diff --git a/notebooks/KBG/KBG_Martinez_PMID_36446582_RunGenoPhenoCorr.ipynb b/notebooks/KBG/KBG_Martinez_PMID_36446582_RunGenoPhenoCorr.ipynb index 9c6a8c34..e08d0a2c 100644 --- a/notebooks/KBG/KBG_Martinez_PMID_36446582_RunGenoPhenoCorr.ipynb +++ b/notebooks/KBG/KBG_Martinez_PMID_36446582_RunGenoPhenoCorr.ipynb @@ -80,28 +80,7 @@ "metadata": { "scrolled": true }, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Expected at least one HPO term per patient, but received none for patient VanDongen2019_P2\n", - "Expected at least one HPO term per patient, but received none for patient VanDongen2019_P12\n", - "Expected at least one HPO term per patient, but received none for patient Reuter2020\n", - "Expected at least one HPO term per patient, but received none for patient Novara, 2017_P10\n", - "Expected at least one variant per patient, but received none for patient Parenti2016_P1\n", - "Expected at least one HPO term per patient, but received none for patient VanDongen2019_P13\n", - "Expected at least one HPO term per patient, but received none for patient VanDongen2019_P8\n", - "Expected at least one HPO term per patient, but received none for patient VanDongen2019_P4\n", - "Expected at least one variant per patient, but received none for patient Low, 2016_P7 (8)\n", - "Expected at least one HPO term per patient, but received none for patient VanDongen2019_P5\n", - "Expected at least one HPO term per patient, but received none for patient KBG31B\n", - "Expected at least one HPO term per patient, but received none for patient VanDongen2019_P9\n", - "Expected at least one HPO term per patient, but received none for patient VanDongen2019_P7\n", - "Expected at least one variant per patient, but received none for patient KBG42\n" - ] - } - ], + "outputs": [], "source": [ "patientCohort = load_phenopacket_folder(fpath_phenopackets, pc)" ] @@ -163,9 +142,9 @@ "\n", "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", "\n", "
ItemDescription
Description of the cohort. 11 individuals were removed from the cohort because they had no HPO terms.Description of the cohort. 14 individuals were removed from the cohort because they had no HPO terms.
Total Individuals340
Excluded Individuals11: Reuter2020;VanDongen2019_P8;VanDongen2019_P5;VanDongen2019_P4;VanDongen2019_P9;VanDongen2019_P2;VanDongen2019_P13;VanDongen2019_P7;KBG31B;VanDongen2019_P12;Novara, 2017_P10
Excluded Individuals14: Novara, 2017_P10;VanDongen2019_P9;VanDongen2019_P2;VanDongen2019_P7;Low, 2016_P7 (8);VanDongen2019_P4;VanDongen2019_P12;KBG42;VanDongen2019_P8;Parenti2016_P1;VanDongen2019_P5;Reuter2020;KBG31B;VanDongen2019_P13
Total Unique HPO Terms28
Total Unique Variants326
" @@ -227,20 +206,20 @@ "\n", "\n", "\n", - "\n", - "\n", - "\n", - "\n", - "\n", + "\n", + "\n", + "\n", + "\n", + "\n", "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", "
HPO TermCount
Counts of annotations to HPO terms for the 340 in the cohort
Abnormality of dental morphology (HP:0006482)224
Abnormality of higher mental function (HP:0011446)220
Intellectual disability (HP:0001249)194
Abnormality of the hand (HP:0001155)189
Neurodevelopmental delay (HP:0012758)176
Abnormality of dental morphology (HP:0006482)223
Abnormality of higher mental function (HP:0011446)218
Intellectual disability (HP:0001249)192
Abnormality of the hand (HP:0001155)186
Neurodevelopmental delay (HP:0012758)174
Short stature (HP:0004322)150
Abnormal external nose morphology (HP:0010938)134
Abnormal eyebrow morphology (HP:0000534)126
Long philtrum (HP:0000343)121
Hearing impairment (HP:0000365)97
Triangular face (HP:0000325)83
Abnormality of the outer ear (HP:0000356)77
Attention deficit hyperactivity disorder (HP:0007018)61
Autistic behavior (HP:0000729)56
Abnormal external nose morphology (HP:0010938)132
Abnormal eyebrow morphology (HP:0000534)125
Long philtrum (HP:0000343)120
Hearing impairment (HP:0000365)96
Triangular face (HP:0000325)82
Abnormality of the outer ear (HP:0000356)76
Attention deficit hyperactivity disorder (HP:0007018)60
Autistic behavior (HP:0000729)54
" ], "text/plain": [ @@ -310,35 +289,34 @@ "c.2408_2412delFRAMESHIFT_VARIANT1016_89284129_89284134_CTTTTT_C\n", "c.1381_1384delFRAMESHIFT_VARIANT816_89285157_89285161_GTTTC_G\n", "c.2398_2401delFRAMESHIFT_VARIANT816_89284140_89284144_TTTTC_T\n", - "c.6792_6793insCFRAMESHIFT_VARIANT516_89279749_89279749_C_CG\n", "c.7481_7482insCFRAMESHIFT_VARIANT516_89275180_89275180_A_AG\n", - "c.2182_2183delFRAMESHIFT_VARIANT316_89284358_89284360_GAT_G\n", - "c.3224_3227delFRAMESHIFT_VARIANT316_89283314_89283318_CCTTT_C\n", + "c.6792_6793insCFRAMESHIFT_VARIANT516_89279749_89279749_C_CG\n", + "c.1977C>GSTOP_GAINED316_89284565_89284565_G_C\n", "c.4406G>ASTOP_GAINED316_89282136_89282136_C_T\n", - "c.2175_2178delFRAMESHIFT_VARIANT316_89284363_89284367_CTTTG_C\n", "c.3832A>TSTOP_GAINED316_89282710_89282710_T_A\n", "c.7570-1G>CSPLICE_ACCEPTOR_VARIANT316_89274958_89274958_C_G\n", - "c.1977C>GSTOP_GAINED316_89284565_89284565_G_C\n", + "c.2182_2183delFRAMESHIFT_VARIANT316_89284358_89284360_GAT_G\n", + "c.2175_2178delFRAMESHIFT_VARIANT316_89284363_89284367_CTTTG_C\n", + "c.3224_3227delFRAMESHIFT_VARIANT316_89283314_89283318_CCTTT_C\n", "c.2197C>TSTOP_GAINED316_89284345_89284345_G_A\n", - "NASTOP_LOST216_88197355_89297194_DEL\n", - "c.1385_1388delFRAMESHIFT_VARIANT216_89285153_89285157_TTTTG_T\n", - "c.7534C>TMISSENSE_VARIANT216_89275128_89275128_G_A\n", + "c.5488G>TSTOP_GAINED216_89281054_89281054_C_A\n", "c.2329_2332delFRAMESHIFT_VARIANT216_89284209_89284213_TTCTC_T\n", - "c.4087C>TSTOP_GAINED216_89282455_89282455_G_A\n", + "c.1367_1370delFRAMESHIFT_VARIANT216_89285171_89285175_CTTCT_C\n", + "c.3309_3310insAFRAMESHIFT_VARIANT216_89283232_89283232_C_CT\n", + "c.3045delFRAMESHIFT_VARIANT216_89283496_89283497_CG_C\n", + "c.7216C>TSTOP_GAINED216_89279326_89279326_G_A\n", "c.3590_3594delFRAMESHIFT_VARIANT216_89282947_89282952_CTTTTT_C\n", - "c.5488G>TSTOP_GAINED216_89281054_89281054_C_A\n", - "c.4384_4385insAFRAMESHIFT_VARIANT216_89282157_89282157_C_CT\n", + "c.7534C>TMISSENSE_VARIANT216_89275128_89275128_G_A\n", "c.3704_3707delFRAMESHIFT_VARIANT216_89282834_89282838_CTGTT_C\n", - "c.7216C>TSTOP_GAINED216_89279326_89279326_G_A\n", - "c.1367_1370delFRAMESHIFT_VARIANT216_89285171_89285175_CTTCT_C\n", + "c.4087C>TSTOP_GAINED216_89282455_89282455_G_A\n", "c.6513_6514insCFRAMESHIFT_VARIANT216_89280028_89280028_C_CG\n", "c.1318C>TSTOP_GAINED216_89285224_89285224_G_A\n", - "c.3309_3310insAFRAMESHIFT_VARIANT216_89283232_89283232_C_CT\n", - "c.3045delFRAMESHIFT_VARIANT216_89283496_89283497_CG_C\n", + "c.4384_4385insAFRAMESHIFT_VARIANT216_89282157_89282157_C_CT\n", "c.5790C>ASTOP_GAINED216_89280752_89280752_G_T\n", + "c.1385_1388delFRAMESHIFT_VARIANT216_89285153_89285157_TTTTG_T\n", "\n", "

Additionally, the following variants were observed 1 or fewer times: \n", - "c.2412del; c.3334del; c.3310_3311insG; c.4529_4530insC; c.6187G>T; c.5953_5954del; c.4964_4965del; c.4374_4375del; c.3770_3771del; c.4206C>G; c.2828_2829del; c.3771_3772insA; c.2395A>T; c.2593_2594insT; c.5145C>G; c.3019C>T; c.6817_6833del; c.6184del; c.4171C>T; c.7416C>G; c.4218C>A; c.211_226+1del; c.6364_6367del; c.3974del; c.3153del; c.2647G>T; c.2692C>T; c.3221_3222del; c.3931C>T; c.7570_7572del; c.2866G>T; c.3123_3126del; c.7363del; c.2650del; c.3460G>T; c.3582del; c.1893_1894insA; c.548_551del; c.7607G>A; c.7552C>T; c.4391_4392del; c.7834G>T; c.2305del; c.3193A>T; c.7407C>G; c.5123C>A; c.6409_6410del; c.3448C>T; c.3437_3461del; c.7180C>T; c.2367del; c.6682del; c.3046del; c.4498C>T; c.1785_1786delinsTT; c.3198_3199del; 16_87886394_88066394_DEL; c.7000C>T; c.6071_6084del; c.3905_3906del; c.5712_5713insT; c.7192C>T; c.3774_3775del; c.1801C>T; c.7535G>A; c.5205del; c.4408A>T; c.2751_2752insT; c.5146G>T; c.7411_7422del; c.1763C>A; c.4107_4108del; c.4283_4286del; c.3382_3383del; c.2512C>T; c.6701del; c.6472G>T; c.5426_5430del; c.1389_1390insA; c.7356_7357insC; c.6340C>T; c.3295_3296del; c.505G>T; c.4389_4390del; c.2297_2300del; c.1460_1463del; c.1711_1723del; c.5274_5275insC; c.7471A>C; c.4558del; c.4103_4104del; c.3222_3223insA; c.1846G>T; c.7083del; c.1940_1941delinsT; c.6968_6975del; c.5889del; c.915del; c.1173C>G; c.6628G>T; c.520C>T; c.3888_3889insC; c.1285_1286del; c.7470+2T>C; c.6691_6692insG; c.2130del; c.1120G>T; c.2765_2766del; c.5199_5227del; c.3180_3181insA; c.831del; c.4177_4189del; c.3339G>A; c.5957_5958del; c.4528_4529del; c.7753C>T; c.1457C>G; c.7189C>T; c.6015_6016insA; c.6766C>T; c.6053_6057del; c.1731_1732insT; c.867C>G; c.7471-1G>C; c.866_867insA; c.4786G>T; c.3591_3594del; c.3208_3209del.

\n", + "c.1457C>G; c.6015_6016insA; c.3180_3181insA; c.2866G>T; c.3295_3296del; c.3339G>A; c.2130del; c.3448C>T; c.211_226+1del; c.3123_3126del; c.4107_4108del; c.2305del; c.4528_4529del; c.1120G>T; c.4498C>T; c.5199_5227del; c.3460G>T; c.1785_1786delinsTT; c.7552C>T; c.1460_1463del; c.867C>G; c.6968_6975del; c.7834G>T; c.5274_5275insC; c.2650del; c.5205del; c.3046del; c.2765_2766del; 16_87886394_88066394_DEL; c.3770_3771del; c.3198_3199del; c.2692C>T; c.7416C>G; c.7192C>T; c.866_867insA; c.6184del; c.5889del; c.6766C>T; c.1173C>G; c.5957_5958del; c.5953_5954del; c.7607G>A; c.7363del; c.3208_3209del; c.7180C>T; c.6472G>T; c.1846G>T; c.4389_4390del; c.7411_7422del; c.6409_6410del; c.4408A>T; c.4177_4189del; c.3437_3461del; c.7189C>T; c.2512C>T; c.5146G>T; c.3974del; c.1389_1390insA; c.4786G>T; c.6187G>T; c.6682del; c.5712_5713insT; c.4103_4104del; c.7083del; c.7407C>G; c.4206C>G; c.3019C>T; c.6364_6367del; c.2367del; c.2297_2300del; c.520C>T; c.7753C>T; c.2751_2752insT; c.3222_3223insA; c.4171C>T; c.1801C>T; c.915del; c.3221_3222del; c.4391_4392del; c.3905_3906del; c.3582del; c.3334del; c.2828_2829del; c.1285_1286del; c.6053_6057del; c.3774_3775del; c.3771_3772insA; c.7356_7357insC; c.2647G>T; c.4374_4375del; c.5123C>A; c.1893_1894insA; c.4529_4530insC; c.1940_1941delinsT; NA; c.7570_7572del; c.548_551del; c.6071_6084del; c.2412del; c.6691_6692insG; c.3153del; c.2593_2594insT; c.4283_4286del; c.3931C>T; c.3888_3889insC; c.7470+2T>C; c.505G>T; c.7471-1G>C; c.3193A>T; c.1711_1723del; c.3591_3594del; c.5145C>G; c.2395A>T; c.6701del; c.7535G>A; c.3310_3311insG; c.4964_4965del; c.7000C>T; c.4218C>A; c.6340C>T; c.1731_1732insT; c.831del; c.4558del; c.6628G>T; c.6817_6833del; c.7471A>C; c.3382_3383del; c.1763C>A; c.5426_5430del.

\n", "

Use the entry in the \"Key\" column to investigate whether specific variants display genotype-phenotype correlations

