The goal of a clinical analysis is to identify, from millions of patient's variants, a few ones that may explain the disease. Once selected a few variants, they are classified according to a pathogenicity or clinical significance criteria.
For each selected variant, OpenCGA creates a clinical variant that mainly, consists of a list of clinical variant evidences. And each evidence classifies the variant according to a tier, ACGM value, clinical significance, drug response, trait association and functional effect and more.
Clinical analysis classification
OpenCGA provides two types of clinical analysis depending on the outcome:
Analysis that return a clinical analysis interpretation. An interpretation consists of two lists of clinical variants (one for primary findings, and one for secondary findings), a list of panels and the low-coverage regions for that panel genes. OpenCGA implements different interpretation analysis for both rare disease and cancer.