Characterization of genetic sequence variation of 58 STR loci in four major population groups

Nicole M.M. Novroski, Jonathan L. King, Jennifer Churchill Cihlar, Lay Hong Seah, Bruce Budowle

Research output: Contribution to journalArticle

47 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)214-226
Number of pages13
JournalForensic Science International: Genetics
Volume25
DOIs
StatePublished - 1 Nov 2016

Fingerprint

Microsatellite Repeats
Y Chromosome
X Chromosome
Alleles
High-Throughput Nucleotide Sequencing
Chromosomes, Human, Pair 20
Capillary Electrophoresis
Genomics
Gene Frequency
Population

Keywords

  • DNA signature prep kit
  • ForenSeq™
  • Forensic DNA
  • Massively parallel sequencing
  • SNP
  • STR
  • STRait razor
  • Sequence variation

Cite this

@article{729baed7c386438fa08978e01e9bd81f,
title = "Characterization of genetic sequence variation of 58 STR loci in four major population groups",
abstract = "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.",
keywords = "DNA signature prep kit, ForenSeq™, Forensic DNA, Massively parallel sequencing, SNP, STR, STRait razor, Sequence variation",
author = "Novroski, {Nicole M.M.} and King, {Jonathan L.} and Cihlar, {Jennifer Churchill} and Seah, {Lay Hong} and Bruce Budowle",
year = "2016",
month = "11",
day = "1",
doi = "10.1016/j.fsigen.2016.09.007",
language = "English",
volume = "25",
pages = "214--226",
journal = "Forensic Science International: Genetics",
issn = "1872-4973",
publisher = "Elsevier Ireland Ltd",

}

Characterization of genetic sequence variation of 58 STR loci in four major population groups. / Novroski, Nicole M.M.; King, Jonathan L.; Cihlar, Jennifer Churchill; Seah, Lay Hong; Budowle, Bruce.

In: Forensic Science International: Genetics, Vol. 25, 01.11.2016, p. 214-226.

Research output: Contribution to journalArticle

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 - Cihlar, Jennifer Churchill

AU - Seah, Lay Hong

AU - Budowle, Bruce

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

VL - 25

SP - 214

EP - 226

JO - Forensic Science International: Genetics

JF - Forensic Science International: Genetics

SN - 1872-4973

ER -