Comment: This test was performed using a multiplexed nucleic acid amplification test that is labeled Emergence Use Only by the U.S. FDA. Results of this test should not be used as the sole basis for diagnosis, treatment, or other management decisions.A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample.
SARS-CoV-2 Nucleic Acid Method (Comment)
This test was performed using the Roche 6800 COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.Other
Comment: This test was performed using a multiplexed nucleic acid amplification test that is labeled Emergence Use Only by the U.S. FDA. Results of this test should not be used as the sole basis for diagnosis, treatment, or other management decisions.A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample.
SARS-CoV-2 Nucleic Acid Method (Comment)
This test was performed using the Roche 6800 COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.Oropharynx
VUMC CERNER LAB
Specimen (Source)
Anatomical Location / Laterality
Collection Method / Volume
Collection Time
Received Time
Oropharynx
07/27/2022 3:49 PM CDT
07/27/2022 3:58 PM CDT
Resulting Agency Comment
Ordered by Romney H Humphries
Authorizing Provider
Result Type
No Pcp
LAB BODY FLUIDS AND STOOLS ORDERABLES
Performing Organization
Address
City/State/ZIP Code
Phone Number
VUMC CERNER LAB
4605 TVC VUMC1301 Medical Center Drive
NASHVILLE, TN 37232-5310
615-875-5227
SARS-CoV-2 PCR (07/27/2022 3:49 PM CDT)
Component
Value
Ref Range
Test Method
Analysis Time
Performed At
Pathologist Signature
SARS-CoV-2 Nucleic Acid (Result)
Not Detected
Not Detected
VUMC CERNER LAB
Comment: This test was performed using a multiplexed nucleic acid amplification test that is labeled Emergence Use Only by the U.S. FDA. Results of this test should not be used as the sole basis for diagnosis, treatment, or other management decisions.A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample.
SARS-CoV-2 Nucleic Acid Method (Comment)
This test was performed using the Roche 6800 COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.Nasopharynx
VUMC CERNER LAB
Specimen (Source)
Anatomical Location / Laterality
Collection Method / Volume
Collection Time
Received Time
Nasopharynx
07/27/2022 3:49 PM CDT
07/27/2022 3:58 PM CDT
Resulting Agency Comment
Ordered by Romney H Humphries
Authorizing Provider
Result Type
No Pcp
LAB BODY FLUIDS AND STOOLS ORDERABLES
Performing Organization
Address
City/State/ZIP Code
Phone Number
VUMC CERNER LAB
4605 TVC VUMC1301 Medical Center Drive
NASHVILLE, TN 37232-5310
615-875-5227
SARS-CoV-2 PCR (07/27/2022 3:49 PM CDT)
Component
Value
Ref Range
Test Method
Analysis Time
Performed At
Pathologist Signature
SARS-CoV-2 Nucleic Acid (Result)
Not Detected
Not Detected
VUMC CERNER LAB
Comment: This test was performed using a multiplexed nucleic acid amplification test that is labeled Emergence Use Only by the U.S. FDA. Results of this test should not be used as the sole basis for diagnosis, treatment, or other management decisions.A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample.
SARS-CoV-2 Nucleic Acid Method (Comment)
This test was performed using the Roche 6800 COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.Nares
VUMC CERNER LAB
Specimen (Source)
Anatomical Location / Laterality
Collection Method / Volume
Collection Time
Received Time
Nares
07/27/2022 3:49 PM CDT
07/27/2022 3:58 PM CDT
Resulting Agency Comment
Ordered by Romney H Humphries
Authorizing Provider
Result Type
No Pcp
LAB BODY FLUIDS AND STOOLS ORDERABLES
Performing Organization
Address
City/State/ZIP Code
Phone Number
VUMC CERNER LAB
4605 TVC VUMC1301 Medical Center Drive
NASHVILLE, TN 37232-5310
615-875-5227
SARS-CoV-2 PCR (07/27/2022 3:49 PM CDT)
Component
Value
Ref Range
Test Method
Analysis Time
Performed At
Pathologist Signature
SARS-CoV-2 Nucleic Acid (Result)
Not Detected
Not Detected
VUMC CERNER LAB
Comment: This test was performed using a multiplexed nucleic acid amplification test that is labeled Emergence Use Only by the U.S. FDA. Results of this test should not be used as the sole basis for diagnosis, treatment, or other management decisions.A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample.
SARS-CoV-2 Nucleic Acid Method (Comment)
This test was performed using the Roche 6800 COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.BAL
VUMC CERNER LAB
Specimen (Source)
Anatomical Location / Laterality
Collection Method / Volume
Collection Time
Received Time
BAL
07/27/2022 3:49 PM CDT
07/27/2022 3:58 PM CDT
Resulting Agency Comment
Ordered by Romney H Humphries
Authorizing Provider
Result Type
No Pcp
LAB BODY FLUIDS AND STOOLS ORDERABLES
Performing Organization
Address
City/State/ZIP Code
Phone Number
VUMC CERNER LAB
4605 TVC VUMC1301 Medical Center Drive
NASHVILLE, TN 37232-5310
615-875-5227
(ABNORMAL) Hepatitis C IgG w/Rfx PCR (05/12/2022 6:00 AM CDT)
Component
Value
Ref Range
Test Method
Analysis Time
Performed At
Pathologist Signature
Hepatitis C Antibody
Positive (A)
Negative
VUMC CERNER LAB
Comment: Negative: Antibodies to HCV not detected; does not exclude possibility of infection with HCV.Equivocal: Antibodies to HCV may or may not be present; repeat serologic testing in approximately 8 weeks or nucleic acid testing is recommended to assess possible infection. Positive: Presumptive history of HCV infection; nucleic acid testing recommended to document viral replication.
Specimen (Source)
Anatomical Location / Laterality
Collection Method / Volume
Collection Time
Received Time
Blood
05/12/2022 6:00 AM CDT
05/12/2022 11:30 AM CDT
Authorizing Provider
Result Type
Charles W Stratton MD
LAB BLOOD ORDERABLES
Performing Organization
Address
City/State/ZIP Code
Phone Number
VUMC CERNER LAB
4605 TVC VUMC1301 Medical Center Drive
NASHVILLE, TN 37232-5310
615-875-5227
Cytogenomic SNP microarray (04/04/2022 11:55 AM CDT)
Specimen (Source)
Anatomical Location / Laterality
Collection Method / Volume
Collection Time
Received Time
Blood
04/04/2022 11:55 AM CDT
04/18/2022 2:46 PM CDT
Narrative
VUMC CERNER LAB - 04/18/2022 2:57 PM CDTMICROARRAY REPORT- Corrected Request#: CG-22-0000006 Service date: 4/4/2022 11:55 Microarray Result: Normal female Microarray Interpretation: SNP chromosomal microarray analysis (CMA) of a blood sample from this patient demonstrated no copy number changes of known clinical significance. No large regions of homozygosity (ROH) were detected. The ISCN nomenclature describing this result is: arr(X,1-22)x2. Electronically signed out by: Benfield, Luis A on 04/18/2022 ___________________________________________________________________ Clinical indication: Specimen List: Blood Date in Lab: 4/18/2022 14:46 Date Collected: 4/4/2022 11:55 ___________________________________________________________________ Disclaimer: Copy number gains less than 400 kb in size and copy number losses less than 200 kb in size will not be reported unless they represent a known or suspected clinically relevant imbalance. The reporting of copy number variants less than 100 kb in size is at the discretion of the laboratory and some clinically relevant copy number changes under 50 kb may not be reported due to limitations in probe coverage in certain genomic regions. Copy number changes of any size with no apparent clinical significance (likely benign or benign) have not been discussed in this report but may be available upon request. Regions of homozygosity (ROH) less than 10 Mb in size will not be reported unless the ROH is clinically relevant for potential uniparental disomy. Genome-wide ROH under 2% will not be reported. Copy number variants less than 200 kb associated with a carrier status for autosomal recessive conditions will not be reported unless specifically indicated in the reason for referral. This microarray was designed and manufactured by Affymetrix for the sole purpose of identifying DNA copy number gains and losses associated with chromosomal imbalances and regions of homozygosity (ROH) associated with uniparental isodisomy (isoUPD).This microarray will detect aneuploidy, deletions and duplications of loci represented on the microarray. \u00a0It will not detect balanced alterations including: reciprocal translocations, inversions and balanced insertions. It will not detect point mutations and imbalances less than 10 kb. \u00a0Failure to detect an alteration at any locus does not exclude the diagnosis of any of the disorders represented on the microarray. This assay is not designed to detect mosaic gains and losses and its performance in detecting mosaicism has not been established. This test was developed and its performance characteristics determined by Affymetrix as required by CLIA \u00c2\u201988 regulations. This test is used for clinical purposes and the accuracy and precision has been established and verified by this laboratory. This test has not been cleared or approved by the U.S. Food and Drug Administration. Interpretation of copy number variants is performed using VUMC-laboratory maintained databases as well as the following resources: Database of Genomic Variants (http://dgv.tcag.ca/dgv/app/home) Online Mendelian Inheritance in Man (http://www.omim.org/) UCSC Genome Bioinformatics (http://genome.ucsc.edu/cgi-bin/hgGateway) ClinGen Clinical Genome Resource (http://www.ncbi.nlm.nih.gov/projects/dbvar/clingen) DECIPHER Database (https://decipher.sanger.ac.uk/browser) PubMed-NCBI (http://www.ncbi.nlm.nih.gov/pubmed) Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen). PMID: 31690835 Method: Microarray platform: ThermoFisher Scientific CytoScanTM HD Cytogenetics Solution Version: 1.1 (Based on UCSC hg19 assembly) Number of loci analyzed: 2,696,550 Mean probe spacing: <700 bp Testing performed at Vanderbilt Cytogenetics One Hundred Oaks Laboratory, Suite 21100, 719 Thompson Ln, Nashville, TN 37204 \u00a0phone 615-875-0228, fax 615-875-0234
Resulting Agency Comment
testing comment
Authorizing Provider
Result Type
Carda Testprovqa MD
LAB GENETIC TESTING
Performing Organization
Address
City/State/ZIP Code
Phone Number
VUMC CERNER LAB
4605 TVC VUMC1301 Medical Center Drive
NASHVILLE, TN 37232-5310
615-875-5227
Pharmacogenomics (03/31/2022 5:36 PM CDT)
Specimen (Source)
Anatomical Location / Laterality
Collection Method / Volume
Collection Time
Received Time
DNA
03/31/2022 5:36 PM CDT
03/31/2022 5:44 PM CDT
Narrative
VUMC CERNER LAB - 03/31/2022 5:51 PM CDTPharmacogenomics: Final Report Request #: MD-22-0000041 Service Date: 3/31/2022 17:36 Reason for Request: Genotyping for Determination of Drug Efficacy, Dosage and Safety Type of Specimen: DNA Date Received: 3/31/2022 17:44 Date Reported: 3/31/2022 17:51 Interpretation: Results from this assay may indicate dosage adjustments or medication alternatives that should be considered for this patient. Additional information regarding the implications of these results is available at www.mydruggenome.org. For VUMC patients, clinical decision support regarding the management of this patient with respect to specific drugs based upon the patient''s genotype as listed below is available in the patient''s electronic medical record under Genomic Indicators. Clinical decision support may also be provided for some drugs through order entry and medication prescribing tools utilized within the VUMC system. Comments: Results: CYP2C19 - \u00a0Cancelled CYP2C9 - \u00a0 Cancelled CYP2D6 - \u00a0 Cancelled CYP3A5 - \u00a0 Cancelled CYP4F2 - \u00a0 Cancelled DPYD - \u00a0 \u00a0 Cancelled NUDT15 - \u00a0 Cancelled SLCO1B1 - \u00a0Cancelled TPMT - \u00a0 \u00a0 Cancelled VKORC1 - \u00a0 Cancelled These results should be correlated with other laboratory and clinical findings and additional testing should be considered if clinically indicated. Methodology: DNA was extracted from this specimen and screened for 37 variants in 10 genes that are associated with drug absorption, distribution, metabolism, excretion or response. The reported genotypes were determined using PCR amplification and oligonucleotide primers specific for each interrogated region of the genes listed within this panel. Fluorophore labeled probes were used to identify each variant. Variants analyzed in this assay include: CYP2C19 *2, *3, *4, *6, *8, *17; CYP2C9 *2, *3, *6, *8; CYP3A5 *3, *6, *7; CYP4F2 *3; DPYD *2A, *13, c.557A>G, c.1236G>A (HapB3), c.2846A>T; \u00a0NUDT15 *2 or *3; SLCO1B1 *5; TPMT *2, *3B, *3C, *4; VKORC1 promoter variant c.-1639G>A; and CYP2D6 copy number and variants *2, *2A, *3, *4, *6, *7, *9, *10, *17, *29 and *41. A *1 allele is considered the reference (normal) sequence and is reported if none of the variants analyzed for a particular gene is detected. This assay is specific for the variants listed above and cannot exclude the presence of other variants within these genes that may affect the pharmacologic function of the protein product encoded by these genes. In most cases, variants for a particular gene exist on separate alleles; however, for individuals in which multiple variants in the same gene are detected, this assay cannot determine if the variants are on the same allele or on different alleles. Further, due to the highly polymorphic nature of these regions, rare variants may exist that could affect the sensitivity or specificity of this assay and lead to a false-negative or a false-positive result. Electronically signed out by: Barba, Elizabeth on 03/31/2022 This assay has not been cleared or approved by the US Food and Drug Administration. The performance of this assay was tested and validated prior to use for patient testing. This test is used for clinical purposes and should not be regarded as investigational or research. This laboratory is regulated by the Clinical Laboratory Improvement Act of 1988.
Authorizing Provider
Result Type
Carda Testprovqa MD
LAB GENETIC TESTING
Performing Organization
Address
City/State/ZIP Code
Phone Number
VUMC CERNER LAB
4605 TVC VUMC1301 Medical Center Drive
NASHVILLE, TN 37232-5310
615-875-5227
Drug Toxicology Monitoring Base Pnl w/Conf, Oral Fl-QSTD (03/29/2022 1:53 PM CDT)
Component
Value
Ref Range
Test Method
Analysis Time
Performed At
Pathologist Signature
Drug Toxicology Monitoring Base Pnl w/Conf, Oral Fl
VPLS clients: \u00a0 See separate report sent to client.VUMC patients: \u00a0Results faxed to Vanderbilt Medical Record.
VUMC CERNER LAB
Comment: This test was performed at: Quest Laboratory,Location Varies,,,,,,
Comment: This test was performed using a multiplexed nucleic acid amplification test that is labeled Emergence Use Only by the U.S. FDA. Results of this test should not be used as the sole basis for diagnosis, treatment, or other management decisions.A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample.
SARS-CoV-2 Nucleic Acid Method (Comment)
This test was performed using the Hologic Panther COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.Nares
VUMC CERNER LAB
Specimen (Source)
Anatomical Location / Laterality
Collection Method / Volume
Collection Time
Received Time
Nares
03/11/2022 1:05 PM CST
03/11/2022 1:46 PM CST
Authorizing Provider
Result Type
Adam Clark Seegmiller MD
LAB BODY FLUIDS AND STOOLS ORDERABLES
Performing Organization
Address
City/State/ZIP Code
Phone Number
VUMC CERNER LAB
4605 TVC VUMC1301 Medical Center Drive
NASHVILLE, TN 37232-5310
615-875-5227
FISH ALL Pnl (03/11/2022 1:05 PM CST)
Specimen (Source)
Anatomical Location / Laterality
Collection Method / Volume
Collection Time
Received Time
Blood
03/11/2022 1:05 PM CST
03/11/2022 1:09 PM CST
Narrative
VUMC CERNER LAB - 03/11/2022 1:27 PM CSTFISH REPORT Request#:CG-22-0000003 Service date:3/11/2022 13:05 FISH IMPRESSION: Abnormal for homozygous deletion of CDKN2A locus at 9p21 in __% of cells. FISH KARYOTYPE: nuc ish (DXZ1x1,DYZ3x1,D18Z1x2)[200] COMMENTS: Results of the FISH studies with the 21 DNA probes described above were analyzed in at least 200 cells per probe and no abnormal signal patterns were detected for the target regions of chromosomes 1, 4, 7, 9, 10, 11, 12, 14, 17, 19, 21, and 22. Normal cut off values for probes: 1.0% for t(1;19) PBX1/TCF3 1.0% for t(9;22) BCR/ABL1 1.0% for KMT2A (11q23) 1.0% for t(12;21) ETV6/RUNX1 1.0% for IKZF1/CEP7 3.0% for CEP 4 2.0% for CEP 10 2.0% for CEP 17 1.0% for CDKN2A/CEP9 (9p21) 1.0% for IGH breakapart 1.0% for ABL2 breakapart 1.0% for ABL1 breakapart These probes were developed by Vysis and their performance characteristics determined by VUMC as required by the CLIA ''88 regulations. \u00a0These probes have not been cleared or approved by the U.S. Food and Drug administration. Ferrin Courtney Wheeler, PhD, FACMG reviewed and approved Electronically signed out by: Mavrak, Geoffrey A on 03/11/2022 Clinical History: \u00a0ALL Specimen List: Blood Date In Lab: 3/11/2022 13:09 Date Collected: 3/11/2022 13:05 Testing performed at Vanderbilt Cytogenetics One Hundred Oaks Laboratory, Suite 21100, 719 Thompson Ln, Nashville, TN 37204 \u00a0phone 615-875-0228, fax 615-875-0234
Authorizing Provider
Result Type
Adam Clark Seegmiller MD
LAB GENETIC TESTING
Performing Organization
Address
City/State/ZIP Code
Phone Number
VUMC CERNER LAB
4605 TVC VUMC1301 Medical Center Drive
NASHVILLE, TN 37232-5310
615-875-5227
(ABNORMAL) Culture Bact Bld Adult (03/11/2022 8:51 AM CST)
Component
Value
Ref Range
Test Method
Analysis Time
Performed At
Pathologist Signature
Final Report
Gram positive cocci; restreak for isolation Isolated from Aerobic bottleStaphylococcus aureus
Request#:CG-22-0000003 Service date:3/11/2022 13:05
FISH IMPRESSION:
Abnormal for homozygous deletion of CDKN2A locus at 9p21 in __% of cells.
FISH KARYOTYPE:
nuc ish (DXZ1x1,DYZ3x1,D18Z1x2)[200]
\u00a0 \u00a0 \u00a0
COMMENTS:
Results of the FISH studies with the 21 DNA probes described above were analyzed in at least 200 cells per probe and no abnormal signal patterns were detected for the target regions of chromosomes 1, 4, 7, 9, 10, 11, 12, 14, 17, 19, 21, and 22.
