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Carvalho Gontijo C, Porras-Hurtado LG, Freire-Aradas A, Fondevila M, Santos C, Salas A, Henao J, Isaza C, Beltrán L, Nogueira Silbiger V, Castillo A, Ibarra A, Moreno Chavez F, Söchtig J, Ruiz Y, Barreto G, Rondon F, Zabala W, Borjas L, de Oliveira SF, Carracedo A, Lareu MV, Phillips C. Corrigendum to "PIMA: A population informative multiplex for the Americas" [Forensic Sci. Int.: Genet. 44 (2020) 102200]. Forensic Sci Int Genet 2020; 48:102320. [PMID: 32574992 DOI: 10.1016/j.fsigen.2020.102320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/28/2020] [Indexed: 11/29/2022]
Affiliation(s)
- C Carvalho Gontijo
- Forensic Genetics Unit, University of Santiago de Compostela, Spain; Human Genetics Laboratory, Institute of Biological Sciences, University of Brasília, Brazil
| | - L G Porras-Hurtado
- Forensic Genetics Unit, University of Santiago de Compostela, Spain; Medical Genetics Laboratory, Human Molecular Genetics Research Group, Technology University of Pereira, Colombia
| | - A Freire-Aradas
- Forensic Genetics Unit, University of Santiago de Compostela, Spain
| | - M Fondevila
- Forensic Genetics Unit, University of Santiago de Compostela, Spain
| | - C Santos
- Forensic Genetics Unit, University of Santiago de Compostela, Spain
| | - A Salas
- Forensic Genetics Unit, University of Santiago de Compostela, Spain
| | - J Henao
- Medical Genetics Laboratory, Human Molecular Genetics Research Group, Technology University of Pereira, Colombia
| | - C Isaza
- Medical Genetics Laboratory, Human Molecular Genetics Research Group, Technology University of Pereira, Colombia
| | - L Beltrán
- Medical Genetics Laboratory, Human Molecular Genetics Research Group, Technology University of Pereira, Colombia; Health Science Faculty, Unidad Central del Valle del Cauca, Tulua, Colombia
| | - V Nogueira Silbiger
- Department of Clinical and Toxicological Analysis, Health Sciences Center, Federal University of Rio Grande do Norte, Brazil
| | - A Castillo
- Medical Genetic Laboratory, Industrial University of Santander (UIS), Colombia
| | - A Ibarra
- Medical Genetics Laboratory, University of Antioquia, Colombia
| | - F Moreno Chavez
- Servicio Médico Legal, Ministry of Justice and Human Rights of Chile, Santiago, Chile
| | - J Söchtig
- Forensic Genetics Unit, University of Santiago de Compostela, Spain
| | - Y Ruiz
- Forensic Genetics Unit, University of Santiago de Compostela, Spain
| | - G Barreto
- Human Molecular Genetics Research Group, University of Valle, Colombia
| | - F Rondon
- School of Biology, Industrial University of Santander (UIS), Colombia
| | - W Zabala
- Molecular Genetics Laboratory, Medical Genetics Unit, University of Zulia, Venezuela
| | - L Borjas
- Molecular Genetics Laboratory, Medical Genetics Unit, University of Zulia, Venezuela
| | - S F de Oliveira
- Human Genetics Laboratory, Institute of Biological Sciences, University of Brasília, Brazil.
| | - A Carracedo
- Forensic Genetics Unit, University of Santiago de Compostela, Spain; Grupo de Medicina Xenómica, CIBERER, University of Santiago de Compostela, Spain
| | - M V Lareu
- Forensic Genetics Unit, University of Santiago de Compostela, Spain
| | - C Phillips
- Forensic Genetics Unit, University of Santiago de Compostela, Spain.
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Carvalho Gontijo C, Porras-Hurtado LG, Freire-Aradas A, Fondevila M, Santos C, Salas A, Henao J, Isaza C, Beltrán L, Nogueira Silbiger V, Castillo A, Ibarra A, Moreno Chavez F, Söchtig J, Ruiz Y, Barreto G, Rondon F, Zabala W, Borjas L, de Oliveira SF, Carracedo A, Lareu MV, Phillips C. PIMA: A population informative multiplex for the Americas. Forensic Sci Int Genet 2019; 44:102200. [PMID: 31760353 DOI: 10.1016/j.fsigen.2019.102200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/01/2019] [Indexed: 11/26/2022]
Abstract
We describe an ancestry-informative autosomal SNP multiplex designed to be a small-scale, flexible panel that can complement uniparental markers in assessing the American variability (i.e. pre-Colombian) found in contemporary indigenous American populations. This study centered on choosing SNPs with the specific characteristics of: 1) extreme allele frequency differences between indigenous Americans and the African, European and East Asian population groups that contribute to present-day population variation in the Americas; 2) high informativeness-for-assignment In values; and 3) well-spaced genomic distribution and chromosomal separation from existing small-scale forensic ancestry marker sets. The resulting capillary electrophoresis SNaPshot single base extension test was named: PIMA (Population Informative Multiplex for the Americas), comprising 26 autosomal SNPs, a single X-chromosome SNP plus the amelogenin sex marker adapted for SNaPshot. PIMA complements the established 34plex forensic ancestry panel to provide a powerful and simple tool for the analysis of American populations, including those with admixed histories, commonly encountered in America. Comparing the results obtained with the combined marker panels of PIMA and 34plex to SNP data from a much larger ancestry panel allowed us to gauge their relative efficiency. PIMA+34plex gives equivalent power to the 314-SNP 'LACE' genomic ancestry control panel, while requiring a much smaller genotyping effort. The ancestry profiles and genetic structure of 22 populations spread across the American continent were estimated using PIMA+34plex data, and those estimates were contrasted with information provided by uniparental markers (mtDNA and Y-chromosome loci) for a small set of admixed individuals from Venezuela. Our results indicate that an American genetic component is efficiently detected in contemporary American populations using a small set of ancestry informative SNPs, and these co-ancestry estimates are consistent with the known history and demography of the Americas. The small scale and high population differentiation power of PIMA, particularly when combined with 34plex, provides a practical and powerful tool for genetic studies of American populations as well as forensic DNA analyses.
