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Sequencing of autosomal, mitochondrial and Y-chromosomal forensic markers in the People of the British Isles cohort detects population structure dominated by patrilineages.
Forensic Sci Int Genet. 2022 07; 59:102725.FS

Abstract

Short tandem repeat (STR) polymorphisms are traditionally assessed by measuring allele lengths via capillary electrophoresis (CE). Massively parallel sequencing (MPS) reveals differences among alleles of the same length, thus improving discrimination, but also identifying groups of alleles likely related by descent. These may have relatively restricted geographical distributions and thus MPS could detect population structure more effectively than CE-based analysis. We addressed this question by applying an MPS multiplex, the Promega PowerSeq™ Auto/Mito/Y System prototype, to 362 individuals chosen to represent a wide geographical spread from the People of the British Isles (PoBI) cohort, which represents at least three generations of local rural ancestry. As well as 22 autosomal STRs (aSTRs; equivalent to PowerPlex Fusion loci) the system sequences 23 Y-STRs (the PowerPlexY 23 loci) and the control region (CR) of mitochondrial DNA (mtDNA), allowing population structure to be compared across biparentally and uniparentally inherited segments of the genome. For all loci, FST-based tests of population structure were done based on historical, linguistic, and geographical partitions, and for aSTRs the clustering algorithm STRUCTURE was also applied. STRs were considered using both length and sequence. Sequencing increased aSTR allele diversity by 87.5% compared to CE-based designations, reducing random match probability to 1.25E-30, compared to a CE-based 6.72E-27. Significant population structure was detectable in just one pairwise comparison (Central/South East England compared to the rest), and for sequence-based alleles only. The 362 samples carried 308 distinct mtDNA CR haplotypes corresponding to 13 broad haplogroups, representing a haplotype diversity of 0.9985 (± 0.0005), and a haplotype match probability of 0.0043. No significant population structure was observed. Y-STR haplotypes belonged to ten broad predicted Y-haplogroups. Allele diversity increased by 33% when considered at the sequence rather than length level, although haplotype diversity was unchanged at 0.999969 (± 0.000001); haplotype match probability was 2.79E-03. In contrast to the biparentally and maternally inherited loci, Y-STR haplotypes showed significant population structure at several levels, but most markedly in a comparison of regions subject to Anglo-Saxon influence in the east with the rest of the sample. This was evident for both length- and sequence-based allele designations, with no systematic difference between the two. We conclude that MPS analysis of aSTRs or Y-STRs does not generally reveal stronger population structure than length-based analysis, that UK maternal lineages are not significantly structured, and that Y-STR haplotypes reveal significant population structure that may reflect the Anglo-Saxon migrations to Britain in the 6th century.

Authors+Show Affiliations

Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH UK.Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headley Way, Oxford OX3 9DS UK.Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headley Way, Oxford OX3 9DS UK.Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH UK. Electronic address: jw418@le.ac.uk.Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH UK. Electronic address: maj4@le.ac.uk.

Pub Type(s)