Normal cut off values for probes:
1.0% for t(1;19) PBX1/TCF3 1.0% for t(9;22) BCR/ABL1 1.0% for KMT2A (11q23) 1.0% for t(12;21) ETV6/RUNX1 1.0% for IKZF1/CEP7 3.0% for CEP 4 2.0% for CEP 10 2.0% for CEP 17 1.0% for CDKN2A/CEP9 (9p21) 1.0% for IGH breakapart 1.0% for ABL2 breakapart 1.0% for ABL1 breakapart
These probes were developed by Vysis and their performance characteristics determined by VUMC as required by the CLIA ''88 regulations. \u00a0These probes have not been cleared or approved by the U.S. Food and Drug administration.
Ferrin Courtney Wheeler, PhD, FACMG reviewed and approved
Electronically signed out by: Mavrak, Geoffrey A
on 03/11/2022
Clinical History: \u00a0ALL Specimen List: Blood Date In Lab: 3/11/2022 13:09 Date Collected: 3/11/2022 13:05
Reason for Request: Genotyping for Determination of Drug Efficacy, Dosage and Safety
Type of Specimen: DNA
Date Received: 3/31/2022 17:44
Date Reported: 3/31/2022 17:51
Interpretation: Results from this assay may indicate dosage adjustments or medication alternatives that should be considered for this patient. Additional information regarding the implications of these results is available at www.mydruggenome.org.
For VUMC patients, clinical decision support regarding the management of this patient with respect to specific drugs based upon the patient''s genotype as listed below is available in the patient''s electronic medical record under Genomic Indicators. Clinical decision support may also be provided for some drugs through order entry and medication prescribing tools utilized within the VUMC system.
Comments:
Results:
CYP2C19 - \u00a0Cancelled
CYP2C9 - \u00a0 Cancelled
CYP2D6 - \u00a0 Cancelled \u00a0
CYP3A5 - \u00a0 Cancelled
CYP4F2 - \u00a0 Cancelled
DPYD - \u00a0 \u00a0 Cancelled
NUDT15 - \u00a0 Cancelled
SLCO1B1 - \u00a0Cancelled \u00a0 \u00a0 \u00a0
TPMT - \u00a0 \u00a0 Cancelled
VKORC1 - \u00a0 Cancelled \u00a0 \u00a0 \u00a0 These results should be correlated with other laboratory and clinical findings and additional testing should be considered if clinically indicated. \u00a0 \u00a0
Methodology:
DNA was extracted from this specimen and screened for 37 variants in 10 genes that are associated with drug absorption, distribution, metabolism, excretion or response. The reported genotypes were determined using PCR amplification and oligonucleotide primers specific for each interrogated region of the genes listed within this panel. Fluorophore labeled probes were used to identify each variant.
Variants analyzed in this assay include: CYP2C19 *2, *3, *4, *6, *8, *17; CYP2C9 *2, *3, *6, *8; CYP3A5 *3, *6, *7; CYP4F2 *3; DPYD *2A, *13, c.557A>G, c.1236G>A (HapB3), c.2846A>T; \u00a0NUDT15 *2 or *3; SLCO1B1 *5; TPMT *2, *3B, *3C, *4; VKORC1 promoter variant c.-1639G>A; and CYP2D6 copy number and variants *2, *2A, *3, *4, *6, *7, *9, *10, *17, *29 and *41. A *1 allele is considered the reference (normal) sequence and is reported if none of the variants analyzed for a particular gene is detected. This assay is specific for the variants listed above and cannot exclude the presence of other variants within these genes that may affect the pharmacologic function of the protein product encoded by these genes. In most cases, variants for a particular gene exist on separate alleles; however, for individuals in which multiple variants in the same gene are detected, this assay cannot determine if the variants are on the same allele or on different alleles. Further, due to the highly polymorphic nature of these regions, rare variants may exist that could affect the sensitivity or specificity of this assay and lead to a false-negative or a false-positive result.
Electronically signed out by: Barba, Elizabeth
on 03/31/2022
This assay has not been cleared or approved by the US Food and Drug Administration. The performance of this assay was tested and validated prior to use for patient testing. This test is used for clinical purposes and should not be regarded as investigational or research. This laboratory is regulated by the Clinical Laboratory Improvement Act of 1988.", "extension": [{"url": "http://hl7.org/fhir/R4/specimen.html", "extension": [{"url": "specimen source", "valueString": "DNA"}, {"url": "specimen collection time", "valueDateTime": "2022-03-31T22:36:00Z"}, {"url": "specimen receive time", "valueDateTime": "2022-03-31T22:44:00Z"}, {"url": "observation entry reference value", "valueString": "#Result.1.2.840.114350.1.13.478.3.7.2.798268.2061345.Narrative"}]}], "subject": {"reference": "Patient/8f17ebaf-226e-4565-a8e4-1fd09cc4f25a"}, "performer": [{"display": "VUMC CERNER LAB", "reference": "Organization/e3ece69c-0968-59c9-47dd-f16db731621a"}]}, "request": {"method": "PUT", "url": "Observation/2e9477e8-412b-905c-270f-16ca12bff791"}}, {"fullUrl": "urn:uuid:ed66ccf7-584a-1142-b9a4-8fe01b6f21fb", "resource": {"resourceType": "Observation", "id": "ed66ccf7-584a-1142-b9a4-8fe01b6f21fb", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"], "source": "ecr"}, "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.798268", "value": "2061345"}], "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "laboratory"}]}], "status": "final", "effectiveDateTime": "2022-03-31T22:51:17Z", "valueCodeableConcept": {"coding": [{"code": "16", "system": "urn:oid:1.2.840.114350.1.72.1.5007"}]}, "extension": [{"url": "http://hl7.org/fhir/R4/specimen.html", "extension": [{"url": "specimen source", "valueString": "DNA"}, {"url": "specimen collection time", "valueDateTime": "2022-03-31T22:36:00Z"}, {"url": "specimen receive time", "valueDateTime": "2022-03-31T22:44:00Z"}]}], "subject": {"reference": "Patient/8f17ebaf-226e-4565-a8e4-1fd09cc4f25a"}}, "request": {"method": "PUT", "url": "Observation/ed66ccf7-584a-1142-b9a4-8fe01b6f21fb"}}, {"fullUrl": "urn:uuid:b0f590a6-4bf5-7add-9716-2bd3ba6defb2", "resource": {"resourceType": "DiagnosticReport", "id": "b0f590a6-4bf5-7add-9716-2bd3ba6defb2", "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.798268", "value": "2061347"}], "status": "final", "code": {"coding": [{"code": "118330", "display": "Cytogenomic SNP microarray", "system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.696580"}]}, "effectivePeriod": {"start": "2022-04-04T16:55:00Z", "end": "2022-04-04T16:55:00Z"}, "subject": {"reference": "Patient/8f17ebaf-226e-4565-a8e4-1fd09cc4f25a"}, "performer": [{"reference": "Organization/22c6cdd0-bde1-e220-9ba4-2c2802f795ad"}], "result": [{"reference": "Observation/2a4f8fb5-f957-3c30-1353-a30aa441a12b"}, {"reference": "Observation/2e70be1d-fa6c-0256-cf67-f695f5bba1ac"}, {"reference": "Observation/97b316f7-bb96-051f-adba-72ddc4ae5825"}], "meta": {"source": "ecr"}}, "request": {"method": "PUT", "url": "DiagnosticReport/b0f590a6-4bf5-7add-9716-2bd3ba6defb2"}}, {"fullUrl": "urn:uuid:2a4f8fb5-f957-3c30-1353-a30aa441a12b", "resource": {"resourceType": "Observation", "id": "2a4f8fb5-f957-3c30-1353-a30aa441a12b", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"], "source": "ecr"}, "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.7.798268.1000", "value": "2061347"}], "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "laboratory"}]}], "status": "final", "code": {"coding": [{"code": "NAR", "system": "urn:oid:1.2.840.114350.1.72.1.5220"}]}, "effectiveDateTime": "2022-04-18T19:57:02Z", "valueString": "MICROARRAY REPORT- Corrected
Request#: CG-22-0000006 Service date: 4/4/2022 11:55
Microarray Result: Normal female
Microarray Interpretation: SNP chromosomal microarray analysis (CMA) of a blood sample from this patient demonstrated no copy number changes of known clinical significance. No large regions of homozygosity (ROH) were detected. The ISCN nomenclature describing this result is: arr(X,1-22)x2. Electronically signed out by: Benfield, Luis A
on 04/18/2022 ___________________________________________________________________
Clinical indication: Specimen List: Blood Date in Lab: 4/18/2022 14:46 Date Collected: 4/4/2022 11:55 ___________________________________________________________________
Disclaimer:
Copy number gains less than 400 kb in size and copy number losses less than 200 kb in size will not be reported unless they represent a known or suspected clinically relevant imbalance. The reporting of copy number variants less than 100 kb in size is at the discretion of the laboratory and some clinically relevant copy number changes under 50 kb may not be reported due to limitations in probe coverage in certain genomic regions. Copy number changes of any size with no apparent clinical significance (likely benign or benign) have not been discussed in this report but may be available upon request. Regions of homozygosity (ROH) less than 10 Mb in size will not be reported unless the ROH is clinically relevant for potential uniparental disomy. Genome-wide ROH under 2% will not be reported. Copy number variants less than 200 kb associated with a carrier status for autosomal recessive conditions will not be reported unless specifically indicated in the reason for referral.
This microarray was designed and manufactured by Affymetrix for the sole purpose of identifying DNA copy number gains and losses associated with chromosomal imbalances and regions of homozygosity (ROH) associated with uniparental isodisomy (isoUPD).This microarray will detect aneuploidy, deletions and duplications of loci represented on the microarray. \u00a0It will not detect balanced alterations including: reciprocal translocations, inversions and balanced insertions. It will not detect point mutations and imbalances less than 10 kb. \u00a0Failure to detect an alteration at any locus does not exclude the diagnosis of any of the disorders represented on the microarray. This assay is not designed to detect mosaic gains and losses and its performance in detecting mosaicism has not been established. This test was developed and its performance characteristics determined by Affymetrix as required by CLIA \u00c2\u201988 regulations. This test is used for clinical purposes and the accuracy and precision has been established and verified by this laboratory. This test has not been cleared or approved by the U.S. Food and Drug Administration.
Interpretation of copy number variants is performed using VUMC-laboratory maintained databases as well as the following resources: Database of Genomic Variants (http://dgv.tcag.ca/dgv/app/home) Online Mendelian Inheritance in Man (http://www.omim.org/) UCSC Genome Bioinformatics (http://genome.ucsc.edu/cgi-bin/hgGateway) ClinGen Clinical Genome Resource (http://www.ncbi.nlm.nih.gov/projects/dbvar/clingen) DECIPHER Database (https://decipher.sanger.ac.uk/browser) PubMed-NCBI (http://www.ncbi.nlm.nih.gov/pubmed) Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen). PMID: 31690835
Method: Microarray platform: ThermoFisher Scientific CytoScanTM HD Cytogenetics Solution Version: 1.1 (Based on UCSC hg19 assembly) Number of loci analyzed: 2,696,550 Mean probe spacing: <700 bp
Testing performed at Vanderbilt Cytogenetics One Hundred Oaks Laboratory, Suite 21100, 719 Thompson Ln, Nashville, TN 37204 \u00a0phone 615-875-0228, fax 615-875-0234", "extension": [{"url": "http://hl7.org/fhir/R4/specimen.html", "extension": [{"url": "specimen source", "valueString": "Blood"}, {"url": "specimen collection time", "valueDateTime": "2022-04-04T16:55:00Z"}, {"url": "specimen receive time", "valueDateTime": "2022-04-18T19:46:00Z"}, {"url": "observation entry reference value", "valueString": "#Result.1.2.840.114350.1.13.478.3.7.2.798268.2061347.Narrative"}]}], "subject": {"reference": "Patient/8f17ebaf-226e-4565-a8e4-1fd09cc4f25a"}, "performer": [{"display": "VUMC CERNER LAB", "reference": "Organization/e3ece69c-0968-59c9-47dd-f16db731621a"}]}, "request": {"method": "PUT", "url": "Observation/2a4f8fb5-f957-3c30-1353-a30aa441a12b"}}, {"fullUrl": "urn:uuid:2e70be1d-fa6c-0256-cf67-f695f5bba1ac", "resource": {"resourceType": "Observation", "id": 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A not detected result indicates that the test did not detect the virus in the sample."}], "extension": [{"url": "http://hl7.org/fhir/R4/specimen.html", "extension": [{"url": "specimen source", "valueString": "Oropharynx"}, {"url": "specimen collection time", "valueDateTime": "2022-07-27T20:49:00Z"}, {"url": "specimen receive time", "valueDateTime": "2022-07-27T20:58:00Z"}, {"url": "observation entry reference value", "valueString": "#Result.1.2.840.114350.1.13.478.3.7.2.798268.2122246.Comp1"}]}, {"url": "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code", "coding": [{"code": "840539006", "system": "http://snomed.info/sct"}]}], "subject": {"reference": "Patient/8f17ebaf-226e-4565-a8e4-1fd09cc4f25a"}, "performer": [{"display": "VUMC CERNER LAB", "reference": "Organization/e3ece69c-0968-59c9-47dd-f16db731621a"}]}, "request": {"method": "PUT", "url": "Observation/55d8ed97-c896-4612-48a3-7427e3225e9b"}}, {"fullUrl": "urn:uuid:b4bc2708-6174-3295-5ddf-0484b06ae3b4", "resource": {"resourceType": "Observation", "id": "b4bc2708-6174-3295-5ddf-0484b06ae3b4", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"], "source": "ecr"}, "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.6.798268.2000", "value": "2122246.2"}], "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "laboratory"}]}], "status": "final", "code": {"coding": [{"code": "16535", "display": "SARS-CoV-2 Nucleic Acid Method (Comment)", "system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.768282"}]}, "effectiveDateTime": "2022-07-28T14:01:16Z", "valueString": "Oropharynx This test was performed using the Roche 6800 COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.", "extension": [{"url": "http://hl7.org/fhir/R4/specimen.html", "extension": [{"url": "specimen source", "valueString": "Oropharynx"}, {"url": "specimen collection time", "valueDateTime": "2022-07-27T20:49:00Z"}, {"url": "specimen receive time", "valueDateTime": "2022-07-27T20:58:00Z"}, {"url": "observation entry reference value", "valueString": "#Result.1.2.840.114350.1.13.478.3.7.2.798268.2122246.Comp2"}]}], "subject": {"reference": "Patient/8f17ebaf-226e-4565-a8e4-1fd09cc4f25a"}, "performer": [{"display": "VUMC CERNER LAB", "reference": "Organization/e3ece69c-0968-59c9-47dd-f16db731621a"}]}, "request": {"method": "PUT", "url": "Observation/b4bc2708-6174-3295-5ddf-0484b06ae3b4"}}, {"fullUrl": "urn:uuid:26531afa-b417-3fc1-1ab4-ac0fe728c034", "resource": {"resourceType": "Observation", "id": "26531afa-b417-3fc1-1ab4-ac0fe728c034", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"], "source": "ecr"}, "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.7.798268.71", "value": "2122246"}], "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "laboratory"}]}], "status": "final", "code": {"coding": [{"code": "RAC", "system": "urn:oid:1.2.840.114350.1.72.1.5220"}]}, "effectiveDateTime": "2022-07-28T14:01:16Z", "valueString": "Ordered by Romney H Humphries", "extension": [{"url": "http://hl7.org/fhir/R4/specimen.html", "extension": [{"url": "specimen source", "valueString": "Oropharynx"}, {"url": "specimen collection time", "valueDateTime": "2022-07-27T20:49:00Z"}, {"url": "specimen receive time", "valueDateTime": "2022-07-27T20:58:00Z"}, {"url": "observation entry reference value", "valueString": "#Result.1.2.840.114350.1.13.478.3.7.2.798268.2122246.ResultingAgencyComment"}]}], "subject": {"reference": "Patient/8f17ebaf-226e-4565-a8e4-1fd09cc4f25a"}}, "request": {"method": "PUT", "url": "Observation/26531afa-b417-3fc1-1ab4-ac0fe728c034"}}, {"fullUrl": "urn:uuid:c0bcac36-62c5-5224-7b19-96161329bdeb", "resource": {"resourceType": "Observation", "id": "c0bcac36-62c5-5224-7b19-96161329bdeb", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"], "source": "ecr"}, "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.798268", "value": "2122246"}], "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "laboratory"}]}], "status": "final", "code": {"coding": [{"code": "56850-1", "display": "Lab Interpretation", "system": "http://loinc.org"}]}, "effectiveDateTime": "2022-07-28T14:01:16Z", "valueString": "Abnormal", "extension": [{"url": "http://hl7.org/fhir/R4/specimen.html", "extension": [{"url": "specimen source", "valueString": "Oropharynx"}, {"url": "specimen collection time", "valueDateTime": "2022-07-27T20:49:00Z"}, {"url": "specimen receive time", "valueDateTime": "2022-07-27T20:58:00Z"}]}], "subject": {"reference": "Patient/8f17ebaf-226e-4565-a8e4-1fd09cc4f25a"}}, "request": {"method": "PUT", "url": "Observation/c0bcac36-62c5-5224-7b19-96161329bdeb"}}, {"fullUrl": "urn:uuid:a1f13b27-0d59-f1db-2ab8-978b752be322", "resource": {"resourceType": "Observation", "id": "a1f13b27-0d59-f1db-2ab8-978b752be322", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"], "source": "ecr"}, "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.798268", "value": "2122246"}], "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "laboratory"}]}], "status": "final", "effectiveDateTime": "2022-07-28T14:01:16Z", "valueCodeableConcept": {"coding": [{"code": "16", "system": "urn:oid:1.2.840.114350.1.72.1.5007"}]}, "extension": [{"url": "http://hl7.org/fhir/R4/specimen.html", "extension": [{"url": "specimen source", "valueString": "Oropharynx"}, {"url": "specimen collection time", "valueDateTime": "2022-07-27T20:49:00Z"}, {"url": "specimen receive time", "valueDateTime": "2022-07-27T20:58:00Z"}]}], "subject": {"reference": "Patient/8f17ebaf-226e-4565-a8e4-1fd09cc4f25a"}}, "request": {"method": "PUT", "url": "Observation/a1f13b27-0d59-f1db-2ab8-978b752be322"}}, {"fullUrl": "urn:uuid:590d2c83-924b-707c-73f4-3aa9b4f1359d", "resource": {"resourceType": "DiagnosticReport", "id": "590d2c83-924b-707c-73f4-3aa9b4f1359d", "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.798268", "value": "2122247"}], "status": "final", "code": {"coding": [{"code": "191589", "display": "SARS-CoV-2 PCR", "system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.696580"}]}, "effectivePeriod": {"start": "2022-07-27T20:49:00Z", "end": "2022-07-27T20:49:00Z"}, "subject": {"reference": "Patient/8f17ebaf-226e-4565-a8e4-1fd09cc4f25a"}, "performer": [{"reference": "Organization/22c6cdd0-bde1-e220-9ba4-2c2802f795ad"}], "result": [{"reference": "Observation/259c0261-e650-24f3-7ccf-ec69871a431a"}, {"reference": "Observation/d2b4826f-802c-87d2-20ac-34dade169167"}, {"reference": "Observation/7dbb8280-9206-097a-3b7a-c2dfc712459e"}, {"reference": "Observation/01eb7b0c-1ce3-ff8b-cb73-e85b6c8ee41c"}, {"reference": "Observation/d218e3d4-5585-f9f0-a926-c2740482ac49"}], "meta": {"source": "ecr"}}, "request": {"method": "PUT", "url": "DiagnosticReport/590d2c83-924b-707c-73f4-3aa9b4f1359d"}}, {"fullUrl": "urn:uuid:259c0261-e650-24f3-7ccf-ec69871a431a", "resource": {"resourceType": "Observation", "id": "259c0261-e650-24f3-7ccf-ec69871a431a", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"], "source": "ecr"}, "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.6.798268.2000", "value": "2122247.1"}], "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "laboratory"}]}], "status": "final", "code": {"coding": [{"code": "94533-7", "display": "SARS-CoV-2 Nucleic Acid (Result)", "system": "http://loinc.org"}]}, "effectiveDateTime": "2022-07-28T14:01:17Z", "valueString": "Detected", "referenceRange": [{"text": "Not Detected"}], "interpretation": [{"coding": [{"code": "A", "display": "Abnormal", "system": "http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation"}]}], "note": [{"text": "This test was performed using a multiplexed nucleic acid amplification test that is labeled Emergence Use Only by the U.S. FDA. Results of this test should not be used as the sole basis for diagnosis, treatment, or other management decisions. A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample."