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Forensic DNA Phenotyping: Predicting human appearance from crime scene material for investigative purposes. Forensic Sci Int Genet 2015; 18:33-48. [DOI: 10.1016/j.fsigen.2015.02.003] [Citation(s) in RCA: 227] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 01/29/2015] [Accepted: 02/11/2015] [Indexed: 01/17/2023]
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Dario P, Mouriño H, Oliveira AR, Lucas I, Ribeiro T, Porto MJ, Costa Santos J, Dias D, Corte Real F. Assessment of IrisPlex-based multiplex for eye and skin color prediction with application to a Portuguese population. Int J Legal Med 2015; 129:1191-200. [PMID: 26289415 DOI: 10.1007/s00414-015-1248-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 08/12/2015] [Indexed: 11/26/2022]
Abstract
DNA phenotyping research is one of the most emergent areas of forensic genetics. Predictions of externally visible characteristics are possible through analysis of single nucleotide polymorphisms. These tools can provide police with "intelligence" in cases where there are no obvious suspects and unknown biological samples found at the crime scene do not result in any criminal DNA database hits. IrisPlex, an eye color prediction assay, revealed high prediction rates for blue and brown eye color in European populations. However, this is less predictive in some non-European populations, probably due to admixing. When compared to other European countries, Portugal has a relatively admixed population, resulting from a genetic influx derived from its proximity to and historical relations with numerous African territories. The aim of this work was to evaluate the utility of IrisPlex in the Portuguese population. Furthermore, the possibility of supplementing this multiplex with additional markers to also achieve skin color prediction within this population was evaluated. For that, IrisPlex was augmented with additional SNP loci. Eye and skin color prediction was estimated using the multinomial logistic regression and binomial logistic regression models, respectively. The results demonstrated eye color prediction accuracies of the IrisPlex system of 90 and 60% for brown and blue eye color, respectively, and 77% for intermediate eye color, after allele frequency adjustment. With regard to skin color, it was possible to achieve a prediction accuracy of 93%. In the future, phenotypic determination multiplexes must include additional loci to permit skin color prediction as presented in this study as this can be an advantageous tool for forensic investigation.
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Affiliation(s)
- Paulo Dario
- INMLCF - National Institute of Legal Medicine and Forensic Sciences, Largo da Sé Nova, 3000-213, Coimbra, Portugal.
- Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016, Lisboa, Portugal.
- CENCIFOR - Forensic Sciences Centre, Largo da Sé Nova, 3000-213, Coimbra, Portugal.
- CESAM - Centre for Environmental and Marine Studies, Edifício C2, Campo Grande, 1749-016, Lisboa, Portugal.
| | - Helena Mouriño
- Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016, Lisboa, Portugal
| | - Ana Rita Oliveira
- Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016, Lisboa, Portugal
- CESAM - Centre for Environmental and Marine Studies, Edifício C2, Campo Grande, 1749-016, Lisboa, Portugal
| | - Isabel Lucas
- INMLCF - National Institute of Legal Medicine and Forensic Sciences, Largo da Sé Nova, 3000-213, Coimbra, Portugal
| | - Teresa Ribeiro
- INMLCF - National Institute of Legal Medicine and Forensic Sciences, Largo da Sé Nova, 3000-213, Coimbra, Portugal
- CENCIFOR - Forensic Sciences Centre, Largo da Sé Nova, 3000-213, Coimbra, Portugal
| | - Maria João Porto
- INMLCF - National Institute of Legal Medicine and Forensic Sciences, Largo da Sé Nova, 3000-213, Coimbra, Portugal
- CENCIFOR - Forensic Sciences Centre, Largo da Sé Nova, 3000-213, Coimbra, Portugal
| | - Jorge Costa Santos
- INMLCF - National Institute of Legal Medicine and Forensic Sciences, Largo da Sé Nova, 3000-213, Coimbra, Portugal
- CENCIFOR - Forensic Sciences Centre, Largo da Sé Nova, 3000-213, Coimbra, Portugal
