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Genetic analysis of Southern Brazil subjects using the PowerSeq™ AUTO/Y system for short tandem repeat sequencing.
Forensic Sci Int Genet. 2018 03; 33:129-135.FS

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.

Authors+Show Affiliations

Molecular Biomedical Sciences, North Carolina State University, 1060 William Moore Dr., Raleigh, NC, 27607, USA; Forensic Sciences Institute, North Carolina State University, 1060 William Moore Dr., Raleigh, NC, 27607, USA. Electronic address: silva_deborah@hotmail.com.Laboratory of Human and Molecular Genetics, Pontificia Universidade Catolica do Rio Grande do Sul,Av. Ipiranga 6681, Porto Alegre, RS, 90619-900, Brazil.Molecular Biomedical Sciences, North Carolina State University, 1060 William Moore Dr., Raleigh, NC, 27607, USA; Forensic Sciences Institute, North Carolina State University, 1060 William Moore Dr., Raleigh, NC, 27607, USA.Molecular Biomedical Sciences, North Carolina State University, 1060 William Moore Dr., Raleigh, NC, 27607, USA; Forensic Sciences Institute, North Carolina State University, 1060 William Moore Dr., Raleigh, NC, 27607, USA.Laboratory of Human and Molecular Genetics, Pontificia Universidade Catolica do Rio Grande do Sul,Av. Ipiranga 6681, Porto Alegre, RS, 90619-900, Brazil.Molecular Biomedical Sciences, North Carolina State University, 1060 William Moore Dr., Raleigh, NC, 27607, USA; Forensic Sciences Institute, North Carolina State University, 1060 William Moore Dr., Raleigh, NC, 27607, USA.

Pub Type(s)

Journal Article
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

29275088

Citation

Silva, Deborah S B S., et al. "Genetic Analysis of Southern Brazil Subjects Using the PowerSeq™ AUTO/Y System for Short Tandem Repeat Sequencing." Forensic Science International. Genetics, vol. 33, 2018, pp. 129-135.
Silva DSBS, Sawitzki FR, Scheible MKR, et al. Genetic analysis of Southern Brazil subjects using the PowerSeq™ AUTO/Y system for short tandem repeat sequencing. Forensic Sci Int Genet. 2018;33:129-135.
Silva, D. S. B. S., Sawitzki, F. R., Scheible, M. K. R., Bailey, S. F., Alho, C. S., & Faith, S. A. (2018). Genetic analysis of Southern Brazil subjects using the PowerSeq™ AUTO/Y system for short tandem repeat sequencing. Forensic Science International. Genetics, 33, 129-135. https://doi.org/10.1016/j.fsigen.2017.12.008
Silva DSBS, et al. Genetic Analysis of Southern Brazil Subjects Using the PowerSeq™ AUTO/Y System for Short Tandem Repeat Sequencing. Forensic Sci Int Genet. 2018;33:129-135. PubMed PMID: 29275088.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genetic analysis of Southern Brazil subjects using the PowerSeq™ AUTO/Y system for short tandem repeat sequencing. AU - Silva,Deborah S B S, AU - Sawitzki,Fernanda R, AU - Scheible,Melissa K R, AU - Bailey,Sarah F, AU - Alho,Clarice S, AU - Faith,Seth A, Y1 - 2017/12/16/ PY - 2017/09/07/received PY - 2017/12/12/revised PY - 2017/12/15/accepted PY - 2017/12/25/pubmed PY - 2018/10/23/medline PY - 2017/12/25/entrez KW - PowerSeq™ AUTO/Y system KW - Sequence variation KW - Short tandem repeat KW - South Brazil SP - 129 EP - 135 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 33 N2 - 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. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/29275088/Genetic_analysis_of_Southern_Brazil_subjects_using_the_PowerSeq™_AUTO/Y_system_for_short_tandem_repeat_sequencing_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1872-4973(17)30294-6 DB - PRIME DP - Unbound Medicine ER -