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Global patterns of STR sequence variation: Sequencing the CEPH human genome diversity panel for 58 forensic STRs using the Illumina ForenSeq DNA Signature Prep Kit.
Electrophoresis. 2018 11; 39(21):2708-2724.E

Abstract

The 944 individuals of the CEPH human genome diversity panel (HGDP-CEPH), a standard sample set of 51 globally distributed populations, were sequenced using the Illumina ForenSeq™ DNA Signature Prep Kit. The ForenSeq™ system is a single multiplex for the MiSeq/FGx™ massively parallel sequencing instrument, comprising: amelogenin, 27 autosomal STRs, 24 Y-STRs, 7 X-STRs, and 94 SNPforID+Kiddlab autosomal ID-SNPs (plus optionally detected ancestry and phenotyping SNP sets). We report in detail the patterns of sequence variation observed in the repeat regions of the 58 forensic STR loci typed by the ForenSeq™ system. Sequence alleles were characterized and repeat region structures annotated by aligning the ForenSeq™ sequence output to the latest GRCh38 human reference sequence, necessitating the reversal and re-alignment of STR allele sequences reported by the Forenseq™ system in 20 of 58 STRs (plus the reverse alleles in two Y-STRs with duplicated-inverted repeat regions). Individual population sample sizes of the HGDP-CEPH panel do not allow reliable inferences to be made about levels of genetic variability in low frequency STR alleles-where particular sequence variants are found in only a few individuals; but we assessed the occurrence of both population-specific sequence variants and singleton observations; finding each of these in a sizeable proportion of HGDP-CEPH samples, with consequences for planning the co-ordinated compilation of sequence variation on a much larger scale than was required before by forensic laboratories now adopting massively parallel sequencing.

Authors+Show Affiliations

Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain.King's Forensics, King's College London, London, UK. Verogen Inc., San Diego, USA.King's Forensics, King's College London, London, UK.Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain.Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain.Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain.Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain.Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain.Verogen Inc., San Diego, USA.Verogen Inc., San Diego, USA.King's Forensics, King's College London, London, UK.Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain. Genomic Medicine Group, University of Santiago de Compostela, Galicia, Spain.Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

30101987

Citation

Phillips, Christopher, et al. "Global Patterns of STR Sequence Variation: Sequencing the CEPH Human Genome Diversity Panel for 58 Forensic STRs Using the Illumina ForenSeq DNA Signature Prep Kit." Electrophoresis, vol. 39, no. 21, 2018, pp. 2708-2724.
Phillips C, Devesse L, Ballard D, et al. Global patterns of STR sequence variation: Sequencing the CEPH human genome diversity panel for 58 forensic STRs using the Illumina ForenSeq DNA Signature Prep Kit. Electrophoresis. 2018;39(21):2708-2724.
Phillips, C., Devesse, L., Ballard, D., van Weert, L., de la Puente, M., Melis, S., Álvarez Iglesias, V., Freire-Aradas, A., Oldroyd, N., Holt, C., Syndercombe Court, D., Carracedo, Á., & Lareu, M. V. (2018). Global patterns of STR sequence variation: Sequencing the CEPH human genome diversity panel for 58 forensic STRs using the Illumina ForenSeq DNA Signature Prep Kit. Electrophoresis, 39(21), 2708-2724. https://doi.org/10.1002/elps.201800117
Phillips C, et al. Global Patterns of STR Sequence Variation: Sequencing the CEPH Human Genome Diversity Panel for 58 Forensic STRs Using the Illumina ForenSeq DNA Signature Prep Kit. Electrophoresis. 2018;39(21):2708-2724. PubMed PMID: 30101987.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Global patterns of STR sequence variation: Sequencing the CEPH human genome diversity panel for 58 forensic STRs using the Illumina ForenSeq DNA Signature Prep Kit. AU - Phillips,Christopher, AU - Devesse,Laurence, AU - Ballard,David, AU - van Weert,Leanne, AU - de la Puente,Maria, AU - Melis,Stefania, AU - Álvarez Iglesias,Vanessa, AU - Freire-Aradas,Ana, AU - Oldroyd,Nicola, AU - Holt,Cydne, AU - Syndercombe Court,Denise, AU - Carracedo,Ángel, AU - Lareu,Maria Victoria, Y1 - 2018/09/03/ PY - 2018/03/04/received PY - 2018/07/02/revised PY - 2018/07/26/accepted PY - 2018/8/14/pubmed PY - 2019/10/8/medline PY - 2018/8/14/entrez KW - Autosomal STRs KW - CEPH Human genome diversity panel KW - Massively parallel sequencing KW - STR KW - X-STRs SP - 2708 EP - 2724 JF - Electrophoresis JO - Electrophoresis VL - 39 IS - 21 N2 - The 944 individuals of the CEPH human genome diversity panel (HGDP-CEPH), a standard sample set of 51 globally distributed populations, were sequenced using the Illumina ForenSeq™ DNA Signature Prep Kit. The ForenSeq™ system is a single multiplex for the MiSeq/FGx™ massively parallel sequencing instrument, comprising: amelogenin, 27 autosomal STRs, 24 Y-STRs, 7 X-STRs, and 94 SNPforID+Kiddlab autosomal ID-SNPs (plus optionally detected ancestry and phenotyping SNP sets). We report in detail the patterns of sequence variation observed in the repeat regions of the 58 forensic STR loci typed by the ForenSeq™ system. Sequence alleles were characterized and repeat region structures annotated by aligning the ForenSeq™ sequence output to the latest GRCh38 human reference sequence, necessitating the reversal and re-alignment of STR allele sequences reported by the Forenseq™ system in 20 of 58 STRs (plus the reverse alleles in two Y-STRs with duplicated-inverted repeat regions). Individual population sample sizes of the HGDP-CEPH panel do not allow reliable inferences to be made about levels of genetic variability in low frequency STR alleles-where particular sequence variants are found in only a few individuals; but we assessed the occurrence of both population-specific sequence variants and singleton observations; finding each of these in a sizeable proportion of HGDP-CEPH samples, with consequences for planning the co-ordinated compilation of sequence variation on a much larger scale than was required before by forensic laboratories now adopting massively parallel sequencing. SN - 1522-2683 UR - https://www.unboundmedicine.com/medline/citation/30101987/Global_patterns_of_STR_sequence_variation:_Sequencing_the_CEPH_human_genome_diversity_panel_for_58_forensic_STRs_using_the_Illumina_ForenSeq_DNA_Signature_Prep_Kit_ L2 - https://doi.org/10.1002/elps.201800117 DB - PRIME DP - Unbound Medicine ER -