- Faculty of Medicine, University of Lisbon, Av. Professor Egas Moniz, 1649-028, Lisboa, Portugal
| | - Deodália Dias
- Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016, Lisboa, Portugal
- CESAM - Centre for Environmental and Marine Studies, Edifício C2, Campo Grande, 1749-016, Lisboa, Portugal
| | - Francisco Corte Real
- INMLCF - National Institute of Legal Medicine and Forensic Sciences, Largo da Sé Nova, 3000-213, Coimbra, Portugal
- CENCIFOR - Forensic Sciences Centre, Largo da Sé Nova, 3000-213, Coimbra, Portugal
- Faculty of Medicine, University of Coimbra, Rua Larga, 3004-504, Coimbra, Portugal
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103
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Söchtig J, Phillips C, Maroñas O, Gómez-Tato A, Cruz R, Alvarez-Dios J, de Cal MÁC, Ruiz Y, Reich K, Fondevila M, Carracedo Á, Lareu MV. Exploration of SNP variants affecting hair colour prediction in Europeans. Int J Legal Med 2015; 129:963-75. [PMID: 26162598 DOI: 10.1007/s00414-015-1226-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 06/23/2015] [Indexed: 10/23/2022]
Abstract
DNA profiling is a key tool for forensic analysis; however, current methods identify a suspect either by direct comparison or from DNA database searches. In cases with unidentified suspects, prediction of visible physical traits e.g. pigmentation or hair distribution of the DNA donors can provide important probative information. This study aimed to explore single nucleotide polymorphism (SNP) variants for their effect on hair colour prediction. A discovery panel of 63 SNPs consisting of already established hair colour markers from the HIrisPlex hair colour phenotyping assay as well as additional markers for which associations to human pigmentation traits were previously identified was used to develop multiplex assays based on SNaPshot single-base extension technology. A genotyping study was performed on a range of European populations (n = 605). Hair colour phenotyping was accomplished by matching donor's hair to a graded colour category system of reference shades and photography. Since multiple SNPs in combination contribute in varying degrees to hair colour predictability in Europeans, we aimed to compile a compact marker set that could provide a reliable hair colour inference from the fewest SNPs. The predictive approach developed uses a naïve Bayes classifier to provide hair colour assignment probabilities for the SNP profiles of the key SNPs and was embedded into the Snipper online SNP classifier ( http://mathgene.usc.es/snipper/ ). Results indicate that red, blond, brown and black hair colours are predictable with informative probabilities in a high proportion of cases. Our study resulted in the identification of 12 most strongly associated SNPs to hair pigmentation variation in six genes.
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Affiliation(s)
- Jens Söchtig
- Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, A Coruña, Spain
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Lin L, Yee SW, Kim RB, Giacomini KM. SLC transporters as therapeutic targets: emerging opportunities. Nat Rev Drug Discov 2015; 14:543-60. [PMID: 26111766 DOI: 10.1038/nrd4626] [Citation(s) in RCA: 512] [Impact Index Per Article: 56.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Solute carrier (SLC) transporters - a family of more than 300 membrane-bound proteins that facilitate the transport of a wide array of substrates across biological membranes - have important roles in physiological processes ranging from the cellular uptake of nutrients to the absorption of drugs and other xenobiotics. Several classes of marketed drugs target well-known SLC transporters, such as neurotransmitter transporters, and human genetic studies have provided powerful insight into the roles of more-recently characterized SLC transporters in both rare and common diseases, indicating a wealth of new therapeutic opportunities. This Review summarizes knowledge on the roles of SLC transporters in human disease, describes strategies to target such transporters, and highlights current and investigational drugs that modulate SLC transporters, as well as promising drug targets.
