GeT-RM Project and Browser Deanna M. Church @deannachurch
Jun 24, 2015
GeT-RM Project and Browser
Deanna M. Church
@deannachurch
Project Team
Lisa Kalman, CDCBirgit Funke, Harvard PartnersMadhuri Hegde, Emory
Guidance and Direction ImplementationChen Chao, NCBIDouglas Slotta, NCBIJonathon Trow, NCBIPeter Meric, NCBIVictor Ananiev, NCBIDaniel Frishberg, NCBIChunlei Liu, NCBIMaryam Halavi, NCBIWendy Rubinstein, NCBIDeanna Church, NCBI
Submitting LabsARUP Laboratories Baylor College of Medicine Medical Genetics LaboratoryBroad Institute of MIT and HarvardEmory Genetics LaboratoryGeneDxGenomics and Pathology Services at Washington University in St. LouisHarvard School of Public HealthIlluminaLaboratory for Molecular MedicineNational Institute of Standards and TechnologyUniversity of California, San Francisco Department of Laboratory MedicineUniversity of Chicago
http://www.ncbi.nlm.nih.gov/variation/tools/get-rm/details/
http://www.ncbi.nlm.nih.gov/variation/tools/get-rm
Calls
Tests
cSRA
ConcordantDiscordantNA
Target audience: Clinical testing labsSubmissions from: Clinical and Research labs
Lab Provided Validation
Variants validated in this sample using another platformVariants validated in another sample using another platformVariants seen in other samples from submitting lab using this platformVariants seen in public data setVariants that are novelVariants that were not assessed
Based on May 2013 Data release
Based on May 2013 Data release
http://www.ncbi.nlm.nih.gov/variation/tools/get-rm
MCL1
Looking forward
Analysis
Web tools
Genotype support analysis based on alignmentsDevelopment of consensus genotype setInvestigation of discordant regionsComparison to paralogous sequence variant (PSV) sitesComparison to GRCh38
Calculation of FP and FN rates Link to browser for review
Improved gene navigationAddition of PSV data tracks