GME Variome
Overview
The Greater Middle East (GME) Variome Project is aimed at generating a coding base reference for the countries found in the Greater Middle East. Illumina Connected Annotations presents variant frequencies for the Greater Middle Eastern population.
Publication
Scott, E. M., Halees, A., Itan, Y., Spencer, E. G., He, Y., Azab, M. A., Gabriel, S. B., Belkadi, A., Boisson, B., Abel, L., Clark, A. G., Greater Middle East Variome Consortium, Alkuraya, F. S., Casanova, J. L., & Gleeson, J. G. (2016). Characterization of Greater Middle Eastern genetic variation for enhanced disease gene discovery. Nature genetics, 48(9), 1071–1076. https://doi.org/10.1038/ng.3592
TSV Extraction
chrom pos ref alt AA filter FunctionGVS geneFunction Gene GeneID SIFT_pred GERP++ AF GME_GC GME_AC GME_AF NWA NEA AP Israel SD TP CA FunctionGVS_new Priority Polyphen2_HVAR_pred LRT_pred MutationTaster_pred rsid OMIM_MIM OMIM_Disease AA_AC EA_AC rsid_link position_link
1 69134 A G A VQSRTrancheSNP99.90to100.00 nonsynonymous_SNV exonic OR4F5 79501 T 2.31 96:0:5 10,192 0.04950495049504951 4:0:0 59:0:2 12:0:0 0:0:0 6:0:0 9:0:2 13:0:2 nonsynonymous_SNV MODERATE B N N none - - none none - http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&org=human&position=chr1%3A69134-69133
1 69270 A G A PASS synonymous_SNV exonic OR4F5 79501 . . 93:38:240 518,224 0.6981132075471698 5:5:11 63:30:86 12:5:28 1:0:2 2:2:18 7:3:46 7:2:52 synonymous_SNV LOW . . . rs201219564 - - none none http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?searchType=adhoc_search&type=rs&rs=rs201219564 http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&org=human&position=chr1%3A69270-69269
1 69428 T G T PASS nonsynonymous_SNV exonic OR4F5 79501 D 0.891 676:44:15 74,1396 0.050340136054421766 43:0:2 313:16:10 88:7:3 6:0:0 44:8:0 102:9:0 102:4:2 nonsynonymous_SNV MODERATE D N N rs140739101 - - 14,3808 313,6535 http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?searchType=adhoc_search&type=rs&rs=rs140739101 http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&org=human&position=chr1%3A69428-69427
Parsing
We parse the GME tsv file and extract the following columns:
- chrom
- pos
- ref
- alt
- filter
- GME_AC
- GME_AF
GRCh37 liftover
The data is not available for GRCh38 on GME website. We performed a liftover from GRCh37 to GRCh38 using CrossMap.
Download URL
http://igm.ucsd.edu/gme/download.shtml
JSON output
"gmeVariome":{
"allAc":10,
"allAn":202,
"allAf":0.049504,
"failedFilter":true
}
Field | Type | Notes |
---|---|---|
allAc | int | GME allele count |
allAn | int | GME allele number |
allAf | float | GME allele frequency |
failedFilter | bool | True if this variant failed any filters |