TY - JOUR
T1 - Novel Y-chromosome Short Tandem Repeat Variants Detected Through the Use of Massively Parallel Sequencing
AU - Warshauer, David H.
AU - Churchill, Jennifer D.
AU - Novroski, Nicole
AU - King, Jonathan L.
AU - Budowle, Bruce
N1 - Funding Information:
This work was supported in part by the grant “Development of Reference Sample DNA Profiling for Databases Using Next Generation Sequencing Technologies” (Award No. 2012-DN-BXK033) awarded to BB 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. The authors also would like to thank Illumina for its support during this study.
Publisher Copyright:
© 2015 The Authors.
PY - 2015/8
Y1 - 2015/8
N2 - Massively parallel sequencing (MPS) technology is capable of determining the sizes of short tandem repeat (STR) alleles as well as their individual nucleotide sequences. Thus, single nucleotide polymorphisms (SNPs) within the repeat regions of STRs and variations in the pattern of repeat units in a given repeat motif can be used to differentiate alleles of the same length. In this study, MPS was used to sequence 28 forensically-relevant Y-chromosome STRs in a set of 41 DNA samples from the 3 major U.S. population groups (African Americans, Caucasians, and Hispanics). The resulting sequence data, which were analyzed with STRait Razor v2.0, revealed 37 unique allele sequence variants that have not been previously reported. Of these, 19 sequences were variations of documented sequences resulting from the presence of intra-repeat SNPs or alternative repeat unit patterns. Despite a limited sampling, two of the most frequently-observed variants were found only in African American samples. The remaining 18 variants represented allele sequences for which there were no published data with which to compare. These findings illustrate the great potential of MPS with regard to increasing the resolving power of STR typing and emphasize the need for sample population characterization of STR alleles.
AB - Massively parallel sequencing (MPS) technology is capable of determining the sizes of short tandem repeat (STR) alleles as well as their individual nucleotide sequences. Thus, single nucleotide polymorphisms (SNPs) within the repeat regions of STRs and variations in the pattern of repeat units in a given repeat motif can be used to differentiate alleles of the same length. In this study, MPS was used to sequence 28 forensically-relevant Y-chromosome STRs in a set of 41 DNA samples from the 3 major U.S. population groups (African Americans, Caucasians, and Hispanics). The resulting sequence data, which were analyzed with STRait Razor v2.0, revealed 37 unique allele sequence variants that have not been previously reported. Of these, 19 sequences were variations of documented sequences resulting from the presence of intra-repeat SNPs or alternative repeat unit patterns. Despite a limited sampling, two of the most frequently-observed variants were found only in African American samples. The remaining 18 variants represented allele sequences for which there were no published data with which to compare. These findings illustrate the great potential of MPS with regard to increasing the resolving power of STR typing and emphasize the need for sample population characterization of STR alleles.
KW - Allele variants
KW - Massively parallel sequencing
KW - Nextera
KW - STRait Razor
KW - Sequence polymorphism
KW - Y-STR
UR - http://www.scopus.com/inward/record.url?scp=84944415530&partnerID=8YFLogxK
U2 - 10.1016/j.gpb.2015.08.001
DO - 10.1016/j.gpb.2015.08.001
M3 - Article
C2 - 26391384
AN - SCOPUS:84944415530
SN - 1672-0229
VL - 13
SP - 250
EP - 257
JO - Genomics, Proteomics and Bioinformatics
JF - Genomics, Proteomics and Bioinformatics
IS - 4
M1 - 162
ER -