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Forensic characterization of Brazilian regional populations through massive parallel sequencing of 124 SNPs included in HID ion Ampliseq Identity Panel.
Forensic Sci Int Genet. 2019 05; 40:74-84.FS

Abstract

Use of Massive Parallel Sequencing (MPS) techniques has been investigated by forensic community aiming introduction of such methods in routine forensic casework analyses. Interesting features presented by MPS include high-throughput, ability to simultaneous genotyping of significant number of samples and forensic markers, workflow automation, among others. Emergence of single nucleotide polymorphism (SNP) as forensic relevant markers was facilitated in this process, since concurrent typing of larger marker sets is necessary for obtaining same levels of individual discrimination provided by other marker categories. In this context, HID Ion Ampliseq Identity Panel is a commercial solution with forensic purposes comprising simultaneous analysis of 90 highly informative autosomal SNPs and 34 Y -chromosome superior clade SNPs for male lineage haplotyping. SNP typing can be obtained with smaller amplicons, and this panel was designed for efficient processing of critical or challenging forensic samples. In this work, a sample of 432 individuals from all five Brazilian geopolitical regions was evaluated with this panel, in order to access feasibility of this panel use in a national basis. Results obtained for all five regions, including forensic parameters, show that this marker set can be efficiently employed for Brazilian nationals in human identification or kinship determination applications, due to high levels of genetic discriminative information content displayed by Brazilians. Interpopulation comparison studies were executed among Brazilian regional populations and 26 worldwide populations, in order to access genetic stratification occurrence. Some levels of population structure were identified, and impact on database design was discussed. Y-chromosome haplotyping of Brazilian samples revealed high levels of European ancestry in Brazilian male lineages, and utility of haplotyping in real forensic casework is addressed. Finally, genotyping and sequencing efficiency with this panel were addressed, as an effort to appraise the adequacy of this panel use in Brazilian national forensic demands.

Authors+Show Affiliations

Setor Técnico-Científico, Superintendência Regional de Polícia Federal do RS, Porto Alegre, Brazil; Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil; Instituto Nacional de Ciência e Tecnologia INCT Ciências Forenses, Porto Alegre, Brazil. Electronic address: e.avila@edu.pucrs.br.Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil; Instituto Nacional de Ciência e Tecnologia INCT Ciências Forenses, Porto Alegre, Brazil.

Pub Type(s)

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

Language

eng

PubMed ID

30780121

Citation

Avila, Eduardo, et al. "Forensic Characterization of Brazilian Regional Populations Through Massive Parallel Sequencing of 124 SNPs Included in HID Ion Ampliseq Identity Panel." Forensic Science International. Genetics, vol. 40, 2019, pp. 74-84.
Avila E, Felkl AB, Graebin P, et al. Forensic characterization of Brazilian regional populations through massive parallel sequencing of 124 SNPs included in HID ion Ampliseq Identity Panel. Forensic Sci Int Genet. 2019;40:74-84.
Avila, E., Felkl, A. B., Graebin, P., Nunes, C. P., & Alho, C. S. (2019). Forensic characterization of Brazilian regional populations through massive parallel sequencing of 124 SNPs included in HID ion Ampliseq Identity Panel. Forensic Science International. Genetics, 40, 74-84. https://doi.org/10.1016/j.fsigen.2019.02.012
Avila E, et al. Forensic Characterization of Brazilian Regional Populations Through Massive Parallel Sequencing of 124 SNPs Included in HID Ion Ampliseq Identity Panel. Forensic Sci Int Genet. 2019;40:74-84. PubMed PMID: 30780121.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Forensic characterization of Brazilian regional populations through massive parallel sequencing of 124 SNPs included in HID ion Ampliseq Identity Panel. AU - Avila,Eduardo, AU - Felkl,Aline Brugnera, AU - Graebin,Pietra, AU - Nunes,Cláudia Paiva, AU - Alho,Clarice Sampaio, Y1 - 2019/02/13/ PY - 2018/10/01/received PY - 2019/02/11/revised PY - 2019/02/11/accepted PY - 2019/2/20/pubmed PY - 2019/4/26/medline PY - 2019/2/20/entrez KW - Brazilian population KW - Forensics KW - HID Ion Ampliseq Identity Panel KW - Massive Parallel Sequencing KW - SNP KW - Y-haplotypes SP - 74 EP - 84 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 40 N2 - Use of Massive Parallel Sequencing (MPS) techniques has been investigated by forensic community aiming introduction of such methods in routine forensic casework analyses. Interesting features presented by MPS include high-throughput, ability to simultaneous genotyping of significant number of samples and forensic markers, workflow automation, among others. Emergence of single nucleotide polymorphism (SNP) as forensic relevant markers was facilitated in this process, since concurrent typing of larger marker sets is necessary for obtaining same levels of individual discrimination provided by other marker categories. In this context, HID Ion Ampliseq Identity Panel is a commercial solution with forensic purposes comprising simultaneous analysis of 90 highly informative autosomal SNPs and 34 Y -chromosome superior clade SNPs for male lineage haplotyping. SNP typing can be obtained with smaller amplicons, and this panel was designed for efficient processing of critical or challenging forensic samples. In this work, a sample of 432 individuals from all five Brazilian geopolitical regions was evaluated with this panel, in order to access feasibility of this panel use in a national basis. Results obtained for all five regions, including forensic parameters, show that this marker set can be efficiently employed for Brazilian nationals in human identification or kinship determination applications, due to high levels of genetic discriminative information content displayed by Brazilians. Interpopulation comparison studies were executed among Brazilian regional populations and 26 worldwide populations, in order to access genetic stratification occurrence. Some levels of population structure were identified, and impact on database design was discussed. Y-chromosome haplotyping of Brazilian samples revealed high levels of European ancestry in Brazilian male lineages, and utility of haplotyping in real forensic casework is addressed. Finally, genotyping and sequencing efficiency with this panel were addressed, as an effort to appraise the adequacy of this panel use in Brazilian national forensic demands. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/30780121/Forensic_characterization_of_Brazilian_regional_populations_through_massive_parallel_sequencing_of_124_SNPs_included_in_HID_ion_Ampliseq_Identity_Panel_ DB - PRIME DP - Unbound Medicine ER -