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 - Churchill, Jennifer D.
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
N1 - Funding Information:
This study was partly supported by a National Institute of Justice grant 2014-DN-BX-K024 to Sreetharan Kanthaswamy and David Glenn Smith and a research grant to Kelly L McCulloh from the UC Davis Forensic Science Graduate Program. Additionally, the authors would like to thank Illumina for kindly providing library preparation and sequencing reagents.
Publisher Copyright:
© 2017 Elsevier B.V.
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
C2 - 28273507
AN - SCOPUS:85014408685
SN - 1872-4973
VL - 28
SP - 146
EP - 154
JO - Forensic Science International: Genetics
JF - Forensic Science International: Genetics
ER -