" ], "text/plain": [ @@ -362,346 +340,346 @@ { "data": { "text/plain": [ - "['Kim, 2015_P1',\n", - " 'KBG15',\n", - " 'Goldenberg2016_P32',\n", - " 'Parenti2021_P3',\n", - " 'Parenti2021_P23',\n", - " 'Gnazzo, 2020_P26',\n", - " 'Goldenberg2016_P20',\n", - " 'Low, 2016_P18 (12)',\n", - " 'Miyatake, 2013',\n", + "['Scarano, 2013_P10',\n", + " 'Ockeloen2015_P18',\n", + " 'Parenti2021_P12',\n", + " 'Murray, 2017_P6 (3.2)',\n", " 'Kutkowska-Kazmierczak2021_P23',\n", - " 'Low, 2016_P28 (25)',\n", + " 'Kutkowska-Kazmierczak2021_P16',\n", + " 'Gnazzo, 2020_P2',\n", + " 'KBG58',\n", + " 'Ockeloen2015_P7',\n", + " 'Goldenberg2016_P27',\n", + " 'Kutkowska-Kazmierczak2021_P15',\n", + " 'Gnazzo, 2020_P11',\n", + " 'Parenti2021_P19',\n", + " 'KBG33',\n", + " 'Ockeloen2015_P10',\n", + " 'KBG10B',\n", + " 'Sirmaci2011_P5',\n", + " 'Goldenberg2016_P3',\n", + " 'KBG17',\n", + " 'Walz2015_Pf',\n", + " 'Parenti2021_P11',\n", + " 'Gnazzo, 2020_P28',\n", + " 'Khalifa, 2013_P1B',\n", " 'VanDongen2019_P1',\n", - " 'Low, 2016_P7 (8)',\n", - " 'Low, 2016_P4 (5)',\n", - " 'Kutkowska-Kazmierczak2021_P9',\n", - " 'Low, 2016_P27 (24)',\n", - " 'Sayed, 2020_P2',\n", - " 'KBG50',\n", - " 'Gnazzo, 2020_P7',\n", - " 'KBG48',\n", + " 'Gnazzo, 2020_P26',\n", " 'KBG11',\n", - " 'Low, 2016_P5 (6)',\n", - " 'Walz2015_PE',\n", - " 'Reuter2020',\n", + " 'Gnazzo, 2020_P19',\n", + " 'Kutkowska-Kazmierczak2021_P1',\n", + " 'KBG41',\n", + " 'Gnazzo, 2020_P12',\n", + " 'Ockeloen2015_P9',\n", + " 'Murray, 2017_P2 (1.2)',\n", + " 'Gnazzo, 2020_P14',\n", + " 'Gnazzo, 2020_P27',\n", + " 'KBG38',\n", + " 'Novara, 2017_P10',\n", + " 'Goldenberg2016_P32',\n", + " 'Sirmaci2011_P2/F1? (previously published Tekin, 2004)',\n", + " 'Low, 2016_P14 (2)',\n", + " 'Murray, 2017_P12 (9.1)',\n", + " 'Murray, 2017_P9 (5.1.)',\n", + " 'Youngs2011',\n", + " 'Parenti2021_P16',\n", + " 'Goldenberg2016_P29',\n", + " 'Parenti2016_P2',\n", + " 'Murray, 2017_P1 (1.1)',\n", + " 'Gnazzo, 2020_P3',\n", + " 'KBG10A',\n", + " 'Scarano, 2013_P12',\n", + " 'Gnazzo, 2020_P23',\n", + " 'KBG22',\n", + " 'Sirmaci2011_P2',\n", + " 'Ockeloen2015_P20',\n", + " 'KBG2',\n", + " 'Miyatake, 2017_P2',\n", + " 'Low, 2016_P3 (4)',\n", + " 'Parenti2021_P18',\n", + " 'Ockeloen2015_P15',\n", + " 'VanDongen2019_P6',\n", + " 'Low2017',\n", + " 'KBG12',\n", + " 'Walz2015_PC',\n", + " 'KBG35',\n", + " 'Goldenberg2016_P1',\n", + " 'KBG66',\n", + " 'Gnazzo, 2020_P10',\n", " 'Parenti2021_P14',\n", - " 'Kim, 2015_P3',\n", - " 'Cucco, 2020 (Patient B)',\n", - " 'Low, 2016_P6 (7)',\n", - " 'VanDongen2019_P13',\n", + " 'Isrie, 2012_P1',\n", + " 'Novara, 2017_P8',\n", + " 'KBG45',\n", + " 'Goldenberg2016_P39',\n", + " 'Ockeloen2015_P2',\n", + " 'Goldenberg2016_P21',\n", + " 'Behnert, 2018',\n", + " 'Kutkowska-Kazmierczak2021_P14',\n", + " 'Novara, 2017_P9',\n", + " 'Ockeloen2015_P12',\n", + " 'Gnazzo, 2020_P6',\n", + " 'Low, 2016_P2 (26)',\n", + " 'Miyatake, 2017_P3',\n", + " 'VanDongen2019_P12',\n", + " 'Low, 2016_P12 (13)',\n", + " 'Low, 2016_P23 (17)',\n", + " 'Parenti2021_P7',\n", + " 'Kutkowska-Kazmierczak2021_P10',\n", + " 'Ockeloen2015_P1',\n", + " 'Sirmaci2011_P3/F1? (previously published Tekin, 2004)',\n", + " 'Low, 2016_P21 (15)',\n", + " 'KBG29',\n", + " 'KBG25',\n", + " 'Willemsen2010_P4',\n", + " 'KBG9',\n", + " 'KBG37',\n", + " 'Parenti2021_P1',\n", + " 'Walz2015_PB',\n", + " 'KBG3',\n", " 'Goldenberg2016_P12',\n", - " 'KBG65',\n", + " 'KBG26',\n", + " 'Murray, 2017_P3 (1.3)',\n", + " 'Low, 2016_P6 (7)',\n", + " 'KBG16',\n", + " 'Kleyner, 2016',\n", + " 'Miyatake, 2013',\n", " 'KBG42',\n", - " 'Murray, 2017_P4 (2.1)',\n", - " 'KBG13',\n", - " 'Goldenberg2016_P30',\n", - " 'Isrie, 2012_P1',\n", - " 'Sirmaci2011_P1/F1? (previously published Tekin, 2004)',\n", - " 'Gnazzo, 2020_P24',\n", - " 'Sirmaci2011_P3',\n", - " 'Goldenberg2016_P2',\n", - " 'Scarano, 2013_P12',\n", - " 'Kutkowska-Kazmierczak2021_P7',\n", - " 'KBG35',\n", - " 'Goldenberg2016_P15',\n", - " 'Scarano, 2013_P1',\n", + " 'Low, 2016_31 (29)',\n", + " 'Parenti2021_P3',\n", + " 'Isrie, 2012_P2',\n", + " 'Ockeloen2015_P4',\n", + " 'Cucco, 2020 (Patient B)',\n", + " 'Gnazzo, 2020_P1',\n", + " 'Goldenberg2016_P9',\n", + " 'Gnazzo, 2020_P29',\n", + " 'Ockeloen2015_P3',\n", + " 'Gnazzo, 2020_P15',\n", + " 'KBG44',\n", " 'Bucerzan2020',\n", - " 'Goldenberg2016_P38',\n", - " 'KBG40',\n", - " 'KBG64',\n", - " 'Parenti2021_P8',\n", - " 'Gnazzo, 2020_P19',\n", - " 'Low, 2016_P15 (3)',\n", - " 'Goldenberg2016_P11',\n", + " 'Ockeloen2015_P11',\n", + " 'Novara, 2017_P5',\n", + " 'KBG7',\n", + " 'Gnazzo, 2020_P4',\n", + " 'Goldenberg2016_P7',\n", + " 'Kutkowska-Kazmierczak2021_P6',\n", + " 'Gnazzo, 2020_P16',\n", + " 'Goldenberg2016_P26',\n", + " 'Parenti2021_P22',\n", " 'Ockeloen2015_P13',\n", - " 'KBG43',\n", - " 'Low, 2016_P22 (16)',\n", - " 'KBG44',\n", - " 'VanDongen2019_P10',\n", - " 'Novara, 2017_P11',\n", - " 'Gnazzo, 2020_P11',\n", - " 'Sirmaci2011_P4 (previously published Brancati, 2004)',\n", - " 'Kutkowska-Kazmierczak2021_P22',\n", - " 'Kutkowska-Kazmierczak2021_P17',\n", - " 'KBG5',\n", + " 'Murray, 2017_P7 (3.3)',\n", + " 'KBG14',\n", + " 'VanDongen2019_P9',\n", + " 'Low, 2016_P16 (9)',\n", + " 'Novara, 2017_P1',\n", + " 'Kutkowska-Kazmierczak2021_P2',\n", + " 'VanDongen2019_P3',\n", " 'VanDongen2019_P8',\n", - " 'Walz2015_Pf',\n", - " 'Kutkowska-Kazmierczak2021_P10',\n", - " 'KBG21',\n", - " 'Low, 2016_P23 (17)',\n", - " 'KBG46',\n", - " 'Bianchi, 2018',\n", - " 'Gnazzo, 2020_P21',\n", - " 'Goldenberg2016_P19',\n", - " 'DeBernardi2018',\n", - " 'Kutkowska-Kazmierczak2021_P13',\n", - " 'Kutkowska-Kazmierczak2021_P5',\n", + " 'Kutkowska-Kazmierczak2021_P9',\n", + " 'Libianto2019',\n", + " 'Murray, 2017_P16 (13.1)',\n", + " 'Ockeloen2015_P5',\n", " 'Crippa2015_P2',\n", - 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'Parenti2021_P17',\n", - " 'Novara, 2017_P1',\n", - " 'Ockeloen2015_P12',\n", - " 'Rentas2021_P1',\n", + " 'Sacharow, 2012_P2',\n", + " 'KBG31A',\n", + " 'Low, 2016_P24 (21)',\n", + " 'Parenti2021_P13',\n", + " 'Low, 2016_P22 (16)',\n", + " 'Willemsen2010_P2',\n", + " 'KBG23',\n", + " 'Low, 2016_P17 (10)',\n", + " 'KBG20',\n", + " 'Goldenberg2016_P34',\n", + " 'Murray, 2017_P8 (4.1)',\n", + " 'Scarano, 2013_P6',\n", + " 'Gnazzo, 2020_P20',\n", + " 'KBG56',\n", + " 'Scarano, 2013_P2',\n", " 'Novara, 2017_P12',\n", - " 'Khalifa, 2013_P1B']" + " 'Low, 2016_P27 (24)',\n", + " 'Scarano, 2013_P3',\n", + " 'Walz2015_PE',\n", + " 'Low, 2016_P5 (6)',\n", + " 'Kutkowska-Kazmierczak2021_P17',\n", + " 'KBG62',\n", + " 'Alves, 2019',\n", + " 'Gnazzo, 2020_P30',\n", + " 'VanDongen2019_P13',\n", + " 'VanDongen2019_P4',\n", + " 'DeBernardi2018',\n", + " 'Kutkowska-Kazmierczak2021_P12',\n", + " 'Low, 2016_P26 (23)',\n", + " 'Sayed, 2020_P2',\n", + " 'Scarano, 2013_P4',\n", + " 'KBG47',\n", + " 'Gnazzo, 2020_P13',\n", + " 'KBG57']" ] }, "execution_count": 12, @@ -724,69 +702,70 @@ { "data": { "text/plain": [ - "[('NP_001243111.1', 325),\n", - " ('NP_037407.4', 325),\n", + "[('NP_037407.4', 325),\n", + " ('NP_001243111.1', 325),\n", " ('NP_001243112.1', 325),\n", " ('NP_872337.2', 45),\n", " ('NP_004924.1', 37),\n", - " ('NP_777577.2', 29),\n", " ('NP_001230208.1', 29),\n", " ('NP_001120686.1', 29),\n", - " ('NP_001305457.1', 25),\n", - " ('NP_000476.1', 25),\n", - " ('NP_001305458.1', 25),\n", - " ('NP_001305461.1', 25),\n", - " ('NP_001305455.1', 25),\n", + " ('NP_777577.2', 29),\n", + " ('NP_057293.1', 25),\n", " ('NP_000503.1', 25),\n", - " ('NP_005178.4', 25),\n", - " ('NP_001305459.1', 25),\n", - " ('NP_001025189.1', 25),\n", - " ('NP_001136336.2', 25),\n", " ('NP_001305454.1', 25),\n", - " ('NP_057293.1', 25),\n", - " ('NP_001305456.1', 25),\n", + " ('NP_001136336.2', 25),\n", + " ('NP_001305457.1', 25),\n", + " ('NP_005178.4', 25),\n", " ('NP_787127.1', 25),\n", - " 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1}),\n", " 'NM_178841.4': Counter({'TRANSCRIPT_ABLATION': 20,\n", " 'TRANSCRIPT_AMPLIFICATION': 1,\n", " 'STOP_LOST': 1,\n", @@ -1329,72 +1258,122 @@ " 'FIVE_PRIME_UTR_VARIANT': 1,\n", " 'THREE_PRIME_UTR_VARIANT': 1,\n", " 'INTRON_VARIANT': 1}),\n", - " 'NM_001318529.2': Counter({'TRANSCRIPT_ABLATION': 24,\n", - " 'TRANSCRIPT_AMPLIFICATION': 1}),\n", - " 'NM_001384919.1': Counter({'TRANSCRIPT_ABLATION': 8,\n", - " 'TRANSCRIPT_AMPLIFICATION': 1,\n", - " 'FEATURE_TRUNCATION': 1,\n", + " 'NM_001384769.1': Counter({'TRANSCRIPT_ABLATION': 35,\n", + " 'TRANSCRIPT_AMPLIFICATION': 2}),\n", + " 'NM_001384775.1': Counter({'TRANSCRIPT_ABLATION': 35,\n", + " 'TRANSCRIPT_AMPLIFICATION': 2}),\n", + " 'NM_001384943.1': Counter({'FEATURE_TRUNCATION': 1,\n", " 'CODING_SEQUENCE_VARIANT': 1,\n", " 'FIVE_PRIME_UTR_VARIANT': 1,\n", - " 'INTRON_VARIANT': 1}),\n", - " 'NM_001184854.2': Counter({'TRANSCRIPT_ABLATION': 5,\n", - " 'UPSTREAM_GENE_VARIANT': 1,\n", - " 'TRANSCRIPT_AMPLIFICATION': 1}),\n", - " 'NM_001385709.2': Counter({'TRANSCRIPT_ABLATION': 24,\n", + " 'INTRON_VARIANT': 1,\n", + " 'TRANSCRIPT_ABLATION': 8,\n", " 'TRANSCRIPT_AMPLIFICATION': 1}),\n", - " 'NM_001351938.2': Counter({'TRANSCRIPT_ABLATION': 5,\n", - " 'UPSTREAM_GENE_VARIANT': 1,\n", + " 'NM_001384928.1': Counter({'FEATURE_TRUNCATION': 1,\n", + " 'CODING_SEQUENCE_VARIANT': 1,\n", + " 'FIVE_PRIME_UTR_VARIANT': 1,\n", + " 'INTRON_VARIANT': 1,\n", + " 'TRANSCRIPT_ABLATION': 8,\n", " 'TRANSCRIPT_AMPLIFICATION': 1}),\n", - " 'NM_153636.3': Counter({'TRANSCRIPT_AMPLIFICATION': 1,\n", - " 'FEATURE_TRUNCATION': 1,\n", - " 'CODING_SEQUENCE_VARIANT': 2,\n", - " 'FIVE_PRIME_UTR_VARIANT': 2,\n", - " 'INTRON_VARIANT': 2}),\n", - " 'NM_001384920.1': Counter({'TRANSCRIPT_ABLATION': 8,\n", + " 'NM_001184856.2': Counter({'TRANSCRIPT_ABLATION': 5,\n", " 'TRANSCRIPT_AMPLIFICATION': 1,\n", - " 'FEATURE_TRUNCATION': 1,\n", + " 'UPSTREAM_GENE_VARIANT': 1}),\n", + " 'NM_004413.4': Counter({'FIVE_PRIME_UTR_VARIANT': 1, 'INTRON_VARIANT': 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Counter({'TRANSCRIPT_ABLATION': 35,\n", + " 'TRANSCRIPT_AMPLIFICATION': 2}),\n", + " 'NM_001243131.1': Counter({'FEATURE_TRUNCATION': 1,\n", + " 'CODING_SEQUENCE_VARIANT': 1,\n", + " 'FIVE_PRIME_UTR_VARIANT': 1,\n", + " 'INTRON_VARIANT': 1,\n", + " 'TRANSCRIPT_AMPLIFICATION': 2,\n", + " 'TRANSCRIPT_ABLATION': 1}),\n", + " 'NM_001384763.1': Counter({'TRANSCRIPT_ABLATION': 35,\n", + " 'TRANSCRIPT_AMPLIFICATION': 2}),\n", + " 'NM_001012759.3': Counter({'TRANSCRIPT_ABLATION': 21,\n", + " 'TRANSCRIPT_AMPLIFICATION': 1}),\n", + " 'NM_153636.3': Counter({'TRANSCRIPT_AMPLIFICATION': 1,\n", + " 'CODING_SEQUENCE_VARIANT': 2,\n", + " 'FIVE_PRIME_UTR_VARIANT': 2,\n", + " 'INTRON_VARIANT': 2,\n", + " 'FEATURE_TRUNCATION': 1}),\n", + " 'NM_001384927.1': Counter({'FEATURE_TRUNCATION': 1,\n", + " 'CODING_SEQUENCE_VARIANT': 1,\n", + " 'FIVE_PRIME_UTR_VARIANT': 1,\n", + " 'INTRON_VARIANT': 1,\n", + " 'TRANSCRIPT_ABLATION': 8,\n", + " 'TRANSCRIPT_AMPLIFICATION': 1}),\n", + " 'NM_033251.2': Counter({'FEATURE_TRUNCATION': 1,\n", + " 'CODING_SEQUENCE_VARIANT': 1,\n", + " 'FIVE_PRIME_UTR_VARIANT': 1,\n", + " 'INTRON_VARIANT': 1,\n", + " 'TRANSCRIPT_AMPLIFICATION': 2,\n", + " 'TRANSCRIPT_ABLATION': 1}),\n", + " 'NM_001384923.1': Counter({'FEATURE_TRUNCATION': 1,\n", + " 'CODING_SEQUENCE_VARIANT': 1,\n", + " 'FIVE_PRIME_UTR_VARIANT': 1,\n", + " 'INTRON_VARIANT': 1,\n", + " 'TRANSCRIPT_ABLATION': 8,\n", " 'TRANSCRIPT_AMPLIFICATION': 1}),\n", - " 'NM_001318528.2': Counter({'TRANSCRIPT_ABLATION': 24,\n", + " 'NM_001030018.2': Counter({'TRANSCRIPT_ABLATION': 24,\n", " 'TRANSCRIPT_AMPLIFICATION': 1}),\n", " 'NM_001318526.2': Counter({'TRANSCRIPT_ABLATION': 24,\n", - " 'TRANSCRIPT_AMPLIFICATION': 1}),\n", - " 'NM_001384763.1': Counter({'TRANSCRIPT_ABLATION': 35,\n", - " 'TRANSCRIPT_AMPLIFICATION': 2}),\n", - " 'NM_001318524.2': Counter({'TRANSCRIPT_ABLATION': 24,\n", - " 'TRANSCRIPT_AMPLIFICATION': 1}),\n", - " 'NM_001384771.1': Counter({'TRANSCRIPT_ABLATION': 35,\n", - " 'TRANSCRIPT_AMPLIFICATION': 2})}" + " 'TRANSCRIPT_AMPLIFICATION': 1})}" ] }, "execution_count": 15, @@ -1454,6 +1433,7 @@ " ProteinMetadata(id=NP_001305459.1, label=Trafficking protein particle complex subunit 2-like protein, features=()),\n", " ProteinMetadata(id=NP_001305461.1, label=Trafficking protein particle complex subunit 2-like protein, features=()),\n", " ProteinMetadata(id=NP_001730.1, label=Carbonic anhydrase 5A, mitochondrial, features=(SimpleProteinFeature(type=FeatureType.DOMAIN, info=FeatureInfo(name=Alpha-carbonic anhydrase, start=39, end=296)),)),\n", + " ProteinMetadata(id=NP_002452.1, label=Diphosphomevalonate decarboxylase, features=()),\n", " ProteinMetadata(id=NP_003110.1, label=Paraplegin, features=(SimpleProteinFeature(type=FeatureType.REGION, info=FeatureInfo(name=Disordered, start=108, end=133)), SimpleProteinFeature(type=FeatureType.REGION, info=FeatureInfo(name=Interaction with PPIF, start=701, end=795)), SimpleProteinFeature(type=FeatureType.REGION, info=FeatureInfo(name=Disordered, start=751, end=795)))),\n", " ProteinMetadata(id=NP_003477.4, label=Large neutral amino acids transporter small subunit 1, features=(SimpleProteinFeature(type=FeatureType.REGION, info=FeatureInfo(name=Disordered, start=1, end=40)),)),\n", " ProteinMetadata(id=NP_004404.1, label=Dipeptidase 1, features=()),\n", @@ -1499,26 +1479,29 @@ "outputs": [], "source": [ "from genophenocorr.analysis import configure_cohort_analysis, CohortAnalysisConfiguration\n", - "from genophenocorr.analysis.predicate import BooleanPredicate, ThisThatPredicate\n", + "from genophenocorr.analysis.predicate import BooleanPredicate, GroupingPredicate\n", "from genophenocorr.model import VariantEffect" ] }, { "cell_type": "code", "execution_count": 18, - "id": "df922d31", + "id": "e3c0b5c1", "metadata": {}, "outputs": [], "source": [ - "config = CohortAnalysisConfiguration(missing_implies_excluded = True, pval_correction='fdr_bh', min_perc_patients_w_hpo=10, include_sv=False)\n", - "\n", - "analysis = configure_cohort_analysis(patientCohort, hpo, config=config)" + "analysis = configure_cohort_analysis(patientCohort, hpo, CohortAnalysisConfiguration(\n", + " missing_implies_excluded = True,\n", + " pval_correction='fdr_bh',\n", + " min_perc_patients_w_hpo=0.1,\n", + " include_sv=True,\n", + " recessive=False))" ] }, { "cell_type": "code", "execution_count": 19, - "id": "57dd0e23", + "id": "91809a38", "metadata": {}, "outputs": [], "source": [ @@ -1527,8 +1510,8 @@ }, { "cell_type": "code", - "execution_count": 28, - "id": "518aa2f8", + "execution_count": 20, + "id": "7a83a5ca", "metadata": {}, "outputs": [ { @@ -1568,454 +1551,382 @@ " \n", " \n", " \n", - " Abnormality of higher mental function [HP:0011446]\n", - " 63\n", - " 26.470588\n", - " 105\n", - " 44.117647\n", - " 0.000347\n", - " 0.003169\n", - " \n", - " \n", - " Abnormality of body height [HP:0000002]\n", - " 28\n", - " 12.334802\n", - " 26\n", - " 11.453744\n", - " 0.000350\n", - " 0.003169\n", - " \n", - " \n", - " Growth delay [HP:0001510]\n", - " 28\n", - " 12.334802\n", - " 26\n", - " 11.453744\n", - " 0.000350\n", - " 0.003169\n", - " \n", - " \n", - " Growth abnormality [HP:0001507]\n", - " 28\n", - " 12.334802\n", - " 26\n", - " 11.453744\n", - " 0.000350\n", - " 0.003169\n", + " Phenotypic abnormality [HP:0000118]\n", + " 137\n", + " 42.024540\n", + " 124\n", + " 38.036810\n", + " 0.000831\n", + " 0.017445\n", " \n", " \n", - " Short stature [HP:0004322]\n", - " 28\n", - " 12.334802\n", - " 26\n", - " 11.453744\n", - " 0.000350\n", - " 0.003169\n", + " All [HP:0000001]\n", + " 137\n", + " 42.024540\n", + " 124\n", + " 38.036810\n", + " 0.000831\n", + " 0.017445\n", " \n", " \n", " Neurodevelopmental abnormality [HP:0012759]\n", - " 66\n", - " 27.500000\n", + " 121\n", + " 38.906752\n", " 113\n", - " 47.083333\n", - " 0.000380\n", - " 0.003169\n", + " 36.334405\n", + " 0.002330\n", + " 0.032621\n", " \n", " \n", - " Intellectual disability [HP:0001249]\n", - " 59\n", - " 25.000000\n", - " 99\n", - " 41.949153\n", - " 0.000488\n", - " 0.003485\n", + " Abnormal nervous system physiology [HP:0012638]\n", + " 125\n", + " 39.808917\n", + " 117\n", + " 37.261146\n", + " 0.004540\n", + " 0.038133\n", " \n", " \n", - " Phenotypic abnormality [HP:0000118]\n", - " 72\n", - " 28.915663\n", - " 124\n", - " 49.799197\n", - " 0.000821\n", - " 0.004169\n", + " Abnormality of the nervous system [HP:0000707]\n", + " 125\n", + " 39.808917\n", + " 117\n", + " 37.261146\n", + " 0.004540\n", + " 0.038133\n", " \n", " \n", - " All [HP:0000001]\n", - " 72\n", - " 28.915663\n", - " 124\n", - " 49.799197\n", - " 0.000821\n", - " 0.004169\n", + " Neurodevelopmental delay [HP:0012758]\n", + " 70\n", + " 26.119403\n", + " 58\n", + " 21.641791\n", + " 0.009995\n", + " 0.069965\n", " \n", " \n", - " Abnormal nervous system physiology [HP:0012638]\n", - " 68\n", - " 28.099174\n", - " 117\n", - " 48.347107\n", - " 0.001023\n", - " 0.004169\n", + " Short stature [HP:0004322]\n", + " 41\n", + " 13.712375\n", + " 26\n", + " 8.695652\n", + " 0.017875\n", + " 0.075074\n", " \n", " \n", - " Abnormality of the nervous system [HP:0000707]\n", - " 68\n", - " 28.099174\n", - " 117\n", - " 48.347107\n", - " 0.001023\n", - " 0.004169\n", + " Abnormality of body height [HP:0000002]\n", + " 41\n", + " 13.712375\n", + " 26\n", + " 8.695652\n", + " 0.017875\n", + " 0.075074\n", " \n", " \n", - " Abnormal nasal morphology [HP:0005105]\n", - " 30\n", - " 14.285714\n", - " 38\n", - " 18.095238\n", - " 0.001167\n", - " 0.004169\n", + " Growth abnormality [HP:0001507]\n", + " 41\n", + " 13.712375\n", + " 26\n", + " 8.695652\n", + " 0.017875\n", + " 0.075074\n", " \n", " \n", - " Abnormality of the nose [HP:0000366]\n", - " 30\n", - " 14.285714\n", - " 38\n", - " 18.095238\n", - " 0.001167\n", - " 0.004169\n", + " Growth delay [HP:0001510]\n", + " 41\n", + " 13.712375\n", + " 26\n", + " 8.695652\n", + " 0.017875\n", + " 0.075074\n", " \n", " \n", - " Abnormal external nose morphology [HP:0010938]\n", - " 30\n", - " 14.285714\n", - " 38\n", - " 18.095238\n", - " 0.001167\n", - " 0.004169\n", + " Abnormality of the ear [HP:0000598]\n", + " 31\n", + " 11.231884\n", + " 19\n", + " 6.884058\n", + " 0.027740\n", + " 0.105918\n", + " \n", + " \n", + " Abnormality of the hand [HP:0001155]\n", + " 58\n", + " 18.649518\n", + " 47\n", + " 15.112540\n", + " 0.054543\n", + " 0.162709\n", " \n", " \n", " Abnormality of limbs [HP:0040064]\n", - " 36\n", - " 15.062762\n", + " 58\n", + " 18.649518\n", " 47\n", - " 19.665272\n", - " 0.005214\n", - " 0.015335\n", + " 15.112540\n", + " 0.054543\n", + " 0.162709\n", " \n", " \n", " Abnormality of the upper limb [HP:0002817]\n", - " 36\n", - " 15.062762\n", + " 58\n", + " 18.649518\n", " 47\n", - " 19.665272\n", - " 0.005214\n", - " 0.015335\n", + " 15.112540\n", + " 0.054543\n", + " 0.162709\n", " \n", " \n", - " Abnormality of the hand [HP:0001155]\n", + " Abnormal ear morphology [HP:0031703]\n", + " 20\n", + " 7.751938\n", + " 12\n", + " 4.651163\n", + " 0.058110\n", + " 0.162709\n", + " \n", + " \n", + " Behavioral abnormality [HP:0000708]\n", " 36\n", - " 15.062762\n", - " 47\n", - " 19.665272\n", - " 0.005214\n", - " 0.015335\n", + " 14.229249\n", + " 31\n", + " 12.252964\n", + " 0.156579\n", + " 0.348855\n", " \n", " \n", " Abnormality of the dentition [HP:0000164]\n", - " 49\n", - " 20.940171\n", + " 81\n", + " 26.384365\n", " 75\n", - " 32.051282\n", - " 0.007331\n", - " 0.019291\n", + " 24.429967\n", + " 0.170658\n", + " 0.348855\n", " \n", " \n", " Abnormality of dental morphology [HP:0006482]\n", - " 49\n", - " 20.940171\n", + " 81\n", + " 26.384365\n", " 75\n", - " 32.051282\n", - " 0.007331\n", - " 0.019291\n", + " 24.429967\n", + " 0.170658\n", + " 0.348855\n", " \n", " \n", - " Neurodevelopmental delay [HP:0012758]\n", - " 35\n", - " 17.326733\n", - " 58\n", - " 28.712871\n", - " 0.012398\n", - " 0.026167\n", + " Abnormality of the face [HP:0000271]\n", + " 86\n", + " 27.388535\n", + " 82\n", + " 26.114650\n", + " 0.174428\n", + " 0.348855\n", " \n", " \n", - " Abnormal hair morphology [HP:0001595]\n", - " 24\n", - " 11.538462\n", - " 32\n", - " 15.384615\n", - " 0.015554\n", - " 0.026167\n", + " Abnormality of head or neck [HP:0000152]\n", + " 86\n", + " 27.388535\n", + " 82\n", + " 26.114650\n", + " 0.174428\n", + " 0.348855\n", " \n", " \n", - " Abnormality of the ocular adnexa [HP:0032039]\n", - " 24\n", - " 11.538462\n", - " 32\n", - " 15.384615\n", - " 0.015554\n", - " 0.026167\n", + " Abnormality of the head [HP:0000234]\n", + " 86\n", + " 27.388535\n", + " 82\n", + " 26.114650\n", + " 0.174428\n", + " 0.348855\n", " \n", " \n", - " Abnormality of the integument [HP:0001574]\n", - " 24\n", - " 11.538462\n", - " 32\n", - " 15.384615\n", - " 0.015554\n", - " 0.026167\n", + " Abnormal ear physiology [HP:0031704]\n", + " 15\n", + " 5.769231\n", + " 10\n", + " 3.846154\n", + " 0.204827\n", + " 0.367695\n", " \n", " \n", - " Abnormality of the orbital region [HP:0000315]\n", - " 24\n", - " 11.538462\n", - " 32\n", - " 15.384615\n", - " 0.015554\n", - " 0.026167\n", + " Hearing abnormality [HP:0000364]\n", + " 15\n", + " 5.769231\n", + " 10\n", + " 3.846154\n", + " 0.204827\n", + " 0.367695\n", " \n", " \n", - " Abnormality of skin adnexa morphology [HP:0011138]\n", - " 24\n", - " 11.538462\n", - " 32\n", - " 15.384615\n", - " 0.015554\n", - " 0.026167\n", + " Abnormal nasal morphology [HP:0005105]\n", + " 41\n", + " 14.855072\n", + " 38\n", + " 13.768116\n", + " 0.231055\n", + " 0.367695\n", " \n", " \n", - " Abnormal eyebrow morphology [HP:0000534]\n", - " 24\n", - " 11.538462\n", - " 32\n", - " 15.384615\n", - " 0.015554\n", - " 0.026167\n", + " Abnormality of the nose [HP:0000366]\n", + " 41\n", + " 14.855072\n", + " 38\n", + " 13.768116\n", + " 0.231055\n", + " 0.367695\n", " \n", " \n", - " Abnormal ocular adnexa morphology [HP:0030669]\n", - " 24\n", - " 11.538462\n", - " 32\n", - " 15.384615\n", - " 0.015554\n", - " 0.026167\n", + " Abnormal external nose morphology [HP:0010938]\n", + " 41\n", + " 14.855072\n", + " 38\n", + " 13.768116\n", + " 0.231055\n", + " 0.367695\n", " \n", " \n", " Abnormal oral morphology [HP:0031816]\n", - " 49\n", - " 20.588235\n", + " 82\n", + " 26.366559\n", " 80\n", - " 33.613445\n", - " 0.016618\n", - " 0.026167\n", + " 25.723473\n", + " 0.255658\n", + " 0.367695\n", " \n", " \n", " Abnormality of the mouth [HP:0000153]\n", - " 49\n", - " 20.588235\n", + " 82\n", + " 26.366559\n", " 80\n", - " 33.613445\n", - " 0.016618\n", - " 0.026167\n", + " 25.723473\n", + " 0.255658\n", + " 0.367695\n", " \n", " \n", " Abnormal oral cavity morphology [HP:0000163]\n", - " 49\n", - " 20.588235\n", - " 80\n", - " 33.613445\n", - " 0.016618\n", - " 0.026167\n", - " \n", - " \n", - " Abnormality of head or neck [HP:0000152]\n", - " 50\n", - " 20.833333\n", " 82\n", - " 34.166667\n", - " 0.017270\n", - " 0.026167\n", + " 26.366559\n", + " 80\n", + " 25.723473\n", + " 0.255658\n", + " 0.367695\n", " \n", " \n", - " Abnormality of the head [HP:0000234]\n", - " 50\n", - " 20.833333\n", - " 82\n", - " 34.166667\n", - " 0.017270\n", - " 0.026167\n", + " Abnormality of higher mental function [HP:0011446]\n", + " 100\n", + " 32.467532\n", + " 105\n", + " 34.090909\n", + " 0.276268\n", + " 0.367695\n", " \n", " \n", - " Abnormality of the face [HP:0000271]\n", - " 50\n", - " 20.833333\n", - " 82\n", - " 34.166667\n", - " 0.017270\n", - " 0.026167\n", + " Intellectual disability [HP:0001249]\n", + " 93\n", + " 30.491803\n", + " 99\n", + " 32.459016\n", + " 0.284542\n", + " 0.367695\n", " \n", " \n", - " Abnormality of the ear [HP:0000598]\n", - " 16\n", - " 7.729469\n", - " 19\n", - " 9.178744\n", - " 0.025832\n", - " 0.037988\n", + " Abnormality of the integument [HP:0001574]\n", + " 35\n", + " 12.773723\n", + " 32\n", + " 11.678832\n", + " 0.323922\n", + " 0.367695\n", " \n", " \n", - " Hearing impairment [HP:0000365]\n", - " 10\n", - " 5.102041\n", - " 10\n", - " 5.102041\n", - " 0.035540\n", - " 0.048028\n", + " Abnormality of the ocular adnexa [HP:0032039]\n", + " 35\n", + " 12.773723\n", + " 32\n", + " 11.678832\n", + " 0.323922\n", + " 0.367695\n", " \n", " \n", - " Hearing abnormality [HP:0000364]\n", - " 10\n", - " 5.102041\n", - " 10\n", - " 5.102041\n", - " 0.035540\n", - " 0.048028\n", + " Abnormal hair morphology [HP:0001595]\n", + " 35\n", + " 12.773723\n", + " 32\n", + " 11.678832\n", + " 0.323922\n", + " 0.367695\n", " \n", " \n", - " Abnormal ear physiology [HP:0031704]\n", - " 10\n", - " 5.102041\n", - " 10\n", - " 5.102041\n", - " 0.035540\n", - " 0.048028\n", + " Abnormal ocular adnexa morphology [HP:0030669]\n", + " 35\n", + " 12.773723\n", + " 32\n", + " 11.678832\n", + " 0.323922\n", + " 0.367695\n", " \n", " \n", - " Behavioral abnormality [HP:0000708]\n", - " 19\n", - " 10.106383\n", - " 31\n", - " 16.489362\n", - " 0.066085\n", - " 0.086955\n", + " Abnormality of skin adnexa morphology [HP:0011138]\n", + " 35\n", + " 12.773723\n", + " 32\n", + " 11.678832\n", + " 0.323922\n", + " 0.367695\n", " \n", " \n", - " Abnormality of the outer ear [HP:0000356]\n", - " 10\n", - " 5.154639\n", - " 12\n", - " 6.185567\n", - " 0.077609\n", - " 0.097011\n", + " Abnormality of the orbital region [HP:0000315]\n", + " 35\n", + " 12.773723\n", + " 32\n", + " 11.678832\n", + " 0.323922\n", + " 0.367695\n", " \n", " \n", - " Abnormal ear morphology [HP:0031703]\n", - " 10\n", - " 5.154639\n", - " 12\n", - " 6.185567\n", - " 0.077609\n", - " 0.097011\n", + " Triangular face [HP:0000325]\n", + " 23\n", + " 8.949416\n", + " 22\n", + " 8.560311\n", + " 0.512910\n", + " 0.552365\n", " \n", " \n", - " Abnormality of the philtrum [HP:0000288]\n", - " 21\n", - " 9.813084\n", - " 33\n", - " 15.420561\n", - " 0.086224\n", - " 0.097982\n", + " Abnormal facial shape [HP:0001999]\n", + " 23\n", + " 8.949416\n", + " 22\n", + " 8.560311\n", + " 0.512910\n", + " 0.552365\n", " \n", " \n", " Abnormal lip morphology [HP:0000159]\n", - " 21\n", - " 9.813084\n", + " 31\n", + " 11.111111\n", " 33\n", - " 15.420561\n", - " 0.086224\n", - " 0.097982\n", + " 11.827957\n", + " 0.669860\n", + " 0.669860\n", " \n", " \n", - " Abnormal upper lip morphology [HP:0000177]\n", - " 21\n", - " 9.813084\n", + " Abnormality of the philtrum [HP:0000288]\n", + " 31\n", + " 11.111111\n", " 33\n", - " 15.420561\n", - " 0.086224\n", - " 0.097982\n", + " 11.827957\n", + " 0.669860\n", + " 0.669860\n", " \n", " \n", - " Long philtrum [HP:0000343]\n", - " 21\n", - " 9.813084\n", + " Abnormal upper lip morphology [HP:0000177]\n", + " 31\n", + " 11.111111\n", " 33\n", - " 15.420561\n", - " 0.086224\n", - " 0.097982\n", - " \n", - " \n", - " Short attention span [HP:0000736]\n", - " 12\n", - " 6.486486\n", - " 18\n", - " 9.729730\n", - " 0.114005\n", - " 0.121282\n", - " \n", - " \n", - " Attention deficit hyperactivity disorder [HP:0007018]\n", - " 12\n", - " 6.486486\n", - " 18\n", - " 9.729730\n", - " 0.114005\n", - " 0.121282\n", - " \n", - " \n", - " Hyperactivity [HP:0000752]\n", - " 12\n", - " 6.486486\n", - " 18\n", - " 9.729730\n", - " 0.114005\n", - " 0.121282\n", - " \n", - " \n", - " Abnormal facial shape [HP:0001999]\n", - " 14\n", - " 7.291667\n", - " 22\n", - " 11.458333\n", - " 0.148845\n", - " 0.151883\n", - " \n", - " \n", - " Triangular face [HP:0000325]\n", - " 14\n", - " 7.291667\n", - " 22\n", - " 11.458333\n", - " 0.148845\n", - " 0.151883\n", - " \n", - " \n", - " Autistic behavior [HP:0000729]\n", - " 13\n", - " 7.142857\n", - " 22\n", - " 12.087912\n", - " 0.205130\n", - " 0.205130\n", + " 11.827957\n", + " 0.669860\n", + " 0.669860\n", " \n", " \n", "\n", @@ -2024,165 +1935,141 @@ "text/plain": [ "FRAMESHIFT_VARIANT on NM_013275.6 No Yes \\\n", " Count Percent Count \n", - "Abnormality of higher mental function [HP:0011446] 63 26.470588 105 \n", - "Abnormality of body height [HP:0000002] 28 12.334802 26 \n", - "Growth delay [HP:0001510] 28 12.334802 26 \n", - "Growth abnormality [HP:0001507] 28 12.334802 26 \n", - "Short stature [HP:0004322] 28 12.334802 26 \n", - "Neurodevelopmental abnormality [HP:0012759] 66 27.500000 113 \n", - "Intellectual disability [HP:0001249] 59 25.000000 99 \n", - "Phenotypic abnormality [HP:0000118] 72 28.915663 124 \n", - "All [HP:0000001] 72 28.915663 124 \n", - "Abnormal nervous system physiology [HP:0012638] 68 28.099174 117 \n", - "Abnormality of the nervous system [HP:0000707] 68 28.099174 117 \n", - "Abnormal nasal morphology [HP:0005105] 30 14.285714 38 \n", - "Abnormality of the nose [HP:0000366] 30 14.285714 38 \n", - "Abnormal external nose morphology [HP:0010938] 30 14.285714 38 \n", - "Abnormality of limbs [HP:0040064] 36 15.062762 47 \n", - "Abnormality of the upper limb [HP:0002817] 36 15.062762 47 \n", - "Abnormality of the hand [HP:0001155] 36 15.062762 47 \n", - "Abnormality of the dentition [HP:0000164] 49 20.940171 75 \n", - "Abnormality of dental morphology [HP:0006482] 49 20.940171 75 \n", - "Neurodevelopmental delay [HP:0012758] 35 17.326733 58 \n", - "Abnormal hair morphology [HP:0001595] 24 11.538462 32 \n", - "Abnormality of the ocular adnexa [HP:0032039] 24 11.538462 32 \n", - "Abnormality of the integument [HP:0001574] 24 11.538462 32 \n", - "Abnormality of the orbital region [HP:0000315] 24 11.538462 32 \n", - "Abnormality of skin adnexa morphology [HP:0011138] 24 11.538462 32 \n", - "Abnormal eyebrow morphology [HP:0000534] 24 11.538462 32 \n", - "Abnormal ocular adnexa morphology [HP:0030669] 24 11.538462 32 \n", - "Abnormal oral morphology [HP:0031816] 49 20.588235 80 \n", - "Abnormality of the mouth [HP:0000153] 49 20.588235 80 \n", - "Abnormal oral cavity morphology [HP:0000163] 49 20.588235 80 \n", - "Abnormality of head or neck [HP:0000152] 50 20.833333 82 \n", - "Abnormality of the head [HP:0000234] 50 20.833333 82 \n", - "Abnormality of the face [HP:0000271] 50 20.833333 82 \n", - "Abnormality of the ear [HP:0000598] 16 7.729469 19 \n", - "Hearing impairment [HP:0000365] 10 5.102041 10 \n", - "Hearing abnormality [HP:0000364] 10 5.102041 10 \n", - "Abnormal ear physiology [HP:0031704] 10 5.102041 10 \n", - "Behavioral abnormality [HP:0000708] 19 10.106383 31 \n", - "Abnormality of the outer ear [HP:0000356] 10 5.154639 12 \n", - "Abnormal ear morphology [HP:0031703] 10 5.154639 12 \n", - "Abnormality of the philtrum [HP:0000288] 21 9.813084 33 \n", - "Abnormal lip morphology [HP:0000159] 21 9.813084 33 \n", - "Abnormal upper lip morphology [HP:0000177] 21 9.813084 33 \n", - "Long philtrum [HP:0000343] 21 9.813084 33 \n", - "Short attention span [HP:0000736] 12 6.486486 18 \n", - "Attention deficit hyperactivity disorder [HP:00... 12 6.486486 18 \n", - "Hyperactivity [HP:0000752] 12 6.486486 18 \n", - "Abnormal facial shape [HP:0001999] 14 7.291667 22 \n", - "Triangular face [HP:0000325] 14 7.291667 22 \n", - "Autistic behavior [HP:0000729] 13 7.142857 22 \n", + "Phenotypic abnormality [HP:0000118] 137 42.024540 124 \n", + "All [HP:0000001] 137 42.024540 124 \n", + "Neurodevelopmental abnormality [HP:0012759] 121 38.906752 113 \n", + "Abnormal nervous system physiology [HP:0012638] 125 39.808917 117 \n", + "Abnormality of the nervous system [HP:0000707] 125 39.808917 117 \n", + "Neurodevelopmental delay [HP:0012758] 70 26.119403 58 \n", + "Short stature [HP:0004322] 41 13.712375 26 \n", + "Abnormality of body height [HP:0000002] 41 13.712375 26 \n", + "Growth abnormality [HP:0001507] 41 13.712375 26 \n", + "Growth delay [HP:0001510] 41 13.712375 26 \n", + "Abnormality of the ear [HP:0000598] 31 11.231884 19 \n", + "Abnormality of the hand [HP:0001155] 58 18.649518 47 \n", + "Abnormality of limbs [HP:0040064] 58 18.649518 47 \n", + "Abnormality of the upper limb [HP:0002817] 58 18.649518 47 \n", + "Abnormal ear morphology [HP:0031703] 20 7.751938 12 \n", + "Behavioral abnormality [HP:0000708] 36 14.229249 31 \n", + "Abnormality of the dentition [HP:0000164] 81 26.384365 75 \n", + "Abnormality of dental morphology [HP:0006482] 81 26.384365 75 \n", + "Abnormality of the face [HP:0000271] 86 27.388535 82 \n", + "Abnormality of head or neck [HP:0000152] 86 27.388535 82 \n", + "Abnormality of the head [HP:0000234] 86 27.388535 82 \n", + "Abnormal ear physiology [HP:0031704] 15 5.769231 10 \n", + "Hearing abnormality [HP:0000364] 15 5.769231 10 \n", + "Abnormal nasal morphology [HP:0005105] 41 14.855072 38 \n", + "Abnormality of the nose [HP:0000366] 41 14.855072 38 \n", + "Abnormal external nose morphology [HP:0010938] 41 14.855072 38 \n", + "Abnormal oral morphology [HP:0031816] 82 26.366559 80 \n", + "Abnormality of the mouth [HP:0000153] 82 26.366559 80 \n", + "Abnormal oral cavity morphology [HP:0000163] 82 26.366559 80 \n", + "Abnormality of higher mental function [HP:0011446] 100 32.467532 105 \n", + "Intellectual disability [HP:0001249] 93 30.491803 99 \n", + "Abnormality of the integument [HP:0001574] 35 12.773723 32 \n", + "Abnormality of the ocular adnexa [HP:0032039] 35 12.773723 32 \n", + "Abnormal hair morphology [HP:0001595] 35 12.773723 32 \n", + "Abnormal ocular adnexa morphology [HP:0030669] 35 12.773723 32 \n", + "Abnormality of skin adnexa morphology [HP:0011138] 35 12.773723 32 \n", + "Abnormality of the orbital region [HP:0000315] 35 12.773723 32 \n", + "Triangular face [HP:0000325] 23 8.949416 22 \n", + "Abnormal facial shape [HP:0001999] 23 8.949416 22 \n", + "Abnormal lip morphology [HP:0000159] 31 11.111111 33 \n", + "Abnormality of the philtrum [HP:0000288] 31 11.111111 33 \n", + "Abnormal upper lip morphology [HP:0000177] 31 11.111111 33 \n", "\n", "FRAMESHIFT_VARIANT on NM_013275.6 \\\n", " Percent p value \n", - "Abnormality of higher mental function [HP:0011446] 44.117647 0.000347 \n", - "Abnormality of body height [HP:0000002] 11.453744 0.000350 \n", - "Growth delay [HP:0001510] 11.453744 0.000350 \n", - "Growth abnormality [HP:0001507] 11.453744 0.000350 \n", - "Short stature [HP:0004322] 11.453744 0.000350 \n", - "Neurodevelopmental abnormality [HP:0012759] 47.083333 0.000380 \n", - "Intellectual disability [HP:0001249] 41.949153 0.000488 \n", - "Phenotypic abnormality [HP:0000118] 49.799197 0.000821 \n", - "All [HP:0000001] 49.799197 0.000821 \n", - "Abnormal nervous system physiology [HP:0012638] 48.347107 0.001023 \n", - "Abnormality of the nervous system [HP:0000707] 48.347107 0.001023 \n", - "Abnormal nasal morphology [HP:0005105] 18.095238 0.001167 \n", - "Abnormality of the nose [HP:0000366] 18.095238 0.001167 \n", - "Abnormal external nose morphology [HP:0010938] 18.095238 0.001167 \n", - "Abnormality of limbs [HP:0040064] 19.665272 0.005214 \n", - "Abnormality of the upper limb [HP:0002817] 19.665272 0.005214 \n", - "Abnormality of the hand [HP:0001155] 19.665272 0.005214 \n", - "Abnormality of the dentition [HP:0000164] 32.051282 0.007331 \n", - "Abnormality of dental morphology [HP:0006482] 32.051282 0.007331 \n", - "Neurodevelopmental delay [HP:0012758] 28.712871 0.012398 \n", - "Abnormal hair morphology [HP:0001595] 15.384615 0.015554 \n", - "Abnormality of the ocular adnexa [HP:0032039] 15.384615 0.015554 \n", - "Abnormality of the integument [HP:0001574] 15.384615 0.015554 \n", - "Abnormality of the orbital region [HP:0000315] 15.384615 0.015554 \n", - "Abnormality of skin adnexa morphology [HP:0011138] 15.384615 0.015554 \n", - "Abnormal eyebrow morphology [HP:0000534] 15.384615 0.015554 \n", - "Abnormal ocular adnexa morphology [HP:0030669] 15.384615 0.015554 \n", - "Abnormal oral morphology [HP:0031816] 33.613445 0.016618 \n", - "Abnormality of the mouth [HP:0000153] 33.613445 0.016618 \n", - "Abnormal oral cavity morphology [HP:0000163] 33.613445 0.016618 \n", - "Abnormality of head or neck [HP:0000152] 34.166667 0.017270 \n", - "Abnormality of the head [HP:0000234] 34.166667 0.017270 \n", - "Abnormality of the face [HP:0000271] 34.166667 0.017270 \n", - "Abnormality of the ear [HP:0000598] 9.178744 0.025832 \n", - "Hearing impairment [HP:0000365] 5.102041 0.035540 \n", - "Hearing abnormality [HP:0000364] 5.102041 0.035540 \n", - "Abnormal ear physiology [HP:0031704] 5.102041 0.035540 \n", - "Behavioral abnormality [HP:0000708] 16.489362 0.066085 \n", - "Abnormality of the outer ear [HP:0000356] 6.185567 0.077609 \n", - "Abnormal ear morphology [HP:0031703] 6.185567 0.077609 \n", - "Abnormality of the philtrum [HP:0000288] 15.420561 0.086224 \n", - "Abnormal lip morphology [HP:0000159] 15.420561 0.086224 \n", - "Abnormal upper lip morphology [HP:0000177] 15.420561 0.086224 \n", - "Long philtrum [HP:0000343] 15.420561 0.086224 \n", - "Short attention span [HP:0000736] 9.729730 0.114005 \n", - "Attention deficit hyperactivity disorder [HP:00... 