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FDP Data Capture Entry

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Matt W. Wright edited this page Jan 31, 2020 · 36 revisions

Part 1: Entering Variant and Data Source Information

Example

Variant ID

ClinGen Canonical Allele ID (CaID) / ClinVar Variation ID (ClinVar ID)

  • Required: either or (CaID preferable)
  • ClinGen CaID's can be found here
  • ClinVar Variation IDs are available only for variants that have been submitted to ClinVar and can be found here

Note: CaIDs may not be available for certain types of variants such as CNVs; in these cases, the ClinVar ID can be used

Canonical Allele HGVS Notation

  • Required: RefSeq (ex. NM_#)
  • Required: "c." or "g." ("p." is optional)
  • HGVS notation help

Comments: The Ca/ClinVar IDs are used as the primary variant identifiers within the FDRepo database; at least one is required for the data to be uploaded to the VCI. These identifiers may also be useful for downstream data querying purposes. Gene and HGVS notation details are not needed by the VCI but will be stored in the FDRepo database and are helpful for curators to recognize and track their data entries within the spreadsheet.

Data Source

Contribution Source

  • Indicates where the data is coming from
  • Required: "PMID" or "DOI" (PMID preferred if available)

Note: The PMID/DOI requirement helps to ensure that functional data going into the VCI has been peer-reviewed or (at the least) is publically available online, allowing users of the VCI to access the data source if needed.

Contribution Affiliation

  • Indicates who is entering this data into the spreadsheet/VCI
  • Required: Affiliation code and label

Note: For users affiliated with a ClinGen Variant Curation Expert Panel (VCEP) or Working Group, affiliation code and labels can be found here.

Associated Condition

  • Indicates disease/phenotype context under which the variant is being evaluated (this is ultimately determined by the curator entering the data, who makes this judgment using the information in the data source (PMID/DOI))
  • Required: use of ontology code and label
  • Please use a MONDO ID term

Note: The associated condition entered is not required for the VCI; however, it is stored in the FDRepo database for potential downstream querying purposes.

Part 2: Entering Experimental Methods, Materials, and Effects

Example

For each experiment performed, ontology terms must be used in describing the method, material(s) and effect(s); this facilitates a much more controlled and consistent (i.e. reusable) vocabulary when describing these key functional assay elements. These ontologies are also used for data querying purposes.

Ontology terms can be found by using the Ontology Lookup Service. We provide some examples of useful ontologies below; however, curators may use whatever they determine is most appropriate (is accurate and can be reusable across studies performed in the respective gene/disease they are curating).

Note: To ensure appropriate ontology terms are being used we suggest they are selected by (or in coordination with) ClinGen VCEPs or experts who have familiarity with the aggregate functional assay literature (for the specific gene(s) they are entering data for).

Method

  • Indicates the type of method used
  • Required: use of ontology term code and label

Material(s)

  • Indicates the materials used and if they were patient-derived
  • Required: use of ontology term code and label
  • Required: Patient sourced "Yes" or "No"; if "Yes", patient genotype (i.e. was the patient heterozygous or homozygous for this variant?)
  • Patient genotype must be entered using the Genotype Ontology (GENO); options include: GENO:0000135 (heterozygous) or GENO:0000136 (homozygous)

Example:

Note: Materials entered should be only those which are importantly relevant to the evaluation of the data in applying PS3/BS3 codes.

Effect(s)

  • Indicates what was being assessed or measured in the experiment
  • Required: use of ontology term code and label

Effect value

  • Indicates effect output
  • Required: qualitative term or quantitative (use if available) value
  • Recommended qualitative terms: Normal, Abnormal, Increased, Decreased
  • Recommended quantitative value format: % (of normal)

Effect comments

  • free text box
  • can be used to enter any additional information about the effect/effect value that may be important to include

Example:

Part 3: Entering Quality Control Parameters

Example

Experimental Repeats

  • Required: either a number value or "Not reported"

Normal control

  • Required: free text description of the normal (wild-type) control used

Validation control

  • Validation controls refer to known pathogenic and/or benign variant controls included in the study; these establish the assay output range which can be expected for these classes of variants
  • Required: "Yes" or "No"
  • Required: If "Yes", a free text description of the validation controls used

Statistical analysis

  • Required: "Yes" or "No"
  • Required: If "Yes", a free text description of the statistical analysis result reported

Feedback and Comments? Please email us at: [email protected]

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