Zeitschrift für Bioanalyse und Biomedizin

The Identification of Functional Non-Synonymous SNP in Human ATPBinding Cassette (ABC), Subfamily Member 7 Gene: Application of Bioinformatics Tools in Biomedicine

Abstract

Pornlada Nuchnoi, Duangdao Nantakomol, Vasunun Chumchua, Chotiros Plabplueng, Chartchalerm Isarankura-Na-Ayudhya and Virapong Prachayasittikul

The prediction of functional single nucleotide polymorphism (SNP) is promising in modern genetics analysis. Computational biology technology has facilitated an increase in the successful rate of genetic association study and reduced the cost of genotyping. In the present study, we applied various bioinformatics tools for the selection of high potentially functional nsSNP and determined the linkage disequilibrium (LD) structure of ATP-binding cassette transporter member 7 (ABCA7) genes in HapMap populations. Two functional polymorphisms (rs3752233 and rs3752246) were identified on the basis of less protein stability, a low likelihood of mutability, a changing of protein structure and function. Interestingly, a completed LD between rs3752233 (R463H) and rs4147918 (Q1686R) was detected in Utah residents with ancestry from northern and western Europe (CEU) populations. In addition, the difference of the LD pattern between the populations observed highlighted the essential role of the construction of an LD map for designing and interpreting genetic association study. Studies herein convey the empirical guidelines for conduction of ABCA7 genetic association study via bioinformatics and computational application.