9.729730 0.114005 \n", - "Hyperactivity [HP:0000752] 9.729730 0.114005 \n", - "Abnormal facial shape [HP:0001999] 11.458333 0.148845 \n", - "Triangular face [HP:0000325] 11.458333 0.148845 \n", - "Autistic behavior [HP:0000729] 12.087912 0.205130 \n", + "Phenotypic abnormality [HP:0000118] 38.036810 0.000831 \n", + "All [HP:0000001] 38.036810 0.000831 \n", + "Neurodevelopmental abnormality [HP:0012759] 36.334405 0.002330 \n", + "Abnormal nervous system physiology [HP:0012638] 37.261146 0.004540 \n", + "Abnormality of the nervous system [HP:0000707] 37.261146 0.004540 \n", + "Neurodevelopmental delay [HP:0012758] 21.641791 0.009995 \n", + "Short stature [HP:0004322] 8.695652 0.017875 \n", + "Abnormality of body height [HP:0000002] 8.695652 0.017875 \n", + "Growth abnormality [HP:0001507] 8.695652 0.017875 \n", + "Growth delay [HP:0001510] 8.695652 0.017875 \n", + "Abnormality of the ear [HP:0000598] 6.884058 0.027740 \n", + "Abnormality of the hand [HP:0001155] 15.112540 0.054543 \n", + "Abnormality of limbs [HP:0040064] 15.112540 0.054543 \n", + "Abnormality of the upper limb [HP:0002817] 15.112540 0.054543 \n", + "Abnormal ear morphology [HP:0031703] 4.651163 0.058110 \n", + "Behavioral abnormality [HP:0000708] 12.252964 0.156579 \n", + "Abnormality of the dentition [HP:0000164] 24.429967 0.170658 \n", + "Abnormality of dental morphology [HP:0006482] 24.429967 0.170658 \n", + "Abnormality of the face [HP:0000271] 26.114650 0.174428 \n", + "Abnormality of head or neck [HP:0000152] 26.114650 0.174428 \n", + "Abnormality of the head [HP:0000234] 26.114650 0.174428 \n", + "Abnormal ear physiology [HP:0031704] 3.846154 0.204827 \n", + "Hearing abnormality [HP:0000364] 3.846154 0.204827 \n", + "Abnormal nasal morphology [HP:0005105] 13.768116 0.231055 \n", + "Abnormality of the nose [HP:0000366] 13.768116 0.231055 \n", + "Abnormal external nose morphology [HP:0010938] 13.768116 0.231055 \n", + "Abnormal oral morphology [HP:0031816] 25.723473 0.255658 \n", + "Abnormality of the mouth [HP:0000153] 25.723473 0.255658 \n", + "Abnormal oral cavity morphology [HP:0000163] 25.723473 0.255658 \n", + "Abnormality of higher mental function [HP:0011446] 34.090909 0.276268 \n", + "Intellectual disability [HP:0001249] 32.459016 0.284542 \n", + "Abnormality of the integument [HP:0001574] 11.678832 0.323922 \n", + "Abnormality of the ocular adnexa [HP:0032039] 11.678832 0.323922 \n", + "Abnormal hair morphology [HP:0001595] 11.678832 0.323922 \n", + "Abnormal ocular adnexa morphology [HP:0030669] 11.678832 0.323922 \n", + "Abnormality of skin adnexa morphology [HP:0011138] 11.678832 0.323922 \n", + "Abnormality of the orbital region [HP:0000315] 11.678832 0.323922 \n", + "Triangular face [HP:0000325] 8.560311 0.512910 \n", + "Abnormal facial shape [HP:0001999] 8.560311 0.512910 \n", + "Abnormal lip morphology [HP:0000159] 11.827957 0.669860 \n", + "Abnormality of the philtrum [HP:0000288] 11.827957 0.669860 \n", + "Abnormal upper lip morphology [HP:0000177] 11.827957 0.669860 \n", "\n", "FRAMESHIFT_VARIANT on NM_013275.6 \n", " Corrected p value \n", - "Abnormality of higher mental function [HP:0011446] 0.003169 \n", - "Abnormality of body height [HP:0000002] 0.003169 \n", - "Growth delay [HP:0001510] 0.003169 \n", - "Growth abnormality [HP:0001507] 0.003169 \n", - "Short stature [HP:0004322] 0.003169 \n", - "Neurodevelopmental abnormality [HP:0012759] 0.003169 \n", - "Intellectual disability [HP:0001249] 0.003485 \n", - "Phenotypic abnormality [HP:0000118] 0.004169 \n", - "All [HP:0000001] 0.004169 \n", - "Abnormal nervous system physiology [HP:0012638] 0.004169 \n", - "Abnormality of the nervous system [HP:0000707] 0.004169 \n", - "Abnormal nasal morphology [HP:0005105] 0.004169 \n", - "Abnormality of the nose [HP:0000366] 0.004169 \n", - "Abnormal external nose morphology [HP:0010938] 0.004169 \n", - "Abnormality of limbs [HP:0040064] 0.015335 \n", - "Abnormality of the upper limb [HP:0002817] 0.015335 \n", - "Abnormality of the hand [HP:0001155] 0.015335 \n", - "Abnormality of the dentition [HP:0000164] 0.019291 \n", - "Abnormality of dental morphology [HP:0006482] 0.019291 \n", - "Neurodevelopmental delay [HP:0012758] 0.026167 \n", - "Abnormal hair morphology [HP:0001595] 0.026167 \n", - "Abnormality of the ocular adnexa [HP:0032039] 0.026167 \n", - "Abnormality of the integument [HP:0001574] 0.026167 \n", - "Abnormality of the orbital region [HP:0000315] 0.026167 \n", - "Abnormality of skin adnexa morphology [HP:0011138] 0.026167 \n", - "Abnormal eyebrow morphology [HP:0000534] 0.026167 \n", - "Abnormal ocular adnexa morphology [HP:0030669] 0.026167 \n", - "Abnormal oral morphology [HP:0031816] 0.026167 \n", - "Abnormality of the mouth [HP:0000153] 0.026167 \n", - "Abnormal oral cavity morphology [HP:0000163] 0.026167 \n", - "Abnormality of head or neck [HP:0000152] 0.026167 \n", - "Abnormality of the head [HP:0000234] 0.026167 \n", - "Abnormality of the face [HP:0000271] 0.026167 \n", - "Abnormality of the ear [HP:0000598] 0.037988 \n", - "Hearing impairment [HP:0000365] 0.048028 \n", - "Hearing abnormality [HP:0000364] 0.048028 \n", - "Abnormal ear physiology [HP:0031704] 0.048028 \n", - "Behavioral abnormality [HP:0000708] 0.086955 \n", - "Abnormality of the outer ear [HP:0000356] 0.097011 \n", - "Abnormal ear morphology [HP:0031703] 0.097011 \n", - "Abnormality of the philtrum [HP:0000288] 0.097982 \n", - "Abnormal lip morphology [HP:0000159] 0.097982 \n", - "Abnormal upper lip morphology [HP:0000177] 0.097982 \n", - "Long philtrum [HP:0000343] 0.097982 \n", - "Short attention span [HP:0000736] 0.121282 \n", - "Attention deficit hyperactivity disorder [HP:00... 0.121282 \n", - "Hyperactivity [HP:0000752] 0.121282 \n", - "Abnormal facial shape [HP:0001999] 0.151883 \n", - "Triangular face [HP:0000325] 0.151883 \n", - "Autistic behavior [HP:0000729] 0.205130 " + "Phenotypic abnormality [HP:0000118] 0.017445 \n", + "All [HP:0000001] 0.017445 \n", + "Neurodevelopmental abnormality [HP:0012759] 0.032621 \n", + "Abnormal nervous system physiology [HP:0012638] 0.038133 \n", + "Abnormality of the nervous system [HP:0000707] 0.038133 \n", + "Neurodevelopmental delay [HP:0012758] 0.069965 \n", + "Short stature [HP:0004322] 0.075074 \n", + "Abnormality of body height [HP:0000002] 0.075074 \n", + "Growth abnormality [HP:0001507] 0.075074 \n", + "Growth delay [HP:0001510] 0.075074 \n", + "Abnormality of the ear [HP:0000598] 0.105918 \n", + "Abnormality of the hand [HP:0001155] 0.162709 \n", + "Abnormality of limbs [HP:0040064] 0.162709 \n", + "Abnormality of the upper limb [HP:0002817] 0.162709 \n", + "Abnormal ear morphology [HP:0031703] 0.162709 \n", + "Behavioral abnormality [HP:0000708] 0.348855 \n", + "Abnormality of the dentition [HP:0000164] 0.348855 \n", + "Abnormality of dental morphology [HP:0006482] 0.348855 \n", + "Abnormality of the face [HP:0000271] 0.348855 \n", + "Abnormality of head or neck [HP:0000152] 0.348855 \n", + "Abnormality of the head [HP:0000234] 0.348855 \n", + "Abnormal ear physiology [HP:0031704] 0.367695 \n", + "Hearing abnormality [HP:0000364] 0.367695 \n", + "Abnormal nasal morphology [HP:0005105] 0.367695 \n", + "Abnormality of the nose [HP:0000366] 0.367695 \n", + "Abnormal external nose morphology [HP:0010938] 0.367695 \n", + "Abnormal oral morphology [HP:0031816] 0.367695 \n", + "Abnormality of the mouth [HP:0000153] 0.367695 \n", + "Abnormal oral cavity morphology [HP:0000163] 0.367695 \n", + "Abnormality of higher mental function [HP:0011446] 0.367695 \n", + "Intellectual disability [HP:0001249] 0.367695 \n", + "Abnormality of the integument [HP:0001574] 0.367695 \n", + "Abnormality of the ocular adnexa [HP:0032039] 0.367695 \n", + "Abnormal hair morphology [HP:0001595] 0.367695 \n", + "Abnormal ocular adnexa morphology [HP:0030669] 0.367695 \n", + "Abnormality of skin adnexa morphology [HP:0011138] 0.367695 \n", + "Abnormality of the orbital region [HP:0000315] 0.367695 \n", + "Triangular face [HP:0000325] 0.552365 \n", + "Abnormal facial shape [HP:0001999] 0.552365 \n", + "Abnormal lip morphology [HP:0000159] 0.669860 \n", + "Abnormality of the philtrum [HP:0000288] 0.669860 \n", + "Abnormal upper lip morphology [HP:0000177] 0.669860 " ] }, - "execution_count": 28, + "execution_count": 20, "metadata": {}, "output_type": "execute_result" } @@ -2195,7 +2082,7 @@ { "cell_type": "code", "execution_count": 21, - "id": "1c2c01fd", + "id": "57dd0e23", "metadata": {}, "outputs": [], "source": [ @@ -2204,7 +2091,7 @@ }, { "cell_type": "code", - "execution_count": 27, + "execution_count": 22, "id": "a586d8ff", "metadata": {}, "outputs": [ @@ -2246,453 +2133,381 @@ " \n", " \n", " Phenotypic abnormality [HP:0000118]\n", - " 177\n", - " 71.084337\n", + " 242\n", + " 74.233129\n", " 19\n", - " 7.630522\n", - " 0.009174\n", - " 0.200338\n", + " 5.828221\n", + " 0.004307\n", + " 0.090438\n", " \n", " \n", " All [HP:0000001]\n", - " 177\n", - " 71.084337\n", + " 242\n", + " 74.233129\n", " 19\n", - " 7.630522\n", - " 0.009174\n", - " 0.200338\n", - " \n", - " \n", - " Abnormality of higher mental function [HP:0011446]\n", - " 152\n", - " 63.865546\n", - " 16\n", - " 6.722689\n", - " 0.019099\n", - " 0.200338\n", + " 5.828221\n", + " 0.004307\n", + " 0.090438\n", " \n", " \n", " Abnormal nervous system physiology [HP:0012638]\n", - " 166\n", - " 68.595041\n", + " 223\n", + " 71.019108\n", " 19\n", - " 7.851240\n", - " 0.023529\n", - " 0.200338\n", + " 6.050955\n", + " 0.024006\n", + " 0.252063\n", " \n", " \n", " Abnormality of the nervous system [HP:0000707]\n", - " 166\n", - " 68.595041\n", + " 223\n", + " 71.019108\n", " 19\n", - " 7.851240\n", - " 0.023529\n", - " 0.200338\n", + " 6.050955\n", + " 0.024006\n", + " 0.252063\n", " \n", " \n", - " Intellectual disability [HP:0001249]\n", - " 143\n", - " 60.593220\n", - " 15\n", - " 6.355932\n", - " 0.024041\n", - " 0.200338\n", + " Abnormality of the ear [HP:0000598]\n", + " 49\n", + " 17.753623\n", + " 1\n", + " 0.362319\n", + " 0.037354\n", + " 0.313770\n", " \n", " \n", " Neurodevelopmental abnormality [HP:0012759]\n", - " 160\n", - " 66.666667\n", + " 215\n", + " 69.131833\n", " 19\n", - " 7.916667\n", - " 0.048016\n", - " 0.340029\n", + " 6.109325\n", + " 0.048989\n", + " 0.342924\n", " \n", " \n", - " Abnormality of the ear [HP:0000598]\n", - " 34\n", - " 16.425121\n", + " Abnormality of higher mental function [HP:0011446]\n", + " 189\n", + " 61.363636\n", + " 16\n", + " 5.194805\n", + " 0.072214\n", + " 0.426679\n", + " \n", + " \n", + " Intellectual disability [HP:0001249]\n", + " 177\n", + " 58.032787\n", + " 15\n", + " 4.918033\n", + " 0.081272\n", + " 0.426679\n", + " \n", + " \n", + " Abnormal ear morphology [HP:0031703]\n", + " 31\n", + " 12.015504\n", " 1\n", - " 0.483092\n", - " 0.054405\n", - " 0.340029\n", + " 0.387597\n", + " 0.218309\n", + " 0.707731\n", " \n", " \n", - " Abnormality of dental morphology [HP:0006482]\n", - " 112\n", - " 47.863248\n", - " 12\n", - " 5.128205\n", - " 0.169816\n", - " 0.538860\n", + " Behavioral abnormality [HP:0000708]\n", + " 63\n", + " 24.901186\n", + " 4\n", + " 1.581028\n", + " 0.241365\n", + " 0.707731\n", " \n", " \n", " Abnormality of the dentition [HP:0000164]\n", - " 112\n", - " 47.863248\n", + " 144\n", + " 46.905537\n", " 12\n", - " 5.128205\n", - " 0.169816\n", - " 0.538860\n", + " 3.908795\n", + " 0.250659\n", + " 0.707731\n", " \n", " \n", - " Autistic behavior [HP:0000729]\n", - " 33\n", - " 18.131868\n", - " 2\n", - " 1.098901\n", - " 0.175721\n", - " 0.538860\n", + " Abnormality of dental morphology [HP:0006482]\n", + " 144\n", + " 46.905537\n", + " 12\n", + " 3.908795\n", + " 0.250659\n", + " 0.707731\n", " \n", " \n", " Abnormality of head or neck [HP:0000152]\n", - " 118\n", - " 49.166667\n", + " 154\n", + " 49.044586\n", " 14\n", - " 5.833333\n", - " 0.185604\n", - " 0.538860\n", + " 4.458599\n", + " 0.265996\n", + " 0.707731\n", " \n", " \n", " Abnormality of the head [HP:0000234]\n", - " 118\n", - " 49.166667\n", + " 154\n", + " 49.044586\n", " 14\n", - " 5.833333\n", - " 0.185604\n", - " 0.538860\n", + " 4.458599\n", + " 0.265996\n", + " 0.707731\n", " \n", " \n", " Abnormality of the face [HP:0000271]\n", - " 118\n", - " 49.166667\n", - " 14\n", - " 5.833333\n", - " 0.185604\n", - " 0.538860\n", - " \n", - " \n", - " Behavioral abnormality [HP:0000708]\n", - " 46\n", - " 24.468085\n", - " 4\n", - " 2.127660\n", - " 0.231875\n", - " 0.538860\n", + " 154\n", + " 49.044586\n", + " 14\n", + " 4.458599\n", + " 0.265996\n", + " 0.707731\n", " \n", " \n", - " Abnormality of the upper limb [HP:0002817]\n", - " 75\n", - " 31.380753\n", + " Abnormality of the hand [HP:0001155]\n", + " 97\n", + " 31.189711\n", " 8\n", - " 3.347280\n", - " 0.238015\n", - " 0.538860\n", + " 2.572347\n", + " 0.326465\n", + " 0.707731\n", " \n", " \n", - " Abnormality of the hand [HP:0001155]\n", - " 75\n", - " 31.380753\n", + " Abnormality of the upper limb [HP:0002817]\n", + " 97\n", + " 31.189711\n", " 8\n", - " 3.347280\n", - " 0.238015\n", - " 0.538860\n", + " 2.572347\n", + " 0.326465\n", + " 0.707731\n", " \n", " \n", " Abnormality of limbs [HP:0040064]\n", - " 75\n", - " 31.380753\n", + " 97\n", + " 31.189711\n", " 8\n", - " 3.347280\n", - " 0.238015\n", - " 0.538860\n", + " 2.572347\n", + " 0.326465\n", + " 0.707731\n", " \n", " \n", " Abnormal oral morphology [HP:0031816]\n", - " 115\n", - " 48.319328\n", + " 148\n", + " 47.588424\n", " 14\n", - " 5.882353\n", - " 0.252957\n", - " 0.538860\n", + " 4.501608\n", + " 0.353865\n", + " 0.707731\n", " \n", " \n", - " Abnormal oral cavity morphology [HP:0000163]\n", - " 115\n", - " 48.319328\n", + " Abnormality of the mouth [HP:0000153]\n", + " 148\n", + " 47.588424\n", " 14\n", - " 5.882353\n", - " 0.252957\n", - " 0.538860\n", + " 4.501608\n", + " 0.353865\n", + " 0.707731\n", " \n", " \n", - " Abnormality of the mouth [HP:0000153]\n", - " 115\n", - " 48.319328\n", + " Abnormal oral cavity morphology [HP:0000163]\n", + " 148\n", + " 47.588424\n", " 14\n", - " 5.882353\n", - " 0.252957\n", - " 0.538860\n", + " 4.501608\n", + " 0.353865\n", + " 0.707731\n", " \n", " \n", - " Abnormal ear physiology [HP:0031704]\n", - " 19\n", - " 9.693878\n", - " 1\n", - " 0.510204\n", - " 0.319991\n", - " 0.538860\n", + " Neurodevelopmental delay [HP:0012758]\n", + " 117\n", + " 43.656716\n", + " 11\n", + " 4.104478\n", + " 0.425125\n", + " 0.745146\n", " \n", " \n", - " Hearing impairment [HP:0000365]\n", - " 19\n", - " 9.693878\n", + " Abnormal ear physiology [HP:0031704]\n", + " 24\n", + " 9.230769\n", " 1\n", - " 0.510204\n", - " 0.319991\n", - " 0.538860\n", + " 0.384615\n", + " 0.488225\n", + " 0.745146\n", " \n", " \n", " Hearing abnormality [HP:0000364]\n", - " 19\n", - " 9.693878\n", - " 1\n", - " 0.510204\n", - " 0.319991\n", - " 0.538860\n", - " \n", - " \n", - " Abnormal ear morphology [HP:0031703]\n", - " 21\n", - " 10.824742\n", - " 1\n", - " 0.515464\n", - " 0.322677\n", - " 0.538860\n", - " \n", - " \n", - " Abnormality of the outer ear [HP:0000356]\n", - " 21\n", - " 10.824742\n", + " 24\n", + " 9.230769\n", " 1\n", - " 0.515464\n", - " 0.322677\n", - " 0.538860\n", - " \n", - " \n", - " Abnormality of the philtrum [HP:0000288]\n", - " 49\n", - " 22.897196\n", - " 5\n", - " 2.336449\n", - " 0.361864\n", - " 0.538860\n", - " \n", - " \n", - " Abnormal upper lip morphology [HP:0000177]\n", - " 49\n", - " 22.897196\n", - " 5\n", - " 2.336449\n", - " 0.361864\n", - " 0.538860\n", + " 0.384615\n", + " 0.488225\n", + " 0.745146\n", " \n", " \n", - " Long philtrum [HP:0000343]\n", - " 49\n", - " 22.897196\n", + " Growth abnormality [HP:0001507]\n", + " 62\n", + " 20.735786\n", " 5\n", - " 2.336449\n", - " 0.361864\n", - " 0.538860\n", + " 1.672241\n", + " 0.496764\n", + " 0.745146\n", " \n", " \n", - " Abnormal lip morphology [HP:0000159]\n", - " 49\n", - " 22.897196\n", + " Growth delay [HP:0001510]\n", + " 62\n", + " 20.735786\n", " 5\n", - " 2.336449\n", - " 0.361864\n", - " 0.538860\n", + " 1.672241\n", + " 0.496764\n", + " 0.745146\n", " \n", " \n", - " Growth delay [HP:0001510]\n", - " 49\n", - " 21.585903\n", + " Short stature [HP:0004322]\n", + " 62\n", + " 20.735786\n", " 5\n", - " 2.202643\n", - " 0.366424\n", - " 0.538860\n", + " 1.672241\n", + " 0.496764\n", + " 0.745146\n", " \n", " \n", " Abnormality of body height [HP:0000002]\n", - " 49\n", - " 21.585903\n", + " 62\n", + " 20.735786\n", " 5\n", - " 2.202643\n", - " 0.366424\n", - " 0.538860\n", + " 1.672241\n", + " 0.496764\n", + " 0.745146\n", " \n", " \n", - " Short stature [HP:0004322]\n", - " 49\n", - " 21.585903\n", + " Abnormal upper lip morphology [HP:0000177]\n", + " 59\n", + " 21.146953\n", " 5\n", - " 2.202643\n", - " 0.366424\n", - " 0.538860\n", + " 1.792115\n", + " 0.640576\n", + " 0.867877\n", " \n", " \n", - " Growth abnormality [HP:0001507]\n", - " 49\n", - " 21.585903\n", + " Abnormal lip morphology [HP:0000159]\n", + " 59\n", + " 21.146953\n", " 5\n", - " 2.202643\n", - " 0.366424\n", - " 0.538860\n", + " 1.792115\n", + " 0.640576\n", + " 0.867877\n", " \n", " \n", - " Abnormal eyebrow morphology [HP:0000534]\n", - " 50\n", - " 24.038462\n", - " 6\n", - " 2.884615\n", - " 0.503161\n", - " 0.613611\n", + " Abnormality of the philtrum [HP:0000288]\n", + " 59\n", + " 21.146953\n", + " 5\n", + " 1.792115\n", + " 0.640576\n", + " 0.867877\n", " \n", " \n", " Abnormal hair morphology [HP:0001595]\n", - " 50\n", - " 24.038462\n", + " 61\n", + " 22.262774\n", " 6\n", - " 2.884615\n", - " 0.503161\n", - " 0.613611\n", + " 2.189781\n", + " 0.819529\n", + " 0.875043\n", " \n", " \n", " Abnormal ocular adnexa morphology [HP:0030669]\n", - " 50\n", - " 24.038462\n", + " 61\n", + " 22.262774\n", " 6\n", - " 2.884615\n", - " 0.503161\n", - " 0.613611\n", + " 2.189781\n", + " 0.819529\n", + " 0.875043\n", " \n", " \n", - " Abnormality of the integument [HP:0001574]\n", - " 50\n", - " 24.038462\n", + " Abnormality of skin adnexa morphology [HP:0011138]\n", + " 61\n", + " 22.262774\n", " 6\n", - " 2.884615\n", - " 0.503161\n", - " 0.613611\n", + " 2.189781\n", + " 0.819529\n", + " 0.875043\n", " \n", " \n", " Abnormality of the ocular adnexa [HP:0032039]\n", - " 50\n", - " 24.038462\n", + " 61\n", + " 22.262774\n", " 6\n", - " 2.884615\n", - " 0.503161\n", - " 0.613611\n", + " 2.189781\n", + " 0.819529\n", + " 0.875043\n", " \n", " \n", - " Abnormality of the orbital region [HP:0000315]\n", - " 50\n", - " 24.038462\n", + " Abnormality of the integument [HP:0001574]\n", + " 61\n", + " 22.262774\n", " 6\n", - " 2.884615\n", - " 0.503161\n", - " 0.613611\n", + " 2.189781\n", + " 0.819529\n", + " 0.875043\n", " \n", " \n", - " Abnormality of skin adnexa morphology [HP:0011138]\n", - " 50\n", - " 24.038462\n", + " Abnormality of the orbital region [HP:0000315]\n", + " 61\n", + " 22.262774\n", " 6\n", - " 2.884615\n", - " 0.503161\n", - " 0.613611\n", - " \n", - " \n", - " Neurodevelopmental delay [HP:0012758]\n", - " 82\n", - " 40.594059\n", - " 11\n", - " 5.445545\n", - " 0.541222\n", - " 0.644312\n", + " 2.189781\n", + " 0.819529\n", + " 0.875043\n", " \n", " \n", - " Attention deficit hyperactivity disorder [HP:0007018]\n", - " 27\n", - " 14.594595\n", - " 3\n", - " 1.621622\n", - " 0.773679\n", - " 0.835742\n", - " \n", - " \n", - " Short attention span [HP:0000736]\n", - " 27\n", - " 14.594595\n", - " 3\n", - " 1.621622\n", - " 0.773679\n", - " 0.835742\n", + " Abnormal external nose morphology [HP:0010938]\n", + " 70\n", + " 25.362319\n", + " 9\n", + " 3.260870\n", + " 0.833375\n", + " 0.875043\n", " \n", " \n", - " Hyperactivity [HP:0000752]\n", - " 27\n", - " 14.594595\n", - " 3\n", - " 1.621622\n", - " 0.773679\n", - " 0.835742\n", + " Abnormal nasal morphology [HP:0005105]\n", + " 70\n", + " 25.362319\n", + " 9\n", + " 3.260870\n", + " 0.833375\n", + " 0.875043\n", " \n", " \n", - " Abnormal facial shape [HP:0001999]\n", - " 32\n", - " 16.666667\n", - " 4\n", - " 2.083333\n", - " 0.790818\n", - " 0.835742\n", + " Abnormality of the nose [HP:0000366]\n", + " 70\n", + " 25.362319\n", + " 9\n", + " 3.260870\n", + " 0.833375\n", + " 0.875043\n", " \n", " \n", " Triangular face [HP:0000325]\n", - " 32\n", - " 16.666667\n", + " 41\n", + " 15.953307\n", " 4\n", - " 2.083333\n", - " 0.790818\n", - " 0.835742\n", - " \n", - " \n", - " Abnormal nasal morphology [HP:0005105]\n", - " 59\n", - " 28.095238\n", - " 9\n", - " 4.285714\n", - " 0.835742\n", - " 0.835742\n", - " \n", - " \n", - " Abnormal external nose morphology [HP:0010938]\n", - " 59\n", - " 28.095238\n", - " 9\n", - " 4.285714\n", - " 0.835742\n", - " 0.835742\n", + " 1.556420\n", + " 1.000000\n", + " 1.000000\n", " \n", " \n", - " Abnormality of the nose [HP:0000366]\n", - " 59\n", - " 28.095238\n", - " 9\n", - " 4.285714\n", - " 0.835742\n", - " 0.835742\n", + " Abnormal facial shape [HP:0001999]\n", + " 41\n", + " 15.953307\n", + " 4\n", + " 1.556420\n", + " 1.000000\n", + " 1.000000\n", " \n", " \n", "\n", @@ -2701,218 +2516,186 @@ "text/plain": [ ">=1 allele of the variant 16_89284634_89284639_GTGTTT_G No \\\n", " Count Percent \n", - "Phenotypic abnormality [HP:0000118] 177 71.084337 \n", - "All [HP:0000001] 177 71.084337 \n", - "Abnormality of higher mental function [HP:0011446] 152 63.865546 \n", - "Abnormal nervous system physiology [HP:0012638] 166 68.595041 \n", - "Abnormality of the nervous system [HP:0000707] 166 68.595041 \n", - "Intellectual disability [HP:0001249] 143 60.593220 \n", - "Neurodevelopmental abnormality [HP:0012759] 160 66.666667 \n", - "Abnormality of the ear [HP:0000598] 34 16.425121 \n", - "Abnormality of dental morphology [HP:0006482] 112 47.863248 \n", - "Abnormality of the dentition [HP:0000164] 112 47.863248 \n", - "Autistic behavior [HP:0000729] 33 18.131868 \n", - "Abnormality of head or neck [HP:0000152] 118 49.166667 \n", - "Abnormality of the head [HP:0000234] 118 49.166667 \n", - "Abnormality of the face [HP:0000271] 118 49.166667 \n", - "Behavioral abnormality [HP:0000708] 46 24.468085 \n", - "Abnormality of the upper limb [HP:0002817] 75 31.380753 \n", - "Abnormality of the hand [HP:0001155] 75 31.380753 \n", - "Abnormality of limbs [HP:0040064] 75 31.380753 \n", - "Abnormal oral morphology [HP:0031816] 115 48.319328 \n", - "Abnormal oral cavity morphology [HP:0000163] 115 48.319328 \n", - "Abnormality of the mouth [HP:0000153] 115 48.319328 \n", - "Abnormal ear physiology [HP:0031704] 19 9.693878 \n", - "Hearing impairment [HP:0000365] 19 9.693878 \n", - "Hearing abnormality [HP:0000364] 19 9.693878 \n", - "Abnormal ear morphology [HP:0031703] 21 10.824742 \n", - "Abnormality of the outer ear [HP:0000356] 21 10.824742 \n", - "Abnormality of the philtrum [HP:0000288] 49 22.897196 \n", - "Abnormal upper lip morphology [HP:0000177] 49 22.897196 \n", - "Long philtrum [HP:0000343] 49 22.897196 \n", - "Abnormal lip morphology [HP:0000159] 49 22.897196 \n", - "Growth delay [HP:0001510] 49 21.585903 \n", - "Abnormality of body height [HP:0000002] 49 21.585903 \n", - "Short stature [HP:0004322] 49 21.585903 \n", - "Growth abnormality [HP:0001507] 49 21.585903 \n", - "Abnormal eyebrow morphology [HP:0000534] 50 24.038462 \n", - "Abnormal hair morphology [HP:0001595] 50 24.038462 \n", - "Abnormal ocular adnexa morphology [HP:0030669] 50 24.038462 \n", - "Abnormality of the integument [HP:0001574] 50 24.038462 \n", - "Abnormality of the ocular adnexa [HP:0032039] 50 24.038462 \n", - "Abnormality of the orbital region [HP:0000315] 50 24.038462 \n", - "Abnormality of skin adnexa morphology [HP:0011138] 50 24.038462 \n", - "Neurodevelopmental delay [HP:0012758] 82 40.594059 \n", - "Attention deficit hyperactivity disorder [HP:00... 27 14.594595 \n", - "Short attention span [HP:0000736] 27 14.594595 \n", - "Hyperactivity [HP:0000752] 27 14.594595 \n", - "Abnormal facial shape [HP:0001999] 32 16.666667 \n", - "Triangular face [HP:0000325] 32 16.666667 \n", - "Abnormal nasal morphology [HP:0005105] 59 28.095238 \n", - "Abnormal external nose morphology [HP:0010938] 59 28.095238 \n", - "Abnormality of the nose [HP:0000366] 59 28.095238 \n", + "Phenotypic abnormality [HP:0000118] 242 74.233129 \n", + "All [HP:0000001] 242 74.233129 \n", + "Abnormal nervous system physiology [HP:0012638] 223 71.019108 \n", + "Abnormality of the nervous system [HP:0000707] 223 71.019108 \n", + "Abnormality of the ear [HP:0000598] 49 17.753623 \n", + "Neurodevelopmental abnormality [HP:0012759] 215 69.131833 \n", + "Abnormality of higher mental function [HP:0011446] 189 61.363636 \n", + "Intellectual disability [HP:0001249] 177 58.032787 \n", + "Abnormal ear morphology [HP:0031703] 31 12.015504 \n", + "Behavioral abnormality [HP:0000708] 63 24.901186 \n", + "Abnormality of the dentition [HP:0000164] 144 46.905537 \n", + "Abnormality of dental morphology [HP:0006482] 144 46.905537 \n", + "Abnormality of head or neck [HP:0000152] 154 49.044586 \n", + "Abnormality of the head [HP:0000234] 154 49.044586 \n", + "Abnormality of the face [HP:0000271] 154 49.044586 \n", + "Abnormality of the hand [HP:0001155] 97 31.189711 \n", + "Abnormality of the upper limb [HP:0002817] 97 31.189711 \n", + "Abnormality of limbs [HP:0040064] 97 31.189711 \n", + "Abnormal oral morphology [HP:0031816] 148 47.588424 \n", + "Abnormality of the mouth [HP:0000153] 148 47.588424 \n", + "Abnormal oral cavity morphology [HP:0000163] 148 47.588424 \n", + "Neurodevelopmental delay [HP:0012758] 117 43.656716 \n", + "Abnormal ear physiology [HP:0031704] 24 9.230769 \n", + "Hearing abnormality [HP:0000364] 24 9.230769 \n", + "Growth abnormality [HP:0001507] 62 20.735786 \n", + "Growth delay [HP:0001510] 62 20.735786 \n", + "Short stature [HP:0004322] 62 20.735786 \n", + "Abnormality of body height [HP:0000002] 62 20.735786 \n", + "Abnormal upper lip morphology [HP:0000177] 59 21.146953 \n", + "Abnormal lip morphology [HP:0000159] 59 21.146953 \n", + "Abnormality of the philtrum [HP:0000288] 59 21.146953 \n", + "Abnormal hair morphology [HP:0001595] 61 22.262774 \n", + "Abnormal ocular adnexa morphology [HP:0030669] 61 22.262774 \n", + "Abnormality of skin adnexa morphology [HP:0011138] 61 22.262774 \n", + "Abnormality of the ocular adnexa [HP:0032039] 61 22.262774 \n", + "Abnormality of the integument [HP:0001574] 61 22.262774 \n", + "Abnormality of the orbital region [HP:0000315] 61 22.262774 \n", + "Abnormal external nose morphology [HP:0010938] 70 25.362319 \n", + "Abnormal nasal morphology [HP:0005105] 70 25.362319 \n", + "Abnormality of the nose [HP:0000366] 70 25.362319 \n", + "Triangular face [HP:0000325] 41 15.953307 \n", + "Abnormal facial shape [HP:0001999] 41 15.953307 \n", "\n", ">=1 allele of the variant 16_89284634_89284639_GTGTTT_G Yes \\\n", " Count Percent \n", - "Phenotypic abnormality [HP:0000118] 19 7.630522 \n", - "All [HP:0000001] 19 7.630522 \n", - "Abnormality of higher mental function [HP:0011446] 16 6.722689 \n", - "Abnormal nervous system physiology [HP:0012638] 19 7.851240 \n", - "Abnormality of the nervous system [HP:0000707] 19 7.851240 \n", - "Intellectual disability [HP:0001249] 15 6.355932 \n", - "Neurodevelopmental abnormality [HP:0012759] 19 7.916667 \n", - "Abnormality of the ear [HP:0000598] 1 0.483092 \n", - "Abnormality of dental morphology [HP:0006482] 12 5.128205 \n", - "Abnormality of the dentition [HP:0000164] 12 5.128205 \n", - "Autistic behavior [HP:0000729] 2 1.098901 \n", - "Abnormality of head or neck [HP:0000152] 14 5.833333 \n", - "Abnormality of the head [HP:0000234] 14 5.833333 \n", - "Abnormality of the face [HP:0000271] 14 5.833333 \n", - "Behavioral abnormality [HP:0000708] 4 2.127660 \n", - "Abnormality of the upper limb [HP:0002817] 8 3.347280 \n", - "Abnormality of the hand [HP:0001155] 8 3.347280 \n", - "Abnormality of limbs [HP:0040064] 8 3.347280 \n", - "Abnormal oral morphology [HP:0031816] 14 5.882353 \n", - "Abnormal oral cavity morphology [HP:0000163] 14 5.882353 \n", - "Abnormality of the mouth [HP:0000153] 14 5.882353 \n", - "Abnormal ear physiology [HP:0031704] 1 0.510204 \n", - "Hearing impairment [HP:0000365] 1 0.510204 \n", - "Hearing abnormality [HP:0000364] 1 0.510204 \n", - "Abnormal ear morphology [HP:0031703] 1 0.515464 \n", - "Abnormality of the outer ear [HP:0000356] 1 0.515464 \n", - "Abnormality of the philtrum [HP:0000288] 5 2.336449 \n", - "Abnormal upper lip morphology [HP:0000177] 5 2.336449 \n", - "Long philtrum [HP:0000343] 5 2.336449 \n", - "Abnormal lip morphology [HP:0000159] 5 2.336449 \n", - "Growth delay [HP:0001510] 5 2.202643 \n", - "Abnormality of body height [HP:0000002] 5 2.202643 \n", - "Short stature [HP:0004322] 5 2.202643 \n", - "Growth abnormality [HP:0001507] 5 2.202643 \n", - "Abnormal eyebrow morphology [HP:0000534] 6 2.884615 \n", - "Abnormal hair morphology [HP:0001595] 6 2.884615 \n", - "Abnormal ocular adnexa morphology [HP:0030669] 6 2.884615 \n", - "Abnormality of the integument [HP:0001574] 6 2.884615 \n", - "Abnormality of the ocular adnexa [HP:0032039] 6 2.884615 \n", - "Abnormality of the orbital region [HP:0000315] 6 2.884615 \n", - "Abnormality of skin adnexa morphology [HP:0011138] 6 2.884615 \n", - "Neurodevelopmental delay [HP:0012758] 11 5.445545 \n", - "Attention deficit hyperactivity disorder [HP:00... 3 1.621622 \n", - "Short attention span [HP:0000736] 3 1.621622 \n", - "Hyperactivity [HP:0000752] 3 1.621622 \n", - "Abnormal facial shape [HP:0001999] 4 2.083333 \n", - "Triangular face [HP:0000325] 4 2.083333 \n", - "Abnormal nasal morphology [HP:0005105] 9 4.285714 \n", - "Abnormal external nose morphology [HP:0010938] 9 4.285714 \n", - "Abnormality of the nose [HP:0000366] 9 4.285714 \n", + "Phenotypic abnormality [HP:0000118] 19 5.828221 \n", + "All [HP:0000001] 19 5.828221 \n", + "Abnormal nervous system physiology [HP:0012638] 19 6.050955 \n", + "Abnormality of the nervous system [HP:0000707] 19 6.050955 \n", + "Abnormality of the ear [HP:0000598] 1 0.362319 \n", + "Neurodevelopmental abnormality [HP:0012759] 19 6.109325 \n", + "Abnormality of higher mental function [HP:0011446] 16 5.194805 \n", + "Intellectual disability [HP:0001249] 15 4.918033 \n", + "Abnormal ear morphology [HP:0031703] 1 0.387597 \n", + "Behavioral abnormality [HP:0000708] 4 1.581028 \n", + "Abnormality of the dentition [HP:0000164] 12 3.908795 \n", + "Abnormality of dental morphology [HP:0006482] 12 3.908795 \n", + "Abnormality of head or neck [HP:0000152] 14 4.458599 \n", + "Abnormality of the head [HP:0000234] 14 4.458599 \n", + "Abnormality of the face [HP:0000271] 14 4.458599 \n", + "Abnormality of the hand [HP:0001155] 8 2.572347 \n", + "Abnormality of the upper limb [HP:0002817] 8 2.572347 \n", + "Abnormality of limbs [HP:0040064] 8 2.572347 \n", + "Abnormal oral morphology [HP:0031816] 14 4.501608 \n", + "Abnormality of the mouth [HP:0000153] 14 4.501608 \n", + "Abnormal oral cavity morphology [HP:0000163] 14 4.501608 \n", + "Neurodevelopmental delay [HP:0012758] 11 4.104478 \n", + "Abnormal ear physiology [HP:0031704] 1 0.384615 \n", + "Hearing abnormality [HP:0000364] 1 0.384615 \n", + "Growth abnormality [HP:0001507] 5 1.672241 \n", + "Growth delay [HP:0001510] 5 1.672241 \n", + "Short stature [HP:0004322] 5 1.672241 \n", + "Abnormality of body height [HP:0000002] 5 1.672241 \n", + "Abnormal upper lip morphology [HP:0000177] 5 1.792115 \n", + "Abnormal lip morphology [HP:0000159] 5 1.792115 \n", + "Abnormality of the philtrum [HP:0000288] 5 1.792115 \n", + "Abnormal hair morphology [HP:0001595] 6 2.189781 \n", + "Abnormal ocular adnexa morphology [HP:0030669] 6 2.189781 \n", + "Abnormality of skin adnexa morphology [HP:0011138] 6 2.189781 \n", + "Abnormality of the ocular adnexa [HP:0032039] 6 2.189781 \n", + "Abnormality of the integument [HP:0001574] 6 2.189781 \n", + "Abnormality of the orbital region [HP:0000315] 6 2.189781 \n", + "Abnormal external nose morphology [HP:0010938] 9 3.260870 \n", + "Abnormal nasal morphology [HP:0005105] 9 3.260870 \n", + "Abnormality of the nose [HP:0000366] 9 3.260870 \n", + "Triangular face [HP:0000325] 4 1.556420 \n", + "Abnormal facial shape [HP:0001999] 4 1.556420 \n", "\n", ">=1 allele of the variant 16_89284634_89284639_GTGTTT_G \\\n", " p value \n", - "Phenotypic abnormality [HP:0000118] 0.009174 \n", - "All [HP:0000001] 0.009174 \n", - "Abnormality of higher mental function [HP:0011446] 0.019099 \n", - "Abnormal nervous system physiology [HP:0012638] 0.023529 \n", - "Abnormality of the nervous system [HP:0000707] 0.023529 \n", - "Intellectual disability [HP:0001249] 0.024041 \n", - "Neurodevelopmental abnormality [HP:0012759] 0.048016 \n", - "Abnormality of the ear [HP:0000598] 0.054405 \n", - "Abnormality of dental morphology [HP:0006482] 0.169816 \n", - "Abnormality of the dentition [HP:0000164] 0.169816 \n", - "Autistic behavior [HP:0000729] 0.175721 \n", - "Abnormality of head or neck [HP:0000152] 0.185604 \n", - "Abnormality of the head [HP:0000234] 0.185604 \n", - "Abnormality of the face [HP:0000271] 0.185604 \n", - "Behavioral abnormality [HP:0000708] 0.231875 \n", - "Abnormality of the upper limb [HP:0002817] 0.238015 \n", - "Abnormality of the hand [HP:0001155] 0.238015 \n", - "Abnormality of limbs [HP:0040064] 0.238015 \n", - "Abnormal oral morphology [HP:0031816] 0.252957 \n", - "Abnormal oral cavity morphology [HP:0000163] 0.252957 \n", - "Abnormality of the mouth [HP:0000153] 0.252957 \n", - "Abnormal ear physiology [HP:0031704] 0.319991 \n", - "Hearing impairment [HP:0000365] 0.319991 \n", - "Hearing abnormality [HP:0000364] 0.319991 \n", - "Abnormal ear morphology [HP:0031703] 0.322677 \n", - "Abnormality of the outer ear [HP:0000356] 0.322677 \n", - "Abnormality of the philtrum [HP:0000288] 0.361864 \n", - "Abnormal upper lip morphology [HP:0000177] 0.361864 \n", - "Long philtrum [HP:0000343] 0.361864 \n", - "Abnormal lip morphology [HP:0000159] 0.361864 \n", - "Growth delay [HP:0001510] 0.366424 \n", - "Abnormality of body height [HP:0000002] 0.366424 \n", - "Short stature [HP:0004322] 0.366424 \n", - "Growth abnormality [HP:0001507] 0.366424 \n", - "Abnormal eyebrow morphology [HP:0000534] 0.503161 \n", - "Abnormal hair morphology [HP:0001595] 0.503161 \n", - "Abnormal ocular adnexa morphology [HP:0030669] 0.503161 \n", - "Abnormality of the integument [HP:0001574] 0.503161 \n", - "Abnormality of the ocular adnexa [HP:0032039] 0.503161 \n", - "Abnormality of the orbital region [HP:0000315] 0.503161 \n", - "Abnormality of skin adnexa morphology [HP:0011138] 0.503161 \n", - "Neurodevelopmental delay [HP:0012758] 0.541222 \n", - "Attention deficit hyperactivity disorder [HP:00... 