}], "extension": [{"url": "http://hl7.org/fhir/R4/specimen.html", "extension": [{"url": "specimen source", "valueString": "Other"}, {"url": "specimen collection time", "valueDateTime": "2022-07-27T20:49:00Z"}, {"url": "specimen receive time", "valueDateTime": "2022-07-27T20:58:00Z"}, {"url": "observation entry reference value", "valueString": "#Result.1.2.840.114350.1.13.478.3.7.2.798268.2122247.Comp1"}]}, {"url": "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code", "coding": [{"code": "840539006", "system": "http://snomed.info/sct"}]}], "subject": {"reference": "Patient/8f17ebaf-226e-4565-a8e4-1fd09cc4f25a"}, "performer": [{"display": "VUMC CERNER LAB", "reference": "Organization/e3ece69c-0968-59c9-47dd-f16db731621a"}]}, "request": {"method": "PUT", "url": "Observation/259c0261-e650-24f3-7ccf-ec69871a431a"}}, {"fullUrl": "urn:uuid:d2b4826f-802c-87d2-20ac-34dade169167", "resource": {"resourceType": "Observation", "id": "d2b4826f-802c-87d2-20ac-34dade169167", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"], "source": "ecr"}, "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.6.798268.2000", "value": "2122247.2"}], "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "laboratory"}]}], "status": "final", "code": {"coding": [{"code": "16535", "display": "SARS-CoV-2 Nucleic Acid Method (Comment)", "system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.768282"}]}, "effectiveDateTime": "2022-07-28T14:01:17Z", "valueString": "Other This test was performed using the Roche 6800 COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.", "extension": [{"url": "http://hl7.org/fhir/R4/specimen.html", "extension": [{"url": "specimen source", "valueString": "Other"}, {"url": "specimen collection time", "valueDateTime": "2022-07-27T20:49:00Z"}, {"url": "specimen receive time", "valueDateTime": "2022-07-27T20:58:00Z"}, {"url": "observation entry reference value", "valueString": "#Result.1.2.840.114350.1.13.478.3.7.2.798268.2122247.Comp2"}]}], "subject": {"reference": "Patient/8f17ebaf-226e-4565-a8e4-1fd09cc4f25a"}, "performer": [{"display": "VUMC CERNER LAB", "reference": "Organization/e3ece69c-0968-59c9-47dd-f16db731621a"}]}, "request": {"method": "PUT", "url": "Observation/d2b4826f-802c-87d2-20ac-34dade169167"}}, {"fullUrl": "urn:uuid:7dbb8280-9206-097a-3b7a-c2dfc712459e", "resource": {"resourceType": "Observation", "id": "7dbb8280-9206-097a-3b7a-c2dfc712459e", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"], "source": "ecr"}, "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.7.798268.71", "value": "2122247"}], "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "laboratory"}]}], "status": "final", "code": {"coding": [{"code": "RAC", "system": "urn:oid:1.2.840.114350.1.72.1.5220"}]}, "effectiveDateTime": "2022-07-28T14:01:17Z", "valueString": "Ordered by Romney H Humphries", "extension": [{"url": "http://hl7.org/fhir/R4/specimen.html", "extension": [{"url": "specimen source", "valueString": "Other"}, {"url": "specimen collection time", "valueDateTime": "2022-07-27T20:49:00Z"}, {"url": "specimen receive time", "valueDateTime": "2022-07-27T20:58:00Z"}, {"url": "observation entry reference value", "valueString": "#Result.1.2.840.114350.1.13.478.3.7.2.798268.2122247.ResultingAgencyComment"}]}], "subject": {"reference": "Patient/8f17ebaf-226e-4565-a8e4-1fd09cc4f25a"}}, "request": {"method": "PUT", "url": "Observation/7dbb8280-9206-097a-3b7a-c2dfc712459e"}}, {"fullUrl": "urn:uuid:01eb7b0c-1ce3-ff8b-cb73-e85b6c8ee41c", "resource": {"resourceType": "Observation", "id": "01eb7b0c-1ce3-ff8b-cb73-e85b6c8ee41c", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"], "source": "ecr"}, "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.798268", "value": "2122247"}], "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "laboratory"}]}], "status": "final", "code": {"coding": [{"code": "56850-1", "display": "Lab Interpretation", "system": "http://loinc.org"}]}, "effectiveDateTime": "2022-07-28T14:01:17Z", "valueString": "Abnormal", "extension": [{"url": "http://hl7.org/fhir/R4/specimen.html", "extension": [{"url": "specimen source", "valueString": "Other"}, {"url": "specimen collection time", "valueDateTime": "2022-07-27T20:49:00Z"}, {"url": "specimen receive time", "valueDateTime": "2022-07-27T20:58:00Z"}]}], "subject": {"reference": "Patient/8f17ebaf-226e-4565-a8e4-1fd09cc4f25a"}}, "request": {"method": "PUT", "url": "Observation/01eb7b0c-1ce3-ff8b-cb73-e85b6c8ee41c"}}, {"fullUrl": "urn:uuid:d218e3d4-5585-f9f0-a926-c2740482ac49", "resource": {"resourceType": "Observation", "id": "d218e3d4-5585-f9f0-a926-c2740482ac49", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"], "source": "ecr"}, "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.798268", "value": "2122247"}], "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "laboratory"}]}], "status": "final", "effectiveDateTime": "2022-07-28T14:01:17Z", "valueCodeableConcept": {"coding": [{"code": "16", "system": "urn:oid:1.2.840.114350.1.72.1.5007"}]}, "extension": [{"url": "http://hl7.org/fhir/R4/specimen.html", "extension": [{"url": "specimen source", "valueString": "Other"}, {"url": "specimen collection time", "valueDateTime": "2022-07-27T20:49:00Z"}, {"url": "specimen receive time", "valueDateTime": "2022-07-27T20:58:00Z"}]}], "subject": {"reference": "Patient/8f17ebaf-226e-4565-a8e4-1fd09cc4f25a"}}, "request": {"method": "PUT", "url": "Observation/d218e3d4-5585-f9f0-a926-c2740482ac49"}}, {"fullUrl": "urn:uuid:1cfb73a5-128f-a51c-c396-fb20cd8e2456", "resource": {"resourceType": "Observation", "id": "1cfb73a5-128f-a51c-c396-fb20cd8e2456", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"], "source": "ecr"}, "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.1.1040.1", "value": "Z31828^^72166-2"}], "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "social-history"}]}], "status": "final", "code": {"coding": [{"code": "72166-2", "display": "Tobacco smoking status NHIS", "system": "http://loinc.org"}]}, "valueCodeableConcept": {"coding": [{"code": "266927001", "display": "Tobacco smoking consumption unknown", "system": "http://snomed.info/sct"}]}, "subject": {"reference": "Patient/8f17ebaf-226e-4565-a8e4-1fd09cc4f25a"}}, "request": {"method": "PUT", "url": "Observation/1cfb73a5-128f-a51c-c396-fb20cd8e2456"}}, {"fullUrl": "urn:uuid:", "resource": {"resourceType": "Observation", "meta": {"profile": ["http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"], "source": "ecr"}}, "request": {"method": "PUT", "url": "Observation/"}}, {"fullUrl": "urn:uuid:f5e25af7-945a-cf66-d2d0-8942935165a2", "resource": {"resourceType": "Immunization", "id": "f5e25af7-945a-cf66-d2d0-8942935165a2", "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.768076", "value": "86940"}], "occurrenceDateTime": "2021-01-22", "note": {"text": "SARS-COV-2 (COVID-19) Spikevax Vaccine, Moderna"}, "vaccineCode": {"coding": [{"code": "80777-273-10", "system": "urn:oid:2.16.840.1.113883.6.69"}]}, "lotNumber": "LLSFJK", "manufacturer": {"reference": "Organization/57fcc148-b440-3a80-749b-780325e9680d"}, "status": "completed", "primarySource": true, "patient": {"reference": "Patient/8f17ebaf-226e-4565-a8e4-1fd09cc4f25a"}, "meta": {"source": "ecr"}}, "request": {"method": "PUT", "url": "Immunization/f5e25af7-945a-cf66-d2d0-8942935165a2"}}, {"fullUrl": "urn:uuid:57fcc148-b440-3a80-749b-780325e9680d", "resource": {"resourceType": "Organization", "id": "57fcc148-b440-3a80-749b-780325e9680d", "name": "Moderna US, Inc.", "meta": {"source": "ecr"}}, "request": {"method": "PUT", "url": "Organization/57fcc148-b440-3a80-749b-780325e9680d"}}, {"fullUrl": "urn:uuid:875c24ee-6be0-066b-ca5f-e73b2d914f5b", "resource": {"resourceType": "Immunization", "id": "875c24ee-6be0-066b-ca5f-e73b2d914f5b", "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.768076", "value": "90497"}], "occurrenceDateTime": "2020-09-08", "note": {"text": "Hep B, adult vaccine (Engerix/Recombivax)"}, "vaccineCode": {"coding": [{"display": "Hep B, adult vaccine (Engerix/Recombivax)"}]}, "status": "completed", "primarySource": true, "meta": {"source": "ecr"}}, "request": {"method": "PUT", "url": "Immunization/875c24ee-6be0-066b-ca5f-e73b2d914f5b"}}, {"fullUrl": "urn:uuid:3c8af1dd-2983-5d97-d5f1-f6dd57e9eba1", "resource": {"resourceType": "Immunization", "id": "3c8af1dd-2983-5d97-d5f1-f6dd57e9eba1", "identifier": [{"system": "urn:oid:1.2.840.114350.1.13.478.3.7.2.768076", "value": "90499"}], "occurrenceDateTime": "2021-06-15", "note": {"text": "DTaP, 5 pertussis antigens vaccine (DAPTACEL)"}, "vaccineCode": {"coding": [{"display": "DTaP, 5 pertussis antigens vaccine (DAPTACEL)"}]}, "status": "completed", "primarySource": true, "meta": {"source": "ecr"}}, "request": {"method": "PUT", "url": "Immunization/3c8af1dd-2983-5d97-d5f1-f6dd57e9eba1"}}]}') ON CONFLICT (ecr_id) DO NOTHING;
+WITH inserted_data AS (
+ INSERT INTO ecr_data (
+ eICR_ID, patient_name_last, patient_name_first, patient_birth_date, data_source, report_date
+ ) VALUES (
+ '1.2.840.114350.1.13.478.3.7.8.688883.230886', 'ZTEST', 'APPLE', '1965-10-05', 'DB', '2022-02-18'
+ )
+ ON CONFLICT (eICR_ID) DO NOTHING
+ RETURNING eICR_ID
+), inserted_condition AS (
+ INSERT INTO ecr_rr_conditions (uuid, eICR_ID, condition)
+ VALUES (uuid_generate_v4(), (SELECT eICR_ID FROM inserted_data), 'Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder),Viral hepatitis type C (disorder),Viral hepatitis type C (disorder),Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder),Plague (disorder),Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder)')
+ RETURNING uuid
+)
+INSERT INTO ecr_rr_rule_summaries (uuid, ecr_rr_conditions_id, rule_summary)
+VALUES (uuid_generate_v4(), (SELECT uuid FROM inserted_condition), 'Detection of SARS-CoV-2 nucleic acid in a clinical or post-mortem specimen by any method,Detection of Hepatitis C virus antibody in a clinical specimen by any method,Detection of Hepatitis C virus antibody in a clinical specimen by any method,COVID-19 (as a diagnosis or active problem),Detection of SARS-CoV-2 nucleic acid in a clinical or post-mortem specimen by any method,Plague (as a diagnosis or active problem),Detection of SARS-CoV-2 nucleic acid in a clinical or post-mortem specimen by any method')
+RETURNING (SELECT eICR_ID FROM inserted_data);
\ No newline at end of file
diff --git a/containers/ecr-viewer/cypress/docker-compose.yml b/containers/ecr-viewer/cypress/docker-compose.yml
new file mode 100644
index 0000000000..fdd6dbc026
--- /dev/null
+++ b/containers/ecr-viewer/cypress/docker-compose.yml
@@ -0,0 +1,32 @@
+services:
+ # PostgreSQL database
+ postgres:
+ image: "postgres:alpine"
+ ports:
+ - "5432:5432"
+ volumes:
+ - ../sql/core.sql:/docker-entrypoint-initdb.d/core.sql
+ - ../seed-scripts/sql/01-init.sql:/docker-entrypoint-initdb.d/01-init.sql
+ - ./assets/data.sql:/docker-entrypoint-initdb.d/data.sql
+ - ../seed-scripts/sql/.pgpass/:/usr/local/lib/.pgpass
+ environment:
+ - POSTGRES_USER=postgres
+ - PGUSER=postgres
+ - POSTGRES_PASSWORD=pw
+ - POSTGRES_DB=ecr_viewer_db
+ healthcheck:
+ test: ["CMD-SHELL", "pg_isready"]
+ interval: 2s
+ timeout: 5s
+ retries: 20
+
+ # Next.js app
+ ecr-viewer:
+ build:
+ context: ../../..
+ dockerfile: ./containers/ecr-viewer/Dockerfile
+ ports:
+ - "3000:3000"
+ environment:
+ - DATABASE_URL=${DATABASE_URL:-postgres://postgres:pw@db:5432/ecr_viewer_db}
+ - APP_ENV=${APP_ENV:-prod}
diff --git a/containers/ecr-viewer/cypress/e2e/app.cy.tsx b/containers/ecr-viewer/cypress/e2e/app.cy.tsx
index 11d60eef8c..e5e711026e 100644
--- a/containers/ecr-viewer/cypress/e2e/app.cy.tsx
+++ b/containers/ecr-viewer/cypress/e2e/app.cy.tsx
@@ -2,11 +2,13 @@ describe("Happy Path", () => {
it("Should load the eCR Viewer for a known ID", () => {
// Visit a valid URL
const basePath = Cypress.env("BASE_PATH") || "";
- cy.visit(`${basePath}/view-data?id=6100896d-b520-497c-b2fe-1c111c679274`);
+ cy.visit(
+ `${basePath}/view-data?id=1.2.840.114350.1.13.478.3.7.8.688883.230886`,
+ );
// Gets the expected content
cy.get("#patient-summary").contains("Patient Summary");
- cy.contains("VICTORIA HUNTER");
+ cy.contains("APPLE ZTEST");
});
});
diff --git a/containers/ecr-viewer/docker-compose.yml b/containers/ecr-viewer/docker-compose.yml
index fe9fb5b815..e78da116b3 100644
--- a/containers/ecr-viewer/docker-compose.yml
+++ b/containers/ecr-viewer/docker-compose.yml
@@ -4,7 +4,8 @@ services:
ports:
- "5432:5432"
volumes:
- - ./seed-scripts/sql/:/docker-entrypoint-initdb.d/
+ - ./sql/core.sql:/docker-entrypoint-initdb.d/core.sql
+ - ./seed-scripts/sql/01-init.sql:/docker-entrypoint-initdb.d/01-init.sql
- ./seed-scripts/sql/.pgpass/:/usr/local/lib/.pgpass
environment:
- POSTGRES_USER=postgres
diff --git a/containers/ecr-viewer/next-env.d.ts b/containers/ecr-viewer/next-env.d.ts
index 4f11a03dc6..40c3d68096 100644
--- a/containers/ecr-viewer/next-env.d.ts
+++ b/containers/ecr-viewer/next-env.d.ts
@@ -2,4 +2,4 @@
///
// NOTE: This file should not be edited
-// see https://nextjs.org/docs/basic-features/typescript for more information.
+// see https://nextjs.org/docs/app/building-your-application/configuring/typescript for more information.
diff --git a/containers/ecr-viewer/package.json b/containers/ecr-viewer/package.json
index 40cd32e5e8..cc413d51a6 100644
--- a/containers/ecr-viewer/package.json
+++ b/containers/ecr-viewer/package.json
@@ -16,7 +16,7 @@
"update-cypress-data": "docker compose -f ./seed-scripts/docker-compose-create-sql.yml up --build --abort-on-container-exit",
"cypress:open": "cypress open",
"cypress:run": "cypress run",
- "cypress:run-local": "cp ./cypress/assets/data.sql ./seed-scripts/sql && docker compose --env-file .env.test up db -d && concurrently --kill-others 'npm run dev' 'npx wait-on http://localhost:3000 && NODE_ENV=dev cypress run ; docker compose down && rm ./seed-scripts/sql/data.sql'",
+ "cypress:run-local": "docker compose -f cypress/docker-compose.yml --env-file .env.test up postgres -d && concurrently --kill-others 'npm run dev' 'npx wait-on http://localhost:3000 && NODE_ENV=dev cypress run ; docker compose down'",
"cypress:run-prod": "NODE_ENV=production cypress run"
},
"dependencies": {
diff --git a/containers/ecr-viewer/seed-scripts/baseECR/cypress/6100896d-b520-497c-b2fe-1c111c679274/CDA_RR.html b/containers/ecr-viewer/seed-scripts/baseECR/cypress/6100896d-b520-497c-b2fe-1c111c679274/CDA_RR.html
deleted file mode 100644
index a456b8cbc4..0000000000
--- a/containers/ecr-viewer/seed-scripts/baseECR/cypress/6100896d-b520-497c-b2fe-1c111c679274/CDA_RR.html
+++ /dev/null
@@ -1,246 +0,0 @@
-
-
-
-
-
- Reportability Response
-
-
-
-
309 EAST HILLCREST AVE
-
- APT 232
-
- INGLEWOOD, CA 90301-2405, US
-
-
-
-
-
Date of Birth
November 15, 1954
-
-
-
Sex
Female
-
-
-
Race
Black or African American
-
-
-
Ethnicity
Not Hispanic or Latino
-
-
-
Preferred Language
Information not available
-
-
-
-
-
-
Primary Information Recipient:
Nielsen, Victoria
-
-
-
Contact info
620 Shadow Lane
-
- Las Vegas, NV 89106, US
-
-
-
-
-
-
-
-
-
eICR Identifier:
6100896d-b520-497c-b2fe-1c111c679274
-
-
-
-
-
-
- Subject:
-
-
Public Health Reporting Communication: one or more conditions are reportable, or may be reportable, to public health.
