Parallel sequencing of 60 X-chromosome genetic markers including STRs, SNPs and InDels

Abstract Massively parallel sequencing (MPS) technology has become popular in forensic studies, due to the general gains of larger multiplexing and the detection of sequence variation. In this study, we present the sequencing results from 100 Chinese individuals at 15 X-STRs, 28 X-SNPs and 17 X-InDels using an in-house assay, since X-chromosome markers are efficiently complement the analysis of autosomal and Y-chromosomal STRs in solving special complex kinship deficiency cases. A total of 100 allelic sequences were obtained at the 15 X-STRs with averaged sequencing coverage of 1120x. And the allele sequencing percentages ranged from 75.21% (DXS10103) to 92.54% (DXS6803). Fully concordant genotypes between MPS and CE were obtained, except at DXS10103 locus. For SNPs and InDels, averaged sequencing coverage are 1658x and 1469x, respectively, with satisfied sequencing performance. However, optimization of primer pool is still necessary to get more balanced performance among all markers and to improve the sensitivety. In brief, results here demonstrated that MPS technology can effectively sequence different markers parallelly and provide detail sequence information, mutation within repeat motifs of STRs or SNPs located in flanking regions. Consequently, MPS analysis of an expanded set of genetic markers on X-chromosome, will be of great practical use in forensic genetics.