A phylogenetic framework facilitates Y-STR variant discovery and classification via massively parallel sequencing

Abstract

Highlights23 Y-chromosomal STRs (PPY23) reanalysed by massively parallel sequencing.Phylogeny-based approach captures wide range of sequence variants in 100 samples.STR variants described in phase with their flanking sequences.Phylogenetic framework clarifies allele nomenclature and mutation processes.

Sequencing of human identification markers in an Uyghur population using the MiSeq FGxTMForensic Genomics System

“…Several commercial sequencing panels were developed for human identification, including the ForenSeq TM DNA Signature Prep Kit (Verogen V R , San Diego, CA, USA), the Precision ID GlobalFiler NGS STR Panel (Thermo Fisher Scientific, Waltham, MA, USA), and the PowerSeq TM 46GY System (Promega, Madison, WI, USA). These assays were tested rigorously by different forensic genetic laboratories, and they produced sequencing results that were concordant with CE-based STR typing assays at a level of sensitivity that is comparable to that of the currently used PCR-CE methods [3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18].…”

Mitigating the effects of reference sequence bias in single-multiplex massively parallel sequencing of the mitochondrial DNA control region

“…We analysed a set of DNA samples that were selected previously to establish a phylogenetic framework for maximum diversity of the male-specific region of the Y chromosome [12]. These samples derive from ethnically diverse individuals including Europeans, Asians and Africans (Table S1).…”

“…A segment of mitochondrial DNA (from position 15,989 to 619, which includes the control region [from 16,024 to 576]) was amplified in a single reaction generating ten overlapping amplicons from 0.5 ng template DNA using the prototype multiplex PowerSeq™ Auto/Mito/Y System (Promega), following the manufacturer’s recommended protocol. Results obtained for the Y-STRs have been published previously [12], and results for autosomal markers will be described elsewhere. In this paper, when we refer to a ‘single-reaction multiplex’, we consider the mtDNA component of the Auto/Mito/Y System only.…”

“…Library preparation and sequencing on a MiSeq® FGx (Illumina) sequencer were performed as described previously [12].…”

“…Quality-checked FASTQ files were generated as described previously [12]. Variants were called using a standard variant calling pipeline, adjusted to amplicon sequencing (omitting the duplicate removal step).…”