-
-
-
-
-
-
- Summary:
-
-
-
Your organization electronically submitted an initial case report to determine if reporting to public health is needed for a patient
-
- "Infection caused by Shiga toxin producing Escherichia coli (disorder)" is reportable to "Local Public Health Agency". The initial case report was sent to "California Department of Public Health". Additional information may be required for this report.
-
-
-
- "Hemolytic uremic syndrome (disorder)" is reportable to "Los Angeles County Department of Public Health". The initial case report was sent to "Los Angeles County Department of Public Health". Additional information may be required for this report.
-
-
-
- "Hemolytic uremic syndrome (disorder)" is reportable to "Nevada State Health Division". The initial case report was sent to "Nevada State Health Division". Additional information may be required for this report.
-
-
-
- "Infection caused by Shiga toxin producing Escherichia coli (disorder)" for "Local Public Health Agency"
-
-
- Reporting is required within "immediate". Reporting to this Public Health Agency is based on "Patient home address"
-
-
-
- > Local Health Department Contact Information (Information only)
-
-
-
-
-
- "Hemolytic uremic syndrome (disorder)" for "Los Angeles County Department of Public Health"
-
-
- "Hemolytic uremic syndrome (disorder)" for "Nevada State Health Division"
-
-
-
-
-
diff --git a/containers/ecr-viewer/seed-scripts/baseECR/cypress/6100896d-b520-497c-b2fe-1c111c679274/CDA_RR.xml b/containers/ecr-viewer/seed-scripts/baseECR/cypress/6100896d-b520-497c-b2fe-1c111c679274/CDA_RR.xml
deleted file mode 100644
index 8d5d9b5e04..0000000000
--- a/containers/ecr-viewer/seed-scripts/baseECR/cypress/6100896d-b520-497c-b2fe-1c111c679274/CDA_RR.xml
+++ /dev/null
@@ -1,2 +0,0 @@
-Reportability Response309 EAST HILLCREST AVEAPT 232INGLEWOODCA90301-2405USVICTORIAHUNTER8515 Georgia Avenue, Suite 700Silver SpringMD20910USAPHL | Association of Public Health Laboratories.8515 Georgia Avenue, Suite 700Silver SpringMD20910US620 Shadow LaneLas VegasNV89106USVictoriaKNielsenHHN-Henderson Hospital1050 W. Galleria DriveHendersonNV89011USA620 Shadow LaneLas VegasNV89106USVictoriaKNielsenHHN-Henderson Hospital1050 W. Galleria DriveHendersonNV89011USA1050 W. Galleria DriveHendersonNV89011USRyanLabuz6900 N. Durango Dr.Las VegasNV89149USSeanMStevens1050 W. Galleria DriveHendersonNV89011USRyanLabuz6900 N. Durango Dr.Las VegasNV89149USSeanMStevens2075 E FLAMINGO RDLAS VEGASNV000000000USStaffPhysicianEd1050 W. Galleria DriveHendersonNV89011USAHHN-Henderson Hospital1050 W. Galleria DriveHendersonNV89011USA. Subject:Public Health Reporting Communication: one or more conditions are reportable, or may be reportable, to public health.Public Health Reporting Communication: one or more conditions are reportable, or may be reportable, to public health.. Summary:Your organization electronically submitted an initial case report to determine if reporting to public health is needed for a patient"Infection caused by Shiga toxin producing Escherichia coli (disorder)" is reportable to "Local Public Health Agency". The initial case report was sent to "California Department of Public Health". Additional information may be required for this report. "Hemolytic uremic syndrome (disorder)" is reportable to "Los Angeles County Department of Public Health". The initial case report was sent to "Los Angeles County Department of Public Health". Additional information may be required for this report. "Hemolytic uremic syndrome (disorder)" is reportable to "Nevada State Health Division". The initial case report was sent to "Nevada State Health Division". Additional information may be required for this report. "Infection caused by Shiga toxin producing Escherichia coli (disorder)" for "Local Public Health Agency" Reporting is required within "immediate". Reporting to this Public Health Agency is based on "Patient home address" > Local Health Department Contact Information (Information only)
"Hemolytic uremic syndrome (disorder)" for "Los Angeles County Department of Public Health" "Hemolytic uremic syndrome (disorder)" for "Nevada State Health Division" > ()
Additional Resources: > (Information only)
> (Information only)
Your organization electronically submitted an initial case report to determine if reporting to public health is needed for a patient.
- California Department of Public HealthCalifornia Department of Public HealthThrombotic thrombocytopenic purpura (TTP) (as a diagnosis or active problem)Local Health Department Contact InformationSouthern Nevada Health District (SNHD)Southern Nevada Health District (SNHD)Los Angeles County Department of Public HealthLos Angeles County Department of Public HealthThrombotic Thrombocytopenic Purpura (TTP) (as a diagnosis or active problem)Nevada State Health DivisionNevada State Health DivisionThrombotic Thrombocytopenic Purpura (TTP) (as a diagnosis or active problem)
\ No newline at end of file
diff --git a/containers/ecr-viewer/seed-scripts/baseECR/cypress/6100896d-b520-497c-b2fe-1c111c679274/CDA_eICR.xml b/containers/ecr-viewer/seed-scripts/baseECR/cypress/6100896d-b520-497c-b2fe-1c111c679274/CDA_eICR.xml
deleted file mode 100644
index 45411d9706..0000000000
--- a/containers/ecr-viewer/seed-scripts/baseECR/cypress/6100896d-b520-497c-b2fe-1c111c679274/CDA_eICR.xml
+++ /dev/null
@@ -1 +0,0 @@
-Initial Public Health Case Report309 EAST HILLCREST AVEAPT 232INGLEWOODCA90301-2405USVICTORIAHUNTER620 Shadow LaneLas VegasNV89106USVictoriaKNielsenHHN-Henderson Hospital1050 W. Galleria DriveHendersonNV89011USA620 Shadow LaneLas VegasNV89106USVictoriaKNielsenHHN-Henderson Hospital1050 W. Galleria DriveHendersonNV89011USA1050 W. Galleria DriveHendersonNV89011USRyanLabuz6900 N. Durango Dr.Las VegasNV89149USSeanMStevens1050 W. Galleria DriveHendersonNV89011USRyanLabuz6900 N. Durango Dr.Las VegasNV89149USSeanMStevens2075 E FLAMINGO RDLAS VEGASNV000000000USStaffPhysicianEd1050 W. Galleria DriveHendersonNV89011USAHHN-Henderson Hospital1050 W. Galleria DriveHendersonNV89011USAPROBLEMS - DIAGNOSES
IMMUNIZATIONSNo ImmunizationInformationSOCIAL HISTORY
Social History Observation
Social History Observation Result
Birth Sex
F
Travel History
COVID- 19 Testing Reason-Screening
Travel History
COVID- 19 Testing Reason-Screening
Travel History
COVID-19 Previously tested-No (qualifier value)
Travel History
Exposure to severe acute respiratory syndrome coronavirus 2 (event)-No (qualifier value)
Travel History
MERS-CoV Travel History-No (qualifier value)
Travel History
TB Risk Score-
Travel History
Symptoms of TB-No symptoms of TB
Travel History
History of tuberculosis (situation)-No known history of exposure to TB
Travel History
C.diff Screening-No (qualifier value)
Travel History
MERS-CoV Symptoms-
Travel History
MRSA Screen Hx MRSA-No (qualifier value)
Travel History
Recent Exposure to Communicable Disease-No (qualifier value)
COVID- 19 Testing Reason-ScreeningCOVID- 19 Testing Reason-ScreeningCOVID-19 Previously tested-No (qualifier value)Exposure to severe acute respiratory syndrome coronavirus 2 (event)-No (qualifier value)MERS-CoV Travel History-No (qualifier value)TB Risk Score-Symptoms of TB-No symptoms of TBHistory of tuberculosis (situation)-No known history of exposure to TBC.diff Screening-No (qualifier value)MERS-CoV Symptoms-MRSA Screen Hx MRSA-No (qualifier value)Recent Exposure to Communicable Disease-No (qualifier value)Plan of TreatmentNo Plan Of Treatment InformationHistory of Present Illness
Narrative Text
Wheezing
Acute URI
Cough
Tachycardia
Reason For Visit
text
ACUTE URI
\ No newline at end of file
diff --git a/containers/ecr-viewer/seed-scripts/baseECR/cypress/61f13d32-b25c-4fb6-998b-73de2dbf87f2/CDA_RR.html b/containers/ecr-viewer/seed-scripts/baseECR/cypress/61f13d32-b25c-4fb6-998b-73de2dbf87f2/CDA_RR.html
new file mode 100644
index 0000000000..d173c6cd55
--- /dev/null
+++ b/containers/ecr-viewer/seed-scripts/baseECR/cypress/61f13d32-b25c-4fb6-998b-73de2dbf87f2/CDA_RR.html
@@ -0,0 +1,274 @@
+
+
+
+
+
+ Reportability Response
+
+
+
+
Primary Home:
+
+ 999 Single Lane
+
+ BEVERLY HILLS, CA 90210, USA
+
+
+
+
+
Date of Birth
October 5, 1965
+
+
+
Sex
Female
+
+
+
Race
White
+
+
+
Ethnicity
Not Hispanic or Latino
+
+
+
Preferred Language
eng
+
+
+
+
+
+
Primary Information Recipient:
,
+
+
+
Contact info
+
+
+
+
+
+
+
eICR Identifier:
1.2.840.114350.1.13.478.3.7.8.688883.230886
+
+
+
+
+
+ Subject:
+
Public Health Reporting Communication: one or more conditions are reportable, or may be reportable, to public health.
+
+
+
+ Summary:
+
Your organization electronically submitted an initial case report to determine if reporting to public health is needed for a patient.
+
+ "Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder)" is reportable to "Local Public Health Agency". The initial case report was sent to "California Department of Public Health". Additional information may be required for this report."Viral hepatitis type C (disorder)" is reportable to "Local Public Health Agency". The initial case report was sent to "California Department of Public Health". Additional information may be required for this report.
+
+
+
+ "Viral hepatitis type C (disorder)" is reportable to "Los Angeles County Department of Public Health". The initial case report was sent to "Los Angeles County Department of Public Health". Additional information may be required for this report."Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder)" is reportable to "Los Angeles County Department of Public Health". The initial case report was sent to "Los Angeles County Department of Public Health". Additional information may be required for this report."Plague (disorder)" is reportable to "Los Angeles County Department of Public Health". The initial case report was sent to "Los Angeles County Department of Public Health". Additional information may be required for this report.
+
+
+
+ "Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder)" is reportable to "Tennessee Department of Health". The initial case report was sent to "Tennessee Department of Health". Additional information may be required for this report.
+
+
+
+ "Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder)" for "Local Public Health Agency"
+
+
+ Reporting is required immediately. Reporting to this Public Health Agency is based on "Patient home address"
+
+
+ "Viral hepatitis type C (disorder)" for "Local Public Health Agency"
+
+
+ Reporting is required within "7 Day(s)". Reporting to this Public Health Agency is based on "Patient home address"
+
+
+
+ > Local Health Department Contact Information (Information only)
+
+
+
+
+
+ "Viral hepatitis type C (disorder)" for "Los Angeles County Department of Public Health"
+
+
+ "Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder)" for "Los Angeles County Department of Public Health"
+
+
+ Reporting is required immediately. Reporting to this Public Health Agency is based on "Patient home address"
+
+
+
+ > CDC COVID-19 webpage (Information only)
+
+
+ > Los Angeles County Department of Public Health Office of the Chief Medical Informatics Officer IRIS System 241 North Figueroa Street Los Angeles, CA 90012 213-288-7696 (Information only)
+
+
+
+
+
+ "Plague (disorder)" for "Los Angeles County Department of Public Health"
+
+
+ "Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder)" for "Tennessee Department of Health"
+
+
+ Reporting is required within "1 Day(s)". Reporting to this Public Health Agency is based on "Provider facility address"
+
+
+
+ > CDC COVID-19 webpage (Information only)
+
+
+ > If you have questions, please contact TDH by phone at (615)741-7247. (Information only)
+
+
+
+
+
+ Additional Resources:
+
+
+
+ > This includes references to more specific COVID reporting guidance for Tennessee. (Information only)
+
+
+ > Link to PDF version of 2021 Tennessee Reportable Conditions. (Information only)
+
+
+
+
+
+
+
+
+
diff --git a/containers/ecr-viewer/seed-scripts/baseECR/cypress/61f13d32-b25c-4fb6-998b-73de2dbf87f2/CDA_RR.xml b/containers/ecr-viewer/seed-scripts/baseECR/cypress/61f13d32-b25c-4fb6-998b-73de2dbf87f2/CDA_RR.xml
new file mode 100644
index 0000000000..efbfbadd99
--- /dev/null
+++ b/containers/ecr-viewer/seed-scripts/baseECR/cypress/61f13d32-b25c-4fb6-998b-73de2dbf87f2/CDA_RR.xml
@@ -0,0 +1,4 @@
+Reportability Response999 Single LaneLOS ANGELESBEVERLY HILLSCA90210USAUSAAppleZtestVanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USA8515 Georgia Avenue, Suite 700Silver SpringMD20910USAPHL | Association of Public Health Laboratories.8515 Georgia Avenue, Suite 700Silver SpringMD20910USVanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USATranscribe OrdersVanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USALabTech MLTLabVanderbilt University Adult Hospital1211 Medical Center DrDAVIDSONNashvilleTN37232Vanderbilt University Medical Center1211 Medical Center DrDAVIDSONNashvilleTN37232Vanderbilt University Medical Center. Subject:Public Health Reporting Communication: one or more conditions are reportable, or may be reportable, to public health. Public Health Reporting Communication: one or more conditions are reportable, or may be reportable, to public health..Summary:Your organization electronically submitted an initial case report to determine if reporting to public health is needed for a patient."Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder)" is reportable to "Local Public Health Agency". The initial case report was sent to "California Department of Public Health". Additional information may be required for this report."Viral hepatitis type C (disorder)" is reportable to "Local Public Health Agency". The initial case report was sent to "California Department of Public Health". Additional information may be required for this report. "Viral hepatitis type C (disorder)" is reportable to "Los Angeles County Department of Public Health". The initial case report was sent to "Los Angeles County Department of Public Health". Additional information may be required for this report."Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder)" is reportable to "Los Angeles County Department of Public Health". The initial case report was sent to "Los Angeles County Department of Public Health". Additional information may be required for this report."Plague (disorder)" is reportable to "Los Angeles County Department of Public Health". The initial case report was sent to "Los Angeles County Department of Public Health". Additional information may be required for this report. "Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder)" is reportable to "Tennessee Department of Health". The initial case report was sent to "Tennessee Department of Health". Additional information may be required for this report. "Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder)" for "Local Public Health Agency" Reporting is required immediately. Reporting to this Public Health Agency is based on "Patient home address" > CDC COVID-19 webpage (Information only)
> Local Health Department Contact Information (Information only)
"Viral hepatitis type C (disorder)" for "Local Public Health Agency" Reporting is required within "7 Day(s)". Reporting to this Public Health Agency is based on "Patient home address" > Local Health Department Contact Information (Information only)
"Viral hepatitis type C (disorder)" for "Los Angeles County Department of Public Health" "Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder)" for "Los Angeles County Department of Public Health" Reporting is required immediately. Reporting to this Public Health Agency is based on "Patient home address" > CDC COVID-19 webpage (Information only)
> Los Angeles County Department of Public Health Office of the Chief Medical Informatics Officer IRIS System 241 North Figueroa Street Los Angeles, CA 90012 213-288-7696 (Information only)
"Plague (disorder)" for "Los Angeles County Department of Public Health" "Disease caused by severe acute respiratory syndrome coronavirus 2 (disorder)" for "Tennessee Department of Health" Reporting is required within "1 Day(s)". Reporting to this Public Health Agency is based on "Provider facility address" > CDC COVID-19 webpage (Information only)
> If you have questions, please contact TDH by phone at (615)741-7247. (Information only)
Additional Resources: > This includes references to more specific COVID reporting guidance for Tennessee. (Information only)
> Link to PDF version of 2021 Tennessee Reportable Conditions. (Information only)
Your organization electronically submitted an initial case report to determine if reporting to public health is needed for a patient. SacramentoCACalifornia Department of Public HealthSacramentoCACalifornia Department of Public HealthDetection of SARS-CoV-2 nucleic acid in a clinical or post-mortem specimen by any methodCDC COVID-19 webpageLocal Health Department Contact InformationSacramentoCACalifornia Department of Public HealthSacramentoCACalifornia Department of Public HealthDetection of Hepatitis C virus antibody in a clinical specimen by any methodLocal Health Department Contact InformationLos Angeles County Department of Public HealthLos Angeles County Department of Public HealthDetection of Hepatitis C virus antibody in a clinical specimen by any methodLos Angeles County Department of Public HealthLos Angeles County Department of Public HealthCOVID-19 (as a diagnosis or active problem)Detection of SARS-CoV-2 nucleic acid in a clinical or post-mortem specimen by any methodCDC COVID-19 webpageLos Angeles County Department of Public Health Office of the Chief Medical Informatics Officer IRIS System 241 North Figueroa Street Los Angeles, CA 90012 213-288-7696Los Angeles County Department of Public HealthLos Angeles County Department of Public HealthPlague (as a diagnosis or active problem)Communicable and Environmental Diseases and Emergency Preparedness
+Andrew Johnson Towerr
+710 James Robertson Parkway, Nashville, TN 37243
+NashvilleTNTennessee Department of HealthTennessee Department of HealthDetection of SARS-CoV-2 nucleic acid in a clinical or post-mortem specimen by any methodCDC COVID-19 webpageIf you have questions, please contact TDH by phone at (615)741-7247.This includes references to more specific COVID reporting guidance for Tennessee.Link to PDF version of 2021 Tennessee Reportable Conditions.