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Affiliation(s)
- Lawrence Lin
- Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, California 94158, USA
| | - Sook Wah Yee
- Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, California 94158, USA
| | - Richard B Kim
- Division of Clinical Pharmacology, Department of Medicine, University of Western Ontario, London Health Science Centre, London, Ontario N6A 5A5, Canada
| | - Kathleen M Giacomini
- 1] Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, California 94158, USA. [2] Institute for Human Genetics, University of California San Francisco, San Francisco, California 94158, USA
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105
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Wei AH, Zang DJ, Zhang Z, Yang XM, Li W. Prenatal Genotyping of Four Common Oculocutaneous Albinism Genes in 51 Chinese Families. J Genet Genomics 2015; 42:279-86. [DOI: 10.1016/j.jgg.2015.05.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 05/17/2015] [Accepted: 05/18/2015] [Indexed: 11/28/2022]
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106
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Maroñas O, Phillips C, Söchtig J, Gomez-Tato A, Cruz R, Alvarez-Dios J, de Cal MC, Ruiz Y, Fondevila M, Carracedo Á, Lareu MV. Development of a forensic skin colour predictive test. Forensic Sci Int Genet 2014; 13:34-44. [DOI: 10.1016/j.fsigen.2014.06.017] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 06/25/2014] [Accepted: 06/30/2014] [Indexed: 11/29/2022]
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107
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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] [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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108
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Yun BM, Song JK, Lee JY. Exploratory investigation of genetic associations with basal cell carcinoma risk: genome-wide association study in Jeju Island, Korea. Asian Pac J Cancer Prev 2014; 15:7443-7. [PMID: 25227856 DOI: 10.7314/apjcp.2014.15.17.7443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AIM Little is known about the genetic associations with Basal cell carcinoma (BCC) risk in non-Caucasian populations, in which BCC is rare, as in Korea. We here conducted a pilot genome-wide association study (GWAS) in 12 patients and 48 standard controls. METHOD A total of 263,511 SNPs were analyzed with the Illumina HumanOmni1 Quad v1.0 DNA Analysis BeadChip for cases and Korean HapMap 570K for controls. RESULTS SNP-based analyses, based on the allele genetic model with adjustment for sex and age showed suggestive associations with BCC risk for 6 SNPs with a P-value (P < 0.0005). However, these associations were not statistically significant after Bonferroni correction: rs1040503, rs2216491, rs13407683, rs4751072, rs9891263, and rs1368474. In addition, results from gene-based analyses showed suggestive associations with BCC risk for 33 candidate genes with a P-value (P <0.0005). Consistent with previous GWAS and replication studies in Caucasian populations, PADI6, RHOU and SLC45A2 were identified as having null associations with BCC (P > 0.05), likely due to the smaller sample size. CONCLUSIONS Although this was a small-scale negative study, to our knowledge, we have conducted the first GWAS for BCC risk in an Asian population. Further large studies in non-Caucasian populations are required to achieve statistical significance and confirm these findings.
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Affiliation(s)
- Byung Min Yun
- Departments of Plastic and Reconstructive Surgery, School of Medicine, Jeju National University , Jeju, Korea E-mail :
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Ghodsinejad Kalahroudi V, Kamalidehghan B, Arasteh Kani A, Aryani O, Tondar M, Ahmadipour F, Chung LY, Houshmand M. Two novel tyrosinase (TYR) gene mutations with pathogenic impact on oculocutaneous albinism type 1 (OCA1). PLoS One 2014; 9:e106656. [PMID: 25216246 PMCID: PMC4162572 DOI: 10.1371/journal.pone.0106656] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Accepted: 08/06/2014] [Indexed: 11/19/2022] Open
Abstract
Oculocutaneous albinism (OCA) is a heterogeneous group of autosomal recessive disorders resulting from mutations of the tyrosinase (TYR) gene and presents with either complete or partial absence of pigment in the skin, hair and eyes due to a defect in an enzyme involved in the production of melanin. In this study, mutations in the TYR gene of 30 unrelated Iranian OCA1 patients and 100 healthy individuals were examined using PCR-sequencing. Additionally, in order to predict the possible effects of new mutations on the structure and function of tyrosinase, these mutations were analyzed by SIFT, PolyPhen and I-Mutant 2 software. Here, two new pathogenic p.C89S and p.H180R mutations were detected in two OCA1 patients. Moreover, the R402Q and S192Y variants, which are common non-pathogenic polymorphisms, were detected in 17.5% and 35% of the patients, respectively. The outcome of this study has extended the genotypic spectrum of OCA1 patients, which paves the way for more efficient carrier detection and genetic counseling.
