Curating Case-Control Information

The top section of the curation interface shows the publication currently being curated.

Case-control studies are those in which statistical analysis is used to evaluate enrichment of variants in cases compared to controls. Each case-control study should be independently assessed based on the criteria outlined in the SOP (Case-Control Data section) to evaluate the quality of the study design. The score status of case-control studies can now also be selected as "Review" or "Contradicts".

All required fields (marked with a star) must be filled in before the curated record for an individual can be saved. The required fields are:

• Case-Control Label, Case Cohort Label and Control Cohort Label are free-text identifiers assigned by the curator. They should be used to uniquely identify the cohorts described in a publication. If possible, use the identifiers given in the publication.

• Disease(s) in Common -- usually select “Copy disease term from Gene-Disease Record”.

• Number of Cases with variant(s) in the gene in question -- fill in the number given in the publication

• Number of Controls with variant(s) in the gene in question -- fill in the number given in the publication

• Number of all Cases genotyped/sequenced -- fill in the number given in the publication

• Number of all Controls genotyped/sequenced -- fill in the number given in the publication

For the sections sections following the Case-Control Label, there is a split screen where Case Cohort information is entered in the left panel and Control Cohort information is entered in the right panel.

In the case cohort "Disease(s) & Phenotype(s)" section, you must enter either disease or phenotype information. Generally, you can simply copy the disease from the gene-disease record. In the "Demographics" and "Methods" subsections, enter as much information as is given in the publication.

Additional required information for both cases and controls must be entered in the "Power" section. Additional information can be entered for both cases and controls in the "Additional Information" section below.

The "Case-Control Evaluation" section enables you to enter information that is used by the GCEP to determine whether the study can be scored. A "Study type" must be entered in order to score the study. The following "Statistics", "Bias Category" and "Comments" subsections facilitate evaluation of the quality of the case-control study.

Case-control studies are evaluated and points are assigned at the discretion of experts. The "Case-Control Score" section now allows the selection of a scoring status that includes the "Review" and "Contradicts" options. To score a study, select "Score" and the appropriate numerical value from the "Score" drop-down menu.