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Valle-Silva GD, Souza FDND, Marcorin L, Pereira ALE, Carratto TMT, Debortoli G, Oliveira MLGD, Fracasso NCDA, Andrade ESD, Donadi EA, Norton HL, Parra EJ, Simões AL, Castelli EC, Mendes-Junior CT. Applicability of the SNPforID 52-plex panel for human identification and ancestry evaluation in a Brazilian population sample by next-generation sequencing. Forensic Sci Int Genet 2019; 40:201-209. [DOI: 10.1016/j.fsigen.2019.03.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 02/19/2019] [Accepted: 03/02/2019] [Indexed: 12/14/2022]
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Goodwin W, Alimat S. Analysis of four PCR/SNaPshot multiplex assays analyzing 52 SNP forID markers. Electrophoresis 2017; 38:1007-1015. [DOI: 10.1002/elps.201600383] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 12/05/2016] [Accepted: 12/10/2016] [Indexed: 11/10/2022]
Affiliation(s)
- William Goodwin
- School of Forensic and Applied Sciences; University of Central Lancashire; Preston United Kingdom of Great Britain and Northern Ireland
| | - Sharizah Alimat
- School of Forensic and Applied Sciences; University of Central Lancashire; Preston United Kingdom of Great Britain and Northern Ireland
- Biotechnology Section; Department of Chemistry Malaysia (MOSTI); Jalan Sultan, Petaling Jaya Selangor Malaysia
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Gomes SM, Bodner M, Souto L, Zimmermann B, Huber G, Strobl C, Röck AW, Achilli A, Olivieri A, Torroni A, Côrte-Real F, Parson W. Human settlement history between Sunda and Sahul: a focus on East Timor (Timor-Leste) and the Pleistocenic mtDNA diversity. BMC Genomics 2015; 16:70. [PMID: 25757516 PMCID: PMC4342813 DOI: 10.1186/s12864-014-1201-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 12/22/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Distinct, partly competing, "waves" have been proposed to explain human migration in(to) today's Island Southeast Asia and Australia based on genetic (and other) evidence. The paucity of high quality and high resolution data has impeded insights so far. In this study, one of the first in a forensic environment, we used the Ion Torrent Personal Genome Machine (PGM) for generating complete mitogenome sequences via stand-alone massively parallel sequencing and describe a standard data validation practice. RESULTS In this first representative investigation on the mitochondrial DNA (mtDNA) variation of East Timor (Timor-Leste) population including >300 individuals, we put special emphasis on the reconstruction of the initial settlement, in particular on the previously poorly resolved haplogroup P1, an indigenous lineage of the Southwest Pacific region. Our results suggest a colonization of southern Sahul (Australia) >37 kya, limited subsequent exchange, and a parallel incubation of initial settlers in northern Sahul (New Guinea) followed by westward migrations <28 kya. CONCLUSIONS The temporal proximity and possible coincidence of these latter dispersals, which encompassed autochthonous haplogroups, with the postulated "later" events of (South) East Asian origin pinpoints a highly dynamic migratory phase.
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Affiliation(s)
- Sibylle M Gomes
- Department of Biology, University of Aveiro, Campus de Santiago, Aveiro, Portugal.
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstr. 44, 6020, Innsbruck, Austria.
| | - Luis Souto
- Department of Biology, University of Aveiro, Campus de Santiago, Aveiro, Portugal.
- Cencifor Centro de Ciências Forenses, Coimbra, Portugal.
| | - Bettina Zimmermann
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstr. 44, 6020, Innsbruck, Austria.
| | - Gabriela Huber
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstr. 44, 6020, Innsbruck, Austria.
| | - Christina Strobl
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstr. 44, 6020, Innsbruck, Austria.
| | - Alexander W Röck
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstr. 44, 6020, Innsbruck, Austria.
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", University of Pavia, Pavia, Italy.
- Dipartimento di Chimica, Biologia e Biotecnologie, University of Perugia, Perugia, Italy.
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", University of Pavia, Pavia, Italy.
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", University of Pavia, Pavia, Italy.
| | | | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstr. 44, 6020, Innsbruck, Austria.
- Penn State Eberly College of Science, University Park, PA, USA.
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Moreira H, Costa H, Tavares F, Souto L. Genetic variation of 12 X-chromosomal STR loci in an East Timor sample. Int J Legal Med 2014; 129:257-8. [DOI: 10.1007/s00414-014-1126-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 11/14/2014] [Indexed: 11/27/2022]
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Canturk KM, Emre R, Kınoglu K, Başpınar B, Sahin F, Ozen M. Current status of the use of single-nucleotide polymorphisms in forensic practices. Genet Test Mol Biomarkers 2014; 18:455-60. [PMID: 24754266 DOI: 10.1089/gtmb.2013.0466] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Forensic geneticists often use short tandem repeats (STRs) to solve cases. However, STRs can be insufficient when DNA samples are degraded due to environmental exposure and mass disasters, alleged and real relatives are genetically related in paternity or kinship analyses, or a suspect is lacking. In such cases, single-nucleotide polymorphisms (SNPs) can provide valuable information and thus should be seriously considered as a tool to help resolve challenging cases. In this review, the current status of SNP analyses in forensic applications and the comparative advantages and disadvantages of SNPs with other biomarkers are discussed.
