- •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.
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.
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- An evaluation of the PowerSeq™ Auto System: a multiplex short tandem repeat marker kit compatible with massively parallel sequencing.Forensic Sci. Int. Genet. 2015; 19: 172-179
- Sequence variation of 22 autosomal STR loci detected by next generation sequencing.Forensic Sci. Int. Genet. 2016; 21: 15-21
- Performance and concordance of the ForenSeq™ system for autosomal and Y chromosome short tandem repeat sequencing of reference-type specimens.Forensic Sci. Int. Genet. 2017; 28 (F.R.): 1-9
- Genetic analysis of the yavapai native americans from West-Central Arizona using the illumina MiSeq FGx™ forensic genomics system.Forensic Sci. Int. Genet. 2016; 24: 18-23
- Sequence-based diversity of 23 autosomal STR loci in Koreans investigated using an in-house massively parallel sequencing panel.Forensic Sci. Int. Genet. 2017; 30: 134-140
- Exomic variants of an elderly cohort of Brazilians in the ABraOM database.Hum. Mutat. 2017; 00: 1-13
- Color and genomic ancestry in Brazilians.Proc. Natl. Acad. Sci. U. S. A. 2003; 100: 177-182
- Updated Brazilian STR allele frequency data using over 100,000 individuals: an analysis of CSF1PO, D3S1358 D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, penta D, Penta E, TH01, TPOX and vWA loci.Forensic Sci. Int. Genet. 2012; 6: 504-509
- Population data of 17 Y-STR loci from Rio Grande do Sul state (South Brazil).Forensic Sci. Int. Genet. 2009; 4: e31-e33
- Genetic data and de novo mutation rates in father-son pairs of 23 Y-STR loci in Southern Brazil population.Int. J. Legal Med. 2015; 129: 1221-1223
- 15 STR loci frequencies with mutation rates in the population from Rio Grande do Sul Southern Brazil.Forensic Sci. Int. Genet. 2009; 3: e35-e38
- Allele frequencies of 20 autosomal STR in the population from Rio Grande do Sul Southern Brazil.Forensic Sci. Int. Genet. 2015; 19: 15-17
- Population data of the 21 autosomal STRs included in the GlobalFiler® kits in population samples from five Brazilian regions.Forensic Sci. Int. Genet. 2017; 26: e28-e30
- Massively parallel sequencing of short tandem repeats-population data and mixture analysis results for the PowerSeq system.Forensic Sci. Int. Genet. 2016; 24: 86-96
- Secure and robust cloud computing for high-throughput forensic microsatellite sequence analysis and databasing.Forensic Sci. Int. Genet. 2017; 31: 40-47
- Massively parallel sequencing of forensic STRs: considerations of the DNA commission of the International Society for Forensic Genetics (ISFG) on minimal nomenclature requirements.Forensic Sci. Int. Genet. 2016; 22: 54-63
- Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment.Mol. Ecol. 2007; 16: 1099-1106
- GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research.Mol. Ecol. Note. 2006; 6: 288-295
- GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update.Bioinformatics. 2012; 28: 2537-2539
- Novel Y-chromosome short tandem repeat variants detected through the use of massively parallel sequencing.Genomics Proteomics Bioinf. 2015; 13: 250-257
- The Y-chromosomal STRs DYS481, DYS570 DYS576 and DYS643.Leg. Med. 2009; 11: S109-S110
Published online: December 16, 2017
Accepted: December 15, 2017
Received in revised form: December 12, 2017
Received: September 7, 2017
© 2017 Elsevier B.V. All rights reserved.