eb302eb9bf4446136c7a81a9839688de53241206 lrnassar Tue Sep 15 14:46:19 2020 -0700 Staging new clinGen composite on beta, and touching up desc page refs #24818 diff --git src/hg/makeDb/trackDb/human/clinGen.html src/hg/makeDb/trackDb/human/clinGen.html index 57ee5dc..a5af4dc 100644 --- src/hg/makeDb/trackDb/human/clinGen.html +++ src/hg/makeDb/trackDb/human/clinGen.html @@ -41,39 +41,39 @@ href="https://www.nlm.nih.gov/">National Center for Biotechnology Information (NCBI) of the National Library of Medicine (NLM) which distributes part of this information through its ClinVar database.

The available data tracks are:

Clinical Genome Resource Structural Variants (ClinGen Structural Variants) - Shows curated copy number variants (CNVs) with sufficient pathogenic or benign evidence as a mechanism for disease from the dbVar study nstd45 (ClinGen Curated Dosage Sensitivity Map-obsoleted).
Clinical Genome Resource Dosage Sensitivity Map Haploinsufficiency (ClinGen Haploinsufficiency) and -Triplosensitivity (ClinGen Triplosensitivity) - +
Clinical Genome Resource Dosage Sensitivity Map Haploinsufficiency (ClinGen Haploinsufficiency) and Triplosensitivity (ClinGen Triplosensitivity) - Shows evidence supporting or refuting haploinsufficiency (loss) and triplosensitivity (gain) as mechanisms for disease at gene-level and larger genomic regions.

A rating system is used to classify the evidence supporting or refuting dosage - sensitivity for individual genes and regions, which takes in consideration the following criteria: + sensitivity for individual genes and regions, which takes into consideration the following criteria: number of causative mutations reported, patterns of inheritance, consistency of phenotype, evidence from large-scale case-control studies, mutational mechanisms, data from public genome variation databases, and expert consensus opinion.

The system is intended to be of a "dynamic nature", with regions being reevaluated periodically to incorporate emerging evidence. The evidence collected is displayed within a publicly available database. Evidence that haploinsufficiency or triplosensitivity of a gene is associated with a specific phenotype will aid in the interpretive assessment of CNVs including that gene.

Display Conventions

Structural Variants are shaded according to variant type, red for CNV loss, blue @@ -88,31 +88,31 @@ clinical significance (benign or pathogenic).

Dosage Scores are used to classify the evidence of the supporting dosage sensitivity map:

0 - no evidence available

1 - little evidence for dosage pathogenicity

2 - some evidence for dosage pathogenicity

3 - sufficient evidence for dosage pathogenicity

30 - gene associated with autosomal recessive phenotype

40 - dosage sensitivity unlikely

For more information on the use of the scores see the ClinGen FAQs. -Items are shaded according to dosage sensitivity type. red for haploinsufficiency, +Items are shaded according to dosage sensitivity type, red for haploinsufficiency, blue for triplosensitivity, and grey for other evidence scores or for genes/regions that have not been evaluated yet or no evidence is available. A light to dark gradient color is used according to the degree of supporting evidence.

Mouseover on items shows the supporting evidence of dosage sensitivity and respective scores. All tracks can be filtered according to the supporting evidence of dosage sensitivity.

These tracks are multi-view composite tracks that contain multiple data types (views). Each view within a track has separate display controls, as described here.