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Affiliation(s)
- C Carvalho Gontijo
- Forensic Genetics Unit, University of Santiago de Compostela, Spain; Human Genetics Laboratory, Institute of Biological Sciences, University of Brasília, Brazil
| | - L G Porras-Hurtado
- Forensic Genetics Unit, University of Santiago de Compostela, Spain; Medical Genetics Laboratory, Human Molecular Genetics Research Group, Technology University of Pereira, Colombia
| | - A Freire-Aradas
- Forensic Genetics Unit, University of Santiago de Compostela, Spain
| | - M Fondevila
- Forensic Genetics Unit, University of Santiago de Compostela, Spain
| | - C Santos
- Forensic Genetics Unit, University of Santiago de Compostela, Spain
| | - A Salas
- Forensic Genetics Unit, University of Santiago de Compostela, Spain
| | - J Henao
- Medical Genetics Laboratory, Human Molecular Genetics Research Group, Technology University of Pereira, Colombia
| | - C Isaza
- Medical Genetics Laboratory, Human Molecular Genetics Research Group, Technology University of Pereira, Colombia
| | - L Beltrán
- Medical Genetics Laboratory, Human Molecular Genetics Research Group, Technology University of Pereira, Colombia; Health Science Faculty, Unidad Central del Valle del Cauca, Tulua, Colombia
| | - V Nogueira Silbiger
- Department of Clinical and Toxicological Analysis, Health Sciences Center, Federal University of Rio Grande do Norte, Brazil
| | - A Castillo
- Medical Genetic Laboratory, Industrial University of Santander (UIS), Colombia
| | - A Ibarra
- Medical Genetics Laboratory, University of Antioquia, Colombia
| | - F Moreno Chavez
- Servicio Médico Legal, Ministry of Justice and Human Rights of Chile, Santiago, Chile
| | - J Söchtig
- Forensic Genetics Unit, University of Santiago de Compostela, Spain
| | - Y Ruiz
- Forensic Genetics Unit, University of Santiago de Compostela, Spain
| | - G Barreto
- Human Molecular Genetics Research Group, University of Valle, Colombia
| | - F Rondon
- Department of Clinical and Toxicological Analysis, Health Sciences Center, Federal University of Rio Grande do Norte, Brazil; Human Molecular Genetics Research Group, University of Valle, Colombia
| | - W Zabala
- Molecular Genetics Laboratory, Medical Genetics Unit, University of Zulia, Venezuela
| | - L Borjas
- Molecular Genetics Laboratory, Medical Genetics Unit, University of Zulia, Venezuela
| | - S F de Oliveira
- Human Genetics Laboratory, Institute of Biological Sciences, University of Brasília, Brazil.
| | - A Carracedo
- Forensic Genetics Unit, University of Santiago de Compostela, Spain; Grupo de Medicina Xenómica, CIBERER, University of Santiago de Compostela, Spain
| | - M V Lareu
- Forensic Genetics Unit, University of Santiago de Compostela, Spain
| | - C Phillips
- Forensic Genetics Unit, University of Santiago de Compostela, Spain.
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Bulbul O, Filoglu G, Zorlu T, Altuncul H, Freire-Aradas A, Söchtig J, Ruiz Y, Klintschar M, Triki-Fendri S, Rebai A, Phillips C, Lareu MV, Carracedo Á, Schneider PM. Inference of biogeographical ancestry across central regions of Eurasia. Int J Legal Med 2015; 130:73-9. [DOI: 10.1007/s00414-015-1246-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 08/10/2015] [Indexed: 11/28/2022]
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Maroñas O, Söchtig J, Ruiz Y, Phillips C, Carracedo Á, Lareu MV. The genetics of skin, hair, and eye color variation and its relevance to forensic pigmentation predictive tests. Forensic Sci Rev 2015; 27:13-40. [PMID: 26227136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
This review examines the potential application of single nucleotide polymorphism (SNP)-based predictive tests for skin, hair, and eye color to forensic analysis in support of police investigations lacking DNA database matches or eyewitness testimony. Brief descriptions of the biology of melanogenesis and the main genes involved are presented in order to understand the basis of common pigmentation variation in humans. We outline the most recently developed forensically sensitive multiplex tests that can be applied to investigative analyses. The review also describes the biology of the SNPs with the closest associations to, and therefore the best predictors for, common variation in eye, hair, and skin pigmentation. Because pigmentation pathways are complex in their patterns, many of the better-studied human albinism traits provide insight into how pigmentation SNPs interact, control, or modify gene expression and show varying degrees of association with the key genes identified to date. These aspects of SNP action are discussed in an overview of each of the functional groups of pigmentation genes.
