Flanking region variation of ForenSeq™ DNA Signature Prep Kit STR and SNP loci in Yavapai Native Americans

Frank R. Wendt, Jonathan L. King, Nicole M.M. Novroski, Jennifer Churchill Cihlar, Jillian Ng, Robert F. Oldt, Kelly L. McCulloh, Jessica A. Weise, David Glenn Smith, Sreetharan Kanthaswamy, Bruce Budowle

Research output: Contribution to journalArticleResearchpeer-review

17 Citations (Scopus)

Abstract

Massively parallel sequencing (MPS) offers advantages over current capillary electrophoresis-based analysis of short tandem repeat (STR) loci for human identification testing. In particular STR repeat motif sequence information can be obtained, thereby increasing the discrimination power of some loci. While sequence variation within the repeat region is observed relatively frequently in some of the commonly used STRs, there is an additional degree of variation found in the flanking regions adjacent to the repeat motif. Repeat motif and flanking region sequence variation have been described for major population groups, however, not for more isolated populations. Flanking region sequence variation in STR and single nucleotide polymorphism (SNP) loci in the Yavapai population was analyzed using the ForenSeq™ DNA Signature Prep Kit and STRait Razor v2s. Seven and 14 autosomal STRs and identity-informative single nucleotide polymorphisms (iiSNPs), respectively, had some degree of flanking region variation. Three and four of these identity-informative loci, respectively, showed ≥5% increase in expected heterozygosity. The combined length- and sequence-based random match probabilities (RMPs) for 27 autosomal STRs were 6.11 × 10−26 and 2.79 × 10−29, respectively. When combined with 94 iiSNPs (a subset of which became microhaplotypes) the combined RMP was 5.49 × 10−63. Analysis of length-based and sequence-based autosomal STRs in STRUCTURE indicated that the Yavapai are most similar to the Hispanic population. While producing minimal increase in X- and Y-STR discrimination potential, access to flanking region data enabled identification of one novel X-STR and three Y-STR alleles relative to previous reports. Five ancestry-informative SNPs (aiSNPs) and two phenotype-informative SNPs (piSNPs) exhibited notable flanking region variation.

Original languageEnglish
Pages (from-to)146-154
Number of pages9
JournalForensic Science International: Genetics
Volume28
DOIs
StatePublished - 1 May 2017

Fingerprint

North American Indians
Microsatellite Repeats
Single Nucleotide Polymorphism
DNA
Population
High-Throughput Nucleotide Sequencing
Forensic Anthropology
Capillary Electrophoresis
Population Groups
Hispanic Americans
Alleles
Phenotype

Keywords

  • Flanking region
  • ForenSeq™ DNA Signature Prep Kit
  • Massively parallel sequencing
  • SNP
  • STR
  • STRait Razor v2s
  • Sequence variation

Cite this

Wendt, Frank R. ; King, Jonathan L. ; Novroski, Nicole M.M. ; Cihlar, Jennifer Churchill ; Ng, Jillian ; Oldt, Robert F. ; McCulloh, Kelly L. ; Weise, Jessica A. ; Smith, David Glenn ; Kanthaswamy, Sreetharan ; Budowle, Bruce. / Flanking region variation of ForenSeq™ DNA Signature Prep Kit STR and SNP loci in Yavapai Native Americans. In: Forensic Science International: Genetics. 2017 ; Vol. 28. pp. 146-154.
@article{36019613912b4a518105ed227c7e4e77,
title = "Flanking region variation of ForenSeq™ DNA Signature Prep Kit STR and SNP loci in Yavapai Native Americans",
abstract = "Massively parallel sequencing (MPS) offers advantages over current capillary electrophoresis-based analysis of short tandem repeat (STR) loci for human identification testing. In particular STR repeat motif sequence information can be obtained, thereby increasing the discrimination power of some loci. While sequence variation within the repeat region is observed relatively frequently in some of the commonly used STRs, there is an additional degree of variation found in the flanking regions adjacent to the repeat motif. Repeat motif and flanking region sequence variation have been described for major population groups, however, not for more isolated populations. Flanking region sequence variation in STR and single nucleotide polymorphism (SNP) loci in the Yavapai population was analyzed using the ForenSeq™ DNA Signature Prep Kit and STRait Razor v2s. Seven and 14 autosomal STRs and identity-informative single nucleotide polymorphisms (iiSNPs), respectively, had some degree of flanking region variation. Three and four of these identity-informative loci, respectively, showed ≥5{\%} increase in expected heterozygosity. The combined length- and sequence-based random match probabilities (RMPs) for 27 autosomal STRs were 6.11 × 10−26 and 2.79 × 10−29, respectively. When combined with 94 iiSNPs (a subset of which became microhaplotypes) the combined RMP was 5.49 × 10−63. Analysis of length-based and sequence-based autosomal STRs in STRUCTURE indicated that the Yavapai are most similar to the Hispanic population. While producing minimal increase in X- and Y-STR discrimination potential, access to flanking region data enabled identification of one novel X-STR and three Y-STR alleles relative to previous reports. Five ancestry-informative SNPs (aiSNPs) and two phenotype-informative SNPs (piSNPs) exhibited notable flanking region variation.",
keywords = "Flanking region, ForenSeq™ DNA Signature Prep Kit, Massively parallel sequencing, SNP, STR, STRait Razor v2s, Sequence variation",
author = "Wendt, {Frank R.} and King, {Jonathan L.} and Novroski, {Nicole M.M.} and Cihlar, {Jennifer Churchill} and Jillian Ng and Oldt, {Robert F.} and McCulloh, {Kelly L.} and Weise, {Jessica A.} and Smith, {David Glenn} and Sreetharan Kanthaswamy and Bruce Budowle",
year = "2017",
month = "5",
day = "1",
doi = "10.1016/j.fsigen.2017.02.014",
language = "English",
volume = "28",
pages = "146--154",
journal = "Forensic Science International: Genetics",
issn = "1872-4973",
publisher = "Elsevier Ireland Ltd",