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Wei YL, Qin CJ, Liu HB, Jia J, Hu L, Li CX. Validation of 58 autosomal individual identification SNPs in three Chinese populations. Croat Med J 2014; 55:10-3. [PMID: 24577821 PMCID: PMC3944413 DOI: 10.3325/cmj.2014.55.10] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Aim To genotype and evaluate a panel of single-nucleotide polymorphisms for individual identification (IISNPs) in three Chinese populations: Chinese Han, Uyghur, and Tibetan. Methods Two previously identified panels of IISNPs, 86 unlinked IISNPs and SNPforID 52-plex markers, were pooled and analyzed. Four SNPs were included in both panels. In total, 132 SNPs were typed on Sequenom MassARRAY® platform in 330 individuals from Han Chinese, Uyghur, and Tibetan populations. Population genetic indices and forensic parameters were determined for all studied markers. Results No significant deviation from Hardy-Weinberg equilibrium was observed for any of the SNPs in 3 populations. Expected heterozygosity (He) ranged from 0.144 to 0.500 in Han Chinese, from 0.197 to 0.500 in Uyghur, and from 0.018 to 0.500 in Tibetan population. Wright's Fst values ranged from 0.0001 to 0.1613. Pairwise linkage disequilibrium (LD) calculations for all 132 SNPs showed no significant LD across the populations (r2<0.147). A subset of 58 unlinked IISNPs (r2<0.094) with He>0.450 and Fst values from 0.0002 to 0.0536 gave match probabilities of 10−25 and a cumulative probability of exclusion of 0.999992. Conclusion The 58 unlinked IISNPs with high heterozygosity have low allele frequency variation among 3 Chinese populations, which makes them excellent candidates for the development of multiplex assays for individual identification and paternity testing.
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Affiliation(s)
| | | | | | | | | | - Cai-Xia Li
- Cai-Xia Li, Institute of Forensic Science, Ministry of Public Security, Muxidi Nanli 17, Xicheng District, Beijing 100038, China,
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Comparison of the genetic background of different Colombian populations using the SNPforID 52plex identification panel. Int J Legal Med 2013; 128:19-25. [PMID: 23665814 DOI: 10.1007/s00414-013-0858-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Accepted: 03/28/2013] [Indexed: 12/17/2022]
Abstract
Various strategies for analysing SNP markers and genotyping have been published with the goal of obtaining informative profiles from biological samples that contain only small amounts of template and/or degraded DNA. In this study, a multiplex assay of 52 autosomal single-nucleotide polymorphisms (SNPs) was used to analyse 438 individuals from urban populations from different regions of Colombia, as well as a sample of 50 Native American individuals of the Pastos ethnic group from Nariño. To determine if significant differences in these 52 SNPs exist between the distinct regions of Colombia, genetic distance and admixture analyses were performed based on the available data for 17 different Colombian population groups and for population groups from Africa, Europe and America. The results demonstrate significant differences between the populations from the Southwest Andean, Central-West Andean, Central-East Andean, Orinoquian and northern Colombian Pacific Coast regions. Most of the regions exhibited a European and Native American admixture. One exception is the population from the region of Chocó (on the northern Pacific Coast), which exhibits a high proportion of African admixture (54 %). From the observed genetic backgrounds, it is possible to conclude that a single reference database for the entire country would not be suitable for forensic purposes. The allele frequencies and the forensically relevant parameters were calculated for all of the markers in each Colombian region with significant values for the combined matching probability (power of discrimination ≥0.99999999999999990) and the combined probability of exclusion (≥0.9990) in trios that were obtained from all of the population groups.
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Børsting C, Mikkelsen M, Morling N. Kinship Analysis with Diallelic SNPs - Experiences with the SNPforID Multiplex in an ISO17025 Accreditated Laboratory. ACTA ACUST UNITED AC 2012; 39:195-201. [PMID: 22851935 DOI: 10.1159/000338957] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 01/27/2012] [Indexed: 11/19/2022]
Abstract
BACKGROUND: The mutation rate of single nucleotide polymorphisms (SNPs) is estimated to be 100,000 times lower than that of short tandem repeats (STRs), which makes SNPs very suitable for relationship testing. The SNPforID multiplex assay was the first SNP typing assay that was a real alternative to the commonly used STR kits in kinship and crime case work and the first SNP assay to be validated in a forensic laboratory accredited according to the ISO17025 standard. METHODS: A total of 54 crime case samples were typed with the SNPforID multiplex assay. 30 samples from relationship cases were sequenced in selected SNP loci. RESULTS: It was demonstrated that mixtures were easily detected with the SNPforID assay by analyzing the signal strengths of the detected alleles. Unusual imbalances in signal strengths that were observed in a few individuals could be explained by unexpected SNPs in one of the primer binding sites. A complicated relationship case with four closely related individuals is presented. CONCLUSION: Mixtures can be detected with bi-allelic SNPs. The SNPforID assay is a very useful supplement to the STR kits in relationship testing.