\ No newline at end of file
diff --git a/containers/ecr-viewer/seed-scripts/baseECR/cypress/6100896d-b520-497c-b2fe-1c111c679274/CDA_eICR.html b/containers/ecr-viewer/seed-scripts/baseECR/cypress/61f13d32-b25c-4fb6-998b-73de2dbf87f2/CDA_eICR.html
similarity index 73%
rename from containers/ecr-viewer/seed-scripts/baseECR/cypress/6100896d-b520-497c-b2fe-1c111c679274/CDA_eICR.html
rename to containers/ecr-viewer/seed-scripts/baseECR/cypress/61f13d32-b25c-4fb6-998b-73de2dbf87f2/CDA_eICR.html
index a22b77a50c..2b4bc8d6d7 100644
--- a/containers/ecr-viewer/seed-scripts/baseECR/cypress/6100896d-b520-497c-b2fe-1c111c679274/CDA_eICR.html
+++ b/containers/ecr-viewer/seed-scripts/baseECR/cypress/61f13d32-b25c-4fb6-998b-73de2dbf87f2/CDA_eICR.html
@@ -1168,7 +1168,7 @@
+
+ Comment:
+
+
+ A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample.
+
+
+ This test was performed using a multiplexed nucleic acid amplification test that is labeled Emergence Use Only by the U.S. FDA. Results of this test should not be used as the sole basis for diagnosis, treatment, or other management decisions.
+
+
+
+
+
+
+
+
SARS-CoV-2 Nucleic Acid Method (Comment)
+
+ Other
+
+
+ This test was performed using the Roche 6800 COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.
+
+
+
+
+ Comment:
+
+
+ A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample.
+
+
+ This test was performed using a multiplexed nucleic acid amplification test that is labeled Emergence Use Only by the U.S. FDA. Results of this test should not be used as the sole basis for diagnosis, treatment, or other management decisions.
+
+
+
+
+
+
+
+
SARS-CoV-2 Nucleic Acid Method (Comment)
+
+ Oropharynx
+
+
+ This test was performed using the Roche 6800 COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.
+
+
+
VUMC CERNER LAB
+
+
+
+
+
+
+
+
+
+
+
+
Specimen (Source)
Anatomical Location / Laterality
Collection Method / Volume
Collection Time
Received Time
+
+
+
+
+
Oropharynx
07/27/2022 3:49 PM CDT
07/27/2022 3:58 PM CDT
+
+
+
+
+
+
+
+
+
Resulting Agency Comment
+
+
+
+
+
+
+ Ordered by Romney H Humphries
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Authorizing Provider
Result Type
+
+
+
+
+
No Pcp
LAB BODY FLUIDS AND STOOLS ORDERABLES
+
+
+
+
+
+
+
+
+
+
+
+
+
Performing Organization
Address
City/State/ZIP Code
Phone Number
+
+
+
+
+
+
VUMC CERNER LAB
+
+
4605 TVC VUMC
+
1301 Medical Center Drive
+
+
NASHVILLE, TN 37232-5310
+
+
615-875-5227
+
+
+
+
+
+
+
+ SARS-CoV-2 PCR (07/27/2022 3:49 PM CDT):
+
+
+
+
+
+
+
+
+
+
+
+
+
Component
Value
Ref Range
Test Method
Analysis Time
Performed At
Pathologist Signature
+
+
+
+
+
SARS-CoV-2 Nucleic Acid (Result)
+ Not Detected
+
Not Detected
VUMC CERNER LAB
+
+
+
+
+ Comment:
+
+
+ A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample.
+
+
+ This test was performed using a multiplexed nucleic acid amplification test that is labeled Emergence Use Only by the U.S. FDA. Results of this test should not be used as the sole basis for diagnosis, treatment, or other management decisions.
+
+
+
+
+
+
+
+
SARS-CoV-2 Nucleic Acid Method (Comment)
+
+ Nasopharynx
+
+
+ This test was performed using the Roche 6800 COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.
+
+
+
VUMC CERNER LAB
+
+
+
+
+
+
+
+
+
+
+
+
Specimen (Source)
Anatomical Location / Laterality
Collection Method / Volume
Collection Time
Received Time
+
+
+
+
+
Nasopharynx
07/27/2022 3:49 PM CDT
07/27/2022 3:58 PM CDT
+
+
+
+
+
+
+
+
+
Resulting Agency Comment
+
+
+
+
+
+
+ Ordered by Romney H Humphries
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Authorizing Provider
Result Type
+
+
+
+
+
No Pcp
LAB BODY FLUIDS AND STOOLS ORDERABLES
+
+
+
+
+
+
+
+
+
+
+
+
+
Performing Organization
Address
City/State/ZIP Code
Phone Number
+
+
+
+
+
+
VUMC CERNER LAB
+
+
4605 TVC VUMC
+
1301 Medical Center Drive
+
+
NASHVILLE, TN 37232-5310
+
+
615-875-5227
+
+
+
+
+
+
+
+ SARS-CoV-2 PCR (07/27/2022 3:49 PM CDT):
+
+
+
+
+
+
+
+
+
+
+
+
+
Component
Value
Ref Range
Test Method
Analysis Time
Performed At
Pathologist Signature
+
+
+
+
+
SARS-CoV-2 Nucleic Acid (Result)
+ Not Detected
+
Not Detected
VUMC CERNER LAB
+
+
+
+
+ Comment:
+
+
+ A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample.
+
+
+ This test was performed using a multiplexed nucleic acid amplification test that is labeled Emergence Use Only by the U.S. FDA. Results of this test should not be used as the sole basis for diagnosis, treatment, or other management decisions.
+
+
+
+
+
+
+
+
SARS-CoV-2 Nucleic Acid Method (Comment)
+
+ Nares
+
+
+ This test was performed using the Roche 6800 COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.
+
+
+
VUMC CERNER LAB
+
+
+
+
+
+
+
+
+
+
+
+
Specimen (Source)
Anatomical Location / Laterality
Collection Method / Volume
Collection Time
Received Time
+
+
+
+
+
Nares
07/27/2022 3:49 PM CDT
07/27/2022 3:58 PM CDT
+
+
+
+
+
+
+
+
+
Resulting Agency Comment
+
+
+
+
+
+
+ Ordered by Romney H Humphries
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Authorizing Provider
Result Type
+
+
+
+
+
No Pcp
LAB BODY FLUIDS AND STOOLS ORDERABLES
+
+
+
+
+
+
+
+
+
+
+
+
+
Performing Organization
Address
City/State/ZIP Code
Phone Number
+
+
+
+
+
+
VUMC CERNER LAB
+
+
4605 TVC VUMC
+
1301 Medical Center Drive
+
+
NASHVILLE, TN 37232-5310
+
+
615-875-5227
+
+
+
+
+
+
+
+ SARS-CoV-2 PCR (07/27/2022 3:49 PM CDT):
+
+
+
+
+
+
+
+
+
+
+
+
+
Component
Value
Ref Range
Test Method
Analysis Time
Performed At
Pathologist Signature
+
+
+
+
+
SARS-CoV-2 Nucleic Acid (Result)
+ Not Detected
+
Not Detected
VUMC CERNER LAB
+
+
+
+
+ Comment:
+
+
+ A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample.
+
+
+ This test was performed using a multiplexed nucleic acid amplification test that is labeled Emergence Use Only by the U.S. FDA. Results of this test should not be used as the sole basis for diagnosis, treatment, or other management decisions.
+
+
+
+
+
+
+
+
SARS-CoV-2 Nucleic Acid Method (Comment)
+
+ BAL
+
+
+ This test was performed using the Roche 6800 COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.
+
+
+
VUMC CERNER LAB
+
+
+
+
+
+
+
+
+
+
+
+
Specimen (Source)
Anatomical Location / Laterality
Collection Method / Volume
Collection Time
Received Time
+
+
+
+
+
BAL
07/27/2022 3:49 PM CDT
07/27/2022 3:58 PM CDT
+
+
+
+
+
+
+
+
+
Resulting Agency Comment
+
+
+
+
+
+
+ Ordered by Romney H Humphries
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Authorizing Provider
Result Type
+
+
+
+
+
No Pcp
LAB BODY FLUIDS AND STOOLS ORDERABLES
+
+
+
+
+
+
+
+
+
+
+
+
+
Performing Organization
Address
City/State/ZIP Code
Phone Number
+
+
+
+
+
+
VUMC CERNER LAB
+
+
4605 TVC VUMC
+
1301 Medical Center Drive
+
+
NASHVILLE, TN 37232-5310
+
+
615-875-5227
+
+
+
+
+
+
+
+ (ABNORMAL) Hepatitis C IgG w/Rfx PCR (05/12/2022 6:00 AM CDT):
+
+
+
+
+
+
+
+
+
+
+
+
+
Component
Value
Ref Range
Test Method
Analysis Time
Performed At
Pathologist Signature
+
+
+
+
+
Hepatitis C Antibody
+ Positive
+ (A)
+
Negative
VUMC CERNER LAB
+
+
+
+
+ Comment:
+
+
+ Positive: Presumptive history of HCV infection; nucleic acid testing recommended to document viral replication.
+
+
+ Equivocal: Antibodies to HCV may or may not be present; repeat serologic testing in approximately 8 weeks or nucleic acid testing is recommended to assess possible infection.
+
+
+ Negative: Antibodies to HCV not detected; does not exclude possibility of infection with HCV.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Specimen (Source)
Anatomical Location / Laterality
Collection Method / Volume
Collection Time
Received Time
+
+
+
+
+
Blood
05/12/2022 6:00 AM CDT
05/12/2022 11:30 AM CDT
+
+
+
+
+
+
+
+
+
+
+
+
+
Authorizing Provider
Result Type
+
+
+
+
+
Charles W Stratton MD
LAB BLOOD ORDERABLES
+
+
+
+
+
+
+
+
+
+
+
+
+
Performing Organization
Address
City/State/ZIP Code
Phone Number
+
+
+
+
+
+
VUMC CERNER LAB
+
+
4605 TVC VUMC
+
1301 Medical Center Drive
+
+
NASHVILLE, TN 37232-5310
+
+
615-875-5227
+
+
+
+
+
+
+
+ Cytogenomic SNP microarray (04/04/2022 11:55 AM CDT):
+
+
+
+
+
+
+
+
Specimen (Source)
Anatomical Location / Laterality
Collection Method / Volume
Collection Time
Received Time
+
+
+
+
+
Blood
04/04/2022 11:55 AM CDT
04/18/2022 2:46 PM CDT
+
+
+
+
+
+
+
+
+
Narrative
+
+
+
+
+
+
VUMC CERNER LAB - 04/18/2022 2:57 PM CDT
+
+ MICROARRAY REPORT- Corrected
+
+
+
+ Request#: CG-22-0000006
+
+ Service date: 4/4/2022 11:55
+
+
+
+ Microarray Result:
+
+ Normal female
+
+
+
+ Microarray Interpretation:
+
+ SNP chromosomal microarray analysis (CMA) of a blood sample from this patient demonstrated no copy number changes of known clinical significance. No large regions of homozygosity (ROH) were detected. The ISCN nomenclature describing this result is: arr(X,1-22)x2.
+
+ Electronically signed out by:
+
+ Benfield, Luis A
+
+
+
+ on 04/18/2022
+
+ ___________________________________________________________________
+
+
+
+ Clinical indication:
+
+ Specimen List: Blood
+
+ Date in Lab: 4/18/2022 14:46
+
+ Date Collected: 4/4/2022 11:55
+
+ ___________________________________________________________________
+
+
+
+ Disclaimer:
+
+
+
+ Copy number gains less than 400 kb in size and copy number losses less than 200 kb in size will not be reported unless they represent a known or suspected clinically relevant imbalance. The reporting of copy number variants less than 100 kb in size is at the discretion of the laboratory and some clinically relevant copy number changes under 50 kb may not be reported due to limitations in probe coverage in certain genomic regions. Copy number changes of any size with no apparent clinical significance (likely benign or benign) have not been discussed in this report but may be available upon request. Regions of homozygosity (ROH) less than 10 Mb in size will not be reported unless the ROH is clinically relevant for potential uniparental disomy. Genome-wide ROH under 2% will not be reported. Copy number variants less than 200 kb associated with a carrier status for autosomal recessive conditions will not be reported unless specifically indicated in the reason for referral.
+
+
+
+ This microarray was designed and manufactured by Affymetrix for the sole purpose of identifying DNA copy number gains and losses associated with chromosomal imbalances and regions of homozygosity (ROH) associated with uniparental isodisomy (isoUPD).This microarray will detect aneuploidy, deletions and duplications of loci represented on the microarray. It will not detect balanced alterations including: reciprocal translocations, inversions and balanced insertions. It will not detect point mutations and imbalances less than 10 kb. Failure to detect an alteration at any locus does not exclude the diagnosis of any of the disorders represented on the microarray. This assay is not designed to detect mosaic gains and losses and its performance in detecting mosaicism has not been established. This test was developed and its performance characteristics determined by Affymetrix as required by CLIA Â’88 regulations. This test is used for clinical purposes and the accuracy and precision has
+
+ been established and verified by this laboratory. This test has not been cleared or approved by the U.S. Food and Drug Administration.
+
+
+
+ Interpretation of copy number variants is performed using VUMC-laboratory maintained databases as well as the following resources:
+
+ Database of Genomic Variants (http://dgv.tcag.ca/dgv/app/home)
+
+ Online Mendelian Inheritance in Man (http://www.omim.org/)
+
+ UCSC Genome Bioinformatics (http://genome.ucsc.edu/cgi-bin/hgGateway)
+
+ ClinGen Clinical Genome Resource (http://www.ncbi.nlm.nih.gov/projects/dbvar/clingen)
+
+ DECIPHER Database (https://decipher.sanger.ac.uk/browser)
+
+ PubMed-NCBI (http://www.ncbi.nlm.nih.gov/pubmed)
+
+ Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen). PMID: 31690835
+
+
+
+ Method:
+
+ Microarray platform: ThermoFisher Scientific CytoScanTM HD Cytogenetics Solution
+
+ Version: 1.1 (Based on UCSC hg19 assembly)
+
+ Number of loci analyzed: 2,696,550
+
+ Mean probe spacing: <700 bp
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Testing performed at Vanderbilt Cytogenetics One Hundred Oaks Laboratory, Suite 21100, 719 Thompson Ln,
+
+ Nashville, TN 37204 phone 615-875-0228, fax 615-875-0234
+
+
+
+
+
+
+
+
+
+
+
Resulting Agency Comment
+
+
+
+
+
+
+ testing comment
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Authorizing Provider
Result Type
+
+
+
+
+
Carda Testprovqa MD
LAB GENETIC TESTING
+
+
+
+
+
+
+
+
+
+
+
+
+
Performing Organization
Address
City/State/ZIP Code
Phone Number
+
+
+
+
+
+
VUMC CERNER LAB
+
+
4605 TVC VUMC
+
1301 Medical Center Drive
+
+
NASHVILLE, TN 37232-5310
+
+
615-875-5227
+
+
+
+
+
+
+
+ Pharmacogenomics (03/31/2022 5:36 PM CDT):
+
+
+
+
+
+
+
+
Specimen (Source)
Anatomical Location / Laterality
Collection Method / Volume
Collection Time
Received Time
+
+
+
+
+
DNA
03/31/2022 5:36 PM CDT
03/31/2022 5:44 PM CDT
+
+
+
+
+
+
+
+
+
Narrative
+
+
+
+
+
+
VUMC CERNER LAB - 03/31/2022 5:51 PM CDT
+
+ Pharmacogenomics: Final Report
+
+
+
+ Request #: MD-22-0000041
+
+
+
+ Service Date: 3/31/2022 17:36
+
+
+
+ Reason for Request: Genotyping for Determination of Drug Efficacy, Dosage and Safety
+
+
+
+ Type of Specimen: DNA
+
+
+
+ Date Received: 3/31/2022 17:44
+
+
+
+ Date Reported: 3/31/2022 17:51
+
+
+
+ Interpretation:
+
+ Results from this assay may indicate dosage adjustments or medication alternatives that should be considered for this patient. Additional information regarding the implications of these results is available at www.mydruggenome.org.
+
+
+
+ For VUMC patients, clinical decision support regarding the management of this patient with respect to specific drugs based upon the patient's genotype as listed below is available in the patient's electronic medical record under Genomic Indicators. Clinical decision support may also be provided for some drugs through order entry and medication prescribing tools utilized within the VUMC system.
+
+
+
+
+
+
+
+ Comments:
+
+
+
+ Results:
+
+
+
+ CYP2C19 - Cancelled
+
+
+
+ CYP2C9 - Cancelled
+
+
+
+ CYP2D6 - Cancelled
+
+
+
+ CYP3A5 - Cancelled
+
+
+
+ CYP4F2 - Cancelled
+
+
+
+ DPYD - Cancelled
+
+
+
+ NUDT15 - Cancelled
+
+
+
+ SLCO1B1 - Cancelled
+
+
+
+ TPMT - Cancelled
+
+
+
+ VKORC1 - Cancelled
+
+
+
+ These results should be correlated with other laboratory and clinical findings and additional testing should be considered if clinically indicated.
+
+
+
+
+
+ Methodology:
+
+
+
+ DNA was extracted from this specimen and screened for 37 variants in 10 genes that are associated with drug absorption, distribution, metabolism, excretion or response. The reported genotypes were determined using PCR amplification and oligonucleotide primers specific for each interrogated region of the genes listed within this panel. Fluorophore labeled probes were used to identify each variant.
+
+
+
+ Variants analyzed in this assay include: CYP2C19 *2, *3, *4, *6, *8, *17; CYP2C9 *2, *3, *6, *8; CYP3A5 *3, *6, *7; CYP4F2 *3; DPYD *2A, *13, c.557A>G, c.1236G>A (HapB3), c.2846A>T; NUDT15 *2 or *3; SLCO1B1 *5; TPMT *2, *3B, *3C, *4; VKORC1 promoter variant c.-1639G>A; and CYP2D6 copy number and variants *2, *2A, *3, *4, *6, *7, *9, *10, *17, *29 and *41. A *1 allele is considered the reference (normal) sequence and is reported if none of the variants analyzed for a particular gene is detected. This assay is specific for the variants listed above and cannot exclude the presence of other variants within these genes that may affect the pharmacologic function of the protein product encoded by these genes. In most cases, variants for a particular gene exist on separate alleles; however, for individuals in which multiple variants in the same gene are detected, this assay cannot determine if the variants are on the same allele or on different alleles. Further, due to the highly polymorphic
+
+ nature of these regions, rare variants may exist that could affect the sensitivity or specificity of this assay and lead to a false-negative or a false-positive result.