0.773679 \n", - "Short attention span [HP:0000736] 0.773679 \n", - "Hyperactivity [HP:0000752] 0.773679 \n", - "Abnormal facial shape [HP:0001999] 0.790818 \n", - "Triangular face [HP:0000325] 0.790818 \n", - "Abnormal nasal morphology [HP:0005105] 0.835742 \n", - "Abnormal external nose morphology [HP:0010938] 0.835742 \n", - "Abnormality of the nose [HP:0000366] 0.835742 \n", + "Phenotypic abnormality [HP:0000118] 0.004307 \n", + "All [HP:0000001] 0.004307 \n", + "Abnormal nervous system physiology [HP:0012638] 0.024006 \n", + "Abnormality of the nervous system [HP:0000707] 0.024006 \n", + "Abnormality of the ear [HP:0000598] 0.037354 \n", + "Neurodevelopmental abnormality [HP:0012759] 0.048989 \n", + "Abnormality of higher mental function [HP:0011446] 0.072214 \n", + "Intellectual disability [HP:0001249] 0.081272 \n", + "Abnormal ear morphology [HP:0031703] 0.218309 \n", + "Behavioral abnormality [HP:0000708] 0.241365 \n", + "Abnormality of the dentition [HP:0000164] 0.250659 \n", + "Abnormality of dental morphology [HP:0006482] 0.250659 \n", + "Abnormality of head or neck [HP:0000152] 0.265996 \n", + "Abnormality of the head [HP:0000234] 0.265996 \n", + "Abnormality of the face [HP:0000271] 0.265996 \n", + "Abnormality of the hand [HP:0001155] 0.326465 \n", + "Abnormality of the upper limb [HP:0002817] 0.326465 \n", + "Abnormality of limbs [HP:0040064] 0.326465 \n", + "Abnormal oral morphology [HP:0031816] 0.353865 \n", + "Abnormality of the mouth [HP:0000153] 0.353865 \n", + "Abnormal oral cavity morphology [HP:0000163] 0.353865 \n", + "Neurodevelopmental delay [HP:0012758] 0.425125 \n", + "Abnormal ear physiology [HP:0031704] 0.488225 \n", + "Hearing abnormality [HP:0000364] 0.488225 \n", + "Growth abnormality [HP:0001507] 0.496764 \n", + "Growth delay [HP:0001510] 0.496764 \n", + "Short stature [HP:0004322] 0.496764 \n", + "Abnormality of body height [HP:0000002] 0.496764 \n", + "Abnormal upper lip morphology [HP:0000177] 0.640576 \n", + "Abnormal lip morphology [HP:0000159] 0.640576 \n", + "Abnormality of the philtrum [HP:0000288] 0.640576 \n", + "Abnormal hair morphology [HP:0001595] 0.819529 \n", + "Abnormal ocular adnexa morphology [HP:0030669] 0.819529 \n", + "Abnormality of skin adnexa morphology [HP:0011138] 0.819529 \n", + "Abnormality of the ocular adnexa [HP:0032039] 0.819529 \n", + "Abnormality of the integument [HP:0001574] 0.819529 \n", + "Abnormality of the orbital region [HP:0000315] 0.819529 \n", + "Abnormal external nose morphology [HP:0010938] 0.833375 \n", + "Abnormal nasal morphology [HP:0005105] 0.833375 \n", + "Abnormality of the nose [HP:0000366] 0.833375 \n", + "Triangular face [HP:0000325] 1.000000 \n", + "Abnormal facial shape [HP:0001999] 1.000000 \n", "\n", ">=1 allele of the variant 16_89284634_89284639_GTGTTT_G \n", " Corrected p value \n", - "Phenotypic abnormality [HP:0000118] 0.200338 \n", - "All [HP:0000001] 0.200338 \n", - "Abnormality of higher mental function [HP:0011446] 0.200338 \n", - "Abnormal nervous system physiology [HP:0012638] 0.200338 \n", - "Abnormality of the nervous system [HP:0000707] 0.200338 \n", - "Intellectual disability [HP:0001249] 0.200338 \n", - "Neurodevelopmental abnormality [HP:0012759] 0.340029 \n", - "Abnormality of the ear [HP:0000598] 0.340029 \n", - "Abnormality of dental morphology [HP:0006482] 0.538860 \n", - "Abnormality of the dentition [HP:0000164] 0.538860 \n", - "Autistic behavior [HP:0000729] 0.538860 \n", - "Abnormality of head or neck [HP:0000152] 0.538860 \n", - "Abnormality of the head [HP:0000234] 0.538860 \n", - "Abnormality of the face [HP:0000271] 0.538860 \n", - "Behavioral abnormality [HP:0000708] 0.538860 \n", - "Abnormality of the upper limb [HP:0002817] 0.538860 \n", - "Abnormality of the hand [HP:0001155] 0.538860 \n", - "Abnormality of limbs [HP:0040064] 0.538860 \n", - "Abnormal oral morphology [HP:0031816] 0.538860 \n", - "Abnormal oral cavity morphology [HP:0000163] 0.538860 \n", - "Abnormality of the mouth [HP:0000153] 0.538860 \n", - "Abnormal ear physiology [HP:0031704] 0.538860 \n", - "Hearing impairment [HP:0000365] 0.538860 \n", - "Hearing abnormality [HP:0000364] 0.538860 \n", - "Abnormal ear morphology [HP:0031703] 0.538860 \n", - "Abnormality of the outer ear [HP:0000356] 0.538860 \n", - "Abnormality of the philtrum [HP:0000288] 0.538860 \n", - "Abnormal upper lip morphology [HP:0000177] 0.538860 \n", - "Long philtrum [HP:0000343] 0.538860 \n", - "Abnormal lip morphology [HP:0000159] 0.538860 \n", - "Growth delay [HP:0001510] 0.538860 \n", - "Abnormality of body height [HP:0000002] 0.538860 \n", - "Short stature [HP:0004322] 0.538860 \n", - "Growth abnormality [HP:0001507] 0.538860 \n", - "Abnormal eyebrow morphology [HP:0000534] 0.613611 \n", - "Abnormal hair morphology [HP:0001595] 0.613611 \n", - "Abnormal ocular adnexa morphology [HP:0030669] 0.613611 \n", - "Abnormality of the integument [HP:0001574] 0.613611 \n", - "Abnormality of the ocular adnexa [HP:0032039] 0.613611 \n", - "Abnormality of the orbital region [HP:0000315] 0.613611 \n", - "Abnormality of skin adnexa morphology [HP:0011138] 0.613611 \n", - "Neurodevelopmental delay [HP:0012758] 0.644312 \n", - "Attention deficit hyperactivity disorder [HP:00... 0.835742 \n", - "Short attention span [HP:0000736] 0.835742 \n", - "Hyperactivity [HP:0000752] 0.835742 \n", - "Abnormal facial shape [HP:0001999] 0.835742 \n", - "Triangular face [HP:0000325] 0.835742 \n", - "Abnormal nasal morphology [HP:0005105] 0.835742 \n", - "Abnormal external nose morphology [HP:0010938] 0.835742 \n", - "Abnormality of the nose [HP:0000366] 0.835742 " + "Phenotypic abnormality [HP:0000118] 0.090438 \n", + "All [HP:0000001] 0.090438 \n", + "Abnormal nervous system physiology [HP:0012638] 0.252063 \n", + "Abnormality of the nervous system [HP:0000707] 0.252063 \n", + "Abnormality of the ear [HP:0000598] 0.313770 \n", + "Neurodevelopmental abnormality [HP:0012759] 0.342924 \n", + "Abnormality of higher mental function [HP:0011446] 0.426679 \n", + "Intellectual disability [HP:0001249] 0.426679 \n", + "Abnormal ear morphology [HP:0031703] 0.707731 \n", + "Behavioral abnormality [HP:0000708] 0.707731 \n", + "Abnormality of the dentition [HP:0000164] 0.707731 \n", + "Abnormality of dental morphology [HP:0006482] 0.707731 \n", + "Abnormality of head or neck [HP:0000152] 0.707731 \n", + "Abnormality of the head [HP:0000234] 0.707731 \n", + "Abnormality of the face [HP:0000271] 0.707731 \n", + "Abnormality of the hand [HP:0001155] 0.707731 \n", + "Abnormality of the upper limb [HP:0002817] 0.707731 \n", + "Abnormality of limbs [HP:0040064] 0.707731 \n", + "Abnormal oral morphology [HP:0031816] 0.707731 \n", + "Abnormality of the mouth [HP:0000153] 0.707731 \n", + "Abnormal oral cavity morphology [HP:0000163] 0.707731 \n", + "Neurodevelopmental delay [HP:0012758] 0.745146 \n", + "Abnormal ear physiology [HP:0031704] 0.745146 \n", + "Hearing abnormality [HP:0000364] 0.745146 \n", + "Growth abnormality [HP:0001507] 0.745146 \n", + "Growth delay [HP:0001510] 0.745146 \n", + "Short stature [HP:0004322] 0.745146 \n", + "Abnormality of body height [HP:0000002] 0.745146 \n", + "Abnormal upper lip morphology [HP:0000177] 0.867877 \n", + "Abnormal lip morphology [HP:0000159] 0.867877 \n", + "Abnormality of the philtrum [HP:0000288] 0.867877 \n", + "Abnormal hair morphology [HP:0001595] 0.875043 \n", + "Abnormal ocular adnexa morphology [HP:0030669] 0.875043 \n", + "Abnormality of skin adnexa morphology [HP:0011138] 0.875043 \n", + "Abnormality of the ocular adnexa [HP:0032039] 0.875043 \n", + "Abnormality of the integument [HP:0001574] 0.875043 \n", + "Abnormality of the orbital region [HP:0000315] 0.875043 \n", + "Abnormal external nose morphology [HP:0010938] 0.875043 \n", + "Abnormal nasal morphology [HP:0005105] 0.875043 \n", + "Abnormality of the nose [HP:0000366] 0.875043 \n", + "Triangular face [HP:0000325] 1.000000 \n", + "Abnormal facial shape [HP:0001999] 1.000000 " ] }, - "execution_count": 27, + "execution_count": 22, "metadata": {}, "output_type": "execute_result" } @@ -2975,16 +2758,7 @@ " \n", " \n", " \n", - " Autistic behavior [HP:0000729]\n", - " 2\n", - " 5.714286\n", - " 2\n", - " 5.714286\n", - " 0.267571\n", - " 1.0\n", - " \n", - " \n", - " Abnormality of body height [HP:0000002]\n", + " Short stature [HP:0004322]\n", " 0\n", " 0.000000\n", " 5\n", @@ -2993,7 +2767,7 @@ " 1.0\n", " \n", " \n", - " Growth abnormality [HP:0001507]\n", + " Abnormality of body height [HP:0000002]\n", " 0\n", " 0.000000\n", " 5\n", @@ -3011,7 +2785,7 @@ " 1.0\n", " \n", " \n", - " Short stature [HP:0004322]\n", + " Growth abnormality [HP:0001507]\n", " 0\n", " 0.000000\n", " 5\n", @@ -3047,29 +2821,92 @@ " 1.0\n", " \n", " \n", - " Abnormal external nose morphology [HP:0010938]\n", - " 3\n", - " 7.692308\n", - " 9\n", - " 23.076923\n", + " Abnormal upper lip morphology [HP:0000177]\n", + " 2\n", + " 5.263158\n", + " 5\n", + " 13.157895\n", + " 1.000000\n", + " 1.0\n", + " \n", + " \n", + " Abnormality of the philtrum [HP:0000288]\n", + " 2\n", + " 5.263158\n", + " 5\n", + " 13.157895\n", + " 1.000000\n", + " 1.0\n", + " \n", + " \n", + " Abnormality of head or neck [HP:0000152]\n", + " 4\n", + " 9.523810\n", + " 14\n", + " 33.333333\n", + " 1.000000\n", + " 1.0\n", + " \n", + " \n", + " Abnormality of the head [HP:0000234]\n", + " 4\n", + " 9.523810\n", + " 14\n", + " 33.333333\n", " 1.000000\n", " 1.0\n", " \n", " \n", - " Short attention span [HP:0000736]\n", + " Abnormal ear morphology [HP:0031703]\n", " 0\n", " 0.000000\n", - " 3\n", - " 8.823529\n", + " 1\n", + " 2.857143\n", " 1.000000\n", " 1.0\n", " \n", " \n", - " Neurodevelopmental delay [HP:0012758]\n", - " 3\n", - " 8.108108\n", - " 11\n", - " 29.729730\n", + " Abnormality of the mouth [HP:0000153]\n", + " 4\n", + " 9.523810\n", + " 14\n", + " 33.333333\n", + " 1.000000\n", + " 1.0\n", + " \n", + " \n", + " Abnormal oral cavity morphology [HP:0000163]\n", + " 4\n", + " 9.523810\n", + " 14\n", + " 33.333333\n", + " 1.000000\n", + " 1.0\n", + " \n", + " \n", + " Abnormal ear physiology [HP:0031704]\n", + " 0\n", + " 0.000000\n", + " 1\n", + " 2.857143\n", + " 1.000000\n", + " 1.0\n", + " \n", + " \n", + " Abnormality of the dentition [HP:0000164]\n", + " 4\n", + " 10.000000\n", + " 12\n", + " 30.000000\n", + " 1.000000\n", + " 1.0\n", + " \n", + " \n", + " Abnormality of dental morphology [HP:0006482]\n", + " 4\n", + " 10.000000\n", + " 12\n", + " 30.000000\n", " 1.000000\n", " 1.0\n", " \n", @@ -3101,7 +2938,61 @@ " 1.0\n", " \n", " \n", - " Abnormality of the nose [HP:0000366]\n", + " Abnormal nervous system physiology [HP:0012638]\n", + " 6\n", + " 14.285714\n", + " 19\n", + " 45.238095\n", + " 1.000000\n", + " 1.0\n", + " \n", + " \n", + " Abnormal lip morphology [HP:0000159]\n", + " 2\n", + " 5.263158\n", + " 5\n", + " 13.157895\n", + " 1.000000\n", + " 1.0\n", + " \n", + " \n", + " Abnormality of the face [HP:0000271]\n", + " 4\n", + " 9.523810\n", + " 14\n", + " 33.333333\n", + " 1.000000\n", + " 1.0\n", + " \n", + " \n", + " Intellectual disability [HP:0001249]\n", + " 5\n", + " 12.195122\n", + " 15\n", + " 36.585366\n", + " 1.000000\n", + " 1.0\n", + " \n", + " \n", + " Abnormal oral morphology [HP:0031816]\n", + " 4\n", + " 9.523810\n", + " 14\n", + " 33.333333\n", + " 1.000000\n", + " 1.0\n", + " \n", + " \n", + " Neurodevelopmental delay [HP:0012758]\n", + " 3\n", + " 8.108108\n", + " 11\n", + " 29.729730\n", + " 1.000000\n", + " 1.0\n", + " \n", + " \n", + " Abnormal external nose morphology [HP:0010938]\n", " 3\n", " 7.692308\n", " 9\n", @@ -3119,20 +3010,11 @@ " 1.0\n", " \n", " \n", - " Abnormality of the face [HP:0000271]\n", - " 4\n", - " 9.523810\n", - " 14\n", - " 33.333333\n", - " 1.000000\n", - " 1.0\n", - " \n", - " \n", - " Intellectual disability [HP:0001249]\n", - " 5\n", - " 12.195122\n", - " 15\n", - " 36.585366\n", + " Abnormality of the nose [HP:0000366]\n", + " 3\n", + " 7.692308\n", + " 9\n", + " 23.076923\n", " 1.000000\n", " 1.0\n", " \n", @@ -3209,133 +3091,7 @@ " 1.0\n", " \n", " \n", - " Abnormality of head or neck [HP:0000152]\n", - " 4\n", - " 9.523810\n", - " 14\n", - " 33.333333\n", - " 1.000000\n", - " 1.0\n", - " \n", - " \n", - " Abnormal eyebrow morphology [HP:0000534]\n", - " 2\n", - " 5.263158\n", - " 6\n", - " 15.789474\n", - " 1.000000\n", - " 1.0\n", - " \n", - " \n", - " Abnormality of the philtrum [HP:0000288]\n", - " 2\n", - " 5.263158\n", - " 5\n", - " 13.157895\n", - " 1.000000\n", - " 1.0\n", - " \n", - " \n", - " Long philtrum [HP:0000343]\n", - " 2\n", - " 5.263158\n", - " 5\n", - " 13.157895\n", - " 1.000000\n", - " 1.0\n", - " \n", - " \n", - " Abnormal oral cavity morphology [HP:0000163]\n", - " 4\n", - " 9.523810\n", - " 14\n", - " 33.333333\n", - " 1.000000\n", - " 1.0\n", - " \n", - " \n", - " Abnormal oral morphology [HP:0031816]\n", - " 4\n", - " 9.523810\n", - " 14\n", - " 33.333333\n", - " 1.000000\n", - " 1.0\n", - " \n", - " \n", - " Abnormality of the mouth [HP:0000153]\n", - " 4\n", - " 9.523810\n", - " 14\n", - " 33.333333\n", - " 1.000000\n", - " 1.0\n", - " \n", - " \n", - " Abnormality of the outer ear [HP:0000356]\n", - " 0\n", - " 0.000000\n", - " 1\n", - " 2.857143\n", - " 1.000000\n", - " 1.0\n", - " \n", - " \n", - " Abnormal ear morphology [HP:0031703]\n", - " 0\n", - " 0.000000\n", - " 1\n", - " 2.857143\n", - " 1.000000\n", - " 1.0\n", - " \n", - " \n", - " Abnormality of the ear [HP:0000598]\n", - " 0\n", - " 0.000000\n", - " 1\n", - " 2.857143\n", - " 1.000000\n", - " 1.0\n", - " \n", - " \n", - " Abnormality of dental morphology [HP:0006482]\n", - " 4\n", - " 10.000000\n", - " 12\n", - " 30.000000\n", - " 1.000000\n", - " 1.0\n", - " \n", - " \n", - " Abnormality of the dentition [HP:0000164]\n", - " 4\n", - " 10.000000\n", - " 12\n", - " 30.000000\n", - " 1.000000\n", - " 1.0\n", - " \n", - " \n", - " Abnormal nervous system physiology [HP:0012638]\n", - " 6\n", - " 14.285714\n", - " 19\n", - " 45.238095\n", - " 1.000000\n", - " 1.0\n", - " \n", - " \n", - " Hearing impairment [HP:0000365]\n", - " 0\n", - " 0.000000\n", - " 1\n", - " 2.857143\n", - " 1.000000\n", - " 1.0\n", - " \n", - " \n", - " Abnormal ear physiology [HP:0031704]\n", + " Hearing abnormality [HP:0000364]\n", " 0\n", " 0.000000\n", " 1\n", @@ -3344,7 +3100,7 @@ " 1.0\n", " \n", " \n", - " Abnormality of the hand [HP:0001155]\n", + " Abnormality of limbs [HP:0040064]\n", " 2\n", " 4.761905\n", " 8\n", @@ -3362,52 +3118,7 @@ " 1.0\n", " \n", " \n", - " Abnormality of limbs [HP:0040064]\n", - " 2\n", - " 4.761905\n", - " 8\n", - " 19.047619\n", - " 1.000000\n", - " 1.0\n", - " \n", - " \n", - " Attention deficit hyperactivity disorder [HP:0007018]\n", - " 0\n", - " 0.000000\n", - " 3\n", - " 8.823529\n", - " 1.000000\n", - " 1.0\n", - " \n", - " \n", - " Abnormal lip morphology [HP:0000159]\n", - " 2\n", - " 5.263158\n", - " 5\n", - " 13.157895\n", - " 1.000000\n", - " 1.0\n", - " \n", - " \n", - " Abnormal upper lip morphology [HP:0000177]\n", - " 2\n", - " 5.263158\n", - " 5\n", - " 13.157895\n", - " 1.000000\n", - " 1.0\n", - " \n", - " \n", - " Abnormality of the head [HP:0000234]\n", - " 4\n", - " 9.523810\n", - " 14\n", - " 33.333333\n", - " 1.000000\n", - " 1.0\n", - " \n", - " \n", - " Hearing abnormality [HP:0000364]\n", + " Abnormality of the ear [HP:0000598]\n", " 0\n", " 0.000000\n", " 1\n", @@ -3416,11 +3127,11 @@ " 1.0\n", " \n", " \n", - " Hyperactivity [HP:0000752]\n", - " 0\n", - " 0.000000\n", - " 3\n", - " 8.823529\n", + " Abnormality of the hand [HP:0001155]\n", + " 2\n", + " 4.761905\n", + " 8\n", + " 19.047619\n", " 1.000000\n", " 1.0\n", " \n", @@ -3431,24 +3142,35 @@ "text/plain": [ ">=1 allele of either variant 16_89284129_89284134_CTTTTT_C or variant 16_89284634_89284639_GTGTTT_G First \\\n", " Count \n", - "Autistic behavior [HP:0000729] 2 \n", + "Short stature [HP:0004322] 0 \n", "Abnormality of body height [HP:0000002] 0 \n", - "Growth abnormality [HP:0001507] 0 \n", "Growth delay [HP:0001510] 0 \n", - "Short stature [HP:0004322] 0 \n", + "Growth abnormality [HP:0001507] 0 \n", "Behavioral abnormality [HP:0000708] 2 \n", "Neurodevelopmental abnormality [HP:0012759] 5 \n", "Abnormality of higher mental function [HP:0011446] 6 \n", - "Abnormal external nose morphology [HP:0010938] 3 \n", - "Short attention span [HP:0000736] 0 \n", - "Neurodevelopmental delay [HP:0012758] 3 \n", + "Abnormal upper lip morphology [HP:0000177] 2 \n", + "Abnormality of the philtrum [HP:0000288] 2 \n", + "Abnormality of head or neck [HP:0000152] 4 \n", + "Abnormality of the head [HP:0000234] 4 \n", + "Abnormal ear morphology [HP:0031703] 0 \n", + "Abnormality of the mouth [HP:0000153] 4 \n", + "Abnormal oral cavity morphology [HP:0000163] 4 \n", + "Abnormal ear physiology [HP:0031704] 0 \n", + "Abnormality of the dentition [HP:0000164] 4 \n", + "Abnormality of dental morphology [HP:0006482] 4 \n", "All [HP:0000001] 6 \n", "Phenotypic abnormality [HP:0000118] 6 \n", "Abnormality of the nervous system [HP:0000707] 6 \n", - "Abnormality of the nose [HP:0000366] 3 \n", - "Abnormal nasal morphology [HP:0005105] 3 \n", + "Abnormal nervous system physiology [HP:0012638] 6 \n", + "Abnormal lip morphology [HP:0000159] 2 \n", "Abnormality of the face [HP:0000271] 4 \n", "Intellectual disability [HP:0001249] 5 \n", + "Abnormal oral morphology [HP:0031816] 4 \n", + "Neurodevelopmental delay [HP:0012758] 3 \n", + "Abnormal external nose morphology [HP:0010938] 3 \n", + "Abnormal nasal morphology [HP:0005105] 3 \n", + "Abnormality of the nose [HP:0000366] 3 \n", "Triangular face [HP:0000325] 1 \n", "Abnormal facial shape [HP:0001999] 1 \n", "Abnormal hair morphology [HP:0001595] 2 \n", @@ -3457,51 +3179,43 @@ "Abnormality of the ocular adnexa [HP:0032039] 2 \n", "Abnormality of the integument [HP:0001574] 2 \n", "Abnormality of the orbital region [HP:0000315] 2 \n", - "Abnormality of head or neck [HP:0000152] 4 \n", - "Abnormal eyebrow morphology [HP:0000534] 2 \n", - "Abnormality of the philtrum [HP:0000288] 2 \n", - "Long philtrum [HP:0000343] 2 \n", - "Abnormal oral cavity morphology [HP:0000163] 4 \n", - "Abnormal oral morphology [HP:0031816] 4 \n", - "Abnormality of the mouth [HP:0000153] 4 \n", - "Abnormality of the outer ear [HP:0000356] 0 \n", - "Abnormal ear morphology [HP:0031703] 0 \n", + "Hearing abnormality [HP:0000364] 0 \n", + "Abnormality of limbs [HP:0040064] 2 \n", + "Abnormality of the upper limb [HP:0002817] 2 \n", "Abnormality of the ear [HP:0000598] 0 \n", - "Abnormality of dental morphology [HP:0006482] 4 \n", - "Abnormality of the dentition [HP:0000164] 4 \n", - "Abnormal nervous system physiology [HP:0012638] 6 \n", - "Hearing impairment [HP:0000365] 0 \n", - "Abnormal ear physiology [HP:0031704] 0 \n", "Abnormality of the hand [HP:0001155] 2 \n", - "Abnormality of the upper limb [HP:0002817] 2 \n", - "Abnormality of limbs [HP:0040064] 2 \n", - "Attention deficit hyperactivity disorder [HP:00... 0 \n", - "Abnormal lip morphology [HP:0000159] 2 \n", - "Abnormal upper lip morphology [HP:0000177] 2 \n", - "Abnormality of the head [HP:0000234] 4 \n", - "Hearing abnormality [HP:0000364] 0 \n", - "Hyperactivity [HP:0000752] 0 \n", "\n", ">=1 allele of either variant 16_89284129_89284134_CTTTTT_C or variant 16_89284634_89284639_GTGTTT_G \\\n", " Percent \n", - "Autistic behavior [HP:0000729] 5.714286 \n", + "Short stature [HP:0004322] 0.000000 \n", "Abnormality of body height [HP:0000002] 0.000000 \n", - "Growth abnormality [HP:0001507] 0.000000 \n", "Growth delay [HP:0001510] 0.000000 \n", - "Short stature [HP:0004322] 0.000000 \n", + "Growth abnormality [HP:0001507] 0.000000 \n", "Behavioral abnormality [HP:0000708] 5.714286 \n", "Neurodevelopmental abnormality [HP:0012759] 11.904762 \n", "Abnormality of higher mental function [HP:0011446] 14.634146 \n", - "Abnormal external nose morphology [HP:0010938] 7.692308 \n", - "Short attention span [HP:0000736] 0.000000 \n", - "Neurodevelopmental delay [HP:0012758] 8.108108 \n", + "Abnormal upper lip morphology [HP:0000177] 5.263158 \n", + "Abnormality of the philtrum [HP:0000288] 5.263158 \n", + "Abnormality of head or neck [HP:0000152] 9.523810 \n", + "Abnormality of the head [HP:0000234] 9.523810 \n", + "Abnormal ear morphology [HP:0031703] 0.000000 \n", + "Abnormality of the mouth [HP:0000153] 9.523810 \n", + "Abnormal oral cavity morphology [HP:0000163] 9.523810 \n", + "Abnormal ear physiology [HP:0031704] 0.000000 \n", + "Abnormality of the dentition [HP:0000164] 10.000000 \n", + "Abnormality of dental morphology [HP:0006482] 10.000000 \n", "All [HP:0000001] 14.285714 \n", "Phenotypic abnormality [HP:0000118] 14.285714 \n", "Abnormality of the nervous system [HP:0000707] 14.285714 \n", - "Abnormality of the nose [HP:0000366] 7.692308 \n", - "Abnormal nasal morphology [HP:0005105] 7.692308 \n", + "Abnormal nervous system physiology [HP:0012638] 14.285714 \n", + "Abnormal lip morphology [HP:0000159] 5.263158 \n", "Abnormality of the face [HP:0000271] 9.523810 \n", "Intellectual disability [HP:0001249] 12.195122 \n", + "Abnormal oral morphology [HP:0031816] 9.523810 \n", + "Neurodevelopmental delay [HP:0012758] 8.108108 \n", + "Abnormal external nose morphology [HP:0010938] 7.692308 \n", + "Abnormal nasal morphology [HP:0005105] 7.692308 \n", + "Abnormality of the nose [HP:0000366] 7.692308 \n", "Triangular face [HP:0000325] 2.857143 \n", "Abnormal facial shape [HP:0001999] 2.857143 \n", "Abnormal hair morphology [HP:0001595] 5.263158 \n", @@ -3510,51 +3224,43 @@ "Abnormality of the ocular adnexa [HP:0032039] 5.263158 \n", "Abnormality of the integument [HP:0001574] 5.263158 \n", "Abnormality of the orbital region [HP:0000315] 5.263158 \n", - "Abnormality of head or neck [HP:0000152] 9.523810 \n", - "Abnormal eyebrow morphology [HP:0000534] 5.263158 \n", - "Abnormality of the philtrum [HP:0000288] 5.263158 \n", - "Long philtrum [HP:0000343] 5.263158 \n", - "Abnormal oral cavity morphology [HP:0000163] 9.523810 \n", - "Abnormal oral morphology [HP:0031816] 9.523810 \n", - "Abnormality of the mouth [HP:0000153] 9.523810 \n", - "Abnormality of the outer ear [HP:0000356] 0.000000 \n", - "Abnormal ear morphology [HP:0031703] 0.000000 \n", + "Hearing abnormality [HP:0000364] 0.000000 \n", + "Abnormality of limbs [HP:0040064] 4.761905 \n", + "Abnormality of the upper limb [HP:0002817] 4.761905 \n", "Abnormality of the ear [HP:0000598] 0.000000 \n", - "Abnormality of dental morphology [HP:0006482] 10.000000 \n", - "Abnormality of the dentition [HP:0000164] 10.000000 \n", - "Abnormal nervous system physiology [HP:0012638] 14.285714 \n", - "Hearing impairment [HP:0000365] 0.000000 \n", - "Abnormal ear physiology [HP:0031704] 0.000000 \n", "Abnormality of the hand [HP:0001155] 4.761905 \n", - "Abnormality of the upper limb [HP:0002817] 4.761905 \n", - "Abnormality of limbs [HP:0040064] 4.761905 \n", - "Attention deficit hyperactivity disorder [HP:00... 0.000000 \n", - "Abnormal lip morphology [HP:0000159] 5.263158 \n", - "Abnormal upper lip morphology [HP:0000177] 5.263158 \n", - "Abnormality of the head [HP:0000234] 9.523810 \n", - "Hearing abnormality [HP:0000364] 0.000000 \n", - "Hyperactivity [HP:0000752] 0.000000 \n", "\n", ">=1 allele of either variant 16_89284129_89284134_CTTTTT_C or variant 16_89284634_89284639_GTGTTT_G Second \\\n", " Count \n", - "Autistic behavior [HP:0000729] 2 \n", + "Short stature [HP:0004322] 5 \n", "Abnormality of body height [HP:0000002] 5 \n", - "Growth abnormality [HP:0001507] 5 \n", "Growth delay [HP:0001510] 5 \n", - "Short stature [HP:0004322] 5 \n", + "Growth abnormality [HP:0001507] 5 \n", "Behavioral abnormality [HP:0000708] 4 \n", "Neurodevelopmental abnormality [HP:0012759] 19 \n", "Abnormality of higher mental function [HP:0011446] 16 \n", - "Abnormal external nose morphology [HP:0010938] 9 \n", - "Short attention span [HP:0000736] 3 \n", - "Neurodevelopmental delay [HP:0012758] 11 \n", + "Abnormal upper lip morphology [HP:0000177] 5 \n", + "Abnormality of the philtrum [HP:0000288] 5 \n", + "Abnormality of head or neck [HP:0000152] 14 \n", + "Abnormality of the head [HP:0000234] 14 \n", + "Abnormal ear morphology [HP:0031703] 1 \n", + "Abnormality of the mouth [HP:0000153] 14 \n", + "Abnormal oral cavity morphology [HP:0000163] 14 \n", + "Abnormal ear physiology [HP:0031704] 1 \n", + "Abnormality of the dentition [HP:0000164] 12 \n", + "Abnormality of dental morphology [HP:0006482] 12 \n", "All [HP:0000001] 19 \n", "Phenotypic abnormality [HP:0000118] 19 \n", "Abnormality of the nervous system [HP:0000707] 19 \n", - "Abnormality of the nose [HP:0000366] 9 \n", - "Abnormal nasal morphology [HP:0005105] 9 \n", + "Abnormal nervous system physiology [HP:0012638] 19 \n", + "Abnormal lip morphology [HP:0000159] 5 \n", "Abnormality of the face [HP:0000271] 14 \n", "Intellectual disability [HP:0001249] 15 \n", + "Abnormal oral morphology [HP:0031816] 14 \n", + "Neurodevelopmental delay [HP:0012758] 11 \n", + "Abnormal external nose morphology [HP:0010938] 9 \n", + "Abnormal nasal morphology [HP:0005105] 9 \n", + "Abnormality of the nose [HP:0000366] 9 \n", "Triangular face [HP:0000325] 4 \n", "Abnormal facial shape [HP:0001999] 4 \n", "Abnormal hair morphology [HP:0001595] 6 \n", @@ -3563,51 +3269,43 @@ "Abnormality of the ocular adnexa [HP:0032039] 6 \n", "Abnormality of the integument [HP:0001574] 6 \n", "Abnormality of the orbital region [HP:0000315] 6 \n", - "Abnormality of head or neck [HP:0000152] 14 \n", - "Abnormal eyebrow morphology [HP:0000534] 6 \n", - "Abnormality of the philtrum [HP:0000288] 5 \n", - "Long philtrum [HP:0000343] 5 \n", - "Abnormal oral cavity morphology [HP:0000163] 14 \n", - "Abnormal oral morphology [HP:0031816] 14 \n", - "Abnormality of the mouth [HP:0000153] 14 \n", - "Abnormality of the outer ear [HP:0000356] 1 \n", - "Abnormal ear morphology [HP:0031703] 1 \n", + "Hearing abnormality [HP:0000364] 1 \n", + "Abnormality of limbs [HP:0040064] 8 \n", + "Abnormality of the upper limb [HP:0002817] 8 \n", "Abnormality of the ear [HP:0000598] 1 \n", - "Abnormality of dental morphology [HP:0006482] 12 \n", - "Abnormality of the dentition [HP:0000164] 12 \n", - "Abnormal nervous system physiology [HP:0012638] 19 \n", - "Hearing impairment [HP:0000365] 1 \n", - "Abnormal ear physiology [HP:0031704] 1 \n", "Abnormality of the hand [HP:0001155] 8 \n", - "Abnormality of the upper limb [HP:0002817] 8 \n", - "Abnormality of limbs [HP:0040064] 8 \n", - "Attention deficit hyperactivity disorder [HP:00... 3 \n", - "Abnormal lip morphology [HP:0000159] 5 \n", - "Abnormal upper lip morphology [HP:0000177] 5 \n", - "Abnormality of the head [HP:0000234] 14 \n", - "Hearing abnormality [HP:0000364] 1 \n", - "Hyperactivity [HP:0000752] 3 \n", "\n", ">=1 allele of either variant 16_89284129_89284134_CTTTTT_C or variant 16_89284634_89284639_GTGTTT_G \\\n", " Percent \n", - "Autistic behavior [HP:0000729] 5.714286 \n", + "Short stature [HP:0004322] 12.820513 \n", "Abnormality of body height [HP:0000002] 12.820513 \n", - "Growth abnormality [HP:0001507] 12.820513 \n", "Growth delay [HP:0001510] 12.820513 \n", - "Short stature [HP:0004322] 12.820513 \n", + "Growth abnormality [HP:0001507] 12.820513 \n", "Behavioral abnormality [HP:0000708] 11.428571 \n", "Neurodevelopmental abnormality [HP:0012759] 45.238095 \n", "Abnormality of higher mental function [HP:0011446] 39.024390 \n", - "Abnormal external nose morphology [HP:0010938] 23.076923 \n", - "Short attention span [HP:0000736] 8.823529 \n", - "Neurodevelopmental delay [HP:0012758] 29.729730 \n", + "Abnormal upper lip morphology [HP:0000177] 13.157895 \n", + "Abnormality of the philtrum [HP:0000288] 13.157895 \n", + "Abnormality of head or neck [HP:0000152] 33.333333 \n", + "Abnormality of the head [HP:0000234] 33.333333 \n", + "Abnormal ear morphology [HP:0031703] 2.857143 \n", + "Abnormality of the mouth [HP:0000153] 33.333333 \n", + "Abnormal oral cavity morphology [HP:0000163] 33.333333 \n", + "Abnormal ear physiology [HP:0031704] 2.857143 \n", + "Abnormality of the dentition [HP:0000164] 30.000000 \n", + "Abnormality of dental morphology [HP:0006482] 30.000000 \n", "All [HP:0000001] 45.238095 \n", "Phenotypic abnormality [HP:0000118] 45.238095 \n", "Abnormality of the nervous system [HP:0000707] 45.238095 \n", - "Abnormality of the nose [HP:0000366] 23.076923 \n", - "Abnormal nasal morphology [HP:0005105] 23.076923 \n", + "Abnormal nervous system physiology [HP:0012638] 45.238095 \n", + "Abnormal lip morphology [HP:0000159] 13.157895 \n", "Abnormality of the face [HP:0000271] 33.333333 \n", "Intellectual disability [HP:0001249] 36.585366 \n", + "Abnormal oral morphology [HP:0031816] 33.333333 \n", + "Neurodevelopmental delay [HP:0012758] 29.729730 \n", + "Abnormal external nose morphology [HP:0010938] 23.076923 \n", + "Abnormal nasal morphology [HP:0005105] 23.076923 \n", + "Abnormality of the nose [HP:0000366] 23.076923 \n", "Triangular face [HP:0000325] 11.428571 \n", "Abnormal facial shape [HP:0001999] 11.428571 \n", "Abnormal hair morphology [HP:0001595] 15.789474 \n", @@ -3616,51 +3314,43 @@ "Abnormality of the ocular adnexa [HP:0032039] 15.789474 \n", "Abnormality of the integument [HP:0001574] 15.789474 \n", "Abnormality of the orbital region [HP:0000315] 15.789474 \n", - "Abnormality of head or neck [HP:0000152] 33.333333 \n", - "Abnormal eyebrow morphology [HP:0000534] 15.789474 \n", - "Abnormality of the philtrum [HP:0000288] 13.157895 \n", - "Long philtrum [HP:0000343] 13.157895 \n", - "Abnormal oral cavity morphology [HP:0000163] 33.333333 \n", - "Abnormal oral morphology [HP:0031816] 33.333333 \n", - "Abnormality of the mouth [HP:0000153] 33.333333 \n", - "Abnormality of the outer ear [HP:0000356] 2.857143 \n", - "Abnormal ear morphology [HP:0031703] 2.857143 \n", + "Hearing abnormality [HP:0000364] 2.857143 \n", + "Abnormality of limbs [HP:0040064] 19.047619 \n", + "Abnormality of the upper limb [HP:0002817] 19.047619 \n", "Abnormality of the ear [HP:0000598] 2.857143 \n", - "Abnormality of dental morphology [HP:0006482] 30.000000 \n", - "Abnormality of the dentition [HP:0000164] 30.000000 \n", - "Abnormal nervous system physiology [HP:0012638] 45.238095 \n", - "Hearing impairment [HP:0000365] 2.857143 \n", - "Abnormal ear physiology [HP:0031704] 2.857143 \n", "Abnormality of the hand [HP:0001155] 19.047619 \n", - "Abnormality of the upper limb [HP:0002817] 19.047619 \n", - "Abnormality of limbs [HP:0040064] 19.047619 \n", - "Attention deficit hyperactivity disorder [HP:00... 8.823529 \n", - "Abnormal lip morphology [HP:0000159] 13.157895 \n", - "Abnormal upper lip morphology [HP:0000177] 13.157895 \n", - "Abnormality of the head [HP:0000234] 33.333333 \n", - "Hearing abnormality [HP:0000364] 2.857143 \n", - "Hyperactivity [HP:0000752] 8.823529 \n", "\n", ">=1 allele of either variant 16_89284129_89284134_CTTTTT_C or variant 16_89284634_89284639_GTGTTT_G \\\n", " p value \n", - "Autistic behavior [HP:0000729] 0.267571 \n", + "Short stature [HP:0004322] 0.562802 \n", "Abnormality of body height [HP:0000002] 0.562802 \n", - "Growth abnormality [HP:0001507] 0.562802 \n", "Growth delay [HP:0001510] 0.562802 \n", - "Short stature [HP:0004322] 0.562802 \n", + "Growth abnormality [HP:0001507] 0.562802 \n", "Behavioral abnormality [HP:0000708] 0.635267 \n", "Neurodevelopmental abnormality [HP:0012759] 0.720095 \n", "Abnormality of higher mental function [HP:0011446] 0.726865 \n", - "Abnormal external nose morphology [HP:0010938] 1.000000 \n", - "Short attention span [HP:0000736] 1.000000 \n", - "Neurodevelopmental delay [HP:0012758] 1.000000 \n", + "Abnormal upper lip morphology [HP:0000177] 1.000000 \n", + "Abnormality of the philtrum [HP:0000288] 1.000000 \n", + "Abnormality of head or neck [HP:0000152] 1.000000 \n", + "Abnormality of the head [HP:0000234] 1.000000 \n", + "Abnormal ear morphology [HP:0031703] 1.000000 \n", + "Abnormality of the mouth [HP:0000153] 1.000000 \n", + "Abnormal oral cavity morphology [HP:0000163] 1.000000 \n", + "Abnormal ear physiology [HP:0031704] 1.000000 \n", + "Abnormality of the dentition [HP:0000164] 1.000000 \n", + "Abnormality of dental morphology [HP:0006482] 1.000000 \n", "All [HP:0000001] 1.000000 \n", "Phenotypic abnormality [HP:0000118] 1.000000 \n", "Abnormality of the nervous system [HP:0000707] 1.000000 \n", - "Abnormality of the nose [HP:0000366] 1.000000 \n", - "Abnormal nasal morphology [HP:0005105] 1.000000 \n", + "Abnormal nervous system physiology [HP:0012638] 1.000000 \n", + "Abnormal lip morphology [HP:0000159] 1.000000 \n", "Abnormality of the face [HP:0000271] 1.000000 \n", "Intellectual disability [HP:0001249] 1.000000 \n", + "Abnormal oral morphology [HP:0031816] 1.000000 \n", + "Neurodevelopmental delay [HP:0012758] 1.000000 \n", + "Abnormal external nose morphology [HP:0010938] 1.000000 \n", + "Abnormal nasal morphology [HP:0005105] 1.000000 \n", + "Abnormality of the nose [HP:0000366] 1.000000 \n", "Triangular face [HP:0000325] 1.000000 \n", "Abnormal facial shape [HP:0001999] 1.000000 \n", "Abnormal hair morphology [HP:0001595] 1.000000 \n", @@ -3669,51 +3359,43 @@ "Abnormality of the ocular adnexa [HP:0032039] 1.000000 \n", "Abnormality of the integument [HP:0001574] 1.000000 \n", "Abnormality of the orbital region [HP:0000315] 1.000000 \n", - "Abnormality of head or neck [HP:0000152] 1.000000 \n", - "Abnormal eyebrow morphology [HP:0000534] 1.000000 \n", - "Abnormality of the philtrum [HP:0000288] 1.000000 \n", - "Long philtrum [HP:0000343] 1.000000 \n", - "Abnormal oral cavity morphology [HP:0000163] 1.000000 \n", - "Abnormal oral morphology [HP:0031816] 1.000000 \n", - "Abnormality of the mouth [HP:0000153] 1.000000 \n", - "Abnormality of the outer ear [HP:0000356] 1.000000 \n", - "Abnormal ear morphology [HP:0031703] 1.000000 \n", + "Hearing abnormality [HP:0000364] 1.000000 \n", + "Abnormality of limbs [HP:0040064] 1.000000 \n", + "Abnormality of the upper limb [HP:0002817] 1.000000 \n", "Abnormality of the ear [HP:0000598] 1.000000 \n", - "Abnormality of dental morphology [HP:0006482] 1.000000 \n", - "Abnormality of the dentition [HP:0000164] 1.000000 \n", - "Abnormal nervous system physiology [HP:0012638] 1.000000 \n", - "Hearing impairment [HP:0000365] 1.000000 \n", - "Abnormal ear physiology [HP:0031704] 1.000000 \n", "Abnormality of the hand [HP:0001155] 1.000000 \n", - "Abnormality of the upper limb [HP:0002817] 1.000000 \n", - "Abnormality of limbs [HP:0040064] 1.000000 \n", - "Attention deficit hyperactivity disorder [HP:00... 