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Affiliation(s)
- Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Denmark
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Børsting C, Tomas C, Morling N. Typing of 49 autosomal SNPs by single base extension and capillary electrophoresis for forensic genetic testing. Methods Mol Biol 2012; 830:87-107. [PMID: 22139655 DOI: 10.1007/978-1-61779-461-2_7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
We describe a method for simultaneous amplification of 49 autosomal single nucleotide polymorphisms (SNPs) by multiplex PCR and detection of the SNP alleles by single base extension (SBE) and capillary electrophoresis. All the SNPs may be amplified from only 100 pg of genomic DNA and the length of the amplicons range from 65 to 115 bp. The high sensitivity and the short amplicon sizes make the assay very suitable for typing of degraded DNA samples, and the low mutation rate of SNPs makes the assay very useful for relationship testing. Combined, these advantages make the assay well suited for disaster victim identifications, where the DNA from the victims may be highly degraded and the victims are identified via investigation of their relatives. The assay was validated according to the ISO 17025 standard and used for routine case work in our laboratory.
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Affiliation(s)
- Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark.
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Børsting C, Morling N. Reinvestigations of six unusual paternity cases by typing of autosomal single-nucleotide polymorphisms. Transfusion 2011; 52:425-30. [PMID: 21790631 DOI: 10.1111/j.1537-2995.2011.03260.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND In some relationship cases, the initial investigations of autosomal short tandem repeats (STRs) lead to an ambiguous conclusion and supplementary investigations become necessary. STUDY DESIGN AND METHODS Six unusual paternity cases were previously investigated by other researchers and published as case work examples in forensic journals. Here, the cases were reinvestigated by typing the samples for 49 autosomal single-nucleotide polymorphisms (SNPs) using the SNPforID multiplex assay. RESULTS Three cases were solved by the SNP investigation without the need for any additional testing. In two cases, the SNP results supported the conclusions based on STRs. In the last case, the SNP results spoke in favor of paternity, and the combined paternity index based on autosomal STRs and SNPs was 12.3 billion. Nevertheless, the alleged father was excluded by X-chromosome typing. CONCLUSION The case work examples underline the importance of performing supplementary investigations, and they advocate for the implementation of several panels that may be used in the highly unusual cases. Panels with SNPs or other markers with low mutation probabilities are preferable as supplementary markers, because the risk of detecting (additional) mutations is very low.
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Affiliation(s)
- Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
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Hou L, Phillips C, Azaro M, Brzustowicz LM, Bartlett CW. Validation of a cost-efficient multi-purpose SNP panel for disease based research. PLoS One 2011; 6:e19699. [PMID: 21611176 PMCID: PMC3096622 DOI: 10.1371/journal.pone.0019699] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 04/13/2011] [Indexed: 12/04/2022] Open
Abstract
Background Here we present convergent methodologies using theoretical calculations, empirical assessment on in-house and publicly available datasets as well as in silico simulations, that validate a panel of SNPs for a variety of necessary tasks in human genetics disease research before resources are committed to larger-scale genotyping studies on those samples. While large-scale well-funded human genetic studies routinely have up to a million SNP genotypes, samples in a human genetics laboratory that are not yet part of such studies may be productively utilized in pilot projects or as part of targeted follow-up work though such smaller scale applications require at least some genome-wide genotype data for quality control purposes such as DNA “barcoding” to detect swaps or contamination issues, determining familial relationships between samples and correcting biases due to population effects such as population stratification in pilot studies. Principal Findings Empirical performance in classification of relative types for any two given DNA samples (e.g., full siblings, parental, etc) indicated that for outbred populations the panel performs sufficiently to classify relationship in extended families and therefore also for smaller structures such as trios and for twin zygosity testing. Additionally, familial relationships do not significantly diminish the (mean match) probability of sharing SNP genotypes in pedigrees, further indicating the uniqueness of the “barcode.” Simulation using these SNPs for an African American case-control disease association study demonstrated that population stratification, even in complex admixed samples, can be adequately corrected under a range of disease models using the SNP panel. Conclusion The panel has been validated for use in a variety of human disease genetics research tasks including sample barcoding, relationship verification, population substructure detection and statistical correction. Given the ease of genotyping our specific assay contained herein, this panel represents a useful and economical panel for human geneticists.
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Affiliation(s)
- Liping Hou
- Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States of America
| | - Christopher Phillips
- Forensic Genetics Department, Genomic Medicine Group, University of Santiago de Compostela and Centro Nacional de Genotipado (CeGen), Genomic Medicine Group, Hospital Clínico Universitario, Galicia, Spain
| | - Marco Azaro
- Department of Genetics, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Linda M. Brzustowicz
- Department of Genetics, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Christopher W. Bartlett
- Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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