Targeted capture and sequencing of 1245 SNPs for forensic applications. (September 2019)

• Record Type: Journal Article
• Authors: Wu, Liangjun; Chu, Xufeng; Zheng, Jing; Xiao, Chao; Zhang, Zhe; Huang, Guiyang; Li, Dan; Zhan, Jinbang; Huang, Daixin; Hu, Ping; Xiong, Bo
• Is Part Of: Forensic science international. Volume 42(2019)
• Page Start: 227
• Page End: 234
• Publication Date: 2019-09
• Subjects: SNP -- Molecular inversion probe -- Chinese population -- Paternity test -- Degraded DNA; Forensic genetics -- Periodicals; Génétique légale -- Périodiques; Forensic genetics; Electronic journals; Periodicals; 614.1
• DOI: 10.1016/j.fsigen.2019.07.006
• Languages: English
• ISSNs: 1872-4973

Abstract

Highlights: A 1245 SNPs panel based on MIP-NGS method. An in-house pipeline for SNP genotypes calling was designed. Allele frequencies investigated in 210 individuals from Hubei province, China. Suitable for SNP genotyping of degraded samples in ˜100 bp range. Abstract: Next generation sequencing (NGS) technologies have enabled the possibility of analyzing a large number of SNPs simultaneously from multiple samples in a single experiment, for complementing the shortcomings of STR based methods. To efficiently genotype the desired SNPs, it is critical to optimize the library construction procedures. In this study, we formulated a strategy combining the molecular inversion probe (MIP) based target region capture method and NGS for genotyping 1245 SNPs. All the SNPs we selected exhibited high heterozygosity (minor allele frequency (MAF) > 0.3) according to 1000 genomes data. We applied the method to genotype a population of 210 unrelated individuals from the Hubei province of China and assessed the allele frequencies, Hardy-Weinberg equilibrium and linkage disequilibrium. The MAFs of more than 95% of the SNPs were ≥0.2, and no significant deviation or strong linkage was observed for 98% of the SNPs. The data indicated that, even within a relatively confined region, our SNP panel is suitable for individual identifications. Furthermore, we performed paternity test for 7 trio families using low quality DNA samples. The conclusions are in total agreement with these of STR-based analyses, with higher confidence indexes. Finally, we evaluated the performance of the MIP-NGS method with mock degraded DNA samples. We were able to genotype most of the SNPs even when the genomic DNA was sonicated to ˜100 bp range. In summary, we established a highly accurate and cost-effective method of SNP genotyping, which is potentially capable of solving complex issues encountered in forensic practices.