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Aug2013 GeT-RM project and genome browser
This document summarizes the GeT-RM Project and Browser, which collects and analyzes genetic variant data submitted by various clinical and research laboratories. It describes the project team members and submitting labs. It provides information on the types and platforms of tests conducted, validation methods used by labs, read count distributions, and gene-level concordance calculations. It also outlines future analyses, improvements to the browser, and inclusion of paralogous sequence variant data.
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Aug2013 GeT-RM project and genome browser
- 1. GeT-RM Project andBrowser Deanna M. Church @deannachurch GIAB 2013
- 2. ProjectTeam Lisa Kalman, CDC BirgitFunke, Harvard Partners Madhuri Hegde, Emory Guidance and Direction Implementation Chen Chao, NCBI Douglas Slotta, NCBI Jonathon Trow, NCBI Peter Meric, NCBI Victor Ananiev, NCBI Daniel Frishberg, NCBI Chunlei Liu, NCBI Maryam Halavi, NCBI Wendy Rubinstein, NCBI Deanna Church, NCBI
- 3. Submitting Labs ARUP Laboratories BaylorCollege of Medicine Medical Genetics Laboratory Broad Institute of MIT and Harvard Emory Genetics Laboratory GeneDx Genomics and Pathology Services at Washington University in St. Louis Harvard School of Public Health Illumina Laboratory for Molecular Medicine National Institute of Standards and Technology University of California, San Francisco Department of Laboratory Medicine University of Chicago http://www.ncbi.nlm.nih.gov/variation/tools/get-rm/details/
- 4. http://www.ncbi.nlm.nih.gov/variation/tools/get-rm Calls Tests cSRA Concordant Discordant NA Target audience: Clinicaltesting labs Submissions from: Clinical and Research labs
- 5. Twelve submitting labsto date Twelve custom scripts to regularize data Defined formats here: http://www.ncbi.nlm.nih.gov/projects/variation/get-rm
- 6. Platforms 0 5 10 15 20 25 30 HiSeq 2000 HiSeq2500 MiSeq Ion Torrent Sanger 454 NA12878Tests by Platform
- 7. Lab ProvidedValidation Variants validatedin this sample using another platform Variants validated in another sample using another platform Variants seen in other samples from submitting lab using this platform Variants seen in public data set Variants that are novel Variants that were not assessed
- 8. 0 50 100 150 200 250 0 10 50100 500 1000 5000 Number of Variant Read Count Bins Suppor ng Read Counts Based on May 2013 Data release
- 9. Based on May2013 Data release
- 10.
- 12. Gene level concordance Σ(max(xi)/Σ T) i = genotype call X = count per call for each variant T = total genotype calls per variant Sums are taken over all variants in a gene. Tested regions taken into account Phasing ignored
- 13. Looking forward Analysis Web tools Genotypesupport analysis based on alignments Development of consensus genotype set Investigation of discordant regions Comparison to paralogous sequence variant (PSV) sites Comparison to GRCh38 Calculation of FP and FN rates Link to browser for review Improved gene navigation Addition of PSV data tracks