+
+
+
+
+
+ Electronically signed out by:
+
+ Barba, Elizabeth
+
+
+
+ on 03/31/2022
+
+
+
+ This assay has not been cleared or approved by the US Food and Drug Administration. The performance of this assay was tested and validated prior to use for patient testing. This test is used for clinical purposes and should not be regarded as investigational or research. This laboratory is regulated by the Clinical Laboratory Improvement Act of 1988.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Authorizing Provider
Result Type
+
+
+
+
+
Carda Testprovqa MD
LAB GENETIC TESTING
+
+
+
+
+
+
+
+
+
+
+
+
+
Performing Organization
Address
City/State/ZIP Code
Phone Number
+
+
+
+
+
+
VUMC CERNER LAB
+
+
4605 TVC VUMC
+
1301 Medical Center Drive
+
+
NASHVILLE, TN 37232-5310
+
+
615-875-5227
+
+
+
+
+
+
+
+ Drug Toxicology Monitoring Base Pnl w/Conf, Oral Fl-QSTD (03/29/2022 1:53 PM CDT):
+
+
+
+
+
+
+
+
+
+
+
+
+
Component
Value
Ref Range
Test Method
Analysis Time
Performed At
Pathologist Signature
+
+
+
+
+
Drug Toxicology Monitoring Base Pnl w/Conf, Oral Fl
+
+ VUMC patients: Results faxed to Vanderbilt Medical Record.
+
+ VPLS clients: See separate report sent to client.
+
+
+
VUMC CERNER LAB
+
+
+
+
+ Comment:
+ This test was performed at: Quest Laboratory,Location Varies,,,,,,
+
+
+
+ Comment:
+
+
+ A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample.
+
+
+ This test was performed using a multiplexed nucleic acid amplification test that is labeled Emergence Use Only by the U.S. FDA. Results of this test should not be used as the sole basis for diagnosis, treatment, or other management decisions.
+
+
+
+
+
+
+
+
SARS-CoV-2 Nucleic Acid Method (Comment)
+
+ Nares
+
+
+ This test was performed using the Hologic Panther COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.
+
+
+
VUMC CERNER LAB
+
+
+
+
+
+
+
+
+
+
+
+
Specimen (Source)
Anatomical Location / Laterality
Collection Method / Volume
Collection Time
Received Time
+
+
+
+
+
Nares
03/11/2022 1:05 PM CST
03/11/2022 1:46 PM CST
+
+
+
+
+
+
+
+
+
+
+
+
+
Authorizing Provider
Result Type
+
+
+
+
+
Adam Clark Seegmiller MD
LAB BODY FLUIDS AND STOOLS ORDERABLES
+
+
+
+
+
+
+
+
+
+
+
+
+
Performing Organization
Address
City/State/ZIP Code
Phone Number
+
+
+
+
+
+
VUMC CERNER LAB
+
+
4605 TVC VUMC
+
1301 Medical Center Drive
+
+
NASHVILLE, TN 37232-5310
+
+
615-875-5227
+
+
+
+
+
+
+
+ FISH ALL Pnl (03/11/2022 1:05 PM CST):
+
+
+
+
+
+
+
+
Specimen (Source)
Anatomical Location / Laterality
Collection Method / Volume
Collection Time
Received Time
+
+
+
+
+
Blood
03/11/2022 1:05 PM CST
03/11/2022 1:09 PM CST
+
+
+
+
+
+
+
+
+
Narrative
+
+
+
+
+
+
VUMC CERNER LAB - 03/11/2022 1:27 PM CST
+
+ FISH REPORT
+
+
+
+ Request#:CG-22-0000003
+
+ Service date:3/11/2022 13:05
+
+
+
+
+
+ FISH IMPRESSION:
+
+
+
+ Abnormal for homozygous deletion of CDKN2A locus at 9p21 in __% of cells.
+
+
+
+ FISH KARYOTYPE:
+
+
+
+
+
+
+
+ nuc ish (DXZ1x1,DYZ3x1,D18Z1x2)[200]
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ COMMENTS:
+
+
+
+
+
+
+
+ Results of the FISH studies with the 21 DNA probes described above were analyzed in at least 200 cells per probe and no abnormal signal patterns were detected for the target regions of chromosomes 1, 4, 7, 9, 10, 11, 12, 14, 17, 19, 21, and 22.
+
+
+
+ Normal cut off values for probes:
+
+
+
+ 1.0% for t(1;19) PBX1/TCF3
+
+ 1.0% for t(9;22) BCR/ABL1
+
+ 1.0% for KMT2A (11q23)
+
+ 1.0% for t(12;21) ETV6/RUNX1
+
+ 1.0% for IKZF1/CEP7
+
+ 3.0% for CEP 4
+
+ 2.0% for CEP 10
+
+ 2.0% for CEP 17
+
+ 1.0% for CDKN2A/CEP9 (9p21)
+
+ 1.0% for IGH breakapart
+
+ 1.0% for ABL2 breakapart
+
+ 1.0% for ABL1 breakapart
+
+
+
+ These probes were developed by Vysis and their performance characteristics determined by VUMC as required by the CLIA '88 regulations. These probes have not been cleared or approved by the U.S. Food and Drug administration.
+
+
+
+
+
+ Ferrin Courtney Wheeler, PhD, FACMG
+
+ reviewed and approved
+
+
+
+ Electronically signed out by:
+
+ Mavrak, Geoffrey A
+
+
+
+ on 03/11/2022
+
+
+
+ Clinical History: ALL
+
+ Specimen List: Blood
+
+ Date In Lab: 3/11/2022 13:09
+
+ Date Collected: 3/11/2022 13:05
+
+
+
+ Testing performed at Vanderbilt Cytogenetics One Hundred Oaks Laboratory, Suite 21100, 719 Thompson Ln,
+
+ Nashville, TN 37204 phone 615-875-0228, fax 615-875-0234
+
- Exposure to severe acute respiratory syndrome coronavirus 2 (event)-No (qualifier value)
-
-
-
-
- Travel History
-
- MERS-CoV Travel History-No (qualifier value)
-
-
-
-
- Travel History
-
- TB Risk Score-
-
-
-
-
- Travel History
-
- Symptoms of TB-No symptoms of TB
-
-
-
-
- Travel History
-
- History of tuberculosis (situation)-No known history of exposure to TB
-
-
-
-
- Travel History
-
- C.diff Screening-No (qualifier value)
-
-
-
-
- Travel History
-
- MERS-CoV Symptoms-
-
-
-
-
- Travel History
-
- MRSA Screen Hx MRSA-No (qualifier value)
-
-
-
-
- Travel History
-
- Recent Exposure to Communicable Disease-No (qualifier value)
-
+
Smoking Tobacco: Never Assessed
-
-
-
-
Plan of Treatment
-
No Plan Of Treatment Information
-
-
-
History of Present Illness
-
-
+
+
+
+
+
-
Narrative Text
+
Sex Assigned at Birth
Date Recorded
-
-
- Wheezing
-
-
-
-
- Acute URI
-
-
-
-
- Cough
-
-
-
-
- Tachycardia
-
+
+
Not on file
+ documented as of this encounter
-
Reason For Visit
+
Encounter Details
-
+
+
+
+
+
+
-
text
+
Date
Type
Department
Care Team
Description
-
-
- ACUTE URI
-
+
+
2/18/22
Transcribe Orders
+
Vanderbilt University Adult Hospital
+
1211 Medical Center Dr
+
Nashville, TN 37232
+
615-322-5000
+
+
Tech, Lab, MLT
+
@@ -2198,21 +4074,21 @@
Reason For Vi
Document maintained by
-
HHN-Henderson Hospital
+
Vanderbilt University Medical Center
Contact
-
+
Work Place
-
1050 W. Galleria Drive
-
Henderson, NV
-
89011, USA
+
3401 West End Ave
+
NASHVILLE, TN
+
37203, USA
-
tel: (Work Place) (702)963-7000
+
tel: (Work Place) +1-615-322-5000
@@ -2228,7 +4104,7 @@
Document Information
-
OID: 6100896d-b520-497c-b2fe-1c111c679274
04/17/2022, 04:17
+
OID: 1.2.840.114350.1.13.478.3.7.8.688883.230886
07/28/2022, 09:01
diff --git a/containers/ecr-viewer/seed-scripts/baseECR/cypress/61f13d32-b25c-4fb6-998b-73de2dbf87f2/CDA_eICR.xml b/containers/ecr-viewer/seed-scripts/baseECR/cypress/61f13d32-b25c-4fb6-998b-73de2dbf87f2/CDA_eICR.xml
new file mode 100644
index 0000000000..ad7e9d3568
--- /dev/null
+++ b/containers/ecr-viewer/seed-scripts/baseECR/cypress/61f13d32-b25c-4fb6-998b-73de2dbf87f2/CDA_eICR.xml
@@ -0,0 +1 @@
+Initial Public Health Case Report999 Single LaneLOS ANGELESBEVERLY HILLSCA90210USAUSAAppleZtestVanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USALabInterfaceVanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USAEpic - Version 10.2Epic - Version 10.2Vanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USAVanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USASister999 Single CourtLOS ANGELEBEVERLY HILLSCA90210USATranscribe OrdersVanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USALabTech MLTLabVanderbilt University Adult Hospital1211 Medical Center DrDAVIDSONNashvilleTN37232Vanderbilt University Medical Center1211 Medical Center DrDAVIDSONNashvilleTN37232Vanderbilt University Medical CenterMiscellaneous NotesNot on filedocumented in this encounterImmunizations
Name
Administration Dates
Next Due
DTaP, 5 pertussis antigens vaccine (DAPTACEL)
06/15/2021
Hep B, adult vaccine (Engerix/Recombivax)
09/08/2020
SARS-COV-2 (COVID-19) Spikevax Vaccine, Moderna
01/22/2021
documented as of this encounterLLSFJKModerna US, Inc.NurseOneFamily MedicineRNVanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USAInternal Medicine719 THOMPSON LANESUITE 20400DAVIDSONNASHVILLETN37204USAVanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USAAdministered MedicationsNot on filedocumented in this encounterPlan of Treatment
Pending Results
Name
Type
Priority
Associated Diagnoses
Date/Time
PCR SARS-CoV-2 and Influenza A/B
Lab
Routine
07/27/2022 3:49 PM CDT
PCR SARS-CoV-2 and Influenza A/B
Lab
Routine
07/27/2022 3:49 PM CDT
PCR SARS-CoV-2 and Influenza A/B
Lab
Routine
07/27/2022 3:49 PM CDT
PCR SARS-CoV-2 and Influenza A/B
Lab
Routine
07/27/2022 3:49 PM CDT
PCR SARS-CoV-2 and Influenza A/B
Lab
Routine
07/27/2022 3:49 PM CDT
Scheduled Orders
Name
Type
Priority
Associated Diagnoses
Order Schedule
PCR Hepatitis C Virus Qt
Lab
Routine
Ordered: 5/12/22
documented as of this encounterPathology1161 21st Avenue SouthC3321 A, Medical Center NorthDAVIDSONNashvilleTN37232-2561USAVanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USAUSAVanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USAProblems
Active Problems
Noted Date
COVID toes
7/13/22
Chest pain on breathing
5/26/22
Type 1 diabetes
2/28/22
Overview: Formatting of this note might be different from the original. BMI Readings from Last 1 Encounters: 08/30/21 28.69 kg/m²
Plague pneumonia
6/16/21
Absence of menstruation
6/12/18
Foot callus
8/11/17
Overview: Formatting of this note might be different from the original. Ouch.
documented as of this encounter (statuses as of 07/28/2022)Cardiology123 SOUTH MAIN STREETSUITE 621DAVIDSONGOODLETTSVILLETN37072USAVanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USAVanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USAReason for VisitNot on fileResults
Comment: A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample.
This test was performed using a multiplexed nucleic acid amplification test that is labeled Emergence Use Only by the U.S. FDA. Results of this test should not be used as the sole basis for diagnosis, treatment, or other management decisions.
SARS-CoV-2 Nucleic Acid Method (Comment)
Other
This test was performed using the Roche 6800 COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.
Comment: A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample.
This test was performed using a multiplexed nucleic acid amplification test that is labeled Emergence Use Only by the U.S. FDA. Results of this test should not be used as the sole basis for diagnosis, treatment, or other management decisions.
SARS-CoV-2 Nucleic Acid Method (Comment)
Oropharynx
This test was performed using the Roche 6800 COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.
VUMC CERNER LAB
Specimen (Source)
Anatomical Location / Laterality
Collection Method / Volume
Collection Time
Received Time
Oropharynx
07/27/2022 3:49 PM CDT
07/27/2022 3:58 PM CDT
Resulting Agency Comment
Ordered by Romney H Humphries
Authorizing Provider
Result Type
No Pcp
LAB BODY FLUIDS AND STOOLS ORDERABLES
Performing Organization
Address
City/State/ZIP Code
Phone Number
VUMC CERNER LAB
4605 TVC VUMC1301 Medical Center Drive
NASHVILLE, TN 37232-5310
615-875-5227
SARS-CoV-2 PCR (07/27/2022 3:49 PM CDT)
Component
Value
Ref Range
Test Method
Analysis Time
Performed At
Pathologist Signature
SARS-CoV-2 Nucleic Acid (Result)
Not Detected
Not Detected
VUMC CERNER LAB
Comment: A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample.
This test was performed using a multiplexed nucleic acid amplification test that is labeled Emergence Use Only by the U.S. FDA. Results of this test should not be used as the sole basis for diagnosis, treatment, or other management decisions.
SARS-CoV-2 Nucleic Acid Method (Comment)
Nasopharynx
This test was performed using the Roche 6800 COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.
VUMC CERNER LAB
Specimen (Source)
Anatomical Location / Laterality
Collection Method / Volume
Collection Time
Received Time
Nasopharynx
07/27/2022 3:49 PM CDT
07/27/2022 3:58 PM CDT
Resulting Agency Comment
Ordered by Romney H Humphries
Authorizing Provider
Result Type
No Pcp
LAB BODY FLUIDS AND STOOLS ORDERABLES
Performing Organization
Address
City/State/ZIP Code
Phone Number
VUMC CERNER LAB
4605 TVC VUMC1301 Medical Center Drive
NASHVILLE, TN 37232-5310
615-875-5227
SARS-CoV-2 PCR (07/27/2022 3:49 PM CDT)
Component
Value
Ref Range
Test Method
Analysis Time
Performed At
Pathologist Signature
SARS-CoV-2 Nucleic Acid (Result)
Not Detected
Not Detected
VUMC CERNER LAB
Comment: A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample.
This test was performed using a multiplexed nucleic acid amplification test that is labeled Emergence Use Only by the U.S. FDA. Results of this test should not be used as the sole basis for diagnosis, treatment, or other management decisions.
SARS-CoV-2 Nucleic Acid Method (Comment)
Nares
This test was performed using the Roche 6800 COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.
VUMC CERNER LAB
Specimen (Source)
Anatomical Location / Laterality
Collection Method / Volume
Collection Time
Received Time
Nares
07/27/2022 3:49 PM CDT
07/27/2022 3:58 PM CDT
Resulting Agency Comment
Ordered by Romney H Humphries
Authorizing Provider
Result Type
No Pcp
LAB BODY FLUIDS AND STOOLS ORDERABLES
Performing Organization
Address
City/State/ZIP Code
Phone Number
VUMC CERNER LAB
4605 TVC VUMC1301 Medical Center Drive
NASHVILLE, TN 37232-5310
615-875-5227
SARS-CoV-2 PCR (07/27/2022 3:49 PM CDT)
Component
Value
Ref Range
Test Method
Analysis Time
Performed At
Pathologist Signature
SARS-CoV-2 Nucleic Acid (Result)
Not Detected
Not Detected
VUMC CERNER LAB
Comment: A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample.
This test was performed using a multiplexed nucleic acid amplification test that is labeled Emergence Use Only by the U.S. FDA. Results of this test should not be used as the sole basis for diagnosis, treatment, or other management decisions.
SARS-CoV-2 Nucleic Acid Method (Comment)
BAL
This test was performed using the Roche 6800 COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.
VUMC CERNER LAB
Specimen (Source)
Anatomical Location / Laterality
Collection Method / Volume
Collection Time
Received Time
BAL
07/27/2022 3:49 PM CDT
07/27/2022 3:58 PM CDT
Resulting Agency Comment
Ordered by Romney H Humphries
Authorizing Provider
Result Type
No Pcp
LAB BODY FLUIDS AND STOOLS ORDERABLES
Performing Organization
Address
City/State/ZIP Code
Phone Number
VUMC CERNER LAB
4605 TVC VUMC1301 Medical Center Drive
NASHVILLE, TN 37232-5310
615-875-5227
(ABNORMAL) Hepatitis C IgG w/Rfx PCR (05/12/2022 6:00 AM CDT)
Component
Value
Ref Range
Test Method
Analysis Time
Performed At
Pathologist Signature
Hepatitis C Antibody
Positive (A)
Negative
VUMC CERNER LAB
Comment: Positive: Presumptive history of HCV infection; nucleic acid testing recommended to document viral replication.
Equivocal: Antibodies to HCV may or may not be present; repeat serologic testing in approximately 8 weeks or nucleic acid testing is recommended to assess possible infection.
Negative: Antibodies to HCV not detected; does not exclude possibility of infection with HCV.
