title: Novel Y-chromosome Short Tandem Repeat Variants Detected Through the Use of Massively Parallel Sequencing.
abstract: 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.
authors.affiliation: Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA.
authors.forename: David H
authors.initials: DH
authors.lastname: Warshauer
authors.affiliation: Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA.
authors.forename: Jennifer D
authors.initials: JD
authors.lastname: Churchill
authors.affiliation: Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA.
authors.forename: Nicole
authors.initials: N
authors.lastname: Novroski
authors.affiliation: Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA.
authors.forename: Jonathan L
authors.initials: JL
authors.lastname: King
authors.affiliation: Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah 21589, Saudi Arabia. Electronic address: Bruce.Budowle@unthsc.edu.
authors.forename: Bruce
authors.initials: B
authors.lastname: Budowle
mesh_terms: D001741:Black or African American / Q000235:genetics; D000483:Alleles; D001483:Base Sequence; D041322:Chromosomes, Human, Y / Q000235:genetics*; D004247:DNA / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006630:Hispanic or Latino / Q000235:genetics; D006801:Humans; D018895:Microsatellite Repeats / Q000235:genetics*; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D014481:United States; D044465:White People / Q000235:genetics
chemical_list: D004247:DNA
keywords: Allele variants; Massively parallel sequencing; Nextera; STRait Razor; Sequence polymorphism; Y-STR