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Sequence-based autosomal STR characterization in four US populations using PowerSeq™ Auto/Y system.
Forensic Sci Int Genet. 2020 09; 48:102311.FS

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.

Authors+Show Affiliations

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.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.NC State University, Molecular Biomedical Sciences, 1060 William Moore Dr., Raleigh, NC, 27607, USA.NC State University, Molecular Biomedical Sciences, 1060 William Moore Dr., Raleigh, NC, 27607, USA.NC State University, Molecular Biomedical Sciences, 1060 William Moore Dr., Raleigh, NC, 27607, USA.DNA Support Unit, Federal Bureau of Investigation Laboratory, 2501 Investigation Parkway, Quantico, VA, 22135, USA.Battelle Memorial Institute, 505 King Ave., Columbus, OH, 43201, USA.Battelle Memorial Institute, 505 King Ave., Columbus, OH, 43201, USA.Battelle Memorial Institute, 505 King Ave., Columbus, OH, 43201, USA.NC State University, College of Veterinary Medicine, Office of Information Technology, 1060 William Moore Dr., Raleigh, NC, 27607, USA.NC State University, College of Veterinary Medicine, Office of Information Technology, 1060 William Moore Dr., Raleigh, NC, 27607, USA.NC State University, Population Health and Pathobiology, 1060 William Moore Dr., Raleigh, NC, 27607, USA.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.

Pub Type(s)

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

Language

eng

PubMed ID

32531758

Citation

Silva, Deborah S B S., et al. "Sequence-based Autosomal STR Characterization in Four US Populations Using PowerSeq™ Auto/Y System." Forensic Science International. Genetics, vol. 48, 2020, p. 102311.
Silva DSBS, Scheible MK, Bailey SF, et al. Sequence-based autosomal STR characterization in four US populations using PowerSeq™ Auto/Y system. Forensic Sci Int Genet. 2020;48:102311.
Silva, D. S. B. S., Scheible, M. K., Bailey, S. F., Williams, C. L., Allwood, J. S., Just, R. S., Schuetter, J., Skomrock, N., Minard-Smith, A., Barker-Scoggins, N., Eichman, C., Meiklejohn, K., & Faith, S. A. (2020). Sequence-based autosomal STR characterization in four US populations using PowerSeq™ Auto/Y system. Forensic Science International. Genetics, 48, 102311. https://doi.org/10.1016/j.fsigen.2020.102311
Silva DSBS, et al. Sequence-based Autosomal STR Characterization in Four US Populations Using PowerSeq™ Auto/Y System. Forensic Sci Int Genet. 2020;48:102311. PubMed PMID: 32531758.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Sequence-based autosomal STR characterization in four US populations using PowerSeq™ Auto/Y system. AU - Silva,Deborah S B S, AU - Scheible,Melissa K, AU - Bailey,Sarah F, AU - Williams,Christopher L, AU - Allwood,Julia S, AU - Just,Rebecca S, AU - Schuetter,Jared, AU - Skomrock,Nicholas, AU - Minard-Smith,Angela, AU - Barker-Scoggins,Nicole, AU - Eichman,Christopher, AU - Meiklejohn,Kelly, AU - Faith,Seth A, Y1 - 2020/05/23/ PY - 2019/08/20/received PY - 2020/04/21/revised PY - 2020/05/14/accepted PY - 2020/6/13/pubmed PY - 2021/7/13/medline PY - 2020/6/13/entrez KW - Isoallele KW - Massively parallel sequencing KW - Population KW - Short tandem repeats SP - 102311 EP - 102311 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 48 N2 - 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. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/32531758/Sequence_based_autosomal_STR_characterization_in_four_US_populations_using_PowerSeq™_Auto/Y_system_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1872-4973(20)30084-3 DB - PRIME DP - Unbound Medicine ER -