Specimen (Source)
Anatomical Location / Laterality
Collection Method / Volume
Collection Time
Received Time
Blood
05/12/2022 6:00 AM CDT
05/12/2022 11:30 AM CDT
Authorizing Provider
Result Type
Charles W Stratton MD
LAB BLOOD ORDERABLES
Performing Organization
Address
City/State/ZIP Code
Phone Number
VUMC CERNER LAB
4605 TVC VUMC1301 Medical Center Drive
NASHVILLE, TN 37232-5310
615-875-5227
Cytogenomic SNP microarray (04/04/2022 11:55 AM CDT)
Specimen (Source)
Anatomical Location / Laterality
Collection Method / Volume
Collection Time
Received Time
Blood
04/04/2022 11:55 AM CDT
04/18/2022 2:46 PM CDT
Narrative
VUMC CERNER LAB - 04/18/2022 2:57 PM CDTMICROARRAY REPORT- Corrected Request#: CG-22-0000006 Service date: 4/4/2022 11:55 Microarray Result: Normal female Microarray Interpretation: SNP chromosomal microarray analysis (CMA) of a blood sample from this patient demonstrated no copy number changes of known clinical significance. No large regions of homozygosity (ROH) were detected. The ISCN nomenclature describing this result is: arr(X,1-22)x2. Electronically signed out by: Benfield, Luis A on 04/18/2022 ___________________________________________________________________ Clinical indication: Specimen List: Blood Date in Lab: 4/18/2022 14:46 Date Collected: 4/4/2022 11:55 ___________________________________________________________________ Disclaimer: Copy number gains less than 400 kb in size and copy number losses less than 200 kb in size will not be reported unless they represent a known or suspected clinically relevant imbalance. The reporting of copy number variants less than 100 kb in size is at the discretion of the laboratory and some clinically relevant copy number changes under 50 kb may not be reported due to limitations in probe coverage in certain genomic regions. Copy number changes of any size with no apparent clinical significance (likely benign or benign) have not been discussed in this report but may be available upon request. Regions of homozygosity (ROH) less than 10 Mb in size will not be reported unless the ROH is clinically relevant for potential uniparental disomy. Genome-wide ROH under 2% will not be reported. Copy number variants less than 200 kb associated with a carrier status for autosomal recessive conditions will not be reported unless specifically indicated in the reason for referral. This microarray was designed and manufactured by Affymetrix for the sole purpose of identifying DNA copy number gains and losses associated with chromosomal imbalances and regions of homozygosity (ROH) associated with uniparental isodisomy (isoUPD).This microarray will detect aneuploidy, deletions and duplications of loci represented on the microarray.  It will not detect balanced alterations including: reciprocal translocations, inversions and balanced insertions. It will not detect point mutations and imbalances less than 10 kb.  Failure to detect an alteration at any locus does not exclude the diagnosis of any of the disorders represented on the microarray. This assay is not designed to detect mosaic gains and losses and its performance in detecting mosaicism has not been established. This test was developed and its performance characteristics determined by Affymetrix as required by CLIA Â’88 regulations. This test is used for clinical purposes and the accuracy and precision has been established and verified by this laboratory. This test has not been cleared or approved by the U.S. Food and Drug Administration. Interpretation of copy number variants is performed using VUMC-laboratory maintained databases as well as the following resources: Database of Genomic Variants (http://dgv.tcag.ca/dgv/app/home) Online Mendelian Inheritance in Man (http://www.omim.org/) UCSC Genome Bioinformatics (http://genome.ucsc.edu/cgi-bin/hgGateway) ClinGen Clinical Genome Resource (http://www.ncbi.nlm.nih.gov/projects/dbvar/clingen) DECIPHER Database (https://decipher.sanger.ac.uk/browser) PubMed-NCBI (http://www.ncbi.nlm.nih.gov/pubmed) Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen). PMID: 31690835 Method: Microarray platform: ThermoFisher Scientific CytoScanTM HD Cytogenetics Solution Version: 1.1 (Based on UCSC hg19 assembly) Number of loci analyzed: 2,696,550 Mean probe spacing: <700 bp Testing performed at Vanderbilt Cytogenetics One Hundred Oaks Laboratory, Suite 21100, 719 Thompson Ln, Nashville, TN 37204  phone 615-875-0228, fax 615-875-0234
Resulting Agency Comment
testing comment
Authorizing Provider
Result Type
Carda Testprovqa MD
LAB GENETIC TESTING
Performing Organization
Address
City/State/ZIP Code
Phone Number
VUMC CERNER LAB
4605 TVC VUMC1301 Medical Center Drive
NASHVILLE, TN 37232-5310
615-875-5227
Pharmacogenomics (03/31/2022 5:36 PM CDT)
Specimen (Source)
Anatomical Location / Laterality
Collection Method / Volume
Collection Time
Received Time
DNA
03/31/2022 5:36 PM CDT
03/31/2022 5:44 PM CDT
Narrative
VUMC CERNER LAB - 03/31/2022 5:51 PM CDTPharmacogenomics: Final Report Request #: MD-22-0000041 Service Date: 3/31/2022 17:36 Reason for Request: Genotyping for Determination of Drug Efficacy, Dosage and Safety Type of Specimen: DNA Date Received: 3/31/2022 17:44 Date Reported: 3/31/2022 17:51 Interpretation: Results from this assay may indicate dosage adjustments or medication alternatives that should be considered for this patient. Additional information regarding the implications of these results is available at www.mydruggenome.org. For VUMC patients, clinical decision support regarding the management of this patient with respect to specific drugs based upon the patient's genotype as listed below is available in the patient's electronic medical record under Genomic Indicators. Clinical decision support may also be provided for some drugs through order entry and medication prescribing tools utilized within the VUMC system. Comments: Results: CYP2C19 -  Cancelled CYP2C9 -  Cancelled CYP2D6 -  Cancelled  CYP3A5 -  Cancelled CYP4F2 -  Cancelled DPYD -   Cancelled NUDT15 -  Cancelled SLCO1B1 -  Cancelled    TPMT -   Cancelled VKORC1 -  Cancelled    These results should be correlated with other laboratory and clinical findings and additional testing should be considered if clinically indicated.   Methodology: DNA was extracted from this specimen and screened for 37 variants in 10 genes that are associated with drug absorption, distribution, metabolism, excretion or response. The reported genotypes were determined using PCR amplification and oligonucleotide primers specific for each interrogated region of the genes listed within this panel. Fluorophore labeled probes were used to identify each variant. Variants analyzed in this assay include: CYP2C19 *2, *3, *4, *6, *8, *17; CYP2C9 *2, *3, *6, *8; CYP3A5 *3, *6, *7; CYP4F2 *3; DPYD *2A, *13, c.557A>G, c.1236G>A (HapB3), c.2846A>T;  NUDT15 *2 or *3; SLCO1B1 *5; TPMT *2, *3B, *3C, *4; VKORC1 promoter variant c.-1639G>A; and CYP2D6 copy number and variants *2, *2A, *3, *4, *6, *7, *9, *10, *17, *29 and *41. A *1 allele is considered the reference (normal) sequence and is reported if none of the variants analyzed for a particular gene is detected. This assay is specific for the variants listed above and cannot exclude the presence of other variants within these genes that may affect the pharmacologic function of the protein product encoded by these genes. In most cases, variants for a particular gene exist on separate alleles; however, for individuals in which multiple variants in the same gene are detected, this assay cannot determine if the variants are on the same allele or on different alleles. Further, due to the highly polymorphic nature of these regions, rare variants may exist that could affect the sensitivity or specificity of this assay and lead to a false-negative or a false-positive result. Electronically signed out by: Barba, Elizabeth on 03/31/2022 This assay has not been cleared or approved by the US Food and Drug Administration. The performance of this assay was tested and validated prior to use for patient testing. This test is used for clinical purposes and should not be regarded as investigational or research. This laboratory is regulated by the Clinical Laboratory Improvement Act of 1988.
Authorizing Provider
Result Type
Carda Testprovqa MD
LAB GENETIC TESTING
Performing Organization
Address
City/State/ZIP Code
Phone Number
VUMC CERNER LAB
4605 TVC VUMC1301 Medical Center Drive
NASHVILLE, TN 37232-5310
615-875-5227
Drug Toxicology Monitoring Base Pnl w/Conf, Oral Fl-QSTD (03/29/2022 1:53 PM CDT)
Component
Value
Ref Range
Test Method
Analysis Time
Performed At
Pathologist Signature
Drug Toxicology Monitoring Base Pnl w/Conf, Oral Fl
VUMC patients: Â Results faxed to Vanderbilt Medical Record. VPLS clients: Â See separate report sent to client.
VUMC CERNER LAB
Comment: This test was performed at: Quest Laboratory,Location Varies,,,,,,
Comment: A detected result is positive and indicates the presence of the virus in the sample. A not detected result indicates that the test did not detect the virus in the sample.
This test was performed using a multiplexed nucleic acid amplification test that is labeled Emergence Use Only by the U.S. FDA. Results of this test should not be used as the sole basis for diagnosis, treatment, or other management decisions.
SARS-CoV-2 Nucleic Acid Method (Comment)
Nares
This test was performed using the Hologic Panther COVID-19 test. This test is currently approved for clinical diagnostic testing under Emergency Use Authorization of the FDA; the result should not be considered experimental or for research purposes.
VUMC CERNER LAB
Specimen (Source)
Anatomical Location / Laterality
Collection Method / Volume
Collection Time
Received Time
Nares
03/11/2022 1:05 PM CST
03/11/2022 1:46 PM CST
Authorizing Provider
Result Type
Adam Clark Seegmiller MD
LAB BODY FLUIDS AND STOOLS ORDERABLES
Performing Organization
Address
City/State/ZIP Code
Phone Number
VUMC CERNER LAB
4605 TVC VUMC1301 Medical Center Drive
NASHVILLE, TN 37232-5310
615-875-5227
FISH ALL Pnl (03/11/2022 1:05 PM CST)
Specimen (Source)
Anatomical Location / Laterality
Collection Method / Volume
Collection Time
Received Time
Blood
03/11/2022 1:05 PM CST
03/11/2022 1:09 PM CST
Narrative
VUMC CERNER LAB - 03/11/2022 1:27 PM CSTFISH REPORT Request#:CG-22-0000003 Service date:3/11/2022 13:05 FISH IMPRESSION: Abnormal for homozygous deletion of CDKN2A locus at 9p21 in __% of cells. FISH KARYOTYPE: nuc ish (DXZ1x1,DYZ3x1,D18Z1x2)[200] Â Â Â COMMENTS: Results of the FISH studies with the 21 DNA probes described above were analyzed in at least 200 cells per probe and no abnormal signal patterns were detected for the target regions of chromosomes 1, 4, 7, 9, 10, 11, 12, 14, 17, 19, 21, and 22. Normal cut off values for probes: 1.0% for t(1;19) PBX1/TCF3 1.0% for t(9;22) BCR/ABL1 1.0% for KMT2A (11q23) 1.0% for t(12;21) ETV6/RUNX1 1.0% for IKZF1/CEP7 3.0% for CEP 4 2.0% for CEP 10 2.0% for CEP 17 1.0% for CDKN2A/CEP9 (9p21) 1.0% for IGH breakapart 1.0% for ABL2 breakapart 1.0% for ABL1 breakapart These probes were developed by Vysis and their performance characteristics determined by VUMC as required by the CLIA '88 regulations. Â These probes have not been cleared or approved by the U.S. Food and Drug administration. Ferrin Courtney Wheeler, PhD, FACMG reviewed and approved Electronically signed out by: Mavrak, Geoffrey A on 03/11/2022 Clinical History: Â ALL Specimen List: Blood Date In Lab: 3/11/2022 13:09 Date Collected: 3/11/2022 13:05 Testing performed at Vanderbilt Cytogenetics One Hundred Oaks Laboratory, Suite 21100, 719 Thompson Ln, Nashville, TN 37204 Â phone 615-875-0228, fax 615-875-0234
Authorizing Provider
Result Type
Adam Clark Seegmiller MD
LAB GENETIC TESTING
Performing Organization
Address
City/State/ZIP Code
Phone Number
VUMC CERNER LAB
4605 TVC VUMC1301 Medical Center Drive
NASHVILLE, TN 37232-5310
615-875-5227
(ABNORMAL) Culture Bact Bld Adult (03/11/2022 8:51 AM CST)
Component
Value
Ref Range
Test Method
Analysis Time
Performed At
Pathologist Signature
Final Report
Staphylococcus aureus Gram positive cocci; restreak for isolation Isolated from Aerobic bottle
(ABNORMAL) Culture Bact Bld Adult (03/10/2022 10:00 AM CST)
Component
Value
Ref Range
Test Method
Analysis Time
Performed At
Pathologist Signature
Final Report
Staphylococcus aureus Gram Positive Cocci Restreak for isolation Isolated from Aerobic bottle
VUMC CERNER LAB
Organism ID
Staphylococcus aureus (POSITIVE)
VUMC CERNER LAB
Specimen (Source)
Anatomical Location / Laterality
Collection Method / Volume
Collection Time
Received Time
Blood (Antecub)
03/10/2022 10:00 AM CST
03/10/2022 2:08 PM CST
Organism
Antibiotic
Method
Susceptibility
Staphylococcus aureus
Ampicillin
MIC
3: Resistant
Staphylococcus aureus
Vancomycin
MIC
0.03: Susceptible
Staphylococcus aureus
Levofloxacin
MIC
2: Intermediate
Authorizing Provider
Result Type
Katelyn Kennedy Atwater MD
LAB MICROBIOLOGY - GENERAL ORDERABLES
Performing Organization
Address
City/State/ZIP Code
Phone Number
VUMC CERNER LAB
4605 TVC VUMC1301 Medical Center Drive
NASHVILLE, TN 37232-5310
615-875-5227
documented in this encounterCulture Bact Bld AdultVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveDAVIDSONNASHVILLETN37232-5310USAVanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USAVanderbilt University Medical Center TSTInternal Medicine719 THOMPSON LANESUITE 38500DAVIDSONNASHVILLETN37204USAKatelynKennedyAtwater MDAntecubFinal ReportVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskyOrganism IDStaphylococcus aureusPOSITIVEVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskyLab InterpretationAbnormalStaphylococcus aureusAmpicillin3: ResistantMICVancomycin0.03: SusceptibleMICLevofloxacin2: IntermediateMICCulture Bact UrineVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveDAVIDSONNASHVILLETN37232-5310USAVanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USAVanderbilt University Medical Center TSTPathology, Hematology1301 MEDICAL CENTER DRIVE4605 THE VANDERBILT CLINICDAVIDSONNASHVILLETN37232USAAdamClarkSeegmiller MDFinal Report>100,000 cfu/ml Proteus mirabilisVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskyOrganism IDProteus mirabilisPOSITIVEVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskyLab InterpretationAbnormalProteus mirabilisAztreonam0.75: ResistantMICCefoxitin0.25: IntermediateMICLevofloxacin0.05: SusceptibleMICCulture Bact Bld AdultVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveDAVIDSONNASHVILLETN37232-5310USAVanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USAVanderbilt University Medical Center TSTPathology, Hematology1301 MEDICAL CENTER DRIVE4605 THE VANDERBILT CLINICDAVIDSONNASHVILLETN37232USAAdamClarkSeegmiller MDAntecubFinal ReportVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskyOrganism IDStaphylococcus aureusPOSITIVEVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskyLab InterpretationAbnormalStaphylococcus aureusAmpicillin0.25: SusceptibleMICRifampin0.75: ResistantMICVancomycin0.05: SusceptibleMICFISH ALL PnlVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveDAVIDSONNASHVILLETN37232-5310USAVanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USAVanderbilt University Medical Center TSTPathology, Hematology1301 MEDICAL CENTER DRIVE4605 THE VANDERBILT CLINICDAVIDSONNASHVILLETN37232USAAdamClarkSeegmiller MDVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskyNarrativeVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310SARS-CoV-2 PCRVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveDAVIDSONNASHVILLETN37232-5310USAVanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USAVanderbilt University Medical Center TSTPathology, Hematology1301 MEDICAL CENTER DRIVE4605 THE VANDERBILT CLINICDAVIDSONNASHVILLETN37232USAAdamClarkSeegmiller MDSARS-CoV-2 Nucleic Acid (Result)Not DetectedVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskyNot DetectedNot DetectedSARS-CoV-2 Nucleic Acid Method (Comment)VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskyCulture Bact CSFVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveDAVIDSONNASHVILLETN37232-5310USAVanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USAVanderbilt University Medical Center TSTPathology, Hematology1301 MEDICAL CENTER DRIVE4605 THE VANDERBILT CLINICDAVIDSONNASHVILLETN37232USAAdamClarkSeegmiller MDFinal ReportLight growth Acinetobacter baumanniiVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskyOrganism IDAcinetobacter baumanniiPOSITIVEVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskyGram Stain Report1+ Gram negative rodVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskyLab InterpretationAbnormalAcinetobacter baumanniiAmikacin0.25: SusceptibleMICAvycaz (Ceftazidime/Avibactam)0.05: IntermediateMICLevofloxacin0.75: ResistantMICCulture Bact CSFVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveDAVIDSONNASHVILLETN37232-5310USAVanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USAVanderbilt University Medical Center TSTPathology, Hematology1301 MEDICAL CENTER DRIVE4605 THE VANDERBILT CLINICDAVIDSONNASHVILLETN37232USAAdamClarkSeegmiller MDFinal ReportModerate growth Neisseria meningitidisVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskyOrganism IDNeisseria meningitidisPOSITIVEVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskyGram Stain ReportVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskyLab InterpretationAbnormalResults CalledVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveDAVIDSONNASHVILLETN37232-5310USAVanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USAVanderbilt University Medical Center TST415 South Pollard StreetVintonVA24179USAEMarkWatts MDTest CalledkVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskyReason CalledQNSVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskyCalled TotestVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskyRead BackYesVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskyCollector IDtest123VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskyDrug Toxicology Monitoring Base Pnl w/Conf, Oral Fl-QSTDVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveDAVIDSONNASHVILLETN37232-5310USAVanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USAVanderbilt