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Affiliation(s)
- Vadieh Ghodsinejad Kalahroudi
- Department of Biology, Kharazmi University, Tehran, Iran
- Department of Medical Genetics, Special Medical Center, Tehran, Iran
| | - Behnam Kamalidehghan
- Department of Pharmacy, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Omid Aryani
- Department of Medical Genetics, Special Medical Center, Tehran, Iran
| | - Mahdi Tondar
- Department of Medical Genetics, Special Medical Center, Tehran, Iran
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, D.C., United States of America
| | - Fatemeh Ahmadipour
- Department of Pharmacy, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Lip Yong Chung
- Department of Pharmacy, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Massoud Houshmand
- Department of Medical Genetics, Special Medical Center, Tehran, Iran
- Department of Medical Genetics, National Institute for Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
- * E-mail:
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110
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López S, García Ó, Yurrebaso I, Flores C, Acosta-Herrera M, Chen H, Gardeazabal J, Careaga JM, Boyano MD, Sánchez A, Ratón-Nieto JA, Sevilla A, Smith-Zubiaga I, de Galdeano AG, Martinez-Cadenas C, Izagirre N, de la Rúa C, Alonso S. The interplay between natural selection and susceptibility to melanoma on allele 374F of SLC45A2 gene in a South European population. PLoS One 2014; 9:e104367. [PMID: 25093503 PMCID: PMC4122405 DOI: 10.1371/journal.pone.0104367] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 07/08/2014] [Indexed: 11/18/2022] Open
Abstract
We aimed to study the selective pressures interacting on SLC45A2 to investigate the interplay between selection and susceptibility to disease. Thus, we enrolled 500 volunteers from a geographically limited population (Basques from the North of Spain) and by resequencing the whole coding region and intron 5 of the 34 most and the 34 least pigmented individuals according to the reflectance distribution, we observed that the polymorphism Leu374Phe (L374F, rs16891982) was statistically associated with skin color variability within this sample. In particular, allele 374F was significantly more frequent among the individuals with lighter skin. Further genotyping an independent set of 558 individuals of a geographically wider population with known ancestry in the Spanish population also revealed that the frequency of L374F was significantly correlated with the incident UV radiation intensity. Selection tests suggest that allele 374F is being positively selected in South Europeans, thus indicating that depigmentation is an adaptive process. Interestingly, by genotyping 119 melanoma samples, we show that this variant is also associated with an increased susceptibility to melanoma in our populations. The ultimate driving force for this adaptation is unknown, but it is compatible with the vitamin D hypothesis. This shows that molecular evolution analysis can be used as a useful technology to predict phenotypic and biomedical consequences in humans.
