Parallel sequencing of 48 Y-chromosome STR and SNP markers

Abstract

Over the last decade, massively parallel sequencing (MPS) has been rapidly developed, bringing many advantages to forensic genomics. It could simultaneously target multiple genetic markers including short tandem repeats (STRs), insertion and deletion polymorphisms (InDels), and single nucleotide polymorphisms (SNPs). In this study, we developed an assay which can simultaneously sequence 22 Y-STRs and 26 Y-SNPs on the MiSeq FGx™ Forensic Genomics System (Illumina, Inc., San Diego, USA). The primers of the markers were designed using the online DesignStudio (Illumina). Subsequently, DNA libraries were established with the TruSeq Amplicon method. For the pilot study, we sequenced 25 unrelated Chinese Han males. A total of 125 sequence-based alleles were observed at the 22 Y-STR loci, with the average depth of coverage (DoC) ranging from 314.9 x to 637.7 × . For the concordant study, the sequencing results of these samples were fully consistent with genotypes called via capillary electrophoresis (CE). For the SNPs, a preferable performance was observed with the average DoC of 836.5 × . However, inter-locus imbalance was observed at some of the markers, which needs substantial improvement of the primer pool. In general, this customized Y-chromosome STR and SNP panel on the MiSeqFGx™ Forensic Genomics System can provide an effective solution for these markers on Y chromosome, which may allow more forensically relevant information to be obtained from limited forensic materials, such as those from sexual assault and rape cases. Besides, it could also facilitate the forensic practices including paternity testing, genetic determination of pedigree and inter-population migration integration.