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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.

Clinical analysis classification

OpenCGA provides two types of clinical analysis depending on the outcome:

Tier calculator

To assign the tier value for the reported events of a selected variant is crucial in clinical analysis. OpenCGA considers three values:

  • Tier 1, variants with strong clinical significance
  • Tier 2, variants with potential clinical significance
  • Tier 3, other findings

OpenCGA implements two algorithms to assign tier values:

  • Default tier calculator
  • GEL-based tier calculator

Default tier calculator

Default tier calculator sets the tier score for each reported event taking into account:

  1. the genomic feature type (VARIANT, GENE or REGION)
  2. the mode of inheritance (MoI) and
  3. the overlap percentage.

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

GEL-based tier calculator sets the tier value for each reported event of a given reported variant taking into account:

  1. the genomic feature type (GENE or REGION),
  2. the mode of inheritance (MoI) and 
  3. the overlap percentage.

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:

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