Sequence-based autosomal STR characterization in four US populations using PowerSeq™ Auto/Y system

Deborah S B S Silva; Melissa K Scheible; Sarah F Bailey; Christopher L Williams; Julia S Allwood; Rebecca S Just; Jared Schuetter; Nicholas Skomrock; Angela Minard-Smith; Nicole Barker-Scoggins; Christopher Eichman; Kelly Meiklejohn; Seth A Faith

doi:10.1016/j.fsigen.2020.102311

Sequence-based autosomal STR characterization in four US populations using PowerSeq™ Auto/Y system

Forensic Sci Int Genet. 2020 Sep:48:102311. doi: 10.1016/j.fsigen.2020.102311. Epub 2020 May 23.

Affiliations

¹ Battelle Memorial Institute, 505 King Ave., Columbus, OH, 43201, USA; NC State University, Molecular Biomedical Sciences, 1060 William Moore Dr., Raleigh, NC, 27607, USA. Electronic address: deborah.silva@hofstra.edu.
² NC State University, Molecular Biomedical Sciences, 1060 William Moore Dr., Raleigh, NC, 27607, USA; NC State University, Population Health and Pathobiology, 1060 William Moore Dr., Raleigh, NC, 27607, USA.
³ NC State University, Molecular Biomedical Sciences, 1060 William Moore Dr., Raleigh, NC, 27607, USA.
⁴ DNA Support Unit, Federal Bureau of Investigation Laboratory, 2501 Investigation Parkway, Quantico, VA, 22135, USA.
⁵ Battelle Memorial Institute, 505 King Ave., Columbus, OH, 43201, USA.
⁶ NC State University, College of Veterinary Medicine, Office of Information Technology, 1060 William Moore Dr., Raleigh, NC, 27607, USA.
⁷ NC State University, Population Health and Pathobiology, 1060 William Moore Dr., Raleigh, NC, 27607, USA.
⁸ Battelle Memorial Institute, 505 King Ave., Columbus, OH, 43201, USA; NC State University, Molecular Biomedical Sciences, 1060 William Moore Dr., Raleigh, NC, 27607, USA; Penn State University Forensic Science Program, 329 Whitmore Laboratory, University Park, PA, 16802, USA.

PMID: 32531758
DOI: 10.1016/j.fsigen.2020.102311

Abstract

The forensic science community is poised to utilize modern advances in massively parallel sequencing (MPS) technologies to better characterize biological samples with higher resolution. A critical component towards the advancement of forensic DNA analysis with these technologies is a comprehensive understanding of the diversity and population distribution of sequence-based short tandem repeat (STR) alleles. Here we analyzed 786 samples of individuals from different population groups, including four of the mostly commonly encountered in forensic casework in the USA. DNA samples were ampliﬁed with the PowerSeq™ Auto/Y System Prototype Kit (Promega Corp.), and sequencing was performed on an Illumina® MiSeq instrument. Sequence data were analyzed using a bioinformatics processing tool, Altius. For additional data analysis and profile comparison, capillary electrophoresis (CE) size-based STR genotypes were generated for a subset of individuals, and where possible, also with a second commercially available MPS STR assay. Autosomal STR loci were analyzed and frequencies were calculated based on sequence composition. Also, population genetics studies were performed, with Hardy-Weinberg equilibrium, polymorphic information content (PIC), and observed and expected heterozygosity all assessed. Overall, sequence-based allelic variants of the repeat region were observed in 20 out of 22 different STR loci commonly used in forensic DNA genotyping, with the highest number of sequence variation observed at locus D12S391. The highest increase in allelic diversity and in PIC through sequence-based genotyping was observed at loci D3S1358 and D8S1179. Such detailed sequence analysis, as the one performed in the present study, is important to help understand the diversity of sequence-based STR alleles across different populations and to demonstrate how such allelic variation can improve statistics used for forensic casework.

Keywords: Isoallele; Massively parallel sequencing; Population; Short tandem repeats.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

DNA Fingerprinting*
Electrophoresis, Capillary
Female
Gene Frequency
Genetics, Population*
Genotype
Heterozygote
High-Throughput Nucleotide Sequencing*
Humans
Male
Microsatellite Repeats*
Polymorphism, Genetic
Racial Groups / genetics*
Sequence Analysis, DNA
United States