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. Nirvana 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