TY - JOUR
T1 - Characterization of genetic sequence variation of 58 STR loci in four major population groups
AU - Novroski, Nicole M.M.
AU - King, Jonathan L.
AU - Churchill, Jennifer D.
AU - Seah, Lay Hong
AU - Budowle, Bruce
N1 - Funding Information:
This work was supported in part by award no. 2015-DN-BX-K067, awarded by the National Institute of Justice, Office of Justice Programs, U.S. Department of Justice. The opinions, findings, and conclusions or recommendations expressed in this publication are those of the authors and do not necessarily reflect those of the U.S. Department of Justice.
Publisher Copyright:
© 2016 Elsevier Ireland Ltd
PY - 2016/11/1
Y1 - 2016/11/1
N2 - Massively parallel sequencing (MPS) can identify sequence variation within short tandem repeat (STR) alleles as well as their nominal allele lengths that traditionally have been obtained by capillary electrophoresis. Using the MiSeq FGx Forensic Genomics System (Illumina), STRait Razor, and in-house excel workbooks, genetic variation was characterized within STR repeat and flanking regions of 27 autosomal, 7 X chromosome and 24 Y-chromosome STR markers in 777 unrelated individuals from four population groups. Seven hundred and forty six autosomal, 227 X chromosome, and 324 Y-chromosome STR alleles were identified by sequence compared with 357 autosomal, 107 X chromosome, and 189 Y-chromosome STR alleles that were identified by length. Within the observed sequence variation, 227 autosomal, 156 X chromosome, and 112 Y-chromosome novel alleles were identified and described. One hundred and seventy six autosomal, 123 X chromosome, and 93 Y-chromosome sequence variants resided within STR repeat regions, and 86 autosomal, 39 X chromosome, and 20 Y-chromosome variants were located in STR flanking regions. Three markers, D18S51, DXS10135, and DYS385a-b had 1, 4, and 1 alleles, respectively, which contained both a novel repeat region variant and a flanking sequence variant in the same nucleotide sequence. There were 50 markers that demonstrated a relative increase in diversity with the variant sequence alleles compared with those of traditional nominal length alleles. These population data illustrate the genetic variation that exists in the commonly used STR markers in the selected population samples and provide allele frequencies for statistical calculations related to STR profiling with MPS data.
AB - Massively parallel sequencing (MPS) can identify sequence variation within short tandem repeat (STR) alleles as well as their nominal allele lengths that traditionally have been obtained by capillary electrophoresis. Using the MiSeq FGx Forensic Genomics System (Illumina), STRait Razor, and in-house excel workbooks, genetic variation was characterized within STR repeat and flanking regions of 27 autosomal, 7 X chromosome and 24 Y-chromosome STR markers in 777 unrelated individuals from four population groups. Seven hundred and forty six autosomal, 227 X chromosome, and 324 Y-chromosome STR alleles were identified by sequence compared with 357 autosomal, 107 X chromosome, and 189 Y-chromosome STR alleles that were identified by length. Within the observed sequence variation, 227 autosomal, 156 X chromosome, and 112 Y-chromosome novel alleles were identified and described. One hundred and seventy six autosomal, 123 X chromosome, and 93 Y-chromosome sequence variants resided within STR repeat regions, and 86 autosomal, 39 X chromosome, and 20 Y-chromosome variants were located in STR flanking regions. Three markers, D18S51, DXS10135, and DYS385a-b had 1, 4, and 1 alleles, respectively, which contained both a novel repeat region variant and a flanking sequence variant in the same nucleotide sequence. There were 50 markers that demonstrated a relative increase in diversity with the variant sequence alleles compared with those of traditional nominal length alleles. These population data illustrate the genetic variation that exists in the commonly used STR markers in the selected population samples and provide allele frequencies for statistical calculations related to STR profiling with MPS data.
KW - DNA signature prep kit
KW - ForenSeq™
KW - Forensic DNA
KW - Massively parallel sequencing
KW - SNP
KW - STR
KW - STRait razor
KW - Sequence variation
UR - http://www.scopus.com/inward/record.url?scp=84989201834&partnerID=8YFLogxK
U2 - 10.1016/j.fsigen.2016.09.007
DO - 10.1016/j.fsigen.2016.09.007
M3 - Article
C2 - 27697609
AN - SCOPUS:84989201834
SN - 1872-4973
VL - 25
SP - 214
EP - 226
JO - Forensic Science International: Genetics
JF - Forensic Science International: Genetics
ER -