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Affiliation(s)
- Saioa López
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Leioa, Bizkaia, Spain
| | - Óscar García
- Ertzaintza Forensic Unit, Erandio, Bizkaia, Spain
| | | | - Carlos Flores
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Tenerife, Spain
- Applied Genomics Group (G2A), Genetics Laboratory, Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, Tenerife, Spain
| | - Marialbert Acosta-Herrera
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Tenerife, Spain
- Research Unit, Universitary Hospital Dr. Negrin, Las Palmas de Gran Canaria, Spain
| | - Hua Chen
- Center for Computational Genetics and Genomics, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Jesús Gardeazabal
- Dermatology Service, BioCruces Health Research Institute, Cruces University Hospital, Cruces-Barakaldo, Bizkaia, Spain
| | - Jesús María Careaga
- Dermatology Service, BioCruces Health Research Institute, Basurto University Hospital, Bilbao, Bizkaia, Spain
| | - María Dolores Boyano
- Department of Cell Biology and Histology, University of the Basque Country UPV/EHU, Leioa, Bizkaia, Spain
| | - Ana Sánchez
- Dermatology Service, BioCruces Health Research Institute, Basurto University Hospital, Bilbao, Bizkaia, Spain
| | - Juan Antonio Ratón-Nieto
- Dermatology Service, BioCruces Health Research Institute, Cruces University Hospital, Cruces-Barakaldo, Bizkaia, Spain
| | - Arrate Sevilla
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Leioa, Bizkaia, Spain
| | - Isabel Smith-Zubiaga
- Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Leioa, Bizkaia, Spain
| | - Alicia García de Galdeano
- Department of Cell Biology and Histology, University of the Basque Country UPV/EHU, Leioa, Bizkaia, Spain
| | | | - Neskuts Izagirre
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Leioa, Bizkaia, Spain
| | - Concepción de la Rúa
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Leioa, Bizkaia, Spain
| | - Santos Alonso
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Leioa, Bizkaia, Spain
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111
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Ali M, Liu X, Pillai EN, Chen P, Khor CC, Ong RTH, Teo YY. Characterizing the genetic differences between two distinct migrant groups from Indo-European and Dravidian speaking populations in India. BMC Genet 2014; 15:86. [PMID: 25053360 PMCID: PMC4120727 DOI: 10.1186/1471-2156-15-86] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 07/11/2014] [Indexed: 12/15/2022] Open
Abstract
Background India is home to many ethnically and linguistically diverse populations. It is hypothesized that history of invasions by people from Persia and Central Asia, who are referred as Aryans in Hindu Holy Scriptures, had a defining role in shaping the Indian population canvas. A shift in spoken languages from Dravidian languages to Indo-European languages around 1500 B.C. is central to the Aryan Invasion Theory. Here we investigate the genetic differences between two sub-populations of India consisting of: (1) The Indo-European language speaking Gujarati Indians with genome-wide data from the International HapMap Project; and (2) the Dravidian language speaking Tamil Indians with genome-wide data from the Singapore Genome Variation Project. Results We implemented three population genetics measures to identify genomic regions that are significantly differentiated between the two Indian populations originating from the north and south of India. These measures singled out genomic regions with: (i) SNPs exhibiting significant variation in allele frequencies in the two Indian populations; and (ii) differential signals of positive natural selection as quantified by the integrated haplotype score (iHS) and cross-population extended haplotype homozygosity (XP-EHH). One of the regions that emerged spans the SLC24A5 gene that has been functionally shown to affect skin pigmentation, with a higher degree of genetic sharing between Gujarati Indians and Europeans. Conclusions Our finding points to a gene-flow from Europe to north India that provides an explanation for the lighter skin tones present in North Indians in comparison to South Indians.
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Affiliation(s)
| | | | | | | | | | | | - Yik-Ying Teo
- Life Sciences Institute, National University of Singapore, Singapore, Singapore.
