Highlights
- •First comprehensive population study of sequence variation in 58 STR markers.
- •Sequence-based genotyping captures both repeat region and flanking region variation.
- •Hundreds of additional alleles were identified by MPS compared with length-based genotyping.
- •Results obtained by MPS and CE are highly concordant.
- •An up-to-date compendium of all known alleles for each marker has been generated.
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.
Keywords
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Article info
Publication history
Published online: September 28, 2016
Accepted:
September 27,
2016
Received in revised form:
September 15,
2016
Received:
August 4,
2016
Identification
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