Parallel sequencing of 87 STR and 294 SNP markers using the prototype of the SifaMPS panel on the MiSeq FGx™ system

• Published in: Forensic science international : genetics Vol. 52; p. 102490
• Main Authors: Tao, Ruiyang, Wang, Shouyu, Chen, Anqi, Xia, Ruocheng, Zhang, Xiaochun, Yang, Qi, Qu, Yiling, Zhang, Suhua, Li, Chengtao
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.05.2021
• Subjects: Forensic genetics; Human identification; Massively parallel sequencing (MPS); MiSeq FGx™ system; Short tandem repeats (STRs); Single nucleotide polymorphisms (SNPs); Single nucleotide polymorphisms (SNPs); Massively parallel sequencing (MPS); Forensic genetics; Human identification; MiSeq FGx™ system; Short tandem repeats (STRs)
• ISSN: 1872-4973; 1878-0326
• DOI: 10.1016/j.fsigen.2021.102490

Massively parallel sequencing (MPS), or next generation sequencing (NGS), is a promising methodology for the detection of short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) in forensic genetics. Here, the prototype SifaMPS Panel is designed to simultaneously target 87 STRs and 294 SNPs with forensic interest in a single multiplex in conjunction with the TruSeq™ Custom Amplicon workflow and MiSeq FGx™ System. Two in-house python scripts are adopted for the fastq-to-genotype interpretation of MPS data concerning STR and SNP, respectively. In the present study, by sequencing 50 Chinese Hans and many other DNA samples involved in validation studies, system parameters including the depth of coverage (DoC), heterozygote balance (Hb) and sequence coverage ratios (SCRs), as well as different forensic parameters of STRs and SNPs in a population study, were calculated to evaluate the overall performance of this new panel and its practicality in forensic application. In general, except for two STRs (DYS505 and DYS449) and one SNP (rs4288409) that performed poorly, the other 85 STRs and 293 SNPs in our panel had good performance that could strengthen efficiency for human identification and paternity testing. In addition, discordant STR genotype results between those generated from capillary electrophoresis (CE) and from the MPS platform were clearly illustrated, and these results could be a useful reference for applying these particular non-CODIS STRs in forensic practice. •The SifaMPS Panel prototype is designed to simultaneously target 87 STRs and 294 SNPs on the MiSeq FGx™ System.•Genetic markers involved in this MPS-STR system could facilitate individual identification and kinship analysis.•Inconsistent STR genotypes between CE and MPS methods were observed, especially for these non-CODIS locus.