Massively Parallel Sequencing Of Forensic Markers: Sequence Variation And Forensic Application

2020-02-28T15:35:19Z (GMT) by Tunde I. Huszar
DNA analyses have been used to aid forensic investigations since 1985 and to date, human identification relies on the typing of polymorphic autosomal short tandem repeats (STRs), supplemented by the use of paternal (Y-chromosomal STRs) and maternal (mitochondrial DNA; mtDNA) lineage markers. To accurately measure the significance of matching genotypes/haplotypes their frequencies in relevant populations must be estimated.
Massively parallel sequencing (MPS) technologies became more cost-effective and therefore more accessible to forensic analysis in the last decade. Many markers and marker types can be simultaneously analysed to observe underlying sequence variants beyond simple length-variation. The distribution of sequence-level variants within and between populations also helps to illuminate population substructure.
In this study, STRs and mtDNA were analysed using MPS first in a diverse global set of samples to establish a framework of variants beyond any single population, followed by the population analysis of a set of 362 samples from the People of the British Isles (PoBI) collection, chosen to represent the core population with minimal admixture in the last two generations. Available data from PoBI also allowed Y-SNP-defined haplogroups to be studied.
Using MPS in these sample sets allowed the description of new STR variants, both within the sequence structure of repeat arrays and their flanking nucleotides. Analysis of the mtDNA control region following PCR with a multi-primer system revealed the importance of accounting for reference sequence bias in data analysis.
The PoBI sample provided an overview of sequence-level variants of forensic markers across The British Isles, and serves as a reference for future MPS-based forensic applications. While mtDNA and autosomal markers show no appreciable population substructure, Y-chromosomal variation revealed clear East-West differentiation, probably reflecting a male-mediated Anglo-Saxon cultural and demographic shift around 500 CE, and correlating with current Celtic-Germanic linguistic divisions.