University Medical Center TSTCardiology123 SOUTH MAIN STREETSUITE 621DAVIDSONGOODLETTSVILLETN37072USACardaTestprovqa MDDrug Toxicology Monitoring Base Pnl w/Conf, Oral FlVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskyPharmacogenomicsVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveDAVIDSONNASHVILLETN37232-5310USAVanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USAVanderbilt University Medical Center TSTCardiology123 SOUTH MAIN STREETSUITE 621DAVIDSONGOODLETTSVILLETN37072USACardaTestprovqa MDVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskyNarrativeVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Cytogenomic SNP microarrayVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveDAVIDSONNASHVILLETN37232-5310USAVanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USAVanderbilt University Medical Center TSTCardiology123 SOUTH MAIN STREETSUITE 621DAVIDSONGOODLETTSVILLETN37072USACardaTestprovqa MDVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskyNarrativeVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Hepatitis C IgG w/Rfx PCRVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveDAVIDSONNASHVILLETN37232-5310USAVanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USAVanderbilt University Medical Center TSTPathology1161 21st Avenue SouthC3321 A, Medical Center NorthDAVIDSONNashvilleTN37232-2561USACharlesWStratton MDHepatitis C AntibodyPositiveAbnormalVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskyNegativeNegativeLab InterpretationAbnormalSARS-CoV-2 PCRVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveDAVIDSONNASHVILLETN37232-5310USAVanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USAVanderbilt University Medical Center TSTUSANoPcpSARS-CoV-2 Nucleic Acid (Result)Not DetectedVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskyNot DetectedNot DetectedSARS-CoV-2 Nucleic Acid Method (Comment)VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskySARS-CoV-2 PCRVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveDAVIDSONNASHVILLETN37232-5310USAVanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USAVanderbilt University Medical Center TSTUSANoPcpSARS-CoV-2 Nucleic Acid (Result)Not DetectedVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskyNot DetectedNot DetectedSARS-CoV-2 Nucleic Acid Method (Comment)VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskySARS-CoV-2 PCRVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveDAVIDSONNASHVILLETN37232-5310USAVanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USAVanderbilt University Medical Center TSTUSANoPcpSARS-CoV-2 Nucleic Acid (Result)Not DetectedVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskyNot DetectedNot DetectedSARS-CoV-2 Nucleic Acid Method (Comment)VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskySARS-CoV-2 PCRVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveDAVIDSONNASHVILLETN37232-5310USAVanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USAVanderbilt University Medical Center TSTUSANoPcpSARS-CoV-2 Nucleic Acid (Result)DetectedAbnormalVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskyNot DetectedNot DetectedSARS-CoV-2 Nucleic Acid Method (Comment)VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskyLab InterpretationAbnormalSARS-CoV-2 PCRVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveDAVIDSONNASHVILLETN37232-5310USAVanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USAVanderbilt University Medical Center TSTUSANoPcpSARS-CoV-2 Nucleic Acid (Result)DetectedAbnormalVUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskyNot DetectedNot DetectedSARS-CoV-2 Nucleic Acid Method (Comment)VUMC CERNER LAB4605 TVC VUMC1301 Medical Center DriveNASHVILLETN37232-5310Adam Seegmiller; Jennifer B. GordetskyLab InterpretationAbnormalSocial History
Tobacco Use
Types
Packs/Day
Years Used
Date
Smoking Tobacco: Never Assessed
Sex Assigned at Birth
Date Recorded
Not on file
documented as of this encounterVanderbilt University Medical Center3401 West End AveDAVIDSONNASHVILLETN37203USAEncounter Details
Date
Type
Department
Care Team
Description
2/18/22
Transcribe Orders
Vanderbilt University Adult Hospital1211 Medical Center DrNashville, TN 37232615-322-5000
Tech, Lab, MLT
LabTechMLTLab1211 Medical Center DrDAVIDSONNashvilleTN37232Vanderbilt University Adult HospitalLab
\ No newline at end of file
diff --git a/containers/ecr-viewer/seed-scripts/create-e2e-sql.py b/containers/ecr-viewer/seed-scripts/create-e2e-sql.py
index 65ed63222d..42ceea385b 100644
--- a/containers/ecr-viewer/seed-scripts/create-e2e-sql.py
+++ b/containers/ecr-viewer/seed-scripts/create-e2e-sql.py
@@ -37,11 +37,22 @@ def save_sql_insert_metadata(metadata):
rule_summary = parsed_values["rule_summary"]
report_date = parsed_values["report_date"]
data_source = "DB"
- query = f"""INSERT INTO fhir_metadata (
- ecr_id,patient_name_last,patient_name_first,patient_birth_date,data_source,reportable_condition,rule_summary,report_date
- ) VALUES (
- '{ecr_id}','{last_name}','{first_name}','{birth_date}','{data_source}','{reportable_condition}','{rule_summary}',{'NULL' if report_date is None else f"'{report_date}'"}
- ) ON CONFLICT (ecr_id) DO NOTHING;\n"""
+ query = f"""WITH inserted_data AS (
+ INSERT INTO ecr_data (
+ eICR_ID, patient_name_last, patient_name_first, patient_birth_date, data_source, report_date
+ ) VALUES (
+ '{ecr_id}', '{last_name}', '{first_name}', '{birth_date}', '{data_source}', {'NULL' if report_date is None else f"'{report_date}'"}
+ )
+ ON CONFLICT (eICR_ID) DO NOTHING
+ RETURNING eICR_ID
+), inserted_condition AS (
+ INSERT INTO ecr_rr_conditions (uuid, eICR_ID, condition)
+ VALUES (uuid_generate_v4(), (SELECT eICR_ID FROM inserted_data), '{reportable_condition}')
+ RETURNING uuid
+)
+INSERT INTO ecr_rr_rule_summaries (uuid, ecr_rr_conditions_id, rule_summary)
+VALUES (uuid_generate_v4(), (SELECT uuid FROM inserted_condition), '{rule_summary}')
+RETURNING (SELECT eICR_ID FROM inserted_data);"""
output_file.write(query)
diff --git a/containers/ecr-viewer/seed-scripts/docker-compose.yml b/containers/ecr-viewer/seed-scripts/docker-compose.yml
index b9f45ef8e4..62fe8236c5 100644
--- a/containers/ecr-viewer/seed-scripts/docker-compose.yml
+++ b/containers/ecr-viewer/seed-scripts/docker-compose.yml
@@ -126,8 +126,8 @@ services:
ports:
- "5432:5432"
volumes:
- - ../sql/:/docker-entrypoint-initdb.d/
- - ./sql/:/docker-entrypoint-initdb.d/
+ - ./sql/01-init.sql:/docker-entrypoint-initdb.d/01-init.sql
+ - ../sql/core.sql:/docker-entrypoint-initdb.d/core.sql
- ./sql/.pgpass/:/usr/local/lib/.pgpass
- db:/var/lib/postgresql/data
environment:
diff --git a/containers/ecr-viewer/seed-scripts/sql/01-init.sql b/containers/ecr-viewer/seed-scripts/sql/01-init.sql
index 6707fe7602..8808d17938 100644
--- a/containers/ecr-viewer/seed-scripts/sql/01-init.sql
+++ b/containers/ecr-viewer/seed-scripts/sql/01-init.sql
@@ -5,18 +5,4 @@ CREATE TABLE IF NOT EXISTS fhir (
data JSONB NOT NULL,
date_created TIMESTAMPTZ NOT NULL DEFAULT NOW(),
PRIMARY KEY (ecr_id)
-);
-
-CREATE TABLE IF NOT EXISTS fhir_metadata(
- ecr_id VARCHAR(200) NOT NULL,
- data_source VARCHAR(2) NOT NULL, -- S3 or DB
- data_link VARCHAR(500), -- Link to the data
- patient_name_first VARCHAR(100) NOT NULL,
- patient_name_last VARCHAR(100) NOT NULL,
- patient_birth_date DATE NOT NULL,
- reportable_condition VARCHAR(10000),
- rule_summary VARCHAR(10000),
- report_date DATE,
- date_created TIMESTAMPTZ NOT NULL DEFAULT NOW(),
- PRIMARY KEY (ecr_id)
-)
\ No newline at end of file
+);
\ No newline at end of file
diff --git a/containers/ecr-viewer/sql/core.sql b/containers/ecr-viewer/sql/core.sql
index 1cdd09296c..fce52e1962 100644
--- a/containers/ecr-viewer/sql/core.sql
+++ b/containers/ecr-viewer/sql/core.sql
@@ -1,10 +1,13 @@
+CREATE EXTENSION IF NOT EXISTS "uuid-ossp";
+
CREATE TABLE ecr_data (
eICR_ID VARCHAR(200) PRIMARY KEY,
data_source VARCHAR(2), -- S3 or DB
- data_link VARCHAR(500), -- Link to the data
+ fhir_reference_link VARCHAR(500), -- Link to the ecr fhir bundle
patient_name_first VARCHAR(100),
patient_name_last VARCHAR(100),
patient_birth_date DATE,
+ date_created TIMESTAMPTZ NOT NULL DEFAULT NOW(),
report_date DATE
);
diff --git a/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts b/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts
index f510036276..a18516f797 100644
--- a/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts
+++ b/containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts
@@ -430,7 +430,7 @@ export const saveMetadataToSqlServer = async (
* @param metadata - The FHIR bundle metadata to be saved.
* @param ecrId - The unique identifier for the Electronic Case Reporting (ECR) associated with the FHIR bundle.
* @returns A promise that resolves when the FHIR bundle metadata is successfully saved to postgres.
- * @throws {Error} Throws an error if the FHIR bundle metadata cannot be saved to postgress.
+ * @throws {Error} Throws an error if the FHIR bundle metadata cannot be saved to postgres.
*/
export const saveMetadataToPostgres = async (
metadata: BundleMetadata,
@@ -442,7 +442,6 @@ export const saveMetadataToPostgres = async (
const { ParameterizedQuery: PQ } = pgPromise;
- let addMetadata = undefined;
if (process.env.METADATA_DATABASE_SCHEMA == "extended") {
return NextResponse.json(
{
@@ -451,27 +450,37 @@ export const saveMetadataToPostgres = async (
},
{ status: 501 },
);
- } else {
- addMetadata = new PQ({
- text: "INSERT INTO fhir_metadata (ecr_id,patient_name_last,patient_name_first,patient_birth_date,data_source,reportable_condition,rule_summary,report_date) VALUES ($1, $2, $3, $4, $5, $6, $7, $8) RETURNING ecr_id",
- values: [
- ecrId,
- metadata.first_name,
- metadata.last_name,
- metadata.birth_date,
- "DB",
- metadata.reportable_condition,
- metadata.rule_summary,
- metadata.report_date,
- ],
- });
}
+ const saveToEcrData = new PQ({
+ text: "INSERT INTO ecr_data (eICR_ID,patient_name_last,patient_name_first,patient_birth_date,data_source,report_date) VALUES ($1, $2, $3, $4, $5, $6) RETURNING eICR_ID",
+ values: [
+ ecrId,
+ metadata.last_name,
+ metadata.first_name,
+ metadata.birth_date,
+ "DB",
+ metadata.report_date,
+ ],
+ });
+
+ const saveRRConditions = new PQ({
+ text: "INSERT INTO ecr_rr_conditions (uuid, eICR_ID, condition) VALUES (uuid_generate_v4(), $1, $2) RETURNING uuid",
+ values: [ecrId, metadata.reportable_condition],
+ });
try {
- const saveECR = await database.one(addMetadata);
+ const saveECR = await database.one(saveToEcrData);
+ const savedRRCondition = await database.one(saveRRConditions);
+
+ const saveRRSummary = new PQ({
+ text: "INSERT INTO ecr_rr_rule_summaries (uuid, ecr_rr_conditions_id,rule_summary) VALUES (uuid_generate_v4(), $1, $2)",
+ values: [savedRRCondition.uuid, metadata.rule_summary],
+ });
+
+ await database.none(saveRRSummary);
return NextResponse.json(
- { message: "Success. Saved metadata to database: " + saveECR.ecr_id },
+ { message: "Success. Saved metadata to database: " + saveECR.eICR_ID },
{ status: 200 },
);
} catch (error: any) {
diff --git a/containers/ecr-viewer/src/app/api/services/listEcrDataService.ts b/containers/ecr-viewer/src/app/api/services/listEcrDataService.ts
index 0e3036db29..283ef40caf 100644
--- a/containers/ecr-viewer/src/app/api/services/listEcrDataService.ts
+++ b/containers/ecr-viewer/src/app/api/services/listEcrDataService.ts
@@ -6,13 +6,13 @@ import {
} from "@/app/services/formatService";
export type EcrMetadataModel = {
- ecr_id: string;
+ eicr_id: string;
data_source: "DB" | "S3";
data_link: string;
patient_name_first: string;
patient_name_last: string;
patient_birth_date: Date;
- reportable_condition: string;
+ condition: string;
rule_summary: string;
report_date: Date;
date_created: Date;
@@ -38,13 +38,14 @@ export async function listEcrData(
startIndex: number,
itemsPerPage: number,
): Promise {
- const fhirMetadataQuery =
- "SELECT ecr_id, patient_name_first, patient_name_last, patient_birth_date, report_date, reportable_condition, rule_summary, date_created FROM fhir_metadata order by date_created DESC OFFSET " +
+ const ecrDataQuery =
+ "SELECT ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date, erc.condition, ers.rule_summary, ed.report_date FROM ecr_data ed LEFT JOIN ecr_rr_conditions erc ON ed.eICR_ID = erc.eICR_ID LEFT JOIN ecr_rr_rule_summaries ers ON erc.uuid = ers.ecr_rr_conditions_id order by ed.report_date DESC OFFSET " +
startIndex +
" ROWS FETCH NEXT " +
itemsPerPage +
" ROWS ONLY";
- let list = await database.manyOrNone(fhirMetadataQuery);
+ const list = await database.manyOrNone(ecrDataQuery);
+
return processMetadata(list);
}
@@ -58,13 +59,13 @@ export const processMetadata = (
): EcrDisplay[] => {
return responseBody.map((object) => {
return {
- ecrId: object.ecr_id || "",
+ ecrId: object.eicr_id || "",
patient_first_name: object.patient_name_first || "",
patient_last_name: object.patient_name_last || "",
patient_date_of_birth: object.patient_birth_date
? formatDate(new Date(object.patient_birth_date!).toISOString())
: "",
- reportable_condition: object.reportable_condition || "",
+ reportable_condition: object.condition || "",
rule_summary: object.rule_summary || "",
date_created: object.date_created
? convertUTCToLocalString(
@@ -81,10 +82,10 @@ export const processMetadata = (
};
/**
- * Retrieves the total number of eCRs stored in the fhir table.
+ * Retrieves the total number of eCRs stored in the ecr_data table.
* @returns A promise resolving to the total number of eCRs.
*/
export const getTotalEcrCount = async (): Promise => {
- let number = await database.one("SELECT count(*) FROM fhir_metadata");
+ let number = await database.one("SELECT count(*) FROM ecr_data");
return number.count;
};
diff --git a/containers/ecr-viewer/src/app/api/tests/listEcrDataService.test.tsx b/containers/ecr-viewer/src/app/api/tests/listEcrDataService.test.tsx
index f771caaa00..e292098ffb 100644
--- a/containers/ecr-viewer/src/app/api/tests/listEcrDataService.test.tsx
+++ b/containers/ecr-viewer/src/app/api/tests/listEcrDataService.test.tsx
@@ -19,26 +19,26 @@ describe("listEcrDataService", () => {
it("should map each object in responseBody to the correct output structure", () => {
const responseBody: EcrMetadataModel[] = [
{
- ecr_id: "ecr1",
+ eicr_id: "ecr1",
date_created: new Date(),
patient_name_first: "Test",
patient_name_last: "Person",
patient_birth_date: new Date(),
report_date: new Date(),
- reportable_condition: "Long",
+ condition: "Long",
rule_summary: "Longer",
data_source: "DB",
data: "",
data_link: "",
},
{
- ecr_id: "ecr2",
+ eicr_id: "ecr2",
date_created: new Date(),
patient_name_first: "Another",
patient_name_last: "Test",
patient_birth_date: new Date(),
report_date: new Date(),
- reportable_condition: "Stuff",
+ condition: "Stuff",
rule_summary: "Other stuff",
data_source: "DB",
data: "",
@@ -103,7 +103,7 @@ describe("listEcrDataService", () => {
database.manyOrNone = jest.fn(() => Promise.resolve([]));
const actual = await listEcrData(startIndex, itemsPerPage);
expect(database.manyOrNone).toHaveBeenCalledExactlyOnceWith(
- "SELECT ecr_id, patient_name_first, patient_name_last, patient_birth_date, report_date, reportable_condition, rule_summary, date_created FROM fhir_metadata order by date_created DESC OFFSET 0 ROWS FETCH NEXT 25 ROWS ONLY",
+ "SELECT ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date, erc.condition, ers.rule_summary, ed.report_date FROM ecr_data ed LEFT JOIN ecr_rr_conditions erc ON ed.eICR_ID = erc.eICR_ID LEFT JOIN ecr_rr_rule_summaries ers ON erc.uuid = ers.ecr_rr_conditions_id order by ed.report_date DESC OFFSET 0 ROWS FETCH NEXT 25 ROWS ONLY",
);
expect(actual).toBeEmpty();
});
@@ -112,13 +112,13 @@ describe("listEcrDataService", () => {
database.manyOrNone<{ EcrMetadataModel }> = jest.fn(() =>
Promise.resolve([
{
- ecr_id: "1234",
+ eicr_id: "1234",
date_created: new Date("2024-06-21T12:00:00Z"),
patient_birth_date: new Date("11/07/1954"),
patient_name_first: "Billy",
patient_name_last: "Bob",
report_date: new Date("06/21/2024 8:00 AM EDT"),
- reportable_condition: "stuff",
+ condition: "stuff",
rule_summary: "yup",
data: "",
data_link: "",
@@ -132,7 +132,7 @@ describe("listEcrDataService", () => {
const actual: EcrDisplay[] = await listEcrData(startIndex, itemsPerPage);
expect(database.manyOrNone).toHaveBeenCalledExactlyOnceWith(
- "SELECT ecr_id, patient_name_first, patient_name_last, patient_birth_date, report_date, reportable_condition, rule_summary, date_created FROM fhir_metadata order by date_created DESC OFFSET 0 ROWS FETCH NEXT 25 ROWS ONLY",
+ "SELECT ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date, erc.condition, ers.rule_summary, ed.report_date FROM ecr_data ed LEFT JOIN ecr_rr_conditions erc ON ed.eICR_ID = erc.eICR_ID LEFT JOIN ecr_rr_rule_summaries ers ON erc.uuid = ers.ecr_rr_conditions_id order by ed.report_date DESC OFFSET 0 ROWS FETCH NEXT 25 ROWS ONLY",
);
expect(actual).toEqual([
{
@@ -152,13 +152,13 @@ describe("listEcrDataService", () => {
database.manyOrNone<{ EcrMetadataModel }> = jest.fn(() =>
Promise.resolve([
{
- ecr_id: "1234",
+ eicr_id: "1234",
date_created: new Date("2024-06-21T12:00:00Z"),
patient_name_first: "boy",
patient_name_last: "lnam",
patient_birth_date: new Date("1990-01-01T05:00:00.000Z"),
report_date: new Date("2024-06-20T04:00:00.000Z"),
- reportable_condition: "sick",
+ condition: "sick",
rule_summary: "stuff",
data: "",
data_link: "",
@@ -171,7 +171,7 @@ describe("listEcrDataService", () => {
let itemsPerPage = 25;
const actual: EcrDisplay[] = await listEcrData(startIndex, itemsPerPage);
expect(database.manyOrNone).toHaveBeenCalledExactlyOnceWith(
- "SELECT ecr_id, patient_name_first, patient_name_last, patient_birth_date, report_date, reportable_condition, rule_summary, date_created FROM fhir_metadata order by date_created DESC OFFSET 0 ROWS FETCH NEXT 25 ROWS ONLY",
+ "SELECT ed.eICR_ID, ed.patient_name_first, ed.patient_name_last, ed.patient_birth_date, ed.date_created, ed.report_date, erc.condition, ers.rule_summary, ed.report_date FROM ecr_data ed LEFT JOIN ecr_rr_conditions erc ON ed.eICR_ID = erc.eICR_ID LEFT JOIN ecr_rr_rule_summaries ers ON erc.uuid = ers.ecr_rr_conditions_id order by ed.report_date DESC OFFSET 0 ROWS FETCH NEXT 25 ROWS ONLY",
);
expect(actual).toEqual([
{