1. GeT-RM Project and Browser
Deanna M. Church
@deannachurch GIAB 2013

2. ProjectTeam
Lisa Kalman, CDC
Birgit Funke, 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
Baylor College 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: Clinical testing labs
Submissions from: Clinical and Research labs

5. Twelve submitting labs to 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 HiSeq 2500 MiSeq Ion Torrent Sanger 454
NA12878Tests by Platform

7. Lab ProvidedValidation
Variants validated in 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 50 100 500 1000 5000
Number
of
Variant
Read Count Bins
Suppor ng Read Counts
Based on May 2013 Data release

9. Based on May 2013 Data release

10. http://www.ncbi.nlm.nih.gov/variation/tools/get-rm

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
Genotype support 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