Add a New Comment

Review comment and Submit

Edit
Comment #1
doc, docx, pdf
Max Size : 10 MB

Comment

GA4GH Categorical Variant Representation (Cat-VRS)

GA4GH has been working on the Categorical Variant Representation Implementation Guide (Cat-VRS).

 

cat-vrs.ga4gh.org

 

There are Broad categories of genomic variants

 

(Suspected) deleterious BRCA 1/2 variants

(Suspected) deleterious gBRCA 1/2 variants

AKT1 variants

ALK fusions

ALK variants

BRAF fusions

BRAF rearrangements

BRAF V600

Deleterious BRCA 1/2 variants

EGFR exon 19 deletion variants

EGFR exon 20 insertion variants

EGFR variants

EZH2 variants

FGFR1 rearrangements

FGFR2 rearrangements

FLT3 variants

FRFR2 : :v 

HER2 (ERBB2) variants

HRR gene variants

IDH1 variants

IDH2 variants

KMT2A translocations

KRAS variants

MET exon 14 skipping variants

Non-resistant EGFR variants

NRG1 fusions

NTRK fusions

PDGFRA exon 18 variants

PDGFRA/B rearrangements

PIK3CA variants

PTEN variants

RET fusions

RET variants

ROS1 fusions

Susceptible FGFR3  variants

Susceptible IDH1 variants

TSC 1/2 variants

Types of constraints :

 

Adjacency constraint

Copy change constraint 

Copy count constraint

Defining allele constraint

Defining location constraint

Feature context constraint

Function constraint

 

Types of recipes:

 

Canonical allele recipe

Categorical CNV recipe

Function variant recipe

Gene fusion recipe

Protein sequence consequence recipe

Variant type

The below 5 are part of Variant Type:

Pathogenic

Likely Pathogenic

Variant of Uncertain Signficance (VUS)

Likely Benign

Benign

 

and of course with Variants:

Test Interpretation

Clnically Significant Copy Number Variations (Clinically Significant CNVs)