1.000000 \n", - "Abnormal lip morphology [HP:0000159] 1.000000 \n", - "Abnormal upper lip morphology [HP:0000177] 1.000000 \n", - "Abnormality of the head [HP:0000234] 1.000000 \n", - "Hearing abnormality [HP:0000364] 1.000000 \n", - "Hyperactivity [HP:0000752] 1.000000 \n", "\n", ">=1 allele of either variant 16_89284129_89284134_CTTTTT_C or variant 16_89284634_89284639_GTGTTT_G \n", " Corrected p value \n", - "Autistic behavior [HP:0000729] 1.0 \n", + "Short stature [HP:0004322] 1.0 \n", "Abnormality of body height [HP:0000002] 1.0 \n", - "Growth abnormality [HP:0001507] 1.0 \n", "Growth delay [HP:0001510] 1.0 \n", - "Short stature [HP:0004322] 1.0 \n", + "Growth abnormality [HP:0001507] 1.0 \n", "Behavioral abnormality [HP:0000708] 1.0 \n", "Neurodevelopmental abnormality [HP:0012759] 1.0 \n", "Abnormality of higher mental function [HP:0011446] 1.0 \n", - "Abnormal external nose morphology [HP:0010938] 1.0 \n", - "Short attention span [HP:0000736] 1.0 \n", - "Neurodevelopmental delay [HP:0012758] 1.0 \n", + "Abnormal upper lip morphology [HP:0000177] 1.0 \n", + "Abnormality of the philtrum [HP:0000288] 1.0 \n", + "Abnormality of head or neck [HP:0000152] 1.0 \n", + "Abnormality of the head [HP:0000234] 1.0 \n", + "Abnormal ear morphology [HP:0031703] 1.0 \n", + "Abnormality of the mouth [HP:0000153] 1.0 \n", + "Abnormal oral cavity morphology [HP:0000163] 1.0 \n", + "Abnormal ear physiology [HP:0031704] 1.0 \n", + "Abnormality of the dentition [HP:0000164] 1.0 \n", + "Abnormality of dental morphology [HP:0006482] 1.0 \n", "All [HP:0000001] 1.0 \n", "Phenotypic abnormality [HP:0000118] 1.0 \n", "Abnormality of the nervous system [HP:0000707] 1.0 \n", - "Abnormality of the nose [HP:0000366] 1.0 \n", - "Abnormal nasal morphology [HP:0005105] 1.0 \n", + "Abnormal nervous system physiology [HP:0012638] 1.0 \n", + "Abnormal lip morphology [HP:0000159] 1.0 \n", "Abnormality of the face [HP:0000271] 1.0 \n", "Intellectual disability [HP:0001249] 1.0 \n", + "Abnormal oral morphology [HP:0031816] 1.0 \n", + "Neurodevelopmental delay [HP:0012758] 1.0 \n", + "Abnormal external nose morphology [HP:0010938] 1.0 \n", + "Abnormal nasal morphology [HP:0005105] 1.0 \n", + "Abnormality of the nose [HP:0000366] 1.0 \n", "Triangular face [HP:0000325] 1.0 \n", "Abnormal facial shape [HP:0001999] 1.0 \n", "Abnormal hair morphology [HP:0001595] 1.0 \n", @@ -3722,30 +3404,11 @@ "Abnormality of the ocular adnexa [HP:0032039] 1.0 \n", "Abnormality of the integument [HP:0001574] 1.0 \n", "Abnormality of the orbital region [HP:0000315] 1.0 \n", - "Abnormality of head or neck [HP:0000152] 1.0 \n", - "Abnormal eyebrow morphology [HP:0000534] 1.0 \n", - "Abnormality of the philtrum [HP:0000288] 1.0 \n", - "Long philtrum [HP:0000343] 1.0 \n", - "Abnormal oral cavity morphology [HP:0000163] 1.0 \n", - "Abnormal oral morphology [HP:0031816] 1.0 \n", - "Abnormality of the mouth [HP:0000153] 1.0 \n", - "Abnormality of the outer ear [HP:0000356] 1.0 \n", - "Abnormal ear morphology [HP:0031703] 1.0 \n", - "Abnormality of the ear [HP:0000598] 1.0 \n", - "Abnormality of dental morphology [HP:0006482] 1.0 \n", - "Abnormality of the dentition [HP:0000164] 1.0 \n", - "Abnormal nervous system physiology [HP:0012638] 1.0 \n", - "Hearing impairment [HP:0000365] 1.0 \n", - "Abnormal ear physiology [HP:0031704] 1.0 \n", - "Abnormality of the hand [HP:0001155] 1.0 \n", - "Abnormality of the upper limb [HP:0002817] 1.0 \n", - "Abnormality of limbs [HP:0040064] 1.0 \n", - "Attention deficit hyperactivity disorder [HP:00... 1.0 \n", - "Abnormal lip morphology [HP:0000159] 1.0 \n", - "Abnormal upper lip morphology [HP:0000177] 1.0 \n", - "Abnormality of the head [HP:0000234] 1.0 \n", "Hearing abnormality [HP:0000364] 1.0 \n", - "Hyperactivity [HP:0000752] 1.0 " + "Abnormality of limbs [HP:0040064] 1.0 \n", + "Abnormality of the upper limb [HP:0002817] 1.0 \n", + "Abnormality of the ear [HP:0000598] 1.0 \n", + "Abnormality of the hand [HP:0001155] 1.0 " ] }, "execution_count": 24, @@ -3758,74 +3421,6 @@ "summary_vd.sort_values(('','p value'))" ] }, - { - "cell_type": "code", - "execution_count": 25, - "id": "f306c5ef", - "metadata": {}, - "outputs": [ - { - "ename": "NameError", - "evalue": "name 'CohortAnalysis' is not defined", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[25], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m analysis2 \u001b[38;5;241m=\u001b[39m \u001b[43mCohortAnalysis\u001b[49m(patientCohort, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mNM_013275.6\u001b[39m\u001b[38;5;124m'\u001b[39m, hpo, include_unmeasured\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m, include_large_SV\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m, \n\u001b[1;32m 2\u001b[0m p_val_correction\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mfdr_bh\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 4\u001b[0m analysis2\u001b[38;5;241m.\u001b[39mcompare_by_exon(\u001b[38;5;241m9\u001b[39m)\n", - "\u001b[0;31mNameError\u001b[0m: name 'CohortAnalysis' is not defined" - ] - } - ], - "source": [ - "analysis2 = CohortAnalysis(patientCohort, 'NM_013275.6', hpo, include_unmeasured=False, include_large_SV=False, \n", - " p_val_correction='fdr_bh')\n", - "\n", - "analysis2.compare_by_exon(9)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "f6861157", - "metadata": {}, - "outputs": [], - "source": [ - "from genophenocorr.model import FeatureType" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "d3c6fd9d", - "metadata": {}, - "outputs": [], - "source": [ - "analysis2.compare_by_protein_feature_type(FeatureType.REGION)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "a97a6a09", - "metadata": {}, - "outputs": [], - "source": [ - "patientCohort.get_protein_features_affected('NM_013275.6')" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "e7e51324", - "metadata": {}, - "outputs": [], - "source": [ - "for var in patientCohort.all_variants:\n", - " print(var.variant_string)\n", - " for tx in var.tx_annotations:\n", - " print(tx.is_preferred)" - ] - }, { "cell_type": "code", "execution_count": null, diff --git a/notebooks/RPGRIP1/RPGRIP1_Beryoskin_PMID_34722527_RunGenoPhenoCorr.ipynb b/notebooks/RPGRIP1/RPGRIP1_Beryoskin_PMID_34722527_RunGenoPhenoCorr.ipynb index c225791e..f5c9ffdc 100644 --- a/notebooks/RPGRIP1/RPGRIP1_Beryoskin_PMID_34722527_RunGenoPhenoCorr.ipynb +++ b/notebooks/RPGRIP1/RPGRIP1_Beryoskin_PMID_34722527_RunGenoPhenoCorr.ipynb @@ -72,17 +72,7 @@ "execution_count": 6, "id": "b0533219", "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Patient 237–523 has unknown alternative variant GNNNN and will not be included.\n", - "Patient 79–194 has unknown alternative variant GNNNN and will not be included.\n", - "Expected at least one variant per patient, but received none for patient 79–194\n" - ] - } - ], + "outputs": [], "source": [ "patientCohort = load_phenopacket_folder(fpath_phenopackets, phenotype_creator)" ] @@ -96,125 +86,124 @@ { "data": { "text/plain": [ - "[('14_21312458_A/-', 25),\n", - " ('14_21312434_deletion', 9),\n", - " ('14_21302531_G/-', 8),\n", - " ('14_21345145_C/T', 8),\n", - " ('14_21325252_G/A', 7),\n", - " ('14_21345140_AAGGCCG/-', 7),\n", - " ('14_21327672_-/T', 6),\n", - " ('14_21303542_C/T', 5),\n", - " ('14_21325265_A/G', 5),\n", - " ('14_21348211_AAAG/-', 4),\n", - " ('14_21326131_C/T', 4),\n", - " ('14_21326545_TTTTTAGTAGAGATGGGATTTCTCCATGTTGGTCAGGCTGGTCTTCAACTCCCGACCTCAGGTGAACCTCCCACCTGAGCCTCCCAAAGTGCTGGGATTACAGACGTGAGCCACCGCGCCTGGCTGAACAAACTTTTTCAAGCTCTGTAATGCTGTCTAGTATCTGTCTTTACTAAAGGCCTGTTGTTTCTTAGTGCATGACTACATAGATATCTGATTATAAACTGAGACCTTAACACTCCCCCATCATTCTCTCACTTCTTTTAAACACTGGACACAAGTTAGAGAGATTTCCACACCAGATCATGACAAACACAAATTTCTTGGATTTTTTTTTTCCTCCCAATGTGGAGCTGAGCTCCATACTGTCTTTCCTAACTTTTATACCTAGGATTGTGGGGGTGTACCAAGAGGGGTCAACTCTTTGACTACAGTCCTGGGAGGGTGAGGTGGGGGTATCCATGTTTTCCTTAGGAAGTGGGGATAGCTGCAGTCAGAAACAACCATATTTAACAAGATTCTGGATGCTCCAGGACATGTATGCAGCTCTCTCCTCAATACAACTGCTTAAAAAAAGGCTGACACTTCTGGACACAACTCCTTTGCCAAACAGGGGAGGCAGTATAAGCCACCTGTTAATCAGTGTTACAAATCAGACATCTGGCATTTCGAAAGAGCCATTTTGCTTAAGTTTTCTTGGGACCACTTGAGGGTAGAGGTAACAGTTTTCTTGGTACAACTAAGGCACAGTAAGCATTTGATAATAGTAATAATAATGCAGCCTTGTTCATTGGCTGGATGACTGATGACAAGCAAGCTGTACTCCTTTTCATACACCCTTCACTATCTCTTCCTGAATCCTAGAGATAACCCATCTTCCCTGATTAATATTCTAACTGCACTGCTGTTTGATTTTACTTCTGAGTGTATCATCATCGTAATTATTTAATGGATGTTAATTAATTGCTGATAAAATATGTTGAAATTAAAAATGGGAAGGAAGTAGATAAGGTGCTGACAAATGCTCACTTGCTTATTTCATGTGATCAGGTCTTATTAATATCTGTTTGTTTCTCAGGTGATTTTAACCTCACTGACCCTGCAGAGAAACCCAACGGATCTATTCAAGTGCAACTGGATTGGAAGTTTCCCTACATACCCCCTGAGAGCTTCCTGAAACCAGAAGCTCAGACTAAGGGGAAGGATACCAAGGACAGTTCAAAGATCTCATCTGAAGAGGAAAAGGCTTCATTTCCTTCCCAGGTAACTCTCCAGGACTCCACAGGTAGCAGATCTCTGCCAATCCTATGGAGCAGATTTGAAGGAGACAGTATTATAG/-',\n", + "[('14_21312457_21312458_GA_G', 25),\n", + " ('14_21312434_21327807_DEL', 9),\n", + " ('14_21345145_21345145_C_T', 8),\n", + " ('14_21302530_21302531_AG_A', 8),\n", + " ('14_21325252_21325252_G_A', 7),\n", + " ('14_21345139_21345146_CAAGGCCG_C', 7),\n", + " ('14_21327671_21327672_A_AT', 6),\n", + " ('14_21303542_21303542_C_T', 5),\n", + " ('14_21325265_21325265_A_G', 5),\n", + " ('14_21326131_21326131_C_T', 4),\n", + " ('14_21327800_21327801_CT_C', 4),\n", + " ('14_21348210_21348214_AAAAG_A', 4),\n", + " ('14_21326544_21327883_ATTTTTAGTAGAGATGGGATTTCTCCATGTTGGTCAGGCTGGTCTTCAACTCCCGACCTCAGGTGAACCTCCCACCTGAGCCTCCCAAAGTGCTGGGATTACAGACGTGAGCCACCGCGCCTGGCTGAACAAACTTTTTCAAGCTCTGTAATGCTGTCTAGTATCTGTCTTTACTAAAGGCCTGTTGTTTCTTAGTGCATGACTACATAGATATCTGATTATAAACTGAGACCTTAACACTCCCCCATCATTCTCTCACTTCTTTTAAACACTGGACACAAGTTAGAGAGATTTCCACACCAGATCATGACAAACACAAATTTCTTGGATTTTTTTTTTCCTCCCAATGTGGAGCTGAGCTCCATACTGTCTTTCCTAACTTTTATACCTAGGATTGTGGGGGTGTACCAAGAGGGGTCAACTCTTTGACTACAGTCCTGGGAGGGTGAGGTGGGGGTATCCATGTTTTCCTTAGGAAGTGGGGATAGCTGCAGTCAGAAACAACCATATTTAACAAGATTCTGGATGCTCCAGGACATGTATGCAGCTCTCTCCTCAATACAACTGCTTAAAAAAAGGCTGACACTTCTGGACACAACTCCTTTGCCAAACAGGGGAGGCAGTATAAGCCACCTGTTAATCAGTGTTACAAATCAGACATCTGGCATTTCGAAAGAGCCATTTTGCTTAAGTTTTCTTGGGACCACTTGAGGGTAGAGGTAACAGTTTTCTTGGTACAACTAAGGCACAGTAAGCATTTGATAATAGTAATAATAATGCAGCCTTGTTCATTGGCTGGATGACTGATGACAAGCAAGCTGTACTCCTTTTCATACACCCTTCACTATCTCTTCCTGAATCCTAGAGATAACCCATCTTCCCTGATTAATATTCTAACTGCACTGCTGTTTGATTTTACTTCTGAGTGTATCATCATCGTAATTATTTAATGGATGTTAATTAATTGCTGATAAAATATGTTGAAATTAAAAATGGGAAGGAAGTAGATAAGGTGCTGACAAATGCTCACTTGCTTATTTCATGTGATCAGGTCTTATTAATATCTGTTTGTTTCTCAGGTGATTTTAACCTCACTGACCCTGCAGAGAAACCCAACGGATCTATTCAAGTGCAACTGGATTGGAAGTTTCCCTACATACCCCCTGAGAGCTTCCTGAAACCAGAAGCTCAGACTAAGGGGAAGGATACCAAGGACAGTTCAAAGATCTCATCTGAAGAGGAAAAGGCTTCATTTCCTTCCCAGGTAACTCTCCAGGACTCCACAGGTAGCAGATCTCTGCCAATCCTATGGAGCAGATTTGAAGGAGACAGTATTATAG_A',\n", " 4),\n", - " ('14_21327801_T/-', 4),\n", - " ('14_21326055_T/G', 3),\n", - " ('14_21328463_C/T', 3),\n", - " ('14_21326072_-/A', 3),\n", - " ('14_21317850_G/T', 3),\n", - " ('14_21294785_G/A', 3),\n", - " ('14_21326125_C/T', 3),\n", - " ('14_21321856_GGAACTGGAG/-', 3),\n", - " ('14_21328469_C/T', 3),\n", - " ('14_21301105_C/T', 3),\n", - " ('14_21325318_C/T', 3),\n", - " ('14_21294745_C/T', 3),\n", - " ('14_21325311_C/A', 2),\n", - " ('14_21317760_C/-', 2),\n", - " ('14_21301114_C/T', 2),\n", - " ('14_21324867_G/A', 2),\n", - " ('14_21325880_C/T', 2),\n", - " ('14_21307824_AG/-', 2),\n", - " ('14_21325405_G/-', 2),\n", - " ('14_21312439_GAGA/-', 2),\n", - " ('14_21303510_C/G', 2),\n", - " ('14_21327708_-/T', 2),\n", - " ('14_21326119_C/T', 2),\n", - " ('14_21325241_GA/-', 2),\n", - " ('14_21301238_G/T', 2),\n", - " ('14_21317769_C/T', 2),\n", - " ('14_21317724_C/T', 2),\n", - " ('14_21324876_C/A', 2),\n", - " ('14_21312466_C/T', 2),\n", - " ('14_21302508_T/-', 2),\n", - " ('14_21320155_T/A', 2),\n", - " ('14_21325330_C/T', 2),\n", - " ('14_21320178_G/T', 2),\n", - " ('14_21324747_A/T', 2),\n", - " ('14_21321257_A/G', 2),\n", - " ('14_21325943_G/T', 2),\n", - " ('14_21326017_C/T', 2),\n", - " ('14_21334696_T/A', 2),\n", - " ('14_21312440_-/A', 2),\n", - " ('14_21351103_G/T', 2),\n", - " ('14_21303544_G/A', 2),\n", - " ('14_21348186_T/A', 2),\n", - " ('14_21317778_C/T', 2),\n", - " ('14_21321929_C/T', 1),\n", - " ('14_21326031_-/T', 1),\n", - " ('14_21348184_-/G', 1),\n", - " ('14_21303543_G/A', 1),\n", - " ('14_21324747_A/C', 1),\n", - " ('14_21325931_A/G', 1),\n", - " ('14_21343084_G/C', 1),\n", - " ('14_21325832_deletion', 1),\n", - " ('14_21321316_C/T', 1),\n", - " ('14_21303373_A/-', 1),\n", - " ('14_21321865_G/-', 1),\n", - " ('14_21312468_A/-', 1),\n", - " ('14_21348167_TTTAG/-', 1),\n", - " ('14_21324616_A/G', 1),\n", - " ('14_21325903_C/T', 1),\n", - " ('14_21280084_deletion', 1),\n", - " ('14_21317847_A/T', 1),\n", - " ('14_21307704_AGAATAATTTAGCGCCTTTCTCTGCAGAGCTTCCATTAAAGAGAAGGTAGAGCTGATTCGACTTAAGA/-',\n", + " ('14_21326055_21326055_T_G', 3),\n", + " ('14_21326071_21326072_T_TA', 3),\n", + " ('14_21325318_21325318_C_T', 3),\n", + " ('14_21294745_21294745_C_T', 3),\n", + " ('14_21328469_21328469_C_T', 3),\n", + " ('14_21321855_21321865_AGGAACTGGAG_A', 3),\n", + " ('14_21301105_21301105_C_T', 3),\n", + " ('14_21326125_21326125_C_T', 3),\n", + " ('14_21328463_21328463_C_T', 3),\n", + " ('14_21317850_21317850_G_T', 3),\n", + " ('14_21294785_21294785_G_A', 3),\n", + " ('14_21312438_21312440_G_GGA', 2),\n", + " ('14_21351103_21351103_G_T', 2),\n", + " ('14_21325880_21325880_C_T', 2),\n", + " ('14_21324876_21324876_C_A', 2),\n", + " ('14_21317769_21317769_C_T', 2),\n", + " ('14_21321257_21321257_A_G', 2),\n", + " ('14_21348186_21348186_T_A', 2),\n", + " ('14_21325240_21325242_GGA_G', 2),\n", + " ('14_21324747_21324747_A_T', 2),\n", + " ('14_21317778_21317778_C_T', 2),\n", + " ('14_21307823_21307825_CAG_C', 2),\n", + " ('14_21325404_21325405_AG_A', 2),\n", + " ('14_21320178_21320178_G_T', 2),\n", + " ('14_21303544_21303544_G_A', 2),\n", + " ('14_21301114_21301114_C_T', 2),\n", + " ('14_21334696_21334696_T_A', 2),\n", + " ('14_21327707_21327708_C_CT', 2),\n", + " ('14_21325311_21325311_C_A', 2),\n", + " ('14_21312466_21312466_C_T', 2),\n", + " ('14_21317759_21317760_GC_G', 2),\n", + " ('14_21325943_21325943_G_T', 2),\n", + " ('14_21317724_21317724_C_T', 2),\n", + " ('14_21312438_21312442_GGAGA_G', 2),\n", + " ('14_21303510_21303510_C_G', 2),\n", + " ('14_21326119_21326119_C_T', 2),\n", + " ('14_21324867_21324867_G_A', 2),\n", + " ('14_21301238_21301238_G_T', 2),\n", + " ('14_21326017_21326017_C_T', 2),\n", + " ('14_21320155_21320155_T_A', 2),\n", + " ('14_21325330_21325330_C_T', 2),\n", + " ('14_21302507_21302508_CT_C', 2),\n", + " ('14_21310608_21310608_G_A', 1),\n", + " ('14_21312500_21312500_T_A', 1),\n", + " ('14_21343054_21343054_A_G', 1),\n", + " ('14_21280084_21343228_DEL', 1),\n", + " ('14_21324875_21324875_C_T', 1),\n", + " ('14_21294674_21294674_T_G', 1),\n", + " ('14_21327670_21327670_C_T', 1),\n", + " ('14_21324747_21324747_A_C', 1),\n", + " ('14_21324934_21324934_C_G', 1),\n", + " ('14_21325063_21325088_ACTGATTGGTAAGTGCCGTTGGCTTC_A', 1),\n", + " ('14_21287940_21288061_DUP', 1),\n", + " ('14_21326029_21326031_C_CTT', 1),\n", + " ('14_21348183_21348184_C_CG', 1),\n", + " ('14_21328499_21328500_GA_G', 1),\n", + " ('14_21326018_21326018_G_A', 1),\n", + " ('14_21348174_21348174_T_G', 1),\n", + " ('14_21301166_21301167_AG_A', 1),\n", + " ('14_21321291_21321295_A_ACTGT', 1),\n", + " ('14_21325898_21325898_G_A', 1),\n", + " ('14_21311823_21311824_GA_G', 1),\n", + " ('14_21325903_21325903_C_T', 1),\n", + " ('14_21325931_21325931_A_G', 1),\n", + " ('14_21300989_21300989_T_A', 1),\n", + " ('14_21312487_21312490_TATG_T', 1),\n", + " ('14_21312467_21312468_GA_G', 1),\n", + " ('14_21320157_21320157_C_T', 1),\n", + " ('14_21326107_21326107_C_T', 1),\n", + " ('14_21325276_21325277_CT_C', 1),\n", + " ('14_21348166_21348171_TTTTAG_T', 1),\n", + " ('14_21327626_21327627_A_AT', 1),\n", + " ('14_21321864_21321865_AG_A', 1),\n", + " ('14_21326039_21326041_C_CTT', 1),\n", + " ('14_21302585_21302585_G_C', 1),\n", + " ('14_21325832_21328627_DEL', 1),\n", + " ('14_21312500_21312504_TAGAA_T', 1),\n", + " ('14_21325927_21325931_C_CCATA', 1),\n", + " ('14_21343084_21343084_G_C', 1),\n", + " ('14_21280084_21288061_DUP', 1),\n", + " ('14_21326174_21326174_G_A', 1),\n", + " ('14_21321402_21321402_G_A', 1),\n", + " ('14_21303372_21303373_TA_T', 1),\n", + " ('14_21325372_21325372_C_T', 1),\n", + " ('14_21303453_21303454_CA_C', 1),\n", + " ('14_21303543_21303543_G_A', 1),\n", + " ('14_21325253_21325253_G_A', 1),\n", + " ('14_21317754_21317754_G_T', 1),\n", + " ('14_21311854_21311858_G_GCCCT', 1),\n", + " ('14_21321316_21321316_C_T', 1),\n", + " ('14_21345188_21345189_AT_A', 1),\n", + " ('14_21325861_21325861_G_A', 1),\n", + " ('14_21324912_21324913_C_CA', 1),\n", + " ('14_21324616_21324616_A_G', 1),\n", + " ('14_21348303_21348303_G_A', 1),\n", + " ('14_21351187_21351190_AAGG_A', 1),\n", + " ('14_21321929_21321929_C_T', 1),\n", + " ('14_21330247_21330386_AGCAGGTGAATTACACTGAGTGGAAGTTCTCAGAGACTAACAGCTTCATAGGTGATGGCTTTAAAAATCAGCACGAGGAAGAGGAAATGACATTATCCCATTCAGCACTGAAACAGAAGGAACCTCTACATCCTGTAAAT_A',\n", " 1),\n", - " ('14_21343054_A/G', 1),\n", - " ('14_21326107_C/T', 1),\n", - " ('14_21310608_G/A', 1),\n", - " ('14_129365_deletion', 1),\n", - " ('14_21348174_T/G', 1),\n", - " ('14_21326018_G/A', 1),\n", - " ('14_21280084_duplication', 1),\n", - " ('14_21325277_T/-', 1),\n", - " ('14_21325861_G/A', 1),\n", - " ('14_21324913_-/A', 1),\n", - " ('14_21330248_GCAGGTGAATTACACTGAGTGGAAGTTCTCAGAGACTAACAGCTTCATAGGTGATGGCTTTAAAAATCAGCACGAGGAAGAGGAAATGACATTATCCCATTCAGCACTGAAACAGAAGGAACCTCTACATCCTGTAAAT/-',\n", - " 1),\n", - " ('14_21327670_C/T', 1),\n", - " ('14_21294674_T/G', 1),\n", - " ('14_21345189_T/-', 1),\n", - " ('14_21320157_C/T', 1),\n", - " ('14_21325372_C/T', 1),\n", - " ('14_21326174_G/A', 1),\n", - " ('14_21300989_T/A', 1),\n", - " ('14_21301167_G/-', 1),\n", - " ('14_21324875_C/T', 1),\n", - " ('14_21312488_ATG/-', 1),\n", - " ('14_21312501_AGAA/-', 1),\n", - " ('14_21325931_-/A', 1),\n", - " ('14_21326041_-/T', 1),\n", - " ('14_21345198_G/A', 1),\n", - " ('14_21311824_A/-', 1),\n", - " ('14_21327627_-/T', 1),\n", - " ('14_21287940_duplication', 1),\n", - " ('14_21303454_A/-', 1),\n", - " ('14_21324865_-/G', 1),\n", - " ('14_21325253_G/A', 1),\n", - " ('14_21324934_C/G', 1),\n", - " ('14_21325064_CTGATTGGTAAGTGCCGTTGGCTTC/-', 1),\n", - " ('14_21312500_T/A', 1),\n", - " ('14_21317754_G/T', 1),\n", - " ('14_21311858_-/T', 1),\n", - " ('14_21348303_G/A', 1),\n", - " ('14_21351188_AGG/-', 1),\n", - " ('14_21321295_-/T', 1),\n", - " ('14_21321402_G/A', 1),\n", - " ('14_21302585_G/C', 1),\n", - " ('14_21325898_G/A', 1),\n", - " ('14_21328500_A/-', 1)]" + " ('14_21324864_21324865_T_TG', 1),\n", + " ('14_21345198_21345198_G_A', 1),\n", + " ('14_21317847_21317847_A_T', 1),\n", + " ('14_21307703_21307771_CAGAATAATTTAGCGCCTTTCTCTGCAGAGCTTCCATTAAAGAGAAGGTAGAGCTGATTCGACTTAAGA_C',\n", + " 1)]" ] }, "execution_count": 7, @@ -235,94 +224,94 @@ { "data": { "text/plain": [ - "{'NM_001377949.1': Counter({'intron_variant': 47,\n", - " 'frameshift_variant': 16,\n", - " 'splice_acceptor_variant': 7,\n", - " 'splice_region_variant': 5,\n", - " 'stop_gained': 18,\n", - " 'missense_variant': 4,\n", - " 'splice_donor_variant': 5,\n", - " 'feature_truncation': 4,\n", - " 'coding_sequence_variant': 7,\n", - " '5_prime_UTR_variant': 3,\n", - " 'inframe_deletion': 1,\n", - " 'splice_donor_5th_base_variant': 2,\n", - " 'synonymous_variant': 1,\n", - " 'splice_polypyrimidine_tract_variant': 1}),\n", - " 'NM_001377948.1': Counter({'frameshift_variant': 24,\n", - " 'splice_acceptor_variant': 7,\n", - " 'missense_variant': 22,\n", - " 'splice_region_variant': 5,\n", - " 'stop_gained': 30,\n", - " 'intron_variant': 9,\n", - " 'splice_donor_variant': 7,\n", - " 'feature_truncation': 4,\n", - " 'coding_sequence_variant': 8,\n", - " '5_prime_UTR_variant': 3,\n", - " 'inframe_deletion': 1,\n", - " 'splice_donor_5th_base_variant': 3,\n", - " 'synonymous_variant': 1,\n", - " 'splice_polypyrimidine_tract_variant': 1}),\n", - " 'NM_001377950.1': Counter({'intron_variant': 49,\n", - " 'frameshift_variant': 16,\n", - " 'splice_acceptor_variant': 6,\n", - " 'splice_region_variant': 5,\n", - " 'stop_gained': 18,\n", - " 'missense_variant': 4,\n", - " 'splice_donor_variant': 5,\n", - " 'feature_truncation': 4,\n", - " 'coding_sequence_variant': 7,\n", - " '5_prime_UTR_variant': 3,\n", - " 'inframe_deletion': 1,\n", - " 'splice_donor_5th_base_variant': 2,\n", - " 'synonymous_variant': 1,\n", - " 'splice_polypyrimidine_tract_variant': 1}),\n", - " 'NM_001377523.1': Counter({'intron_variant': 48,\n", - " 'frameshift_variant': 16,\n", - " 'splice_acceptor_variant': 6,\n", - " 'splice_region_variant': 5,\n", - " 'stop_gained': 18,\n", - " 'missense_variant': 4,\n", - " 'splice_donor_variant': 5,\n", - " 'feature_truncation': 4,\n", - " 'coding_sequence_variant': 7,\n", - " '5_prime_UTR_variant': 3,\n", - " 'inframe_deletion': 1,\n", - " 'splice_donor_5th_base_variant': 2,\n", - " 'synonymous_variant': 1,\n", - " 'splice_polypyrimidine_tract_variant': 1}),\n", - " 'NM_001377951.1': Counter({'intron_variant': 48,\n", - " 'frameshift_variant': 14,\n", - " 'splice_acceptor_variant': 6,\n", - " 'splice_region_variant': 4,\n", - " '5_prime_UTR_variant': 7,\n", - " 'upstream_gene_variant': 9,\n", - " 'stop_gained': 8,\n", - " 'missense_variant': 3,\n", - " 'splice_donor_variant': 5,\n", - " 'feature_truncation': 4,\n", - " 'coding_sequence_variant': 7,\n", - " 'inframe_deletion': 1,\n", - " 'splice_donor_5th_base_variant': 2,\n", - " 'synonymous_variant': 1,\n", - " 'splice_polypyrimidine_tract_variant': 1}),\n", - " 'NM_020366.4': Counter({'frameshift_variant': 38,\n", - " 'splice_acceptor_variant': 8,\n", - " 'missense_variant': 23,\n", - " 'splice_region_variant': 11,\n", - " 'stop_gained': 43,\n", - " 'intron_variant': 12,\n", - " 'inframe_deletion': 2,\n", - " 'splice_donor_variant': 12,\n", - " 'splice_polypyrimidine_tract_variant': 2,\n", - " 'coding_sequence_variant': 11,\n", - " 'start_lost': 3,\n", - " 'feature_truncation': 4,\n", - " 'start_retained_variant': 3,\n", - " '5_prime_UTR_variant': 3,\n", - " 'splice_donor_5th_base_variant': 3,\n", - " 'feature_elongation': 2,\n", - " 'synonymous_variant': 1})}" + "{'NM_001377949.1': Counter({'INTRON_VARIANT': 85,\n", + " 'FEATURE_TRUNCATION': 11,\n", + " 'CODING_SEQUENCE_VARIANT': 16,\n", + " 'FIVE_PRIME_UTR_VARIANT': 10,\n", + " 'SPLICE_ACCEPTOR_VARIANT': 11,\n", + " 'SPLICE_DONOR_VARIANT': 8,\n", + " 'SPLICE_DONOR_5TH_BASE_VARIANT': 4,\n", + " 'FRAMESHIFT_VARIANT': 34,\n", + " 'SPLICE_REGION_VARIANT': 8,\n", + " 'STOP_GAINED': 31,\n", + " 'MISSENSE_VARIANT': 7,\n", + " 'SYNONYMOUS_VARIANT': 1,\n", + " 'INFRAME_DELETION': 1,\n", + " 'SPLICE_POLYPYRIMIDINE_TRACT_VARIANT': 1}),\n", + " 'NM_020366.4': Counter({'MISSENSE_VARIANT': 40,\n", + " 'FEATURE_TRUNCATION': 11,\n", + " 'CODING_SEQUENCE_VARIANT': 20,\n", + " 'INTRON_VARIANT': 22,\n", + " 'STOP_GAINED': 76,\n", + " 'FRAMESHIFT_VARIANT': 93,\n", + " 'SPLICE_ACCEPTOR_VARIANT': 12,\n", + " 'SPLICE_DONOR_VARIANT': 16,\n", + " 'SPLICE_DONOR_5TH_BASE_VARIANT': 5,\n", + " 'SPLICE_REGION_VARIANT': 17,\n", + " 'START_LOST': 3,\n", + " 'FEATURE_ELONGATION': 2,\n", + " 'START_RETAINED_VARIANT': 3,\n", + " 'FIVE_PRIME_UTR_VARIANT': 3,\n", + " 'SYNONYMOUS_VARIANT': 1,\n", + " 'SPLICE_POLYPYRIMIDINE_TRACT_VARIANT': 2,\n", + " 'INFRAME_DELETION': 2}),\n", + " 'NM_001377950.1': Counter({'INTRON_VARIANT': 87,\n", + " 'FEATURE_TRUNCATION': 11,\n", + " 'CODING_SEQUENCE_VARIANT': 16,\n", + " 'FIVE_PRIME_UTR_VARIANT': 10,\n", + " 'SPLICE_ACCEPTOR_VARIANT': 10,\n", + " 'SPLICE_DONOR_VARIANT': 8,\n", + " 'SPLICE_DONOR_5TH_BASE_VARIANT': 4,\n", + " 'FRAMESHIFT_VARIANT': 34,\n", + " 'SPLICE_REGION_VARIANT': 8,\n", + " 'STOP_GAINED': 31,\n", + " 'MISSENSE_VARIANT': 7,\n", + " 'SYNONYMOUS_VARIANT': 1,\n", + " 'INFRAME_DELETION': 1,\n", + " 'SPLICE_POLYPYRIMIDINE_TRACT_VARIANT': 1}),\n", + " 'NM_001377948.1': Counter({'MISSENSE_VARIANT': 39,\n", + " 'FEATURE_TRUNCATION': 11,\n", + " 'CODING_SEQUENCE_VARIANT': 17,\n", + " 'FIVE_PRIME_UTR_VARIANT': 10,\n", + " 'INTRON_VARIANT': 19,\n", + " 'STOP_GAINED': 54,\n", + " 'SPLICE_ACCEPTOR_VARIANT': 11,\n", + " 'SPLICE_DONOR_VARIANT': 10,\n", + " 'SPLICE_DONOR_5TH_BASE_VARIANT': 5,\n", + " 'FRAMESHIFT_VARIANT': 45,\n", + " 'SPLICE_REGION_VARIANT': 8,\n", + " 'SYNONYMOUS_VARIANT': 1,\n", + " 'INFRAME_DELETION': 1,\n", + " 'SPLICE_POLYPYRIMIDINE_TRACT_VARIANT': 1}),\n", + " 'NM_001377523.1': Counter({'INTRON_VARIANT': 86,\n", + " 'FEATURE_TRUNCATION': 11,\n", + " 'CODING_SEQUENCE_VARIANT': 16,\n", + " 'FIVE_PRIME_UTR_VARIANT': 10,\n", + " 'SPLICE_ACCEPTOR_VARIANT': 10,\n", + " 'SPLICE_DONOR_VARIANT': 8,\n", + " 'SPLICE_DONOR_5TH_BASE_VARIANT': 4,\n", + " 'FRAMESHIFT_VARIANT': 34,\n", + " 'SPLICE_REGION_VARIANT': 8,\n", + " 'STOP_GAINED': 31,\n", + " 'MISSENSE_VARIANT': 7,\n", + " 'SYNONYMOUS_VARIANT': 1,\n", + " 'INFRAME_DELETION': 1,\n", + " 'SPLICE_POLYPYRIMIDINE_TRACT_VARIANT': 1}),\n", + " 'NM_001377951.1': Counter({'INTRON_VARIANT': 86,\n", + " 'FEATURE_TRUNCATION': 11,\n", + " 'CODING_SEQUENCE_VARIANT': 16,\n", + " 'FIVE_PRIME_UTR_VARIANT': 15,\n", + " 'SPLICE_ACCEPTOR_VARIANT': 10,\n", + " 'SPLICE_DONOR_VARIANT': 8,\n", + " 'SPLICE_DONOR_5TH_BASE_VARIANT': 4,\n", + " 'FRAMESHIFT_VARIANT': 31,\n", + " 'SPLICE_REGION_VARIANT': 5,\n", + " 'STOP_GAINED': 19,\n", + " 'UPSTREAM_GENE_VARIANT': 13,\n", + " 'SYNONYMOUS_VARIANT': 1,\n", + " 'MISSENSE_VARIANT': 4,\n", + " 'INFRAME_DELETION': 1,\n", + " 'SPLICE_POLYPYRIMIDINE_TRACT_VARIANT': 1})}" ] }, "execution_count": 8, @@ -346,28 +335,28 @@ }, { "cell_type": "code", - "execution_count": 18, - "id": "ef5b47de", + "execution_count": 12, + "id": "3a3ddcdc", "metadata": {}, "outputs": [], "source": [ - "rec_analysis = CohortAnalysis(patientCohort, 'NM_020366.4', hpo, recessive=True, include_unmeasured=False)" + "from genophenocorr.model import VariantEffect\n", + "from genophenocorr.model import FeatureType" ] }, { "cell_type": "code", - "execution_count": 19, - "id": "3a3ddcdc", + "execution_count": 10, + "id": "ef5b47de", "metadata": {}, "outputs": [], "source": [ - "from genophenocorr.constants import VariantEffect\n", - "from genophenocorr.model import FeatureType" + "rec_analysis = CohortAnalysis(patientCohort, 'NM_020366.4', hpo, recessive=True, include_unmeasured=False)" ] }, { "cell_type": "code", - "execution_count": 20, + "execution_count": 14, "id": "19112877", "metadata": {}, "outputs": [ @@ -399,9 +388,9 @@ " \n", " \n", " \n", - " Homozygous frameshift_variant\n", - " Heterozygous frameshift_variant\n", - " No frameshift_variant\n", + " Homozygous missense_variant\n", + " Heterozygous missense_variant\n", + " No missense_variant\n", " \n", " \n", " \n", @@ -418,102 +407,95 @@ " \n", " \n", " \n", - " HP:0001483 (Eye poking)\n", - " 21\n", - " 84.00%\n", - " 2\n", - " 100.00%\n", - " 5\n", - " 41.67%\n", - " 0.024229\n", - " 0.096914\n", - " \n", - " \n", " HP:0012758 (Neurodevelopmental delay)\n", - " 8\n", - " 11.94%\n", " 0\n", " 0.00%\n", - " 4\n", - " 3.31%\n", - " 0.038327\n", - " 0.153306\n", + " 0\n", + " 0.00%\n", + " 12\n", + " 7.06%\n", + " 0.299821\n", + " 1.0\n", " \n", " \n", - " HP:0000613 (Photophobia)\n", - " 12\n", + " HP:0001483 (Eye poking)\n", + " 2\n", + " 50.00%\n", + " 1\n", + " 100.00%\n", + " 25\n", + " 73.53%\n", + " 0.687055\n", + " 1.0\n", + " \n", + " \n", + " HP:0000496 (Abnormality of eye movement)\n", + " 10\n", " 100.00%\n", " 2\n", " 100.00%\n", - " 16\n", + " 79\n", " 100.00%\n", " 1.000000\n", - " 1.000000\n", + " 1.0\n", " \n", " \n", - " HP:0000496 (Abnormality of eye movement)\n", - " 32\n", + " HP:0000613 (Photophobia)\n", + " 7\n", " 100.00%\n", - " 9\n", + " 1\n", " 100.00%\n", - " 50\n", + " 22\n", " 100.00%\n", " 1.000000\n", - " 1.000000\n", + " 1.0\n", " \n", " \n", "\n", "" ], "text/plain": [ - " Homozygous frameshift_variant \\\n", - " Count \n", - "HP:0001483 (Eye poking) 21 \n", - "HP:0012758 (Neurodevelopmental delay) 8 \n", - "HP:0000613 (Photophobia) 12 \n", - "HP:0000496 (Abnormality of eye movement) 32 \n", + " Homozygous missense_variant \\\n", + " Count Percent \n", + "HP:0012758 (Neurodevelopmental delay) 0 0.00% \n", + "HP:0001483 (Eye poking) 2 50.00% \n", + "HP:0000496 (Abnormality of eye movement) 10 100.00% \n", + "HP:0000613 (Photophobia) 7 100.00% \n", "\n", - " \\\n", - " Percent \n", - "HP:0001483 (Eye poking) 84.00% \n", - "HP:0012758 (Neurodevelopmental delay) 11.94% \n", - "HP:0000613 (Photophobia) 100.00% \n", - "HP:0000496 (Abnormality of eye movement) 100.00% \n", - "\n", - " Heterozygous frameshift_variant \\\n", - " Count \n", - "HP:0001483 (Eye poking) 2 \n", - "HP:0012758 (Neurodevelopmental delay) 0 \n", - "HP:0000613 (Photophobia) 2 \n", - "HP:0000496 (Abnormality of eye movement) 9 \n", + " Heterozygous missense_variant \\\n", + " Count \n", + "HP:0012758 (Neurodevelopmental delay) 0 \n", + "HP:0001483 (Eye poking) 1 \n", + "HP:0000496 (Abnormality of eye movement) 2 \n", + "HP:0000613 (Photophobia) 1 \n", "\n", - " No frameshift_variant \\\n", - " Percent Count \n", - "HP:0001483 (Eye poking) 100.00% 5 \n", - "HP:0012758 (Neurodevelopmental delay) 0.00% 4 \n", - "HP:0000613 (Photophobia) 100.00% 16 \n", - "HP:0000496 (Abnormality of eye movement) 100.00% 50 \n", + " No missense_variant \\\n", + " Percent Count \n", + "HP:0012758 (Neurodevelopmental delay) 0.00% 12 \n", + "HP:0001483 (Eye poking) 100.00% 25 \n", + "HP:0000496 (Abnormality of eye movement) 100.00% 79 \n", + "HP:0000613 (Photophobia) 100.00% 22 \n", "\n", " \n", " Percent p-value Corrected p-values \n", - "HP:0001483 (Eye poking) 41.67% 0.024229 0.096914 \n", - "HP:0012758 (Neurodevelopmental delay) 3.31% 0.038327 0.153306 \n", - "HP:0000613 (Photophobia) 100.00% 1.000000 1.000000 \n", - "HP:0000496 (Abnormality of eye movement) 100.00% 1.000000 1.000000 " + "HP:0012758 (Neurodevelopmental delay) 7.06% 0.299821 1.0 \n", + "HP:0001483 (Eye poking) 73.53% 0.687055 1.0 \n", + "HP:0000496 (Abnormality of eye movement) 100.00% 1.000000 1.0 \n", + "HP:0000613 (Photophobia) 100.00% 1.000000 1.0 " ] }, - "execution_count": 20, + "execution_count": 14, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "rec_analysis.compare_by_variant_type(VariantEffect.FRAMESHIFT_VARIANT)" + "rec_analysis.compare_by_variant_type(VariantEffect.MISSENSE_VARIANT)" ] }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 15, "id": "b9bf9ccf", "metadata": {}, "outputs": [], @@ -523,7 +505,7 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": 16, "id": "d835f075", "metadata": {}, "outputs": [ @@ -582,10 +564,10 @@ " 0.648221\n", " \n", " \n", - " HP:0000613 (Photophobia)\n", - " 14\n", + " HP:0000496 (Abnormality of eye movement)\n", + " 41\n", " 100.00%\n", - " 16\n", + " 50\n", " 100.00%\n", " 1.000000\n", " 1.000000\n", @@ -600,10 +582,10 @@ " 1.000000\n", " \n", " \n", - " HP:0000496 (Abnormality of eye movement)\n", - " 41\n", + " HP:0000613 (Photophobia)\n", + " 14\n", " 100.00%\n", - " 50\n", + " 16\n", " 100.00%\n", " 1.000000\n", " 1.000000\n", @@ -617,28 +599,28 @@ " Count Percent \n", "HP:0001483 (Eye poking) 23 85.19% \n", "HP:0012758 (Neurodevelopmental delay) 8 8.99% \n", - "HP:0000613 (Photophobia) 14 100.00% \n", - "HP:0000662 (Nyctalopia) 3 100.00% \n", "HP:0000496 (Abnormality of eye movement) 41 100.00% \n", + "HP:0000662 (Nyctalopia) 3 100.00% \n", + "HP:0000613 (Photophobia) 14 100.00% \n", "\n", " Without frameshift_variant \\\n", " Count Percent \n", "HP:0001483 (Eye poking) 5 41.67% \n", "HP:0012758 (Neurodevelopmental delay) 4 3.31% \n", - "HP:0000613 (Photophobia) 16 100.00% \n", - "HP:0000662 (Nyctalopia) 3 100.00% \n", "HP:0000496 (Abnormality of eye movement) 50 100.00% \n", + "HP:0000662 (Nyctalopia) 3 100.00% \n", + "HP:0000613 (Photophobia) 16 100.00% \n", "\n", " \n", " p-value Corrected p-values \n", "HP:0001483 (Eye poking) 0.016983 0.084915 \n", "HP:0012758 (Neurodevelopmental delay) 0.129644 0.648221 \n", - "HP:0000613 (Photophobia) 1.000000 1.000000 \n", + "HP:0000496 (Abnormality of eye movement) 1.000000 1.000000 \n", "HP:0000662 (Nyctalopia) 1.000000 1.000000 \n", - "HP:0000496 (Abnormality of eye movement) 1.000000 1.000000 " + "HP:0000613 (Photophobia) 1.000000 1.000000 " ] }, - "execution_count": 15, + "execution_count": 16, "metadata": {}, "output_type": "execute_result" } @@ -649,7 +631,7 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": 18, "id": "44006715", "metadata": {}, "outputs": [ @@ -681,8 +663,8 @@ " \n", " \n", " \n", - " With 14_21312458_A/-\n", - " Without 14_21312458_A/-\n", + " With 14_21312457_21312458_GA_G\n", + " Without 14_21312457_21312458_GA_G\n", " \n", " \n", " \n", @@ -715,19 +697,19 @@ " 0.161052\n", " \n", " \n", - " HP:0000613 (Photophobia)\n", - " 5\n", + " HP:0000496 (Abnormality of eye movement)\n", + " 16\n", " 100.00%\n", - " 25\n", + " 75\n", " 100.00%\n", " 1.000000\n", " 1.000000\n", " \n", " \n", - " HP:0000496 (Abnormality of eye movement)\n", - " 16\n", + " HP:0000613 (Photophobia)\n", + " 5\n", " 100.00%\n", - " 75\n", + " 25\n", " 100.00%\n", " 1.000000\n", " 1.000000\n", @@ -737,35 +719,42 @@ "" ], "text/plain": [ - " With 14_21312458_A/- \\\n", - " Count Percent \n", - "HP:0001483 (Eye poking) 16 100.00% \n", - "HP:0012758 (Neurodevelopmental delay) 4 16.00% \n", - "HP:0000613 (Photophobia) 5 100.00% \n", - "HP:0000496 (Abnormality of eye movement) 16 100.00% \n", + " With 14_21312457_21312458_GA_G \\\n", + " Count \n", + "HP:0001483 (Eye poking) 16 \n", + "HP:0012758 (Neurodevelopmental delay) 4 \n", + "HP:0000496 (Abnormality of eye movement) 16 \n", + "HP:0000613 (Photophobia) 5 \n", "\n", - " Without 14_21312458_A/- \\\n", - " Count Percent \n", - "HP:0001483 (Eye poking) 12 52.17% \n", - "HP:0012758 (Neurodevelopmental delay) 8 4.32% \n", - "HP:0000613 (Photophobia) 25 100.00% \n", - "HP:0000496 (Abnormality of eye movement) 75 100.00% \n", + " \\\n", + " Percent \n", + "HP:0001483 (Eye poking) 100.00% \n", + "HP:0012758 (Neurodevelopmental delay) 16.00% \n", + "HP:0000496 (Abnormality of eye movement) 100.00% \n", + "HP:0000613 (Photophobia) 100.00% \n", "\n", - " \n", - " p-value Corrected p-values \n", - "HP:0001483 (Eye poking) 0.000919 0.003677 \n", - "HP:0012758 (Neurodevelopmental delay) 0.040263 0.161052 \n", - "HP:0000613 (Photophobia) 1.000000 1.000000 \n", - "HP:0000496 (Abnormality of eye movement) 1.000000 1.000000 " + " Without 14_21312457_21312458_GA_G \\\n", + " Count \n", + "HP:0001483 (Eye poking) 12 \n", + "HP:0012758 (Neurodevelopmental delay) 8 \n", + "HP:0000496 (Abnormality of eye movement) 75 \n", + "HP:0000613 (Photophobia) 25 \n", + "\n", + " \n", + " Percent p-value Corrected p-values \n", + "HP:0001483 (Eye poking) 52.17% 0.000919 0.003677 \n", + "HP:0012758 (Neurodevelopmental delay) 4.32% 0.040263 0.161052 \n", + "HP:0000496 (Abnormality of eye movement) 100.00% 1.000000 1.000000 \n", + "HP:0000613 (Photophobia) 100.00% 1.000000 1.000000 " ] }, - "execution_count": 16, + "execution_count": 18, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "dom_analysis.compare_by_variant('14_21312458_A/-')" + "dom_analysis.compare_by_variant('14_21312457_21312458_GA_G')" ] }, { diff --git a/notebooks/STXBP1/STXBP1.ipynb b/notebooks/STXBP1/STXBP1.ipynb index 59c27b18..b9a14875 100644 --- a/notebooks/STXBP1/STXBP1.ipynb +++ b/notebooks/STXBP1/STXBP1.ipynb @@ -38,13 +38,13 @@ "name": "stdout", "output_type": "stream", "text": [ - "Loaded HPO v2022-10-05\n" + "Loaded HPO v2023-01-27\n" ] } ], "source": [ "import hpotk\n", - "hpo_purl = \"/Users/robinp/data/hpo/hp.json\"\n", + "hpo_purl = \"../hpo_data/hp.json\"\n", "hpo = hpotk.load_minimal_ontology(hpo_purl)\n", "print(f'Loaded HPO v{hpo.version}')" ] @@ -57,7 +57,7 @@ "outputs": [], "source": [ "from genophenocorr.preprocessing import configure_caching_patient_creator\n", - "patient_creator = configure_caching_patient_creator(hpo)" + "patient_creator = configure_caching_patient_creator(hpo, cache_dir = \"annotations\")" ] }, { @@ -75,78 +75,1351 @@ "execution_count": 5, "id": "3c07a0a5-560a-4970-9f6e-deed8f06fe35", "metadata": {}, + "outputs": [], + "source": [ + "phenopacket_input_folder = \"input\"\n", + "patientCohort = load_phenopacket_folder(pp_directory=phenopacket_input_folder, patient_creator=patient_creator)" + ] + }, + { + "cell_type": "markdown", + "id": "175d2b14-b75a-499a-9251-5154aa31c683", + "metadata": {}, + "source": [ + "

