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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

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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. / Phillips, Christopher; Devesse, Laurence; Ballard, David; van Weert, Leanne; de la Puente, Maria; Melis, Stefania; Álvarez Iglesias, Vanessa; Freire-Aradas, Ana; Oldroyd, Nicola; Holt, Cydne; Syndercombe Court, Denise; Carracedo, Ángel; Lareu, Maria Victoria.

In: Electrophoresis, 13.08.2018.

Research output: Contribution to journalArticle

Harvard

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, MV 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. https://doi.org/10.1002/elps.201800117

APA

Phillips, C., Devesse, L., Ballard, D., van Weert, L., de la Puente, M., Melis, S., ... 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. https://doi.org/10.1002/elps.201800117

Vancouver

Phillips C, Devesse L, Ballard D, van Weert L, de la Puente M, Melis S 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 Aug 13. https://doi.org/10.1002/elps.201800117

Author

Phillips, Christopher ; Devesse, Laurence ; Ballard, David ; van Weert, Leanne ; de la Puente, Maria ; Melis, Stefania ; Álvarez Iglesias, Vanessa ; Freire-Aradas, Ana ; Oldroyd, Nicola ; Holt, Cydne ; Syndercombe Court, Denise ; Carracedo, Ángel ; Lareu, Maria Victoria. / 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. In: Electrophoresis. 2018.

Bibtex Download

@article{50784dac6e1c40df832db42f4059110a,
title = "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",
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.",
keywords = "Autosomal STRs, CEPH Human genome diversity panel, Massively parallel sequencing, STR, X-STRs",
author = "Christopher Phillips and Laurence Devesse and David Ballard and {van Weert}, Leanne and {de la Puente}, Maria and Stefania Melis and {{\'A}lvarez Iglesias}, Vanessa and Ana Freire-Aradas and Nicola Oldroyd and Cydne Holt and {Syndercombe Court}, Denise and {\'A}ngel Carracedo and Lareu, {Maria Victoria}",
year = "2018",
month = "8",
day = "13",
doi = "10.1002/elps.201800117",
language = "English",
journal = "Electrophoresis",
issn = "0173-0835",

}

RIS (suitable for import to EndNote) Download

TY - JOUR

T1 - Global patterns of STR sequence variation

T2 - 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

PY - 2018/8/13

Y1 - 2018/8/13

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.

AB - 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.

KW - Autosomal STRs

KW - CEPH Human genome diversity panel

KW - Massively parallel sequencing

KW - STR

KW - X-STRs

UR - http://www.scopus.com/inward/record.url?scp=85052902391&partnerID=8YFLogxK

U2 - 10.1002/elps.201800117

DO - 10.1002/elps.201800117

M3 - Article

AN - SCOPUS:85052902391

JO - Electrophoresis

JF - Electrophoresis

SN - 0173-0835

ER -

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