Genotyping polymorphic microhaplotype markers through the Illumina® MiSeq platform for forensics. (March 2019)

• Record Type: Journal Article
• Authors: Zhu, Jing; Lv, Meili; Zhou, Nan; Chen, Dan; Jiang, Youjing; Wang, Li; He, Wang; Peng, Duo; Li, Zhilong; Qu, Shengqiu; Wang, Yinji; Wang, Hui; Luo, Haibo; An, Gang; Liang, Weibo; Zhang, Lin
• Is Part Of: Forensic science international. Volume 39(2019)
• Page Start: 1
• Page End: 7
• Publication Date: 2019-03
• Subjects: Microhaplotype -- Massively parallel sequencing (MPS) -- Single nucleotide polymorphisms (SNPs) -- Genetic marker -- Individual identification; Forensic genetics -- Periodicals; Génétique légale -- Périodiques; Forensic genetics; Electronic journals; Periodicals; 614.1
• DOI: 10.1016/j.fsigen.2018.11.005
• Languages: English
• ISSNs: 1872-4973

Abstract

Highlights: A novel nomenclature of microhaplotype marker is proposed. A new Perl-based tool Forensic-Loci-finder (FLfinder) was designed to profile the microhaplotype markers. The direct and accurate genotypes of microhaplotype markers were got using massively parallel sequencing (MPS). 1000 Genomes Phase 3 data was used to give a point that microhaplotype markers have the potential of ancestry inference. Abstract: Microhaplotype markers are emerging forensic genetic markers that have received broad attention in forensics and may supplement existing genetic marker panels. Short tandem repeat polymorphisms (STRPs) and single nucleotide polymorphisms (SNPs) are the general genetic markers at present. Stutter and the high mutation rate of STR markers and the low polymorphism of SNP markers obstruct the solving of certain cases. Kidd proposed microhaplotype markers that encompass 2–4 SNPs. In this study, we screened microhaplotype loci through three criteria, and chose the Illumina ® MiSeq platform to sequence the new markers. A new nomenclature was proposed and Perl-based tool FLfinder was designed to genotype the microhaplotype marker. After counting the number of haplotypes in samples that were sequenced and calculating common forensic parameters, 13 loci with high polymorphism were reported. Twelve of the 13 loci had an average allele coverage ratio (ACR) of 0.72 to 0.92. Structure analysis showed that 2504 samples (1000 genome project) could be divided into 5 groupings of populations, and each one representing a continental origin. The finding indicates that microhaplotype markers could be used for individual identification and ancestry inference, and a new choice is provided for forensic practice in the future.