CohortViewer

\n", + "

The CohortViewer class offers various methods to create tables and graphics to view the data in the cohort.\n", + "It is still very much in progress

" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "id": "a41be80d-0678-4dc3-97b6-2876d69648e0", + "metadata": {}, + "outputs": [], + "source": [ + "from genophenocorr.view import CohortViewer\n", + "from IPython.display import display, HTML" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "id": "1c7c5c1e-8e5e-488a-98ec-85689adff61c", + "metadata": {}, + "outputs": [], + "source": [ + "viewer = CohortViewer(hpo=hpo)" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "id": "ef78af2f", + "metadata": {}, "outputs": [ { - "name": "stderr", - "output_type": "stream", - "text": [ - "Expected a result but got an Error for variant: 9_127684372_127684373_A_A_heterozygous\n" - ] - }, + "data": { + "text/html": [ + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "
ItemDescription
Description of the cohort.
Total Individuals462
Total Unique HPO Terms540
Total Unique Variants462
" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "display(HTML(viewer.cohort_summary_table(patientCohort)))" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "id": "dadb3b22", + "metadata": {}, + "outputs": [ { - "ename": "HTTPError", - "evalue": "400 Client Error: Bad Request for url: https://rest.ensembl.org/vep/human/region/9:127684373-127684373/A?LoF=1&canonical=1&domains=1&hgvs=1&mutfunc=1&numbers=1&protein=1&refseq=1&mane=1&transcript_version=1&variant_class=1", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mHTTPError\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[5], line 2\u001b[0m\n\u001b[1;32m 1\u001b[0m phenopacket_input_folder \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124minput\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m----> 2\u001b[0m patient_list \u001b[38;5;241m=\u001b[39m \u001b[43mload_phenopacket_folder\u001b[49m\u001b[43m(\u001b[49m\u001b[43mpp_directory\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mphenopacket_input_folder\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mpatient_creator\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mpatient_creator\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/GIT/genophenocorr/src/genophenocorr/preprocessing/_phenopacket.py:196\u001b[0m, in \u001b[0;36mload_phenopacket_folder\u001b[0;34m(pp_directory, patient_creator)\u001b[0m\n\u001b[1;32m 193\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mNo JSON Phenopackets were found in \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mpp_directory\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 195\u001b[0m \u001b[38;5;66;03m# turn phenopackets into patients using patient creator\u001b[39;00m\n\u001b[0;32m--> 196\u001b[0m patients \u001b[38;5;241m=\u001b[39m [patient_creator\u001b[38;5;241m.\u001b[39mcreate_patient(pp) \u001b[38;5;28;01mfor\u001b[39;00m pp \u001b[38;5;129;01min\u001b[39;00m pps]\n\u001b[1;32m 198\u001b[0m \u001b[38;5;66;03m# create cohort from patients\u001b[39;00m\n\u001b[1;32m 199\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m Cohort\u001b[38;5;241m.\u001b[39mfrom_patients(patients)\n", - "File \u001b[0;32m~/GIT/genophenocorr/src/genophenocorr/preprocessing/_phenopacket.py:196\u001b[0m, in \u001b[0;36m\u001b[0;34m(.0)\u001b[0m\n\u001b[1;32m 193\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mNo JSON Phenopackets were found in \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mpp_directory\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 195\u001b[0m \u001b[38;5;66;03m# turn phenopackets into patients using patient creator\u001b[39;00m\n\u001b[0;32m--> 196\u001b[0m patients \u001b[38;5;241m=\u001b[39m [\u001b[43mpatient_creator\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate_patient\u001b[49m\u001b[43m(\u001b[49m\u001b[43mpp\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;28;01mfor\u001b[39;00m pp \u001b[38;5;129;01min\u001b[39;00m pps]\n\u001b[1;32m 198\u001b[0m \u001b[38;5;66;03m# create cohort from patients\u001b[39;00m\n\u001b[1;32m 199\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m Cohort\u001b[38;5;241m.\u001b[39mfrom_patients(patients)\n", - "File \u001b[0;32m~/GIT/genophenocorr/src/genophenocorr/preprocessing/_phenopacket.py:116\u001b[0m, in \u001b[0;36mPhenopacketPatientCreator.create_patient\u001b[0;34m(self, item)\u001b[0m\n\u001b[1;32m 108\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"Creates a Patient from the data in a given Phenopacket\u001b[39;00m\n\u001b[1;32m 109\u001b[0m \n\u001b[1;32m 110\u001b[0m \u001b[38;5;124;03mArgs:\u001b[39;00m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 113\u001b[0m \u001b[38;5;124;03m Patient: A Patient object\u001b[39;00m\n\u001b[1;32m 114\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 115\u001b[0m phenotypes \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_add_phenotypes(item)\n\u001b[0;32m--> 116\u001b[0m variants \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_add_variants\u001b[49m\u001b[43m(\u001b[49m\u001b[43mitem\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 117\u001b[0m protein_data \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_add_protein_data(variants)\n\u001b[1;32m 118\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m Patient(item\u001b[38;5;241m.\u001b[39mid, phenotypes, variants, protein_data)\n", - "File \u001b[0;32m~/GIT/genophenocorr/src/genophenocorr/preprocessing/_phenopacket.py:136\u001b[0m, in \u001b[0;36mPhenopacketPatientCreator._add_variants\u001b[0;34m(self, pp)\u001b[0m\n\u001b[1;32m 134\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_logger\u001b[38;5;241m.\u001b[39mwarning(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mPatient \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mpp\u001b[38;5;241m.\u001b[39mid\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m has unknown alternative variant \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mvc\u001b[38;5;241m.\u001b[39malt\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m and will not be included.\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 135\u001b[0m \u001b[38;5;28;01mcontinue\u001b[39;00m\n\u001b[0;32m--> 136\u001b[0m variant \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_func_ann\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mannotate\u001b[49m\u001b[43m(\u001b[49m\u001b[43mvc\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 137\u001b[0m variants_list\u001b[38;5;241m.\u001b[39mappend(variant)\n\u001b[1;32m 138\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n", - "File \u001b[0;32m~/GIT/genophenocorr/src/genophenocorr/preprocessing/_variant.py:227\u001b[0m, in \u001b[0;36mVarCachingFunctionalAnnotator.annotate\u001b[0;34m(self, variant_coordinates)\u001b[0m\n\u001b[1;32m 225\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m annotations\n\u001b[1;32m 226\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 227\u001b[0m ann \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_fallback\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mannotate\u001b[49m\u001b[43m(\u001b[49m\u001b[43mvariant_coordinates\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 228\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cache\u001b[38;5;241m.\u001b[39mstore_annotations(variant_coordinates, ann)\n\u001b[1;32m 229\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m ann\n", - "File \u001b[0;32m~/GIT/genophenocorr/src/genophenocorr/preprocessing/_variant.py:79\u001b[0m, in \u001b[0;36mVepFunctionalAnnotator.annotate\u001b[0;34m(self, variant_coordinates)\u001b[0m\n\u001b[1;32m 71\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mannotate\u001b[39m(\u001b[38;5;28mself\u001b[39m, variant_coordinates: VariantCoordinates) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m Variant:\n\u001b[1;32m 72\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"Creates a Variant object by searching variant coordinates with Variant Effect Predictor (VEP) REST API. \u001b[39;00m\n\u001b[1;32m 73\u001b[0m \n\u001b[1;32m 74\u001b[0m \u001b[38;5;124;03m Args:\u001b[39;00m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 77\u001b[0m \u001b[38;5;124;03m Variant: A Variant object\u001b[39;00m\n\u001b[1;32m 78\u001b[0m \u001b[38;5;124;03m \"\"\"\u001b[39;00m\n\u001b[0;32m---> 79\u001b[0m variant \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_query_vep\u001b[49m\u001b[43m(\u001b[49m\u001b[43mvariant_coordinates\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 80\u001b[0m variant_id \u001b[38;5;241m=\u001b[39m variant\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mid\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m 81\u001b[0m variant_class \u001b[38;5;241m=\u001b[39m variant\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mvariant_class\u001b[39m\u001b[38;5;124m'\u001b[39m)\n", - "File \u001b[0;32m~/GIT/genophenocorr/src/genophenocorr/preprocessing/_variant.py:130\u001b[0m, in \u001b[0;36mVepFunctionalAnnotator._query_vep\u001b[0;34m(self, variant_coordinates)\u001b[0m\n\u001b[1;32m 128\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m r\u001b[38;5;241m.\u001b[39mok:\n\u001b[1;32m 129\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_logging\u001b[38;5;241m.\u001b[39merror(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mExpected a result but got an Error for variant: \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mvariant_coordinates\u001b[38;5;241m.\u001b[39mas_string()\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m--> 130\u001b[0m \u001b[43mr\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mraise_for_status\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 131\u001b[0m results \u001b[38;5;241m=\u001b[39m r\u001b[38;5;241m.\u001b[39mjson()\n\u001b[1;32m 132\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(results, \u001b[38;5;28mlist\u001b[39m):\n", - "File \u001b[0;32m~/GIT/genophenocorr/gpc2venv/lib/python3.8/site-packages/requests/models.py:1021\u001b[0m, in \u001b[0;36mResponse.raise_for_status\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 1016\u001b[0m http_error_msg \u001b[38;5;241m=\u001b[39m (\n\u001b[1;32m 1017\u001b[0m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mstatus_code\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m Server Error: \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mreason\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m for url: \u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39murl\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 1018\u001b[0m )\n\u001b[1;32m 1020\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m http_error_msg:\n\u001b[0;32m-> 1021\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m HTTPError(http_error_msg, response\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m)\n", - "\u001b[0;31mHTTPError\u001b[0m: 400 Client Error: Bad Request for url: https://rest.ensembl.org/vep/human/region/9:127684373-127684373/A?LoF=1&canonical=1&domains=1&hgvs=1&mutfunc=1&numbers=1&protein=1&refseq=1&mane=1&transcript_version=1&variant_class=1" - ] + "data": { + "text/html": [ + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "
VariantEffectCountKey
c.1216C>TMISSENSE_VARIANT199_127675909_127675909_C_T
c.1217G>AMISSENSE_VARIANT199_127675910_127675910_G_A
c.1651C>TMISSENSE_VARIANT189_127682509_127682509_C_T
c.875G>AMISSENSE_VARIANT189_127668160_127668160_G_A
c.416C>TMISSENSE_VARIANT129_127661192_127661192_C_T
c.568C>TMISSENSE_VARIANT119_127663343_127663343_C_T
c.1162C>TSTOP_GAINED109_127675855_127675855_C_T
c.874C>TMISSENSE_VARIANT109_127668159_127668159_C_T
c.1439C>TMISSENSE_VARIANT109_127678510_127678510_C_T
c.364C>TSTOP_GAINED99_127661140_127661140_C_T
c.703C>TSTOP_GAINED89_127666205_127666205_C_T
c.1099C>TSTOP_GAINED69_127673250_127673250_C_T
c.1060T>CMISSENSE_VARIANT59_127673211_127673211_T_C
c.847G>AMISSENSE_VARIANT59_127668132_127668132_G_A
c.388_389delFRAMESHIFT_VARIANT59_127661161_127661163_ACT_A
c.569G>AMISSENSE_VARIANT59_127663344_127663344_G_A
c.795-1G>ASPLICE_ACCEPTOR_VARIANT49_127668079_127668079_G_A
c.734A>GMISSENSE_VARIANT49_127666236_127666236_A_G
c.704G>AMISSENSE_VARIANT49_127666206_127666206_G_A
c.1652G>AMISSENSE_VARIANT49_127682510_127682510_G_A
c.1702+1G>ASPLICE_DONOR_VARIANT49_127682561_127682561_G_A
c.1061G>AMISSENSE_VARIANT39_127673212_127673212_G_A
c.902+1G>ASPLICE_DONOR_VARIANT39_127668188_127668188_G_A
c.57_59delINFRAME_DELETION39_127651621_127651624_TAAA_T
c.1095_1096delFRAMESHIFT_VARIANT39_127673243_127673245_ACT_A
c.1315A>TMISSENSE_VARIANT39_127676709_127676709_A_T
c.758G>AMISSENSE_VARIANT39_127666260_127666260_G_A
c.1249+2T>CSPLICE_DONOR_VARIANT29_127675944_127675944_T_C
c.755T>CMISSENSE_VARIANT29_127666257_127666257_T_C
c.904G>TSTOP_GAINED29_127669899_127669899_G_T
c.83G>ASTOP_GAINED29_127651648_127651648_G_A
c.1206T>ASTOP_GAINED29_127675899_127675899_T_A
c.1630G>CMISSENSE_VARIANT29_127682488_127682488_G_C
c.1631G>AMISSENSE_VARIANT29_127682489_127682489_G_A
c.1029+1G>TSPLICE_DONOR_VARIANT29_127672117_127672117_G_T
c.1038_1039delFRAMESHIFT_VARIANT29_127673187_127673189_ACC_A
c.1631G>TMISSENSE_VARIANT29_127682489_127682489_G_T
c.122T>CMISSENSE_VARIANT29_127653749_127653749_T_C
c.1359+1G>ASPLICE_DONOR_VARIANT29_127676754_127676754_G_A
c.1261G>TSTOP_GAINED29_127676655_127676655_G_T
c.922A>TSTOP_GAINED29_127669917_127669917_A_T
c.795-2A>GSPLICE_ACCEPTOR_VARIANT29_127668078_127668078_A_G
c.703C>GMISSENSE_VARIANT29_127666205_127666205_C_G
c.748C>TSTOP_GAINED29_127666250_127666250_C_T
c.84G>ASTOP_GAINED29_127651649_127651649_G_A
c.998_1000delINFRAME_DELETION29_127672079_127672082_TGAA_T
c.578+1G>ASPLICE_DONOR_VARIANT29_127663354_127663354_G_A
c.733C>GMISSENSE_VARIANT29_127666235_127666235_C_G
c.1565G>ASTOP_GAINED29_127682423_127682423_G_A
\n", + "

Additionally, the following variants were observed 1 or fewer times: \n", + "c.125C>T; c.88-1G>A; c.747dup; c.1645G>A; c.1360-1_1360insC; c.548T>G; c.1482dup; c.1197C>A; c.578+1dup; c.1702+1G>C; c.164T>C; c.1420C>T; c.236C>T; c.360dup; c.227T>C; c.170-12_173del; c.987del; c.1672del; c.1652G>T; c.860T>C; c.87+1G>T; c.1021_1029+1del; c.247-1del; c.374_375del; c.*20C>T; c.16del; c.296A>G; c.1431_1447delinsAT; c.1578_1579del; c.989dup; c.444del; c.437_438del; c.1249G>C; c.771dup; c.420T>A; c.1656C>A; c.1110+1G>A; c.389del; c.679C>A; c.62_64del; c.157G>T; c.268G>C; c.1058_1061del; c.901del; c.794+1G>T; c.1094T>A; c.536T>G; c.308A>C; c.795-1G>C; c.170-2A>G; c.175G>A; c.126C>T; c.961A>T; c.385A>C; c.1193A>G; c.79del; c.1218C>A; c.1328T>G; c.607C>T; c.224A>G; c.88-2A>G; c.325+1G>T; c.685C>T; c.736G>A; c.1130dup; c.167C>G; c.164T>A; c.1606del; c.1347del; c.1303G>T; c.107T>A; c.620A>G; c.430-1G>C; c.754_755del; c.37+1G>A; c.893_894del; c.725del; c.326-1G>T; c.169+1G>A; c.560del; c.268G>T; c.931dup; c.230T>A; c.124T>C; c.41T>G; c.897_898del; c.1461G>A; c.1461G>C; c.1614_1616del; c.1006C>T; c.1194T>G; c.1029+1delinsAA; c.1495_1497del; c.1696_1697delinsA; c.585C>G; c.17T>A; c.1569_1570del; c.1265del; c.9_13del; c.*23C>T; c.217G>C; c.1105G>A; c.1547+1G>A; c.548T>C; c.1249+1G>T; c.1434G>A; c.295T>G; c.1497C>A; c.1708A>G; c.1651C>G; c.714C>A; c.1548-2A>G; c.794+2dup; c.1438C>T; c.1019_1020del; c.1643A>T; c.1030T>G; c.1277T>C; c.663+1G>A; c.1359+1G>T; c.827dup; c.1157del; c.875G>T; c.187A>T; c.539G>A; c.142del; c.551del; c.353T>G; c.88-1G>C; c.167C>A; c.1382dup; c.1250-2A>C; c.1548_1558delinsAT; c.238T>C; c.767T>C; c.1627G>A; c.1387G>T; c.430G>C; c.1607G>A; c.1334A>C; c.1630G>T; c.538T>C; c.661G>T; c.1659del; c.778G>T; c.579-2A>G; c.1324A>G; c.1654T>C; c.721del; c.251T>A; c.1408G>T; c.429+1G>A; c.875G>C; c.663+1G>T; c.1022T>C; c.795-2A>T; c.429+1G>C; c.1249+1G>A; c.1030-1G>A; c.956del; c.533C>T; c.1004C>T; c.1268T>C; c.1157dup; c.232_235del; c.296A>C; c.1462-2A>T; c.1461+1G>A; c.416C>A; c.99delinsTC; c.717del; c.901C>T; c.1769C>T; c.734A>C; c.1082C>T; c.842T>C; c.74del; c.430delinsAGA; c.148dup; c.17T>C; c.749A>G; c.867dup; c.1720A>C; c.54del; c.301G>C; c.60del; c.1105G>C; c.464del; c.1275del; c.1501_1519del; c.586A>T; c.1249G>A; c.751G>A; c.701A>G; c.1105G>T; c.1282del; c.731T>G; c.172del; c.1075C>T; c.37+1_37+2del; c.169+2T>C; c.1661A>G; c.1642A>G; c.1723C>T; c.663+1G>C; c.430-1G>T; c.466T>A; c.518C>A; c.1151dup.

