Highlights
- •Forensic STR loci sequence analysis was performed on a South Brazilian population.
- •Nine of 23 autosomal and six of 23 Y- STRs presented sequence variants.
- •D12S391 and DYS389II were the most polymorphic autosomal and Y loci, respectively.
- •Sequence-based STR analysis resulted in higher genetic population diversity.
- •A previously unreported allele variant was found in the vWA locus.
Abstract
With the advent of Next-Generation Sequencing technology, sequencing of short tandem
repeats (STRs) allows for a more detailed analysis when compared to size-based fragment
methods (capillary electrophoresis-CE). The implementation of high-throughput sequencing
can help uncover deeper genetic diversities of different populations. Subjects from
the South region of Brazil present a particular and more homogeneous ancestry background
when compared to other regions of the country. Both autosomal and Y- STRs have been
analyzed in these individuals; however, all analyses published to date encompass data
from CE-based fragment analysis. In this study, a genetic analysis of 59 individuals
from Southern Brazil was performed on STR sequences. Forensically relevant STRs were
PCR-enriched using a prototype of the PowerSeq™ AUTO/Y system (Promega Corp.). Next-generation
sequencing was performed on an Illumina MiSeq instrument. The raw data (FASTQ files)
were processed using a custom designed sequence processing tool, Altius. Isoalleles, which are sequence-based allelic variants that do not differ in length,
were observed in nine autosomal and in six Y- STRs from the core global forensic marker
set. The number of distinctive alleles based on sequence was higher when compared
to those based on length, 37.3% higher in autosomal STRs and 13.8% higher in Y-STRs.
The most polymorphic autosomal locus was D12S391, which presented 38 different sequence-based
alleles. Among the loci in the Y chromosome, DYS389II presented the highest number
of isoalleles. In comparison to CE analysis, Observed and Expected Heterozygosity,
Polymorphic Information Content (PIC) and Genetic Diversity also presented higher
values when the alleles were analyzed based on their sequence. For autosomal loci,
Polymorphic Information Content (PIC) was 2.6% higher for sequence-based data. Diversity
was 9.3% and 6.5% higher for autosomal and Y markers, respectively. In the analysis
of the repeat structures for the STR loci, a new allele variant was found for allele
18 in the vWA locus. The STR flanking regions were also further investigated and sixteen
variations were observed at nine autosomal STR loci and one Y-STR locus. The results
obtained in this study demonstrate the importance of genetic analysis based on sequencing
and highlight the diversity of the South Brazilian population when characterized by
STR sequencing.
Keywords
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Article info
Publication history
Published online: December 16, 2017
Accepted:
December 15,
2017
Received in revised form:
December 12,
2017
Received:
September 7,
2017
Identification
Copyright
© 2017 Elsevier B.V. All rights reserved.
