Molecular Biology: Open Access

Discovery of Novel DNA Variants in Jordanians Population by Re-Genotyping Affymetrix DMET Arrays Data Using DNA Sequencing

Abstract

Marzooq Ammar AL

The Affymetrix DMETT^MM plus platform (Affymetrix, Santa Clara, CA, USA) is a GeneChip where 1936 SNPs can be genotyped in any given sample at once. The 1936 SNPs were distributed cross 225 genes in the genome. Thirtynine genes on the chip belong to phase I–II drug metabolism, disposition and drug transport gene family. These genes are functional in metabolizing the most widely prescribed anticancer drugs in the world including aromatase inhibitors, tamoxifen and thiopurines groups. In a high-throughput GeneChip array which is based on hybridization with allelespecific probes; genotyping errors are very common which limits the technologies applications; in addition missing calls for many SNPs on the chip immerge as a bigger and more serious problem in high- throughput genotyping methods. This study focuses on re-genotyping these No-call genotypes to maintain sample sizes that are already genotyped by Affymetrix DMETT^MM plus platform. Sixty six different variations were identified, 39 of them had No-call genotypes; our re-genotyping resulted in increasing calling rate from 89.08% to 95.56%. Furthermore, Among the variations that were identified, 8 were non-reported: C.-209T > G in UGT2B7 and -698°C > A in CYP1A2 as promoter variants, c.252G > T in SLC22A6 and c.1356T > C in SLC15A1 as silent mutation, c.1277 + 69°C > T and c.1277 + 82°C > T in SLC22A1 as intronic variants associated with each other and the most important variations are two missense (non- synonymous) in NAT2 gene: D20N c.58G > A and G11S c.31G > A. Affymetrix DMETTMM plus platform.