\n", + "

Use the entry in the \"Key\" column to investigate whether specific variants display genotype-phenotype correlations

" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" } ], "source": [ - "phenopacket_input_folder = \"input\"\n", - "patient_list = load_phenopacket_folder(pp_directory=phenopacket_input_folder, patient_creator=patient_creator)" + "display(HTML(viewer.variants_table(patientCohort, 'NM_003165.6')))" ] }, { "cell_type": "code", - "execution_count": null, - "id": "a41be80d-0678-4dc3-97b6-2876d69648e0", + "execution_count": 13, + "id": "c57441a4", "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "
HPO TermCount
Counts of annotations to HPO terms for the 462 in the cohort
Global developmental delay (HP:0001263)255
Absent speech (HP:0001344)152
Infantile spasms (HP:0012469)143
Seizure (HP:0001250)129
Infantile onset (HP:0003593)121
Hypsarrhythmia (HP:0002521)120
Neonatal onset (HP:0003623)117
Intellectual disability, severe (HP:0010864)106
Inability to walk (HP:0002540)93
Generalized tonic seizure (HP:0010818)92
Multifocal epileptiform discharges (HP:0010841)86
Bilateral tonic-clonic seizure (HP:0002069)84
Ataxia (HP:0001251)82
EEG with burst suppression (HP:0010851)75
Tremor (HP:0001337)73
Focal impaired awareness seizure (HP:0002384)71
EEG with focal epileptiform discharges (HP:0011185)71
Focal-onset seizure (HP:0007359)71
Epileptic spasm (HP:0011097)70
Motor stereotypy (HP:0000733)68
Hypotonia (HP:0001252)67
Delayed speech and language development (HP:0000750)66
Refractory (HP:0031375)63
Severe global developmental delay (HP:0011344)62
Intellectual disability (HP:0001249)54
Generalized myoclonic seizure (HP:0002123)51
Developmental regression (HP:0002376)50
Focal clonic seizure (HP:0002266)50
EEG with generalized slow activity (HP:0010845)47
Infantile muscular hypotonia (HP:0008947)43
EEG with abnormally slow frequencies (HP:0011203)43
Focal tonic seizure (HP:0011167)42
Autistic behavior (HP:0000729)41
Generalized hypotonia (HP:0001290)40
Focal motor seizure (HP:0011153)37
Epileptic encephalopathy (HP:0200134)37
Autism (HP:0000717)33
Sleep disturbance (HP:0002360)33
Axial hypotonia (HP:0008936)29
Dystonia (HP:0001332)27
Intellectual disability, moderate (HP:0002342)25
Gait ataxia (HP:0002066)23
Spastic tetraplegia (HP:0002510)21
Intellectual disability, profound (HP:0002187)21
Profound global developmental delay (HP:0012736)20
Bruxism (HP:0003763)20
Hypomimic face (HP:0000338)19
Gastroesophageal reflux (HP:0002020)19
Strabismus (HP:0000486)18
Poor eye contact (HP:0000817)18
Dyskinesia (HP:0100660)18
Febrile seizure (within the age range of 3 months to 6 years) (HP:0002373)17
Generalized non-motor (absence) seizure (HP:0002121)17
Childhood onset (HP:0011463)17
Scoliosis (HP:0002650)17
Hyperactivity (HP:0000752)17
Delayed CNS myelination (HP:0002188)16
EEG with generalized epileptiform discharges (HP:0011198)16
Intention tremor (HP:0002080)16
Poor head control (HP:0002421)16
Hypoplasia of the corpus callosum (HP:0002079)16
EEG with spike-wave complexes (HP:0010850)16
Neurodevelopmental delay (HP:0012758)16
Spasticity (HP:0001257)15
Moderate global developmental delay (HP:0011343)15
Atonic seizure (HP:0010819)15
Multifocal seizures (HP:0031165)15
Constipation (HP:0002019)14
Microcephaly (HP:0000252)14
Gait disturbance (HP:0001288)14
Interictal epileptiform activity (HP:0011182)14
Bilateral tonic-clonic seizure with focal onset (HP:0007334)14
EEG with focal slow activity (HP:0010843)13
Motor delay (HP:0001270)13
Feeding difficulties (HP:0011968)13
Action tremor (HP:0002345)13
Truncal ataxia (HP:0002078)12
Bilateral multifocal epileptiform discharges (HP:0011189)12
Severe muscular hypotonia (HP:0006829)12
Dysmetria (HP:0001310)12
Limb hypertonia (HP:0002509)12
Self-injurious behavior (HP:0100716)12
Aggressive behavior (HP:0000718)12
Gastrostomy tube feeding in infancy (HP:0011471)12
Intellectual disability, mild (HP:0001256)11
Generalized-onset seizure (HP:0002197)11
Cerebral atrophy (HP:0002059)11
Hypertonia (HP:0001276)11
Broad-based gait (HP:0002136)11
EEG abnormality (HP:0002353)11
Neonatal hypotonia (HP:0001319)11
Status epilepticus (HP:0002133)11
Abnormality of movement (HP:0100022)11
Brain atrophy (HP:0012444)11
EEG with temporal focal spikes (HP:0012018)10
Behavioral abnormality (HP:0000708)10
Stereotypical hand wringing (HP:0012171)10
Spastic tetraparesis (HP:0001285)10
Frontal cortical atrophy (HP:0006913)9
Cerebral visual impairment (HP:0100704)9
Focal myoclonic seizure (HP:0011166)9
Normal interictal EEG (HP:0002372)9
Resting tremor (HP:0002322)9
Language impairment (HP:0002463)9
Cerebral cortical atrophy (HP:0002120)8
Nystagmus (HP:0000639)8
Babinski sign (HP:0003487)8
Myoclonus (HP:0001336)8
EEG with focal sharp waves (HP:0011196)8
Hyperreflexia (HP:0001347)8
Delayed gross motor development (HP:0002194)7
Abnormality of vision (HP:0000504)7
Generalized clonic seizure (HP:0011169)7
Intermittent hyperventilation (HP:0004879)7
Unsteady gait (HP:0002317)7
Bilateral tonic-clonic seizure with generalized onset (HP:0025190)7
Premature birth (HP:0001622)7
EEG with focal spikes (HP:0011193)7
Prominent fingertip pads (HP:0001212)7
Lower limb spasticity (HP:0002061)7
Impulsivity (HP:0100710)7
Focal hemiclonic seizure (HP:0006813)7
Chorea (HP:0002072)6
Cogwheel rigidity (HP:0002396)6
Bradykinesia (HP:0002067)6
Short attention span (HP:0000736)6
Postural instability (HP:0002172)6
Encephalopathy (HP:0001298)6
Impaired social interactions (HP:0000735)6
EEG with occipital focal spikes (HP:0012016)6
Infantile axial hypotonia (HP:0009062)6
Brachycephaly (HP:0000248)5
Macrocephaly (HP:0000256)5
Nocturnal seizures (HP:0031951)5
Impaired pain sensation (HP:0007328)5
Focal autonomic seizure (HP:0011154)5
EEG with spike-wave complexes (<2.5 Hz) (HP:0010847)5
Cognitive impairment (HP:0100543)5
Eczema (HP:0000964)5
Joint hypermobility (HP:0001382)5
Chronic constipation (HP:0012450)5
EEG with frontal focal spike waves (HP:0012010)5
Stereotypical body rocking (HP:0012172)5
Emotional lability (HP:0000712)5
EEG with polyspike wave complexes (HP:0002392)5
Delayed fine motor development (HP:0010862)4
Narrow mouth (HP:0000160)4
Pes valgus (HP:0008081)4
Cerebral hypomyelination (HP:0006808)4
Abnormal eating behavior (HP:0100738)4
Attention deficit hyperactivity disorder (HP:0007018)4
Hand tremor (HP:0002378)4
Spastic diplegia (HP:0001264)4
Limb dystonia (HP:0002451)4
Anxiety (HP:0000739)4
EEG with occipital slowing (HP:0011210)4
Continuous spike and waves during slow sleep (HP:0031491)4
Gait imbalance (HP:0002141)4
Sleep-wake cycle disturbance (HP:0006979)4
Failure to thrive (HP:0001508)4
Progressive microcephaly (HP:0000253)4
Head tremor (HP:0002346)4
Involuntary movements (HP:0004305)4
Focal impaired awareness autonomic seizure (HP:0032755)4
Abnormal facial shape (HP:0001999)4
EEG with temporal sharp waves (HP:0011296)4
EEG with generalized polyspikes (HP:0012001)4
Difficulty walking (HP:0002355)4
Increased body weight (HP:0004324)4
Atypical absence seizure (HP:0007270)4
Joint laxity (HP:0001388)4
Global brain atrophy (HP:0002283)4
Dementia (HP:0000726)3
Upslanted palpebral fissure (HP:0000582)3
Laryngomalacia (HP:0001601)3
Cerebral palsy (HP:0100021)3
Postural tremor (HP:0002174)3
Hypokinesia (HP:0002375)3
Umbilical hernia (HP:0001537)3
Choreoathetosis (HP:0001266)3
Abnormality of the nervous system (HP:0000707)3
EEG with centrotemporal focal spike waves (HP:0012557)3
Abnormal muscle tone (HP:0003808)3
Torticollis (HP:0000473)3
Visual impairment (HP:0000505)3
Skeletal muscle atrophy (HP:0003202)3
Loss of speech (HP:0002371)3
Flat occiput (HP:0005469)3
Head titubation (HP:0002599)3
Loss of ability to walk in first decade (HP:0006794)3
Arachnoid cyst (HP:0100702)3
Mild global developmental delay (HP:0011342)3
Focal motor seizure with version (HP:0011175)3
EEG with frontal focal spikes (HP:0012015)3
Tetraparesis (HP:0002273)3
Inappropriate laughter (HP:0000748)3
Malar flattening (HP:0000272)3
Tapered finger (HP:0001182)3
Delayed myelination (HP:0012448)3
EEG with multifocal slow activity (HP:0010844)3
Slender finger (HP:0001238)3
Irritability (HP:0000737)3
Exaggerated startle response (HP:0002267)3
Ventriculomegaly (HP:0002119)3
Hypermetropia (HP:0000540)3
Astigmatism (HP:0000483)3
Osteopenia (HP:0000938)3
Round face (HP:0000311)2
Hyperintensity of cerebral white matter on MRI (HP:0030890)2
Arm dystonia (HP:0031960)2
Growth delay (HP:0001510)2
EEG with temporal sharp slow waves (HP:0011289)2
Opisthotonus (HP:0002179)2
Focal behavior arrest seizure (HP:0011173)2
Widened subarachnoid space (HP:0012704)2
Focal cortical dysplasia (HP:0032046)2
Focal EEG discharges with secondary generalization (HP:0011188)2
Recurrent hand flapping (HP:0100023)2
Hyperventilation (HP:0002883)2
Secondary microcephaly (HP:0005484)2
Expressive language delay (HP:0002474)2
Focal T2 hyperintense basal ganglia lesion (HP:0007183)2
Periventricular leukomalacia (HP:0006970)2
Abnormal pattern of respiration (HP:0002793)2
Abnormal subarachnoid space morphology (HP:0012703)2
Limb ataxia (HP:0002070)2
Dysphagia (HP:0002015)2
Hearing impairment (HP:0000365)2
Short foot (HP:0001773)2
Ankle clonus (HP:0011448)2
Hemihypsarrhythmia (HP:0011215)2
Juvenile onset (HP:0003621)2
Talipes equinovarus (HP:0001762)2
EEG with changes in voltage (HP:0011201)2
Delayed eruption of teeth (HP:0000684)2
Developmental stagnation (HP:0007281)2
Dysplastic corpus callosum (HP:0006989)2
Limb joint contracture (HP:0003121)2
Short stature (HP:0004322)2
Relative macrocephaly (HP:0004482)2
Typical absence seizure (HP:0011147)2
EEG with parietal focal spikes (HP:0012017)2
Pes planus (HP:0001763)2
Gliosis (HP:0002171)2
Upper limb postural tremor (HP:0007351)2
Upper limb spasticity (HP:0006986)2
Increased theta frequency activity in EEG (HP:0031535)2
Generalized muscle weakness (HP:0003324)2
Epicanthus (HP:0000286)2
Caesarian section (HP:0011410)2
Lower limb hypertonia (HP:0006895)2
Precocious puberty (HP:0000826)2
Status epilepticus without prominent motor symptoms (HP:0031475)2
Inverted nipples (HP:0003186)2
Clinodactyly (HP:0030084)2
Apnea (HP:0002104)2
Poor fine motor coordination (HP:0007010)2
Poor gross motor coordination (HP:0007015)2
Paroxysmal dyskinesia (HP:0007166)2
Rigidity (HP:0002063)2
Enlarged cisterna magna (HP:0002280)2
Obesity (HP:0001513)2
Insomnia (HP:0100785)2
Tip-toe gait (HP:0030051)2
Focal aware seizure (HP:0002349)2
Drooling (HP:0002307)2
Focal hyperkinetic seizure (HP:0011174)2
Hyporeflexia (HP:0001265)2
Abnormal temper tantrums (HP:0025160)2
Death in infancy (HP:0001522)2
Plagiocephaly (HP:0001357)2
Abnormal upper lip morphology (HP:0000177)2
High palate (HP:0000218)2
Protruding ear (HP:0000411)2
Frontal bossing (HP:0002007)2
Depressed nasal bridge (HP:0005280)2
Pain insensitivity (HP:0007021)2
Clumsiness (HP:0002312)2
Lower limb hyperreflexia (HP:0002395)2
Interictal EEG abnormality (HP:0025373)2
Breathing dysregulation (HP:0005957)2
Failure to thrive in infancy (HP:0001531)2
Polyminimyoclonus (HP:0031986)2
Periventricular white matter hyperintensities (HP:0030891)2
Esotropia (HP:0000565)2
Meconium stained amniotic fluid (HP:0012420)2
Poor coordination (HP:0002370)2
Truncal titubation (HP:0030147)2
EEG with focal sharp slow waves (HP:0011195)2
EEG with generalized spikes (HP:0012000)2
Short stepped shuffling gait (HP:0007311)2
Pregnancy exposure (HP:0031437)2
Feeding difficulties in infancy (HP:0008872)2
Limb dysmetria (HP:0002406)2
Low levels of vitamin D (HP:0100512)1
High forehead (HP:0000348)1
Adducted thumb (HP:0001181)1
Hypothyroidism (HP:0000821)1
Decreased CSF homovanillic acid concentration (HP:0003785)1
Decreased CSF 5-hydroxyindolacetic acid concentration (HP:0025455)1
Generalized myoclonic-atonic seizure (HP:0011170)1
Myoclonic spasms (HP:0003739)1
Abnormality of coordination (HP:0011443)1
Psychosis (HP:0000709)1
Polyhydramnios (HP:0001561)1
High pitched voice (HP:0001620)1
Rotary nystagmus (HP:0001583)1
Poor motor coordination (HP:0002275)1
Focal seizure with eyelid myoclonia (HP:0011168)1
Recurrent cystitis (HP:0012786)1
Soft skin (HP:0000977)1
Episodic ataxia (HP:0002131)1
Increased serum lactate (HP:0002151)1
Increased serum pyruvate (HP:0003542)1
Medial flaring of the eyebrow (HP:0010747)1
Prominent eyelashes (HP:0011231)1
Focal hemifacial clonic seizure (HP:0007332)1
Athetosis (HP:0002305)1
Parasomnia (HP:0025234)1
Blue nevus (HP:0100814)1
Hemiplegia/hemiparesis (HP:0004374)1
Talipes (HP:0001883)1
Inguinal hernia (HP:0000023)1
Enamel hypoplasia (HP:0006297)1
Abdominal obesity (HP:0012743)1
Recurrent otitis media (HP:0000403)1
Tented upper lip vermilion (HP:0010804)1
Abnormal CNS myelination (HP:0011400)1
Abnormal choroid plexus morphology (HP:0007376)1
Central nervous system cyst (HP:0030724)1
Peripheral neuropathy (HP:0009830)1
Asthma (HP:0002099)1
Bronchitis (HP:0012387)1
Abnormality of the kidney (HP:0000077)1
Ventricular septal defect (HP:0001629)1
Abnormality of pulmonary circulation (HP:0030875)1
Upper motor neuron dysfunction (HP:0002493)1
Parkinsonism (HP:0001300)1
Generalized hyperreflexia (HP:0007034)1
Decreased activity of mitochondrial complex I (HP:0011923)1
Downslanted palpebral fissures (HP:0000494)1
Anteverted nares (HP:0000463)1
Deeply set eye (HP:0000490)1
Hirsutism (HP:0001007)1
Horizontal eyebrow (HP:0011228)1
Reduced bone mineral density (HP:0004349)1
Abnormality of eye movement (HP:0000496)1
Hyperlordosis (HP:0003307)1
Brisk reflexes (HP:0001348)1
Dysdiadochokinesis (HP:0002075)1
Short philtrum (HP:0000322)1
Thoracic kyphosis (HP:0002942)1
Enlarged sylvian cistern (HP:0100952)1
Focal cortical dysplasia type Ib (HP:0032049)1
Focal cortical dysplasia type III (HP:0032054)1
EEG with frontal sharp waves (HP:0011294)1
Monocular strabismus (HP:0010877)1
Wide nasal bridge (HP:0000431)1
Sleep-wake inversion (HP:0031849)1
Abnormal respiratory system physiology (HP:0002795)1
Everted upper lip vermilion (HP:0010803)1
Death in adolescence (HP:0011421)1
Accessory spleen (HP:0001747)1
Unilateral renal hypoplasia (HP:0012583)1
Pigmentary retinopathy (HP:0000580)1
Proportionate tall stature (HP:0011407)1
Occipital cortical atrophy (HP:0012105)1
Gray matter heterotopia (HP:0002282)1
Oculomotor apraxia (HP:0000657)1
Foot dorsiflexor weakness (HP:0009027)1
Bipolar affective disorder (HP:0007302)1
Ulcerative colitis (HP:0100279)1
Neurogenic bladder (HP:0000011)1
EEG with central focal spikes (HP:0012014)1
Bilateral ptosis (HP:0001488)1
Axial muscle weakness (HP:0003327)1
Enuresis (HP:0000805)1
Speech apraxia (HP:0011098)1
Long toe (HP:0010511)1
Inflexible adherence to routines or rituals (HP:0000732)1
Punctate periventricular T2 hyperintense foci (HP:0030081)1
Apneic episodes in infancy (HP:0005949)1
Non-rapid eye movement parasomnia (HP:0025235)1
Abnormal skull morphology (HP:0000929)1
Triggered by physical trauma (HP:0031135)1
Carious teeth (HP:0000670)1
Dandy-Walker malformation (HP:0001305)1
CNS hypomyelination (HP:0003429)1
Oromotor apraxia (HP:0007301)1
Sleep terror (HP:0030765)1
EEG with parietal focal spike waves (HP:0012012)1
Hyperkinetic movements (HP:0002487)1
Submucous cleft of soft and hard palate (HP:0410031)1
Bifid uvula (HP:0000193)1
Cerebellar atrophy (HP:0001272)1
Agenesis of corpus callosum (HP:0001274)1
Overgrowth (HP:0001548)1
EEG with central sharp slow waves (HP:0011291)1
EEG with parietal sharp slow waves (HP:0011288)1
EEG with intermittent slow activity (HP:0011205)1
Abnormality of brain morphology (HP:0012443)1
Supraventricular tachycardia (HP:0004755)1
Shuffling gait (HP:0002362)1
Hydrocele testis (HP:0000034)1
Unilateral multifocal epileptiform discharges (HP:0011191)1
Somatic sensory dysfunction (HP:0003474)1
Poor hand-eye coordination (HP:0007057)1
Upper limb dysmetria (HP:0020036)1
Restless legs (HP:0012452)1
Elevated brain lactate level by MRS (HP:0012707)1
Progressive gait ataxia (HP:0007240)1
Abnormal corpus callosum morphology (HP:0001273)1
Lumbar hyperlordosis (HP:0002938)1
Polydipsia (HP:0001959)1
Aphasia (HP:0002381)1
Abnormal aggressive, impulsive or violent behavior (HP:0006919)1
Esodeviation (HP:0020045)1
Heart murmur (HP:0030148)1
Abnormal dental enamel morphology (HP:0000682)1
Abnormality of the nose (HP:0000366)1
Intracranial cystic lesion (HP:0010576)1
Hydronephrosis (HP:0000126)1
Laryngeal cleft (HP:0008751)1
2-3 toe syndactyly (HP:0004691)1
Broad forehead (HP:0000337)1
Cupped ear (HP:0000378)1
Abnormal hair pattern (HP:0010720)1
Cerebral white matter atrophy (HP:0012762)1
Decreased activity of mitochondrial respiratory chain (HP:0008972)1
Respiratory distress (HP:0002098)1
Abnormal dentate nucleus morphology (HP:0100321)1
EEG with central sharp waves (HP:0011293)1
Profound static encephalopathy (HP:0007069)1
Pill-rolling tremor (HP:0025387)1
Primary microcephaly (HP:0011451)1
Broad face (HP:0000283)1
Short nose (HP:0003196)1
Broad palm (HP:0001169)1
Broad hallux (HP:0010055)1
Prenatal movement abnormality (HP:0001557)1
Hypoglycemia (HP:0001943)1
Lateral ventricle dilatation (HP:0006956)1
Wide mouth (HP:0000154)1
Simple febrile seizure (HP:0011171)1
Visual hallucinations (HP:0002367)1
Nasogastric tube feeding in infancy (HP:0011470)1
Ventouse delivery (HP:0011412)1
Developmental stagnation at onset of seizures (HP:0006834)1
Recurrent pneumonia (HP:0006532)1
Abnormal brain FDG positron emission tomography (HP:0012658)1
Hyperacusis (HP:0010780)1
EEG with generalized sharp slow waves (HP:0011199)1
Facial hypotonia (HP:0000297)1
Exotropia (HP:0000577)1
Tetraplegia (HP:0002445)1
Prominent forehead (HP:0011220)1
Abnormal eyelid morphology (HP:0000492)1
Abnormality of the outer ear (HP:0000356)1
Precocious puberty in males (HP:0008185)1
Auditory hallucinations (HP:0008765)1
Focal emotional seizure with laughing (HP:0010821)1
Focal dystonia (HP:0004373)1
Brachydactyly (HP:0001156)1
EEG with continuous slow activity (HP:0011204)1
Abnormal cerebral white matter morphology (HP:0002500)1
Moderate sensorineural hearing impairment (HP:0008504)1
Precocious puberty in females (HP:0010465)1
Breech presentation (HP:0001623)1
Eyelid myoclonus (HP:0025097)1
Allergy (HP:0012393)1
Small hand (HP:0200055)1
Spastic hemiparesis (HP:0011099)1
Abnormal cerebral subcortex morphology (HP:0010993)1
Agitation (HP:0000713)1
Maintenance insomnia (HP:0031355)1
Neonatal respiratory distress (HP:0002643)1
Hypertelorism (HP:0000316)1
Obsessive-compulsive behavior (HP:0000722)1
Infectious encephalitis (HP:0002383)1
Oculogyric crisis (HP:0010553)1
Widened cerebral subarachnoid space (HP:0012766)1
Nasogastric tube feeding (HP:0040288)1
Central sleep apnea (HP:0010536)1
Kinetic tremor (HP:0030186)1
Cyanotic episode (HP:0200048)1
Motor deterioration (HP:0002333)1
Abnormality of the face (HP:0000271)1
Stooped posture (HP:0025403)1
Maternal hypertension (HP:0008071)1
Prominent superficial veins (HP:0001015)1
Dermal translucency (HP:0010648)1
Aplasia/Hypoplasia of the nails (HP:0008386)1
Recurrent urinary tract infections (HP:0000010)1
Recurrent upper respiratory tract infections (HP:0002788)1
EEG with frontal sharp slow waves (HP:0011290)1
Deep philtrum (HP:0002002)1
Exaggerated cupid's bow (HP:0002263)1
Echolalia (HP:0010529)1
Exodeviation (HP:0020049)1
Gastrointestinal dysmotility (HP:0002579)1
Gastroparesis (HP:0002578)1
Fatigue (HP:0012378)1
Subependymal nodules (HP:0009716)1
Basal ganglia gliosis (HP:0006999)1
Abnormality of the sphenoid sinus (HP:0430022)1
Titubation (HP:0030187)1
Beta-EEG (HP:0011179)1
Multifocal hyperintensity of cerebral white matter on MRI (HP:0040329)1
Extrapyramidal muscular rigidity (HP:0007076)1
Death in childhood (HP:0003819)1
Poor speech (HP:0002465)1
Expressive aphasia (HP:0002427)1
Hearing abnormality (HP:0000364)1
Ophthalmoplegia (HP:0000602)1
Hip dysplasia (HP:0001385)1
Hip osteoarthritis (HP:0008843)1
EEG with spike-wave complexes (2.5-3.5 Hz) (HP:0010848)1
Focal cortical dysplasia type Ia (HP:0032048)1
Abnormal brainstem MRI signal intensity (HP:0012747)1
Muscle weakness (HP:0001324)1
EEG with focal spike waves (HP:0011197)1
Delayed social development (HP:0012434)1
Upper limb hypertonia (HP:0200049)1
Axial dystonia (HP:0002530)1
EEG with generalized slow activity grade 1 (HP:0011206)1
Phimosis (HP:0001741)1
Hip subluxation (HP:0030043)1
Unilateral cryptorchidism (HP:0012741)1
Bulbous nose (HP:0000414)1
Long eyelashes (HP:0000527)1
Kyphosis (HP:0002808)1
Short neck (HP:0000470)1
" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], "source": [ - "from genophenocorr.model import Cohort\n", - "from genophenocorr.view import CohortViewer\n", - "from IPython.display import display, HTML\n", - "cohort = Cohort.from_patients(patient_list)" + "display(HTML(viewer.hpo_term_counts_table(patientCohort)))" ] }, { - "cell_type": "markdown", - "id": "175d2b14-b75a-499a-9251-5154aa31c683", + "cell_type": "code", + "execution_count": 14, + "id": "dc826732", "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'NM_003165.6': Counter({'FRAMESHIFT_VARIANT': 68,\n", + " 'MISSENSE_VARIANT': 249,\n", + " 'SPLICE_DONOR_VARIANT': 36,\n", + " 'STOP_GAINED': 72,\n", + " 'SPLICE_REGION_VARIANT': 18,\n", + " 'SPLICE_ACCEPTOR_VARIANT': 22,\n", + " 'THREE_PRIME_UTR_VARIANT': 2,\n", + " 'INFRAME_DELETION': 8,\n", + " 'SYNONYMOUS_VARIANT': 4,\n", + " 'PROTEIN_ALTERING_VARIANT': 2,\n", + " 'SPLICE_POLYPYRIMIDINE_TRACT_VARIANT': 1,\n", + " 'INTRON_VARIANT': 1})}" + ] + }, + "execution_count": 14, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ - "

CohortViewer

\n", - "

The CohortViewer class offers various methods to create tables and graphics to view the data in the cohort.\n", - "It is still very much in progress

