149a70c694fe71916a96dda3afeb6139ea764d08 lrnassar Thu Sep 17 09:00:05 2020 -0700 Final touches to desc page, and adding new track pennantIcon refs #24818 diff --git src/hg/makeDb/trackDb/human/clinGen.html src/hg/makeDb/trackDb/human/clinGen.html index 641a3dc..4ea89f7 100644 --- src/hg/makeDb/trackDb/human/clinGen.html +++ src/hg/makeDb/trackDb/human/clinGen.html @@ -41,52 +41,53 @@ 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:

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: number of causative variants 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 +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 or genomic region.

Similarly, a qualitative classification system is used to correlate the evidence of -a gene-disease relationship: "Definitive", "Strong", "Moderate", "Limited", "Animal Model Only", -"No Known Disease Relationship", "Disputed", or "Refuted". +a gene-disease relationship: "Definitive", "Strong", "Moderate", +"Limited", "Animal Model Only", +"No Known Disease Relationship", "Disputed", or "Refuted".

Display Conventions

Haploinsufficiency/Triplosensitivity tracks

Items are shaded according to dosage sensitivity type, red for haploinsufficiency score 3, blue for triplosensitivity score 3, and grey for other evidence scores or not yet evaluated). Mouseover on items shows the supporting evidence of dosage sensitivity. Tracks can be filtered according to the supporting evidence of dosage sensitivity.

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

@@ -156,31 +157,31 @@ Disputed: Conflicting evidence disputing a role for this gene in this disease has arisen since the initial report identifying an association between the gene and disease Refuted: Evidence refuting the role of the gene in the specified disease has been reported and significantly outweighs any evidence supporting the role

The version of the ClinGen Standard Operating Procedures (SOPs) that each gene-disease classification was performed with is provided as well. An older or newer SOP version does not necessarily mean the classification is any more or less valid but is provided for clarity. Each details page also contains a direct link to an evidence summary detailing the rationale behind -the specific classification and information such as a breakdown of the semiquantitative framework, +the specific classification and information such as a breakdown of the semi-qualitative framework, relevant PubMed IDs, the type of data (Genetic vs Experimental Evidence), and a detailed summary.

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.

Data Access

The raw data can be explored interactively with the Table Browser, or the Data Integrator. For automated analysis, the data may be queried from our REST API. Please refer to our mailing list archives @@ -224,18 +225,15 @@ PMID: 22097934; PMC: PMC5008023

Strande NT, Riggs ER, Buchanan AH, Ceyhan-Birsoy O, DiStefano M, Dwight SS, Goldstein J, Ghosh R, Seifert BA, Sneddon TP et al. Evaluating the Clinical Validity of Gene-Disease Associations: An Evidence-Based Framework Developed by the Clinical Genome Resource. Am J Hum Genet. 2017 Jun 1;100(6):895-906. PMID: 28552198; PMC: PMC5473734

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