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

Language

eng

PubMed ID

35640311

Citation

Huszar, Tunde I., et al. "Sequencing of Autosomal, Mitochondrial and Y-chromosomal Forensic Markers in the People of the British Isles Cohort Detects Population Structure Dominated By Patrilineages." Forensic Science International. Genetics, vol. 59, 2022, p. 102725.
Huszar TI, Bodmer WF, Hutnik K, et al. Sequencing of autosomal, mitochondrial and Y-chromosomal forensic markers in the People of the British Isles cohort detects population structure dominated by patrilineages. Forensic Sci Int Genet. 2022;59:102725.
Huszar, T. I., Bodmer, W. F., Hutnik, K., Wetton, J. H., & Jobling, M. A. (2022). Sequencing of autosomal, mitochondrial and Y-chromosomal forensic markers in the People of the British Isles cohort detects population structure dominated by patrilineages. Forensic Science International. Genetics, 59, 102725. https://doi.org/10.1016/j.fsigen.2022.102725
Huszar TI, et al. Sequencing of Autosomal, Mitochondrial and Y-chromosomal Forensic Markers in the People of the British Isles Cohort Detects Population Structure Dominated By Patrilineages. Forensic Sci Int Genet. 2022;59:102725. PubMed PMID: 35640311.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Sequencing of autosomal, mitochondrial and Y-chromosomal forensic markers in the People of the British Isles cohort detects population structure dominated by patrilineages. AU - Huszar,Tunde I, AU - Bodmer,Walter F, AU - Hutnik,Katarzyna, AU - Wetton,Jon H, AU - Jobling,Mark A, Y1 - 2022/05/18/ PY - 2022/02/07/received PY - 2022/05/08/revised PY - 2022/05/13/accepted PY - 2022/6/1/pubmed PY - 2022/6/22/medline PY - 2022/5/31/entrez KW - Autosomal STRs KW - Control region KW - Massively parallel sequencing KW - Mitochondrial DNA KW - People of the British Isles KW - Population structure KW - Short tandem repeat (STR) KW - Single nucleotide polymorphism (SNP) KW - Y-STRs SP - 102725 EP - 102725 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 59 N2 - Short tandem repeat (STR) polymorphisms are traditionally assessed by measuring allele lengths via capillary electrophoresis (CE). Massively parallel sequencing (MPS) reveals differences among alleles of the same length, thus improving discrimination, but also identifying groups of alleles likely related by descent. These may have relatively restricted geographical distributions and thus MPS could detect population structure more effectively than CE-based analysis. We addressed this question by applying an MPS multiplex, the Promega PowerSeq™ Auto/Mito/Y System prototype, to 362 individuals chosen to represent a wide geographical spread from the People of the British Isles (PoBI) cohort, which represents at least three generations of local rural ancestry. As well as 22 autosomal STRs (aSTRs; equivalent to PowerPlex Fusion loci) the system sequences 23 Y-STRs (the PowerPlexY 23 loci) and the control region (CR) of mitochondrial DNA (mtDNA), allowing population structure to be compared across biparentally and uniparentally inherited segments of the genome. For all loci, FST-based tests of population structure were done based on historical, linguistic, and geographical partitions, and for aSTRs the clustering algorithm STRUCTURE was also applied. STRs were considered using both length and sequence. Sequencing increased aSTR allele diversity by 87.5% compared to CE-based designations, reducing random match probability to 1.25E-30, compared to a CE-based 6.72E-27. Significant population structure was detectable in just one pairwise comparison (Central/South East England compared to the rest), and for sequence-based alleles only. The 362 samples carried 308 distinct mtDNA CR haplotypes corresponding to 13 broad haplogroups, representing a haplotype diversity of 0.9985 (± 0.0005), and a haplotype match probability of 0.0043. No significant population structure was observed. Y-STR haplotypes belonged to ten broad predicted Y-haplogroups. Allele diversity increased by 33% when considered at the sequence rather than length level, although haplotype diversity was unchanged at 0.999969 (± 0.000001); haplotype match probability was 2.79E-03. In contrast to the biparentally and maternally inherited loci, Y-STR haplotypes showed significant population structure at several levels, but most markedly in a comparison of regions subject to Anglo-Saxon influence in the east with the rest of the sample. This was evident for both length- and sequence-based allele designations, with no systematic difference between the two. We conclude that MPS analysis of aSTRs or Y-STRs does not generally reveal stronger population structure than length-based analysis, that UK maternal lineages are not significantly structured, and that Y-STR haplotypes reveal significant population structure that may reflect the Anglo-Saxon migrations to Britain in the 6th century. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/35640311/Sequencing_of_autosomal_mitochondrial_and_Y_chromosomal_forensic_markers_in_the_People_of_the_British_Isles_cohort_detects_population_structure_dominated_by_patrilineages_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1872-4973(22)00066-7 DB - PRIME DP - Unbound Medicine ER -