" + "patientCohort.list_data_by_tx('NM_003165.6')" ] }, { "cell_type": "code", - "execution_count": null, - "id": "1c7c5c1e-8e5e-488a-98ec-85689adff61c", + "execution_count": 18, + "id": "cc3cc692", "metadata": {}, "outputs": [], "source": [ - "viewer = CohortViewer(hpo=hpo)" + "from genophenocorr.analysis import CohortAnalysis\n", + "from genophenocorr.model import VariantEffect" ] + }, + { + "cell_type": "code", + "execution_count": 21, + "id": "3a54a6a4", + "metadata": {}, + "outputs": [], + "source": [ + "analysis = CohortAnalysis(patientCohort,'NM_003165.6',hpo,p_val_correction='fdr_bh')" + ] + }, + { + "cell_type": "code", + "execution_count": 22, + "id": "c7ab8b6b", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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With missense_variantWithout missense_variant
CountPercentCountPercentp-valueCorrected p-values
HP:0001251 (Ataxia)4718.88%6630.99%0.0032820.095184
HP:0002376 (Developmental regression)3514.06%157.04%0.0164020.237831
HP:0011097 (Epileptic spasm)9237.40%9947.37%0.0360730.262600
HP:0001252 (Hypotonia)8835.34%9645.07%0.0362210.262600
HP:0003623 (Neonatal onset)5522.09%6229.11%0.0871380.427422
HP:0012469 (Infantile spasms)6928.05%7435.41%0.1050550.427422
HP:0002521 (Hypsarrhythmia)5723.08%6329.72%0.1112640.427422
HP:0002266 (Focal clonic seizure)2510.16%3215.31%0.1179090.427422
HP:0002540 (Inability to walk)5823.29%3817.84%0.1679980.513213
HP:0031375 (Refractory)3915.66%2411.27%0.1769700.513213
HP:0001337 (Tremor)5522.09%5827.23%0.2323870.594057
HP:0002384 (Focal impaired awareness seizure)4317.48%2813.40%0.2458170.594057
HP:0010845 (EEG with generalized slow activity)3012.15%198.96%0.2918500.651050
HP:0001249 (Intellectual disability)10843.37%10147.42%0.3998340.775947
HP:0010818 (Generalized tonic seizure)4618.70%4622.01%0.4131710.775947
HP:0001344 (Absent speech)8634.54%6630.99%0.4286170.775947
HP:0001263 (Global developmental delay)17469.88%15673.24%0.4699260.775947
HP:0011344 (Severe global developmental delay)3614.46%2612.21%0.4969880.775947
HP:0011185 (EEG with focal epileptiform discharges)10843.72%8640.57%0.5083790.775947
HP:0010841 (Multifocal epileptiform discharges)5622.67%4320.28%0.5703020.826938
HP:0010851 (EEG with burst suppression)3815.38%3717.45%0.6129060.846394
HP:0003593 (Infantile onset)6325.30%5827.23%0.6717620.885505
HP:0002069 (Bilateral tonic-clonic seizure)5522.36%4320.57%0.7315280.914891
HP:0001250 (Seizure)22089.43%18990.43%0.7571520.914891
HP:0010864 (Intellectual disability, severe)5622.49%5023.47%0.8249330.949882
HP:0000750 (Delayed speech and language development)11445.78%10046.95%0.8516180.949882
HP:0002123 (Generalized myoclonic seizure)2811.38%2311.00%1.0000001.000000
HP:0000733 (Motor stereotypy)4317.27%3717.37%1.0000001.000000
HP:0007359 (Focal-onset seizure)12350.00%10449.76%1.0000001.000000
\n", + "
" + ], + "text/plain": [ + " With missense_variant \\\n", + " Count \n", + "HP:0001251 (Ataxia) 47 \n", + "HP:0002376 (Developmental regression) 35 \n", + "HP:0011097 (Epileptic spasm) 92 \n", + "HP:0001252 (Hypotonia) 88 \n", + "HP:0003623 (Neonatal onset) 55 \n", + "HP:0012469 (Infantile spasms) 69 \n", + "HP:0002521 (Hypsarrhythmia) 57 \n", + "HP:0002266 (Focal clonic seizure) 25 \n", + "HP:0002540 (Inability to walk) 58 \n", + "HP:0031375 (Refractory) 39 \n", + "HP:0001337 (Tremor) 55 \n", + "HP:0002384 (Focal impaired awareness seizure) 43 \n", + "HP:0010845 (EEG with generalized slow activity) 30 \n", + "HP:0001249 (Intellectual disability) 108 \n", + "HP:0010818 (Generalized tonic seizure) 46 \n", + "HP:0001344 (Absent speech) 86 \n", + "HP:0001263 (Global developmental delay) 174 \n", + "HP:0011344 (Severe global developmental delay) 36 \n", + "HP:0011185 (EEG with focal epileptiform dischar... 108 \n", + "HP:0010841 (Multifocal epileptiform discharges) 56 \n", + "HP:0010851 (EEG with burst suppression) 38 \n", + "HP:0003593 (Infantile onset) 63 \n", + "HP:0002069 (Bilateral tonic-clonic seizure) 55 \n", + "HP:0001250 (Seizure) 220 \n", + "HP:0010864 (Intellectual disability, severe) 56 \n", + "HP:0000750 (Delayed speech and language develop... 114 \n", + "HP:0002123 (Generalized myoclonic seizure) 28 \n", + "HP:0000733 (Motor stereotypy) 43 \n", + "HP:0007359 (Focal-onset seizure) 123 \n", + "\n", + " \\\n", + " Percent \n", + "HP:0001251 (Ataxia) 18.88% \n", + "HP:0002376 (Developmental regression) 14.06% \n", + "HP:0011097 (Epileptic spasm) 37.40% \n", + "HP:0001252 (Hypotonia) 35.34% \n", + "HP:0003623 (Neonatal onset) 22.09% \n", + "HP:0012469 (Infantile spasms) 28.05% \n", + "HP:0002521 (Hypsarrhythmia) 23.08% \n", + "HP:0002266 (Focal clonic seizure) 10.16% \n", + "HP:0002540 (Inability to walk) 23.29% \n", + "HP:0031375 (Refractory) 15.66% \n", + "HP:0001337 (Tremor) 22.09% \n", + "HP:0002384 (Focal impaired awareness seizure) 17.48% \n", + "HP:0010845 (EEG with generalized slow activity) 12.15% \n", + "HP:0001249 (Intellectual disability) 43.37% \n", + "HP:0010818 (Generalized tonic seizure) 18.70% \n", + "HP:0001344 (Absent speech) 34.54% \n", + "HP:0001263 (Global developmental delay) 69.88% \n", + "HP:0011344 (Severe global developmental delay) 14.46% \n", + "HP:0011185 (EEG with focal epileptiform dischar... 43.72% \n", + "HP:0010841 (Multifocal epileptiform discharges) 22.67% \n", + "HP:0010851 (EEG with burst suppression) 15.38% \n", + "HP:0003593 (Infantile onset) 25.30% \n", + "HP:0002069 (Bilateral tonic-clonic seizure) 22.36% \n", + "HP:0001250 (Seizure) 89.43% \n", + "HP:0010864 (Intellectual disability, severe) 22.49% \n", + "HP:0000750 (Delayed speech and language develop... 45.78% \n", + "HP:0002123 (Generalized myoclonic seizure) 11.38% \n", + "HP:0000733 (Motor stereotypy) 17.27% \n", + "HP:0007359 (Focal-onset seizure) 50.00% \n", + "\n", + " Without missense_variant \\\n", + " Count \n", + "HP:0001251 (Ataxia) 66 \n", + "HP:0002376 (Developmental regression) 15 \n", + "HP:0011097 (Epileptic spasm) 99 \n", + "HP:0001252 (Hypotonia) 96 \n", + "HP:0003623 (Neonatal onset) 62 \n", + "HP:0012469 (Infantile spasms) 74 \n", + "HP:0002521 (Hypsarrhythmia) 63 \n", + "HP:0002266 (Focal clonic seizure) 32 \n", + "HP:0002540 (Inability to walk) 38 \n", + "HP:0031375 (Refractory) 24 \n", + "HP:0001337 (Tremor) 58 \n", + "HP:0002384 (Focal impaired awareness seizure) 28 \n", + "HP:0010845 (EEG with generalized slow activity) 19 \n", + "HP:0001249 (Intellectual disability) 101 \n", + "HP:0010818 (Generalized tonic seizure) 46 \n", + "HP:0001344 (Absent speech) 66 \n", + "HP:0001263 (Global developmental delay) 156 \n", + "HP:0011344 (Severe global developmental delay) 26 \n", + "HP:0011185 (EEG with focal epileptiform dischar... 86 \n", + "HP:0010841 (Multifocal epileptiform discharges) 43 \n", + "HP:0010851 (EEG with burst suppression) 37 \n", + "HP:0003593 (Infantile onset) 58 \n", + "HP:0002069 (Bilateral tonic-clonic seizure) 43 \n", + "HP:0001250 (Seizure) 189 \n", + "HP:0010864 (Intellectual disability, severe) 50 \n", + "HP:0000750 (Delayed speech and language develop... 100 \n", + "HP:0002123 (Generalized myoclonic seizure) 23 \n", + "HP:0000733 (Motor stereotypy) 37 \n", + "HP:0007359 (Focal-onset seizure) 104 \n", + "\n", + " \\\n", + " Percent p-value \n", + "HP:0001251 (Ataxia) 30.99% 0.003282 \n", + "HP:0002376 (Developmental regression) 7.04% 0.016402 \n", + "HP:0011097 (Epileptic spasm) 47.37% 0.036073 \n", + "HP:0001252 (Hypotonia) 45.07% 0.036221 \n", + "HP:0003623 (Neonatal onset) 29.11% 0.087138 \n", + "HP:0012469 (Infantile spasms) 35.41% 0.105055 \n", + "HP:0002521 (Hypsarrhythmia) 29.72% 0.111264 \n", + "HP:0002266 (Focal clonic seizure) 15.31% 0.117909 \n", + "HP:0002540 (Inability to walk) 17.84% 0.167998 \n", + "HP:0031375 (Refractory) 11.27% 0.176970 \n", + "HP:0001337 (Tremor) 27.23% 0.232387 \n", + "HP:0002384 (Focal impaired awareness seizure) 13.40% 0.245817 \n", + "HP:0010845 (EEG with generalized slow activity) 8.96% 0.291850 \n", + "HP:0001249 (Intellectual disability) 47.42% 0.399834 \n", + "HP:0010818 (Generalized tonic seizure) 22.01% 0.413171 \n", + "HP:0001344 (Absent speech) 30.99% 0.428617 \n", + "HP:0001263 (Global developmental delay) 73.24% 0.469926 \n", + "HP:0011344 (Severe global developmental delay) 12.21% 0.496988 \n", + "HP:0011185 (EEG with focal epileptiform dischar... 40.57% 0.508379 \n", + "HP:0010841 (Multifocal epileptiform discharges) 20.28% 0.570302 \n", + "HP:0010851 (EEG with burst suppression) 17.45% 0.612906 \n", + "HP:0003593 (Infantile onset) 27.23% 0.671762 \n", + "HP:0002069 (Bilateral tonic-clonic seizure) 20.57% 0.731528 \n", + "HP:0001250 (Seizure) 90.43% 0.757152 \n", + "HP:0010864 (Intellectual disability, severe) 23.47% 0.824933 \n", + "HP:0000750 (Delayed speech and language develop... 46.95% 0.851618 \n", + "HP:0002123 (Generalized myoclonic seizure) 11.00% 1.000000 \n", + "HP:0000733 (Motor stereotypy) 17.37% 1.000000 \n", + "HP:0007359 (Focal-onset seizure) 49.76% 1.000000 \n", + "\n", + " \n", + " Corrected p-values \n", + "HP:0001251 (Ataxia) 0.095184 \n", + "HP:0002376 (Developmental regression) 0.237831 \n", + "HP:0011097 (Epileptic spasm) 0.262600 \n", + "HP:0001252 (Hypotonia) 0.262600 \n", + "HP:0003623 (Neonatal onset) 0.427422 \n", + "HP:0012469 (Infantile spasms) 0.427422 \n", + "HP:0002521 (Hypsarrhythmia) 0.427422 \n", + "HP:0002266 (Focal clonic seizure) 0.427422 \n", + "HP:0002540 (Inability to walk) 0.513213 \n", + "HP:0031375 (Refractory) 0.513213 \n", + "HP:0001337 (Tremor) 0.594057 \n", + "HP:0002384 (Focal impaired awareness seizure) 0.594057 \n", + "HP:0010845 (EEG with generalized slow activity) 0.651050 \n", + "HP:0001249 (Intellectual disability) 0.775947 \n", + "HP:0010818 (Generalized tonic seizure) 0.775947 \n", + "HP:0001344 (Absent speech) 0.775947 \n", + "HP:0001263 (Global developmental delay) 0.775947 \n", + "HP:0011344 (Severe global developmental delay) 0.775947 \n", + "HP:0011185 (EEG with focal epileptiform dischar... 0.775947 \n", + "HP:0010841 (Multifocal epileptiform discharges) 0.826938 \n", + "HP:0010851 (EEG with burst suppression) 0.846394 \n", + "HP:0003593 (Infantile onset) 0.885505 \n", + "HP:0002069 (Bilateral tonic-clonic seizure) 0.914891 \n", + "HP:0001250 (Seizure) 0.914891 \n", + "HP:0010864 (Intellectual disability, severe) 0.949882 \n", + "HP:0000750 (Delayed speech and language develop... 0.949882 \n", + "HP:0002123 (Generalized myoclonic seizure) 1.000000 \n", + "HP:0000733 (Motor stereotypy) 1.000000 \n", + "HP:0007359 (Focal-onset seizure) 1.000000 " + ] + }, + "execution_count": 22, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "analysis.compare_by_variant_type(VariantEffect.MISSENSE_VARIANT)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "f0981332", + "metadata": {}, + "outputs": [], + "source": [] } ], "metadata": { "kernelspec": { - "display_name": "gpc2venv", + "display_name": "enviro", "language": "python", - "name": "gpc2venv" + "name": "enviro" }, "language_info": { "codemirror_mode": { @@ -158,7 +1431,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.10" + "version": "3.10.10" } }, "nbformat": 4, diff --git a/notebooks/SUOX/SUOX_Li_PMID36303223_RunGenoPhenoCorr.ipynb b/notebooks/SUOX/SUOX_Li_PMID36303223_RunGenoPhenoCorr.ipynb index e98b75f8..1b77e036 100644 --- a/notebooks/SUOX/SUOX_Li_PMID36303223_RunGenoPhenoCorr.ipynb +++ b/notebooks/SUOX/SUOX_Li_PMID36303223_RunGenoPhenoCorr.ipynb @@ -82,25 +82,38 @@ { "cell_type": "code", "execution_count": 7, + "id": "bc2ef27b", + "metadata": {}, + "outputs": [], + "source": [ + "from IPython.display import HTML, display\n", + "from genophenocorr.view import CohortViewer\n", + "\n", + "viewer = CohortViewer(hpo)" + ] + }, + { + "cell_type": "code", + "execution_count": 8, "id": "b412e537", "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "[('12_56004589_C/G', 7),\n", - " ('12_56004039_G/A', 3),\n", - " ('12_56004485_C/T', 3),\n", - " ('12_56004765_G/A', 3),\n", - " ('12_56004771_A/T', 2),\n", - " ('12_56004906_TTGT/-', 2),\n", - " ('12_56004273_G/A', 2),\n", - " ('12_56004959_-/C', 2),\n", - " ('12_56004473_G/A', 1),\n", - " ('12_56002674_T/C', 1)]" + "[('12_56004589_56004589_C_G', 7),\n", + " ('12_56004039_56004039_G_A', 3),\n", + " ('12_56004485_56004485_C_T', 3),\n", + " ('12_56004765_56004765_G_A', 3),\n", + " ('12_56004905_56004909_ATTGT_A', 2),\n", + " ('12_56004933_56004959_A_ACAATGTGCAGCCAGACACCGTGGCCC', 2),\n", + " ('12_56004771_56004771_A_T', 2),\n", + " ('12_56004273_56004273_G_A', 2),\n", + " ('12_56004192_56004192_G_A', 1),\n", + " ('12_56004161_56004161_A_C', 1)]" ] }, - "execution_count": 7, + "execution_count": 8, "metadata": {}, "output_type": "execute_result" } @@ -111,7 +124,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 9, "id": "72f35a21", "metadata": {}, "outputs": [ @@ -120,15 +133,15 @@ "text/plain": [ "[('HP:0001250', 28),\n", " ('HP:0001252', 15),\n", - " ('HP:0002071', 11),\n", " ('HP:0001276', 11),\n", + " ('HP:0002071', 11),\n", " ('HP:0000252', 10),\n", " ('HP:0012758', 8),\n", " ('HP:0001083', 7),\n", " ('HP:0034332', 6)]" ] }, - "execution_count": 8, + "execution_count": 9, "metadata": {}, "output_type": "execute_result" } @@ -139,25 +152,25 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 10, "id": "5a03af26", "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "{'NM_001032386.2': Counter({'missense_variant': 22,\n", - " 'stop_gained': 5,\n", - " 'frameshift_variant': 7}),\n", - " 'NM_001032387.2': Counter({'missense_variant': 22,\n", - " 'stop_gained': 5,\n", - " 'frameshift_variant': 7}),\n", - " 'NM_000456.3': Counter({'missense_variant': 22,\n", - " 'stop_gained': 5,\n", - " 'frameshift_variant': 7})}" + "{'NM_001032386.2': Counter({'MISSENSE_VARIANT': 29,\n", + " 'FRAMESHIFT_VARIANT': 9,\n", + " 'STOP_GAINED': 10}),\n", + " 'NM_000456.3': Counter({'MISSENSE_VARIANT': 29,\n", + " 'FRAMESHIFT_VARIANT': 9,\n", + " 'STOP_GAINED': 10}),\n", + " 'NM_001032387.2': Counter({'MISSENSE_VARIANT': 29,\n", + " 'FRAMESHIFT_VARIANT': 9,\n", + " 'STOP_GAINED': 10})}" ] }, - "execution_count": 9, + "execution_count": 10, "metadata": {}, "output_type": "execute_result" } @@ -168,7 +181,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 11, "id": "ba7d8f40", "metadata": {}, "outputs": [ @@ -178,7 +191,7 @@ "35" ] }, - "execution_count": 10, + "execution_count": 11, "metadata": {}, "output_type": "execute_result" } @@ -189,27 +202,29 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 20, "id": "531e077d", "metadata": {}, "outputs": [], "source": [ - "from genophenocorr.analysis import CohortAnalysis" + "from genophenocorr.analysis import CohortAnalysis\n", + "from genophenocorr.model import VariantEffect" ] }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 21, "id": "4b64148d", "metadata": {}, "outputs": [], "source": [ - "analysis = CohortAnalysis(patientCohort, 'NM_000456.3', hpo, include_unmeasured=False, recessive=True)" + "analysis = CohortAnalysis(patientCohort, 'NM_000456.3', hpo, include_unmeasured=False, \n", + " recessive=True, p_val_correction='fdr_bh')" ] }, { "cell_type": "code", - "execution_count": 13, + "execution_count": 22, "id": "f4fb138e", "metadata": {}, "outputs": [ @@ -261,7 +276,7 @@ " 0\n", " 0.00%\n", " 0.023343\n", - " 0.186742\n", + " 0.158119\n", " \n", " \n", " HP:0001252 (Hypotonia)\n", @@ -272,7 +287,7 @@ " 3\n", " 42.86%\n", " 0.039530\n", - " 0.316238\n", + " 0.158119\n", " \n", " \n", " HP:0001250 (Seizure)\n", @@ -283,7 +298,7 @@ " 11\n", " 100.00%\n", " 0.082640\n", - " 0.661118\n", + " 0.220373\n", " \n", " \n", " HP:0002071 (Abnormality of extrapyramidal motor function)\n", @@ -294,7 +309,7 @@ " 2\n", " 25.00%\n", " 0.139377\n", - " 1.000000\n", + " 0.242998\n", " \n", " \n", " HP:0012758 (Neurodevelopmental delay)\n", @@ -305,7 +320,7 @@ " 4\n", " 50.00%\n", " 0.151874\n", - " 1.000000\n", + " 0.242998\n", " \n", " \n", " HP:0001083 (Ectopia lentis)\n", @@ -316,7 +331,7 @@ " 1\n", " 33.33%\n", " 0.334276\n", - " 1.000000\n", + " 0.445701\n", " \n", " \n", " HP:0000252 (Microcephaly)\n", @@ -327,7 +342,7 @@ " 4\n", " 57.14%\n", " 0.849964\n", - " 1.000000\n", + " 0.971388\n", " \n", " \n", " HP:0001276 (Hypertonia)\n", @@ -413,29 +428,28 @@ "\n", " \n", " Corrected p-values \n", - "HP:0034332 (Cognitive regression) 0.186742 \n", - "HP:0001252 (Hypotonia) 0.316238 \n", - "HP:0001250 (Seizure) 0.661118 \n", - "HP:0002071 (Abnormality of extrapyramidal motor... 1.000000 \n", - "HP:0012758 (Neurodevelopmental delay) 1.000000 \n", - "HP:0001083 (Ectopia lentis) 1.000000 \n", - "HP:0000252 (Microcephaly) 1.000000 \n", + "HP:0034332 (Cognitive regression) 0.158119 \n", + "HP:0001252 (Hypotonia) 0.158119 \n", + "HP:0001250 (Seizure) 0.220373 \n", + "HP:0002071 (Abnormality of extrapyramidal motor... 0.242998 \n", + "HP:0012758 (Neurodevelopmental delay) 0.242998 \n", + "HP:0001083 (Ectopia lentis) 0.445701 \n", + "HP:0000252 (Microcephaly) 0.971388 \n", "HP:0001276 (Hypertonia) 1.000000 " ] }, - "execution_count": 13, + "execution_count": 22, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "from genophenocorr.constants import VariantEffect\n", "analysis.compare_by_variant_type(VariantEffect.MISSENSE_VARIANT)" ] }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 19, "id": "743954bd", "metadata": {}, "outputs": [ @@ -460,9 +474,9 @@ " \n", " \n", " \n", - " Homozygous 12_56004589_C/G\n", - " Heterozygous 12_56004589_C/G\n", - " No 12_56004589_C/G\n", + " Homozygous 12_56004589_56004589_C_G\n", + " Heterozygous 12_56004589_56004589_C_G\n", + " No 12_56004589_56004589_C_G\n", " \n", " \n", " \n", @@ -487,7 +501,7 @@ " 14\n", " 77.78%\n", " 0.032869\n", - " 0.26295\n", + " 0.262950\n", " \n", " \n", " HP:0001083 (Ectopia lentis)\n", @@ -498,7 +512,7 @@ " 5\n", " 33.33%\n", " 0.137255\n", - " 1.00000\n", + " 0.468687\n", " \n", " \n", " HP:0012758 (Neurodevelopmental delay)\n", @@ -509,7 +523,7 @@ " 8\n", " 42.11%\n", " 0.175758\n", - " 1.00000\n", + " 0.468687\n", " \n", " \n", " HP:0002071 (Abnormality of extrapyramidal motor function)\n", @@ -520,7 +534,7 @@ " 10\n", " 52.63%\n", " 0.340580\n", - " 1.00000\n", + " 0.681159\n", " \n", " \n", " HP:0034332 (Cognitive regression)\n", @@ -531,7 +545,7 @@ " 6\n", " 31.58%\n", " 0.452851\n", - " 1.00000\n", + " 0.724562\n", " \n", " \n", " HP:0001276 (Hypertonia)\n", @@ -542,7 +556,18 @@ " 9\n", " 50.00%\n", " 0.590062\n", - " 1.00000\n", + " 0.786749\n", + " \n", + " \n", + " HP:0000252 (Microcephaly)\n", + " 1\n", + " 100.00%\n", + " 1\n", + " 33.33%\n", + " 8\n", + " 47.06%\n", + " 1.000000\n", + " 1.000000\n", " \n", " \n", " HP:0001250 (Seizure)\n", @@ -553,34 +578,23 @@ " 22\n", " 78.57%\n", " 1.000000\n", - " 1.00000\n", - " \n", - " \n", - " HP:0000252 (Microcephaly)\n", - " 1\n", - " 100.00%\n", - " 1\n", - " 33.33%\n", - " 8\n", - " 47.06%\n", " 1.000000\n", - " 1.00000\n", " \n", " \n", "\n", "" ], "text/plain": [ - " Homozygous 12_56004589_C/G \\\n", - " Count \n", - "HP:0001252 (Hypotonia) 0 \n", - "HP:0001083 (Ectopia lentis) 0 \n", - "HP:0012758 (Neurodevelopmental delay) 0 \n", - "HP:0002071 (Abnormality of extrapyramidal motor... 0 \n", - "HP:0034332 (Cognitive regression) 0 \n", - "HP:0001276 (Hypertonia) 1 \n", - "HP:0001250 (Seizure) 2 \n", - "HP:0000252 (Microcephaly) 1 \n", + " Homozygous 12_56004589_56004589_C_G \\\n", + " Count \n", + "HP:0001252 (Hypotonia) 0 \n", + "HP:0001083 (Ectopia lentis) 0 \n", + "HP:0012758 (Neurodevelopmental delay) 0 \n", + "HP:0002071 (Abnormality of extrapyramidal motor... 0 \n", + "HP:0034332 (Cognitive regression) 0 \n", + "HP:0001276 (Hypertonia) 1 \n", + "HP:0000252 (Microcephaly) 1 \n", + "HP:0001250 (Seizure) 2 \n", "\n", " \\\n", " Percent \n", @@ -590,19 +604,19 @@ "HP:0002071 (Abnormality of extrapyramidal motor... 0.00% \n", "HP:0034332 (Cognitive regression) 0.00% \n", "HP:0001276 (Hypertonia) 100.00% \n", - "HP:0001250 (Seizure) 100.00% \n", "HP:0000252 (Microcephaly) 100.00% \n", + "HP:0001250 (Seizure) 100.00% \n", "\n", - " Heterozygous 12_56004589_C/G \\\n", - " Count \n", - "HP:0001252 (Hypotonia) 1 \n", - "HP:0001083 (Ectopia lentis) 2 \n", - "HP:0012758 (Neurodevelopmental delay) 0 \n", - "HP:0002071 (Abnormality of extrapyramidal motor... 1 \n", - "HP:0034332 (Cognitive regression) 0 \n", - "HP:0001276 (Hypertonia) 1 \n", - "HP:0001250 (Seizure) 4 \n", - "HP:0000252 (Microcephaly) 1 \n", + " Heterozygous 12_56004589_56004589_C_G \\\n", + " Count \n", + "HP:0001252 (Hypotonia) 1 \n", + "HP:0001083 (Ectopia lentis) 2 \n", + "HP:0012758 (Neurodevelopmental delay) 0 \n", + "HP:0002071 (Abnormality of extrapyramidal motor... 1 \n", + "HP:0034332 (Cognitive regression) 0 \n", + "HP:0001276 (Hypertonia) 1 \n", + "HP:0000252 (Microcephaly) 1 \n", + "HP:0001250 (Seizure) 4 \n", "\n", " \\\n", " Percent \n", @@ -612,50 +626,50 @@ "HP:0002071 (Abnormality of extrapyramidal motor... 20.00% \n", "HP:0034332 (Cognitive regression) 0.00% \n", "HP:0001276 (Hypertonia) 25.00% \n", - "HP:0001250 (Seizure) 80.00% \n", "HP:0000252 (Microcephaly) 33.33% \n", + "HP:0001250 (Seizure) 80.00% \n", "\n", - " No 12_56004589_C/G \\\n", - " Count Percent \n", - "HP:0001252 (Hypotonia) 14 77.78% \n", - "HP:0001083 (Ectopia lentis) 5 33.33% \n", - "HP:0012758 (Neurodevelopmental delay) 8 42.11% \n", - "HP:0002071 (Abnormality of extrapyramidal motor... 10 52.63% \n", - "HP:0034332 (Cognitive regression) 6 31.58% \n", - "HP:0001276 (Hypertonia) 9 50.00% \n", - "HP:0001250 (Seizure) 22 78.57% \n", - "HP:0000252 (Microcephaly) 8 47.06% \n", + " No 12_56004589_56004589_C_G \\\n", + " Count \n", + "HP:0001252 (Hypotonia) 14 \n", + "HP:0001083 (Ectopia lentis) 5 \n", + "HP:0012758 (Neurodevelopmental delay) 8 \n", + "HP:0002071 (Abnormality of extrapyramidal motor... 10 \n", + "HP:0034332 (Cognitive regression) 6 \n", + "HP:0001276 (Hypertonia) 9 \n", + "HP:0000252 (Microcephaly) 8 \n", + "HP:0001250 (Seizure) 22 \n", "\n", - " \\\n", - " p-value \n", - "HP:0001252 (Hypotonia) 0.032869 \n", - "HP:0001083 (Ectopia lentis) 0.137255 \n", - "HP:0012758 (Neurodevelopmental delay) 0.175758 \n", - "HP:0002071 (Abnormality of extrapyramidal motor... 0.340580 \n", - "HP:0034332 (Cognitive regression) 0.452851 \n", - "HP:0001276 (Hypertonia) 0.590062 \n", - "HP:0001250 (Seizure) 1.000000 \n", - "HP:0000252 (Microcephaly) 1.000000 \n", + " \\\n", + " Percent p-value \n", + "HP:0001252 (Hypotonia) 77.78% 0.032869 \n", + "HP:0001083 (Ectopia lentis) 33.33% 0.137255 \n", + "HP:0012758 (Neurodevelopmental delay) 42.11% 0.175758 \n", + "HP:0002071 (Abnormality of extrapyramidal motor... 52.63% 0.340580 \n", + "HP:0034332 (Cognitive regression) 31.58% 0.452851 \n", + "HP:0001276 (Hypertonia) 50.00% 0.590062 \n", + "HP:0000252 (Microcephaly) 47.06% 1.000000 \n", + "HP:0001250 (Seizure) 78.57% 1.000000 \n", "\n", " \n", " Corrected p-values \n", - "HP:0001252 (Hypotonia) 0.26295 \n", - "HP:0001083 (Ectopia lentis) 1.00000 \n", - "HP:0012758 (Neurodevelopmental delay) 1.00000 \n", - "HP:0002071 (Abnormality of extrapyramidal motor... 1.00000 \n", - "HP:0034332 (Cognitive regression) 1.00000 \n", - "HP:0001276 (Hypertonia) 1.00000 \n", - "HP:0001250 (Seizure) 1.00000 \n", - "HP:0000252 (Microcephaly) 1.00000 " + "HP:0001252 (Hypotonia) 0.262950 \n", + "HP:0001083 (Ectopia lentis) 0.468687 \n", + "HP:0012758 (Neurodevelopmental delay) 0.468687 \n", + "HP:0002071 (Abnormality of extrapyramidal motor... 0.681159 \n", + "HP:0034332 (Cognitive regression) 0.724562 \n", + "HP:0001276 (Hypertonia) 0.786749 \n", + "HP:0000252 (Microcephaly) 1.000000 \n", + "HP:0001250 (Seizure) 1.000000 " ] }, - "execution_count": 14, + "execution_count": 19, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "analysis.compare_by_variant('12_56004589_C/G')" + "analysis.compare_by_variant('12_56004589_56004589_C_G')" ] }, { diff --git a/src/genophenocorr/analysis/_analyzers.py b/src/genophenocorr/analysis/_analyzers.py index 82e6ebcd..f34b5e9f 100644 --- a/src/genophenocorr/analysis/_analyzers.py +++ b/src/genophenocorr/analysis/_analyzers.py @@ -242,7 +242,7 @@ def compare_by_variant_effect(self, effect: VariantEffect, tx_id: str): self._transcript = previous return result - def compare_by_variant_type(self, var_type1:VariantEffect, var_type2:VariantEffect = None): + def compare_by_variant_type(self, var_type1:VariantEffect, var_type2:typing.Optional[VariantEffect] = None): """Runs Fisher Exact analysis, finds any correlation between given variant effects across phenotypes. Args: @@ -309,7 +309,7 @@ def compare_by_variant(self, variant1:str, variant2:str = None): final_df.insert(5, ('', "Corrected p-values"), corrected_pvals, True) return final_df.sort_values([('', 'Corrected p-values'), ('', 'p-value')]) - def compare_by_exon(self, exon1:int, exon2:int = None): + def compare_by_exon(self, exon1:int, exon2:typing.Optional[int] = None): """Runs Fisher Exact analysis, finds any correlation between given exons across phenotypes. Args: @@ -341,7 +341,7 @@ def compare_by_exon(self, exon1:int, exon2:int = None): final_df.insert(5, ('', "Corrected p-values"), corrected_pvals, True) return final_df.sort_values([('', 'Corrected p-values'), ('', 'p-value')]) - def compare_by_protein_feature_type(self, feature1:FeatureType, feature2:FeatureType = None): + def compare_by_protein_feature_type(self, feature1:FeatureType, feature2:typing.Optional[FeatureType] = None): """Runs Fisher Exact analysis, finds any correlation between given feature type across phenotypes. Args: @@ -374,7 +374,7 @@ def compare_by_protein_feature_type(self, feature1:FeatureType, feature2:Feature return final_df.sort_values([('', 'Corrected p-values'), ('', 'p-value')]) - def compare_by_protein_feature(self, feature1:str, feature2:str = None): + def compare_by_protein_feature(self, feature1:str, feature2:typing.Optional[str] = None): """Runs Fisher Exact analysis, finds any correlation between given feature and phenotypes. Args: diff --git a/src/genophenocorr/analysis/_commie.py b/src/genophenocorr/analysis/_commie.py index d7425d62..9407ff9e 100644 --- a/src/genophenocorr/analysis/_commie.py +++ b/src/genophenocorr/analysis/_commie.py @@ -14,7 +14,7 @@ from .predicate.phenotype import PropagatingPhenotypeBooleanPredicateFactory, PhenotypePredicateFactory from ._api import CohortAnalysis, GenotypePhenotypeAnalysisResult -from ._stats import run_fisher_exact +from ._stats import run_fisher_exact, run_recessive_fisher_exact def _filter_rare_phenotypes_using_hierarchy(patients: typing.Collection[Patient], @@ -193,7 +193,12 @@ def _run_gp_analysis(self, patients: typing.Iterable[Patient], for pf in phenotypic_features: counts = all_counts.loc[pf] # TODO - this is where we must fail unless we have the contingency table of the right size! - pvals[pf] = run_fisher_exact(counts) + if counts.shape == (2, 2): + pvals[pf] = run_fisher_exact(counts) + elif counts.shape == (3, 2): + pvals[pf] = run_recessive_fisher_exact(counts) + else: + raise ValueError(f"Invalid number of categories. A {counts.shape} table was created. Only (2, 2) and (3, 2) are valid sizes.") # 3) Multiple correction if self._correction is not None: diff --git a/src/genophenocorr/analysis/_config.py b/src/genophenocorr/analysis/_config.py index 11d4e0c5..3552e264 100644 --- a/src/genophenocorr/analysis/_config.py +++ b/src/genophenocorr/analysis/_config.py @@ -9,6 +9,19 @@ from ._commie import CommunistCohortAnalysis +P_VAL_OPTIONS = ['bonferroni', 'b', + 'sidak', 's', + 'holm-sidak', 'hs', + 'holm', 'h', + 'simes-hochberg', 'sh', + 'hommel', 'ho', + 'fdr_bh', + 'fdr_by', + 'fdr_tsbh', + 'fdr_tsbky', + 'fdr_gbs', + None] + class CohortAnalysisConfiguration: """ `CohortAnalysisConfiguration` is a value class for storing :class:`genophenocorr.analysis.CohortAnalysis` @@ -99,8 +112,8 @@ def missing_implies_excluded(self, missing_implies_excluded: bool): if isinstance(missing_implies_excluded, bool): self._missing_implies_excluded = missing_implies_excluded else: - self._logger.warning('Ignoring invalid `missing_implies_excluded` value %s', - missing_implies_excluded) + self._logger.warning('Ignoring invalid `missing_implies_excluded` value %s. Using %s.', + missing_implies_excluded, self._missing_implies_excluded) return self @@ -108,16 +121,26 @@ def pval_correction(self, pval_correction: typing.Optional[str]): """ Set `pval_correction` option. """ - # TODO - check admissible values - self._pval_correction = pval_correction + if pval_correction in P_VAL_OPTIONS: + self._pval_correction = pval_correction + else: + self._logger.warning('Ignoring invalid `pval_correction` value %s. Using %s correction.', pval_correction, self._pval_correction) return self def min_perc_patients_w_hpo(self, min_perc_patients_w_hpo: float): """ Set `min_perc_patients_w_hpo` option. """ - # TODO - check float in range [0,1) - self._min_perc_patients_w_hpo = min_perc_patients_w_hpo + if not isinstance(min_perc_patients_w_hpo, float): + try: + min_perc_patients_w_hpo = float(min_perc_patients_w_hpo) + except ValueError: + self._logger.warning("min_perc_patients_w_hpo must be a number, but was %s. Using %f", min_perc_patients_w_hpo, self._min_perc_patients_w_hpo) + return self + if min_perc_patients_w_hpo > 1 or min_perc_patients_w_hpo <= 0: + self._logger.warning("min_perc_patients_w_hpo must be greater than 0 and at most 1, but was %f. Using %f", min_perc_patients_w_hpo, self._min_perc_patients_w_hpo) + else: + self._min_perc_patients_w_hpo = min_perc_patients_w_hpo return self def include_sv(self, include_sv: bool): @@ -127,7 +150,7 @@ def include_sv(self, include_sv: bool): if isinstance(include_sv, bool): self._include_sv = include_sv else: - self._logger.warning('Ignoring invalid `include_sv` value %s', include_sv) + self._logger.warning('Ignoring invalid `include_sv` value %s. Using %s', include_sv, self._include_sv) return self def build(self) -> CohortAnalysisConfiguration: diff --git a/src/genophenocorr/model/_cohort.py b/src/genophenocorr/model/_cohort.py index 6c3cebb6..6dfb6fff 100644 --- a/src/genophenocorr/model/_cohort.py +++ b/src/genophenocorr/model/_cohort.py @@ -101,7 +101,7 @@ def __hash__(self) -> int: class Cohort(typing.Sized): @staticmethod - def from_patients(members: typing.Sequence[Patient], include_patients_with_no_HPO: bool = False): + def from_patients(members: typing.Sequence[Patient], include_patients_with_no_HPO: bool = False, include_patients_with_no_variants: bool = False): """ Create a cohort from a sequence of patients. @@ -116,6 +116,9 @@ def from_patients(members: typing.Sequence[Patient], include_patients_with_no_HP if len(patient.phenotypes) == 0 and not include_patients_with_no_HPO: excluded_members.append(patient) continue + if len(patient.variants) == 0 and not include_patients_with_no_variants: + excluded_members.append(patient) + continue cohort_phenotypes.update(patient.phenotypes) cohort_variants.update(patient.variants) var_counts.update([var.variant_coordinates.variant_key for var in patient.variants]) diff --git a/src/genophenocorr/model/_protein.py b/src/genophenocorr/model/_protein.py index f928d525..5ff187da 100644 --- a/src/genophenocorr/model/_protein.py +++ b/src/genophenocorr/model/_protein.py @@ -102,6 +102,9 @@ def info(self) -> FeatureInfo: def feature_type(self) -> FeatureType: pass + def to_string(self) -> str: + return f"{self.feature_type.name}-{self.info.name}-{self.info.region}" + class SimpleProteinFeature(ProteinFeature): """A class that represents a protein feature diff --git a/src/genophenocorr/preprocessing/_phenopacket.py b/src/genophenocorr/preprocessing/_phenopacket.py index de6375a4..58801ef8 100644 --- a/src/genophenocorr/preprocessing/_phenopacket.py +++ b/src/genophenocorr/preprocessing/_phenopacket.py @@ -181,15 +181,18 @@ def _add_variants(self, sample_id: str, pp: Phenopacket) -> typing.Sequence[Vari for genomic_interp in interp.diagnosis.genomic_interpretations: vc, gt = self._coord_finder.find_coordinates(genomic_interp) if "N" in vc.alt: - self._logger.warning(f'Patient {pp.id} has unknown alternative variant {vc.alt} and will not be included.') + self._logger.warning('Patient %s has unknown alternative variant %s, this variant will not be included.', pp.id, vc.variant_key) continue tx_annotations = self._func_ann.annotate(vc) + if tx_annotations is None: + self._logger.warning("Patient %s has an error with variant %s, this variant will not be included.", pp.id, vc.variant_key) + continue genotype = Genotypes.single(sample_id, gt) variant = Variant(vc, tx_annotations, genotype) variants_list.append(variant) if len(variants_list) == 0: - self._logger.warning(f'Expected at least one variant per patient, but received none for patient {pp.id}') + self._logger.warning('Expected at least one variant per patient, but received none for patient %s', pp.id) return variants_list def _add_phenotypes(self, pp: Phenopacket) -> typing.Sequence[Phenotype]: diff --git a/src/genophenocorr/preprocessing/_phenotype.py b/src/genophenocorr/preprocessing/_phenotype.py index 79de274f..cb226e54 100644 --- a/src/genophenocorr/preprocessing/_phenotype.py +++ b/src/genophenocorr/preprocessing/_phenotype.py @@ -48,8 +48,9 @@ def create_phenotype(self, term_ids: typing.Iterable[typing.Tuple[str, bool]]) - for term_id, observed in term_ids: term = self._hpo.get_term(term_id) if term is None: - raise ValueError(f'Term ID {term_id} is not present in HPO v{self._hpo.version}') - terms.append((term, observed)) + self._logger.warning("Term %s cannot be found in HPO version %s. It will be ignored.", term_id, self._hpo.version) + else: + terms.append((term, observed)) validation_results = self._validator.validate_all([term[0] for term in terms]) if validation_results.is_ok: return tuple(Phenotype.from_term(term, observed) for term, observed in terms) diff --git a/src/genophenocorr/preprocessing/_vep.py b/src/genophenocorr/preprocessing/_vep.py index 51f29297..6858f0b9 100644 --- a/src/genophenocorr/preprocessing/_vep.py +++ b/src/genophenocorr/preprocessing/_vep.py @@ -8,7 +8,6 @@ from genophenocorr.model.genome import Region from ._api import FunctionalAnnotator, ProteinMetadataService - def verify_start_end_coordinates(vc: VariantCoordinates): """ Converts the 0-based VariantCoordinates to ones that will be interpreted @@ -58,13 +57,15 @@ class VepFunctionalAnnotator(FunctionalAnnotator): def __init__(self, protein_annotator: ProteinMetadataService, include_computational_txs: bool = False): - self._logging = logging.getLogger(__name__) + self._logger = logging.getLogger(__name__) self._protein_annotator = protein_annotator self._url = 'https://rest.ensembl.org/vep/human/region/%s?LoF=1&canonical=1' \ '&domains=1&hgvs=1' \ '&mutfunc=1&numbers=1&protein=1&refseq=1&mane=1' \ '&transcript_version=1&variant_class=1' self._include_computational_txs = include_computational_txs + self._slice_effects = [VariantEffect.SPLICE_ACCEPTOR_VARIANT, VariantEffect.SPLICE_DONOR_VARIANT, VariantEffect.SPLICE_DONOR_5TH_BASE_VARIANT, VariantEffect.SPLICE_POLYPYRIMIDINE_TRACT_VARIANT] + def annotate(self, variant_coordinates: VariantCoordinates) -> typing.Sequence[TranscriptAnnotation]: """Perform functional annotation using Variant Effect Predictor (VEP) REST API. @@ -78,9 +79,8 @@ def annotate(self, variant_coordinates: VariantCoordinates) -> typing.Sequence[T response = self._query_vep(variant_coordinates) annotations = [] if 'transcript_consequences' not in response: - raise ValueError( - f'The VEP response lacked the required `transcript_consequences` field') - + self._logger.error('The VEP response lacked the required `transcript_consequences` field. %s', response) + return None for trans in response['transcript_consequences']: annotation = self._process_item(trans) if annotation is not None: @@ -97,7 +97,7 @@ def _parse_variant_effect(self, effect: str) -> typing.Optional[VariantEffect]: try: var_effect = VariantEffect[effect] except KeyError: - self._logging.warning("VariantEffect %s was not found in our record of possible effects. Please report this issue to the genophenocorr GitHub." , effect) + self._logger.warning("VariantEffect %s was not found in our record of possible effects. Please report this issue to the genophenocorr GitHub.", effect) return None return var_effect @@ -118,7 +118,6 @@ def _process_item(self, item: typing.Dict) -> typing.Optional[TranscriptAnnotati if var_effect is not None: var_effects.append(var_effect) gene_name = item.get('gene_symbol') - exons_effected = item.get('exon') if exons_effected is not None: exons_effected = exons_effected.split('/')[0].split('-') @@ -132,11 +131,8 @@ def _process_item(self, item: typing.Dict) -> typing.Optional[TranscriptAnnotati protein_effect_start = item.get('protein_start') protein_effect_end = item.get('protein_end') if protein_effect_start is None or protein_effect_end is None: - # Does this ever happen? Let's log a warning for now and address the absence of a coordinate later, - # if we see a lot of these warnings popping out. - # Note that Lauren's version of the code had a special branch for missing start, where she set the variable - # to `1` (1-based coordinate). - self._logging.warning('Missing start/end coordinate for %s on protein %s', hgvsc_id, protein_id) + if not any(ve in var_effects for ve in self._slice_effects): + self._logger.warning('Missing start/end coordinate for %s on protein %s. Protein effect will not be included.', hgvsc_id, protein_id) protein_effect = None else: # The coordinates are in 1-based system and we need 0-based. @@ -158,15 +154,17 @@ def _query_vep(self, variant_coordinates: VariantCoordinates) -> dict: api_url = self._url % (verify_start_end_coordinates(variant_coordinates)) r = requests.get(api_url, headers={'Content-Type': 'application/json'}) if not r.ok: - self._logging.error(f"Expected a result but got an Error for variant: {variant_coordinates.variant_key}") - r.raise_for_status() + self._logger.error("Expected a result but got an Error for variant: %s", variant_coordinates.variant_key) + self._logger.error(r.text) + return None results = r.json() if not isinstance(results, list): - self._logging.error(results.get('error')) + self._logger.error(results.get('error')) raise ConnectionError( f"Expected a result but got an Error. See log for details.") if len(results) > 1: - self._logging.error([result.id for result in results]) + self._logger.error("Expected only one variant per request but received %s different variants.", len(results)) + self._logger.error([result.id for result in results]) raise ValueError( f"Expected only one variant per request but received {len(results)} " f"different variants.")