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 reported variant that mainly, consists of a list of reported events or evidences. An each reported event classifies the variant according to it tier, ACGM value, clinical significance, drug response, trait association and functional effect.
OpenCGA provides two types of clinical analysis depending on the outcome:
To assign the tier value for the reported events of a selected variant is crucial in clinical analysis. OpenCGA considers three values:
Default tier calculator sets the tier score for each reported event taking into account:
The default tier calculator is used by the primary findings, secondary findings, customizable interpretation and TEAM-based interpretation analysis.
The following diagram shows how the default tier calculator assigns a tier value:
GEL-based tier calculator sets the tier value for each reported event of a given reported variant taking into account:
The GEL-based tier calculator is used by the interpretation analysis based on GEL algorithms.
The following diagram shows how the GEL-based tier calculator assigns a tier value: