Highlights
- •250 Korean males were sequenced using MPS on PowerPlex® Y23 loci and a Y-SNP (M175) with small-sized amplicons.
- •Discordant genotypes were observed in DYS385, DYS439, and DYS576 between CE and MPS results.
- •12 Y-STR loci showed sequence variation and the most varied alleles occurred in DYS389II through the MPS analysis.
- •SNP, deletion, and insertion were observed in the flanking region of DYS481, DYS576, and DYS385, respectively.
- •Stutter and noise ratios of 23 Y-STRs using the developed MPS system were investigated.
Abstract
Next-generation sequencing (NGS) can produce massively parallel sequencing (MPS) data
for many targeted regions with a high depth of coverage, suggesting its successful
application to the amplicons of forensic genetic markers. In the present study, we
evaluated the practical utility of MPS in Y-chromosome short tandem repeat (Y-STR)
analysis using a multiplex polymerase chain reaction (PCR) system. The multiplex PCR
system simultaneously amplified 24 Y-chromosomal markers, including the PowerPlex®
Y23 loci (DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437,
DYS438, DYS439, DYS448, DYS456, DYS458, DYS481, DYS533, DYS549, DYS570, DYS576, DYS635,
DYS643, and YGATAH4) and the M175 marker with the small-sized amplicons ranging from
85 to 253 bp. The barcoded libraries for the amplicons of the 24 Y-chromosomal markers were
produced using a simplified PCR-based library preparation method and successfully
sequenced using MPS on a MiSeq® System with samples from 250 unrelated Korean males.
The genotyping concordance between MPS and the capillary electrophoresis (CE) method,
as well as the sequence structure of the 23 Y-STRs, were investigated. Three samples
exhibited discordance between the MPS and CE results at DYS385, DYS439, and DYS576.
There were 12 Y-STR loci that showed sequence variations in the alleles by a fragment
size determination, and the most varied alleles occurred in DYS389II with a different
sequence structure in the repeat region. The largest increase in gene diversity between
the CE and MPS results was in DYS437 at +34.41%. Single nucleotide polymorphisms (SNPs),
insertions, and deletions (indels) were observed in the flanking regions of DYS481,
DYS576, and DYS385, respectively. Stutter and noise ratios of the 23 Y-STRs using
the developed MPS system were also investigated. Based on these results, the MPS analysis
system used in this study could facilitate the investigation into the sequences of
the 23 Y-STRs in forensic genetics laboratories.
Keywords
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Article info
Publication history
Published online: August 28, 2016
Accepted:
August 27,
2016
Received in revised form:
August 23,
2016
Received:
February 24,
2016
Identification
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© 2016 Elsevier Ireland Ltd. All rights reserved.
