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Characterization of genetic sequence variation of 58 STR loci in four major population groups.
Forensic Sci Int Genet. 2016 11; 25:214-226.FS

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.

Authors+Show Affiliations

Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd. Fort Worth, TX 76107, USA. Electronic address: Nicole.Novroski@live.unthsc.edu.Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd. Fort Worth, TX 76107, USA.Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd. Fort Worth, TX 76107, USA.Department of Chemistry Malaysia Kuching, Ministry of Science, Technology and Innovation (MOSTI) Malaysia.Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd. Fort Worth, TX 76107, USA; Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia.

Pub Type(s)

Journal Article
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

27697609

Citation

Novroski, Nicole M M., et al. "Characterization of Genetic Sequence Variation of 58 STR Loci in Four Major Population Groups." Forensic Science International. Genetics, vol. 25, 2016, pp. 214-226.
Novroski NMM, King JL, Churchill JD, et al. Characterization of genetic sequence variation of 58 STR loci in four major population groups. Forensic Sci Int Genet. 2016;25:214-226.
Novroski, N. M. M., King, J. L., Churchill, J. D., Seah, L. H., & Budowle, B. (2016). Characterization of genetic sequence variation of 58 STR loci in four major population groups. Forensic Science International. Genetics, 25, 214-226. https://doi.org/10.1016/j.fsigen.2016.09.007
Novroski NMM, et al. Characterization of Genetic Sequence Variation of 58 STR Loci in Four Major Population Groups. Forensic Sci Int Genet. 2016;25:214-226. PubMed PMID: 27697609.
* Article titles in AMA citation format should be in sentence-case
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, Y1 - 2016/09/28/ PY - 2016/08/04/received PY - 2016/09/15/revised PY - 2016/09/27/accepted PY - 2016/10/23/pubmed PY - 2017/6/15/medline PY - 2016/10/5/entrez KW - DNA signature prep kit KW - ForenSeq™ KW - Forensic DNA KW - Massively parallel sequencing KW - SNP KW - STR KW - STRait razor KW - Sequence variation SP - 214 EP - 226 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 25 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. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/27697609/Characterization_of_genetic_sequence_variation_of_58_STR_loci_in_four_major_population_groups_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1872-4973(16)30170-3 DB - PRIME DP - Unbound Medicine ER -