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112
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Kocarnik JM, Park SL, Han J, Dumitrescu L, Cheng I, Wilkens LR, Schumacher FR, Kolonel L, Carlson CS, Crawford DC, Goodloe RJ, Dilks H, Baker P, Richardson D, Ambite JL, Song F, Quresh AA, Zhang M, Duggan D, Hutter C, Hindorff LA, Bush WS, Kooperberg C, Le Marchand L, Peters U. Replication of associations between GWAS SNPs and melanoma risk in the Population Architecture Using Genomics and Epidemiology (PAGE) Study. J Invest Dermatol 2014; 134:2049-2052. [PMID: 24480881 PMCID: PMC4057959 DOI: 10.1038/jid.2014.53] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Jonathan M Kocarnik
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
| | - Sungshim Lani Park
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, USA
| | - Jiali Han
- Channing Laboratory, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA; Department of Epidemiology, Fairbanks School of Public Health, Simon Cancer Center, Indiana University, Indianapolis, Indiana, USA
| | - Logan Dumitrescu
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Iona Cheng
- Cancer Prevention Institute of California, Fremont, California, USA
| | - Lynne R Wilkens
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, USA
| | - Fredrick R Schumacher
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Laurence Kolonel
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, USA
| | - Chris S Carlson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Dana C Crawford
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Robert J Goodloe
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, USA
| | - Holli Dilks
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, USA
| | - Paxton Baker
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, USA
| | - Danielle Richardson
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, USA
| | - José Luis Ambite
- Information Sciences Institute, University of Southern California, Marina del Rey, California, USA
| | - Fengju Song
- Channing Laboratory, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA; Department of Epidemiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Abrar A Quresh
- Department of Dermatology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Mingfeng Zhang
- Department of Dermatology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - David Duggan
- Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Carolyn Hutter
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, NCI, NIH, Bethesda, Maryland, USA
| | - Lucia A Hindorff
- Division of Genomic Medicine, NHGRI, NIH, Bethesda, Maryland, USA
| | - William S Bush
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, USA; Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, USA
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
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113
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Bonilla C, Ness AR, Wills AK, Lawlor DA, Lewis SJ, Davey Smith G. Skin pigmentation, sun exposure and vitamin D levels in children of the Avon Longitudinal Study of Parents and Children. BMC Public Health 2014; 14:597. [PMID: 24924479 PMCID: PMC4067096 DOI: 10.1186/1471-2458-14-597] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 05/27/2014] [Indexed: 11/10/2022] Open
Abstract
Background It has been hypothesised that light skin pigmentation has arisen to ensure adequate levels of vitamin D as human populations moved out of Africa and into higher latitudes. Vitamin D, which is primarily obtained through exposure to sunlight (specifically ultraviolet radiation B (UVR-B)), has been inversely associated with several complex diseases. Greater sun exposure, on the other hand, is a well-known cause of skin cancer. The potential of UVR to be beneficial for some health outcomes but detrimental for others has prompted a public health debate on how to balance the positive and negative consequences of sun exposure. In this study we aimed to determine the validity of the evolutionary hypothesis linking lighter skin with higher vitamin D concentrations in a European population. Additionally, we aimed to examine the influence of pigmentation on personal behaviour towards sunlight exposure and the effects of this behaviour on vitamin D. Methods We combined genetic variants strongly associated with skin colour, tanning or freckling to create genetic scores for each of these phenotypes. We examined the association of the scores with pigmentary traits, sun exposure and serum 25-hydroxyvitamin D (25(OH)D) levels among children of the Avon Longitudinal Study of Parents and Children (ALSPAC, N = 661 to 5649). Results We found that fairer-skinned children, i.e. those with higher pigmentation score values, had higher levels of 25(OH)D (0.6 nmol/l; 95% CI 0.2, 1.0; per unit increase in skin colour score; N = 5649). These children also used more protection against the damaging effects of UVR. Conclusions In this population taking protective measures against sunburn and skin cancer does not seem to remove the positive effect that having a less pigmented skin has on vitamin D production. Our findings require further replication as skin pigmentation showed only a small effect on circulating 25(OH)D.
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Affiliation(s)
- Carolina Bonilla
- School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.