}

Flanking region variation of ForenSeq™ DNA Signature Prep Kit STR and SNP loci in Yavapai Native Americans. / Wendt, Frank R.; King, Jonathan L.; Novroski, Nicole M.M.; Cihlar, Jennifer Churchill; Ng, Jillian; Oldt, Robert F.; McCulloh, Kelly L.; Weise, Jessica A.; Smith, David Glenn; Kanthaswamy, Sreetharan; Budowle, Bruce.

In: Forensic Science International: Genetics, Vol. 28, 01.05.2017, p. 146-154.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - Flanking region variation of ForenSeq™ DNA Signature Prep Kit STR and SNP loci in Yavapai Native Americans

AU - Wendt, Frank R.

AU - King, Jonathan L.

AU - Novroski, Nicole M.M.

AU - Cihlar, Jennifer Churchill

AU - Ng, Jillian

AU - Oldt, Robert F.

AU - McCulloh, Kelly L.

AU - Weise, Jessica A.

AU - Smith, David Glenn

AU - Kanthaswamy, Sreetharan

AU - Budowle, Bruce

PY - 2017/5/1

Y1 - 2017/5/1

N2 - Massively parallel sequencing (MPS) offers advantages over current capillary electrophoresis-based analysis of short tandem repeat (STR) loci for human identification testing. In particular STR repeat motif sequence information can be obtained, thereby increasing the discrimination power of some loci. While sequence variation within the repeat region is observed relatively frequently in some of the commonly used STRs, there is an additional degree of variation found in the flanking regions adjacent to the repeat motif. Repeat motif and flanking region sequence variation have been described for major population groups, however, not for more isolated populations. Flanking region sequence variation in STR and single nucleotide polymorphism (SNP) loci in the Yavapai population was analyzed using the ForenSeq™ DNA Signature Prep Kit and STRait Razor v2s. Seven and 14 autosomal STRs and identity-informative single nucleotide polymorphisms (iiSNPs), respectively, had some degree of flanking region variation. Three and four of these identity-informative loci, respectively, showed ≥5% increase in expected heterozygosity. The combined length- and sequence-based random match probabilities (RMPs) for 27 autosomal STRs were 6.11 × 10−26 and 2.79 × 10−29, respectively. When combined with 94 iiSNPs (a subset of which became microhaplotypes) the combined RMP was 5.49 × 10−63. Analysis of length-based and sequence-based autosomal STRs in STRUCTURE indicated that the Yavapai are most similar to the Hispanic population. While producing minimal increase in X- and Y-STR discrimination potential, access to flanking region data enabled identification of one novel X-STR and three Y-STR alleles relative to previous reports. Five ancestry-informative SNPs (aiSNPs) and two phenotype-informative SNPs (piSNPs) exhibited notable flanking region variation.

AB - Massively parallel sequencing (MPS) offers advantages over current capillary electrophoresis-based analysis of short tandem repeat (STR) loci for human identification testing. In particular STR repeat motif sequence information can be obtained, thereby increasing the discrimination power of some loci. While sequence variation within the repeat region is observed relatively frequently in some of the commonly used STRs, there is an additional degree of variation found in the flanking regions adjacent to the repeat motif. Repeat motif and flanking region sequence variation have been described for major population groups, however, not for more isolated populations. Flanking region sequence variation in STR and single nucleotide polymorphism (SNP) loci in the Yavapai population was analyzed using the ForenSeq™ DNA Signature Prep Kit and STRait Razor v2s. Seven and 14 autosomal STRs and identity-informative single nucleotide polymorphisms (iiSNPs), respectively, had some degree of flanking region variation. Three and four of these identity-informative loci, respectively, showed ≥5% increase in expected heterozygosity. The combined length- and sequence-based random match probabilities (RMPs) for 27 autosomal STRs were 6.11 × 10−26 and 2.79 × 10−29, respectively. When combined with 94 iiSNPs (a subset of which became microhaplotypes) the combined RMP was 5.49 × 10−63. Analysis of length-based and sequence-based autosomal STRs in STRUCTURE indicated that the Yavapai are most similar to the Hispanic population. While producing minimal increase in X- and Y-STR discrimination potential, access to flanking region data enabled identification of one novel X-STR and three Y-STR alleles relative to previous reports. Five ancestry-informative SNPs (aiSNPs) and two phenotype-informative SNPs (piSNPs) exhibited notable flanking region variation.

KW - Flanking region

KW - ForenSeq™ DNA Signature Prep Kit

KW - Massively parallel sequencing

KW - SNP

KW - STR

KW - STRait Razor v2s

KW - Sequence variation

UR - http://www.scopus.com/inward/record.url?scp=85014408685&partnerID=8YFLogxK

U2 - 10.1016/j.fsigen.2017.02.014

DO - 10.1016/j.fsigen.2017.02.014

M3 - Article

VL - 28

SP - 146

EP - 154

JO - Forensic Science International: Genetics

JF - Forensic Science International: Genetics

SN - 1872-4973

ER -