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Affiliation(s)
- O Maroñas
- Unit of Forensic Genetics, Institute of Forensic Science, Genomic Medicine Group, University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | - J Söchtig
- Unit of Forensic Genetics, Institute of Forensic Science, Genomic Medicine Group, University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | - Y Ruiz
- Criminalistics Unit Against Violation of Fundamental Rights (UCCVDF-AMC), Attorney General, Metropolitan Area of Caracas, Santiago de León de Caracas, Venezuela
| | - C Phillips
- Unit of Forensic Genetics, Institute of Forensic Science, Genomic Medicine Group, University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain.
| | - Á Carracedo
- Unit of Forensic Genetics, Institute of Forensic Science, Genomic Medicine Group, University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain
- Center of Excellence in Genomic Medicine Research, King Abdelaziz University, Jeddah, Makkah Province, Saudi Arabia
| | - M V Lareu
- Unit of Forensic Genetics, Institute of Forensic Science, Genomic Medicine Group, University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain
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Freire-Aradas A, Ruiz Y, Phillips C, Maroñas O, Söchtig J, Tato AG, Dios JÁ, de Cal MC, Silbiger V, Luchessi A, Luchessi A, Chiurillo M, Carracedo Á, Lareu M. Exploring iris colour prediction and ancestry inference in admixed populations of South America. Forensic Sci Int Genet 2014; 13:3-9. [DOI: 10.1016/j.fsigen.2014.06.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 05/23/2014] [Accepted: 06/11/2014] [Indexed: 10/25/2022]
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Ruiz Y, Phillips C, Gomez-Tato A, Alvarez-Dios J, Casares de Cal M, Cruz R, Maroñas O, Söchtig J, Fondevila M, Rodriguez-Cid MJ, Carracedo A, Lareu MV. Further development of forensic eye color predictive tests. Forensic Sci Int Genet 2012; 7:28-40. [PMID: 22709892 DOI: 10.1016/j.fsigen.2012.05.009] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 04/20/2012] [Accepted: 05/17/2012] [Indexed: 11/25/2022]
Abstract
In forensic analysis predictive tests for external visible characteristics (or EVCs), including inference of iris color, represent a potentially useful tool to guide criminal investigations. Two recent studies, both focused on forensic testing, have analyzed single nucleotide polymorphism (SNP) genotypes underlying common eye color variation (Mengel-From et al., Forensic Sci. Int. Genet. 4:323 and Walsh et al., Forensic Sci. Int. Genet. 5:170). Each study arrived at different recommendations for eye color predictive tests aiming to type the most closely associated SNPs, although both confirmed rs12913832 in HERC2 as the key predictor, widely recognized as the most strongly associated marker with blue and brown iris colors. Differences between these two studies in identification of other eye color predictors may partly arise from varying approaches to assigning phenotypes, notably those not unequivocally blue or dark brown and therefore occupying an intermediate iris color continuum. We have developed two single base extension assays typing 37 SNPs in pigmentation-associated genes to study SNP-genotype based prediction of eye, skin, and hair color variation. These assays were used to test the performance of different sets of eye color predictors in 416 subjects from six populations of north and south Europe. The presence of a complex and continuous range of intermediate phenotypes distinct from blue and brown eye colors was confirmed by establishing eye color populations compared to genetic clusters defined using Structure software. Our study explored the effect of an expanded SNP combination beyond six markers has on the ability to predict eye color in a forensic test without extending the SNP assay excessively - thus maintaining a balance between the test's predictive value and an ability to reliably type challenging DNA with a multiplex of manageable size. Our evaluation used AUC analysis (area under the receiver operating characteristic curves) and naïve Bayesian likelihood-based classification approaches. To provide flexibility in SNP-based eye color predictive tests in forensic applications we modified an online Bayesian classifier, originally developed for genetic ancestry analysis, to provide a straightforward system to assign eye color likelihoods from a SNP profile combining additional informative markers from the predictors analyzed by our study plus those of Walsh and Mengel-From. Two advantages of the online classifier is the ability to submit incomplete SNP profiles, a common occurrence when typing challenging DNA, and the ability to handle physically linked SNPs showing independent effect, by allowing the user to input frequencies from SNP pairs or larger combinations. This system was used to include the submission of frequency data for the SNP pair rs12913832 and rs1129038: indicated by our study to be the two SNPs most closely associated to eye color.
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Affiliation(s)
- Y Ruiz
- Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Spain
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