Affymetrix Microarray Validation of Qatari Exome Potentially Deleterious SNPs Where the SNP and Gene Have Been Previously Linked to Human Health1.

1Analysis of the exomes in the QE7 14 alleles identified 131 missense coding SNPs where the SNP and gene have been previously identified as linked to human health (Table 1, 4th row). To validate this observation in a larger group of Qataris, the Affymetrix Genome-Wide SNP Array 5.0 was used to assess an independent group of 149 Qataris (QA149, 298 alleles). Of the 2,750 missense potentially deleterious SNPs identified in at least 1 of the QE7 14 alleles, 131 were on the microarray. Of these, 49 were in genes linked to human health, including 16 where both the gene and the SNP are linked to human health. Of these 16, listed are 10 chosen as examples of missense SNPs linked to human health.2Gene symbol and name obtained from the Consensus Coding Sequence (CCDS) NCBI database [32], amino acid substitution position and residues obtained from dbSNP when available, otherwise SIFT online webserver [34]. Transcript position and amino acid substitution were verified to be consistent with the literature.3SNP information includes chromosome amino acid substitution, dbSNP build 134 rsID if available, chromosome, position in GRCh37 human reference genome assembly, reference and alternate allele in QE7. Ref = references; alt = alternative.4Phenotype information from OMIM [12], HGMD [37], PharmGKB [38] or HUGE [39] database.5For more details and references, see Details S1.6Shown is the alternate allele frequency determined by exome sequencing in QE7 individuals.7Shown is the risk allele frequency in the validation set of QA149 individuals (n = 149 Qatari, 298 alleles). Failed genotypes are accounted for in the allele frequency. For statistical comparisons of the QE7 and QA149 allele frequencies, see Figure 2.