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Ding Q, Hu Y, Xu S, Wang CC, Li H, Zhang R, Yan S, Wang J, Jin L. Neanderthal origin of the haplotypes carrying the functional variant Val92Met in the MC1R in modern humans. Mol Biol Evol 2014; 31:1994-2003. [PMID: 24916031 DOI: 10.1093/molbev/msu180] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Skin color is one of the most visible and important phenotypes of modern humans. Melanocyte-stimulating hormone and its receptor played an important role in regulating skin color. In this article, we present evidence of Neanderthal introgression encompassing the melanocyte-stimulating hormone receptor gene MC1R. The haplotypes from Neanderthal introgression diverged with the Altai Neanderthal 103.3 ka, which postdates the anatomically modern human-Neanderthal divergence. We further discovered that all of the putative Neanderthal introgressive haplotypes carry the Val92Met variant, a loss-of-function variant in MC1R that is associated with multiple dermatological traits including skin color and photoaging. Frequency of this Neanderthal introgression is low in Europeans (∼5%), moderate in continental East Asians (∼30%), and high in Taiwanese aborigines (60-70%). As the putative Neanderthal introgressive haplotypes carry a loss-of-function variant that could alter the function of MC1R and is associated with multiple traits related to skin color, we speculate that the Neanderthal introgression may have played an important role in the local adaptation of Eurasians to sunlight intensity.
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Affiliation(s)
- Qiliang Ding
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Ya Hu
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Shuhua Xu
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, China
| | - Chuan-Chao Wang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Hui Li
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Ruyue Zhang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Shi Yan
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, ChinaCAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, China
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Jagirdar K, Smit DJ, Ainger SA, Lee KJ, Brown DL, Chapman B, Zhen Zhao Z, Montgomery GW, Martin NG, Stow JL, Duffy DL, Sturm RA. Molecular analysis of common polymorphisms within the human Tyrosinase locus and genetic association with pigmentation traits. Pigment Cell Melanoma Res 2014; 27:552-64. [PMID: 24739399 DOI: 10.1111/pcmr.12253] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 04/14/2014] [Indexed: 01/13/2023]
Abstract
We have compared the melanogenic activities of cultured melanocytes carrying two common TYR alleles as homozygous 192S-402R wild-type, heterozygous and homozygous variant. This includes assays of TYR protein, DOPAoxidase activity, glycosylation and temperature sensitivity of protein and DOPAoxidase levels. Homozygous wild-type strains on average had higher levels of TYR protein and enzyme activity than other genotypes. Homozygous 402Q/Q melanocytes produced significantly less TYR protein, displayed altered trafficking and glycosylation, with reduced DOPAoxidase. However, near wild-type TYR activity levels could be recovered at lower growth temperature. In a sample population from Southeast Queensland, these two polymorphisms were present on four TYR haplotypes, designated as WT 192S-402R, 192Y-402R and 192S-402Q with a double-variant 192Y-402Q of low frequency at 1.9%. Based on cell culture findings and haplotype associations, we have used an additive model to assess the penetrance of the ten possible TYR genotypes derived from the combination of these haplotypes.
