Analysis of human triallelic SNPs by next-generation sequencing

Ann Hum Genet. 2015 Jul;79(4):275-81. doi: 10.1111/ahg.12114. Epub 2015 Apr 23.

Abstract

Although single-nucleotide polymorphisms (SNPs) have become extremely useful in the study of geneticvariation, triallelic SNPs are still not fully understood. Next-generation sequencing (NGS) is a promising approach to identify triallelic sites in large populations. In this study, we explored exome sequencing data from 221 Chinese individuals, with an average depth of 70-fold. We identified 382,901 SNPs in the study samples, including 2,002 (0.52%) triallelic sites. Among the triallelic SNPs, 17.3% were coding SNPs (cSNPs) and 78.3% were novel. Comparison and analysis revealed that the variant alleles were more likely to result in nonsynonymous variation at triallelic sites. In addition, natural selection seemed to influence triallelic SNPs. However, with the limited sample size assessed, more studies will be required in order to fully characterize the features of triallelic SNPs.

Keywords: mutational directions; natural selection; next-generation sequencing; triallelic SNPs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Asian Continental Ancestry Group / genetics*
  • Gene Frequency
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Polymorphism, Single Nucleotide*
  • Selection, Genetic
  • Sequence Analysis, DNA