Variants Group

Link: https://docs.google.com/document/d/1bcaPqvQeKTtADkyDyOHC9FPbid4Rarb2VPXY3DtHo8o/edit?usp=sharing

Variants Group

People:

• Chunlei Wu - Scripps
• Benjamin Ainscough - WashU
• Alex Pico - Gladstone, UCSF
• Robin Haw - Reactome, OICR
• Sean Mooney - Buck Institute for Research on Aging
• Julian Chytowskl - Buck Institute for Research on Aging
• Chris Mungall - Lawrence Berkeley National Laboratory
• Andrew Su - Scripps
• Bob Stanley - IO Informatics

Gold standard catalogue of SNPs - dbSNP, UniProt, COSMIC, already exist. Although how do we functional categorize these SNPs. Aggregators: SNP Logic, MutDB Other resources: JanaVar - API, Variant - Steven Brenner, myVariant info

ACTION FOR THE DAY - Find a niche that is useful where we can achieve something, e.g. identifier mapping, allele frequencies

If we go with identifier mapping - how do we go from list to annotation, linking variants to genes - use genomic positions rather than exon positions filter the linkages

Federated approaches and indexing

What would people want to query: Genomic location Gene

Versioning - Identifiers would not change but sift scores, allele freq will change

Programmatic Access - webservice

Maintenance - what to do without funding? wikipedia approach. mygene.info model? User contribution would be preferable How to deal with resources that don’t want to share variant info.

UCSC Genome Browser - how to add custom tracks to UCSC.

SNPedia - http://www.snpedia.com/index.php/SNPedia Promotehease - http://www.snpedia.com/index.php/Promethease clinVar will become a repository of clinical significant variants.

DBs/Functional predictors ClinVar dbSNP COSMIC SNPedia -> JSON -> DB -> API dbNSFP SIFT MutDB PupaSuite

Top level should be source, e.g clinvar

Nomenclature for the description of sequence variants - HGVS http://www.hgvs.org/mutnomen/recs.html ICGC DCC uses this e.g. BRAF1 - MU62030 = chr7:g.140453136A>T

Links between variants and other resources - link beyond variants and genes, e.g disease ontology, OMIM, etc.

Vagrant Boxes - http://docs.vagrantup.com/v2/boxes.html