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.

Developmental validation of the MiSeq FGx Forensic Genomics System for Targeted Next Generation Sequencing in Forensic DNA Casework and Database Laboratories

“…In some mixtures, CE data indicate a single source sample or a two-person mixture, where NGS detects alleles from three and upwards of five or more DNA contributors (David Ballard, personal communication). Since NGS detects and identifies intra-STR sequence variants [88][89][90], the total complement of alleles are provided, at the nucleotide level. Mixture studies described here demonstrated the ability of the MiSeq FGx TM System to detect shared, and unshared (unique, obligate) minor contributor alleles at less than 5% of the major donor.…”

Performance and concordance of the ForenSeq™ system for autosomal and Y chromosome short tandem repeat sequencing of reference-type specimens

“…While there are many reasons for this, a primary factor has been the lack of developmentally validated and commercially available start-to-finish kits targeting the marker systems (such as short tandem repeats; STRs) routinely typed for forensic purposes. Several papers in recent years have demonstrated the utility and potential of STR sequencing by NGS methods, however these studies have typically employed custom assays developed in-house ( [2][3][4][5][6][7][8][9][10], for example). An additional barrier to the implementation of STR sequencing had been the absence of software programs specifically intended for STR sequence data assembly, alignment and representation, though this gap has been directly addressed in the past few years by open-source solutions developed with forensic use in mind [11][12][13][14].…”

Massively Parallel Sequencing of Forensic STRs Using the Ion Chef™ and the Ion S5™ XL Systems,

“…Since 2015, the research community has shifted work to Miseq (7,11,12,14,16,(23)(24)(25)(26)(27) and Ion Torrent NGS machines (9,10,13,15,28) because 454 sequencers are no longer supported by their producer. Typing results for 48 autosomal STR markers (11,12,22,24), 29 Y-STR markers (10,24,25), and 9 X-STR markers (24) have been reported. For data analysis, software such as STRait Razor (29,30), MyFLq (31,32), STRinNGS (33) has been developed.…”

“…Sample types including commercial genomic DNA (12,24), blood (4,7,8,10,23), saliva (5,17,23,28), buccal swabs (4,8,24), semen (9,24,28), vaginal secretions (28), skin (28), bone (9,23), and muscle (9) have been successfully genotyped with NGS. Population data for African American, Caucasian, Hispanic (11,25,27), Danish (6), and East Asian (10,27) are documented.…”