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Affiliation(s)
- Kasturee Jagirdar
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld, Australia
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de Cerqueira CCS, Hünemeier T, Gomez-Valdés J, Ramallo V, Volasko-Krause CD, Barbosa AAL, Vargas-Pinilla P, Dornelles RC, Longo D, Rothhammer F, Bedoya G, Canizales-Quinteros S, Acuña-Alonzo V, Gallo C, Poletti G, González-José R, Salzano FM, Callegari-Jacques SM, Schuler-Faccini L, Ruiz-Linares A, Cátira Bortolini M. Implications of the admixture process in skin color molecular assessment. PLoS One 2014; 9:e96886. [PMID: 24809478 PMCID: PMC4014568 DOI: 10.1371/journal.pone.0096886] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 04/12/2014] [Indexed: 12/19/2022] Open
Abstract
The understanding of the complex genotype-phenotype architecture of human pigmentation has clear implications for the evolutionary history of humans, as well as for medical and forensic practices. Although dozens of genes have previously been associated with human skin color, knowledge about this trait remains incomplete. In particular, studies focusing on populations outside the European-North American axis are rare, and, until now, admixed populations have seldom been considered. The present study was designed to help fill this gap. Our objective was to evaluate possible associations of 18 single nucleotide polymorphisms (SNPs), located within nine genes, and one pseudogene with the Melanin Index (MI) in two admixed Brazilian populations (Gaucho, N = 352; Baiano, N = 148) with different histories of geographic and ethnic colonization. Of the total sample, four markers were found to be significantly associated with skin color, but only two (SLC24A5 rs1426654, and SLC45A2 rs16891982) were consistently associated with MI in both samples (Gaucho and Baiano). Therefore, only these 2 SNPs should be preliminarily considered to have forensic significance because they consistently showed the association independently of the admixture level of the populations studied. We do not discard that the other two markers (HERC2 rs1129038 and TYR rs1126809) might be also relevant to admixed samples, but additional studies are necessary to confirm the real importance of these markers for skin pigmentation. Finally, our study shows associations of some SNPs with MI in a modern Brazilian admixed sample, with possible applications in forensic genetics. Some classical genetic markers in Euro-North American populations are not associated with MI in our sample. Our results point out the relevance of considering population differences in selecting an appropriate set of SNPs as phenotype predictors in forensic practice.
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Affiliation(s)
| | - Tábita Hünemeier
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Jorge Gomez-Valdés
- Laboratorio de Antropología Física, Departamento de Anatomía, Facultad de Medicina, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
| | - Virgínia Ramallo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | | | - Pedro Vargas-Pinilla
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Danaê Longo
- Instituto Federal de Educação, Ciência e Tecnologia Farroupilha, Alegrete, Brazil
| | - Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapacá, Facultad de Medicina, Universidad de Chile and Centro de Investigaciones del Hombre en el Desierto, Arica, Chile
| | | | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Victor Acuña-Alonzo
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia, Mexico City, Mexico
| | - Carla Gallo
- Laboratorio de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Giovanni Poletti
- Laboratorio de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | | | - Francisco Mauro Salzano
- Departamento de Estatística, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Sídia Maria Callegari-Jacques
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Departamento de Estatística, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Lavínia Schuler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- INAGEMP – Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil
| | - Andrés Ruiz-Linares
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London, United Kingdom
| | - Maria Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- * E-mail:
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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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Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the last 5,000 y. Proc Natl Acad Sci U S A 2014; 111:4832-7. [PMID: 24616518 DOI: 10.1073/pnas.1316513111] [Citation(s) in RCA: 154] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Pigmentation is a polygenic trait encompassing some of the most visible phenotypic variation observed in humans. Here we present direct estimates of selection acting on functional alleles in three key genes known to be involved in human pigmentation pathways--HERC2, SLC45A2, and TYR--using allele frequency estimates from Eneolithic, Bronze Age, and modern Eastern European samples and forward simulations. Neutrality was overwhelmingly rejected for all alleles studied, with point estimates of selection ranging from around 2-10% per generation. Our results provide direct evidence that strong selection favoring lighter skin, hair, and eye pigmentation has been operating in European populations over the last 5,000 y.
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119
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Durso DF, Bydlowski SP, Hutz MH, Suarez-Kurtz G, Magalhães TR, Junho Pena SD. Association of genetic variants with self-assessed color categories in Brazilians. PLoS One 2014; 9:e83926. [PMID: 24416183 PMCID: PMC3885524 DOI: 10.1371/journal.pone.0083926] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 11/09/2013] [Indexed: 01/07/2023] Open
Abstract
The Brazilian population was formed by extensive admixture of three different ancestral roots: Amerindians, Europeans and Africans. Our previous work has shown that at an individual level, ancestry, as estimated using molecular markers, was a poor predictor of color in Brazilians. We now investigate if SNPs known to be associated with human skin pigmentation can be used to predict color in Brazilians. For that, we studied the association of fifteen SNPs, previously known to be linked with skin color, in 243 unrelated Brazilian individuals self-identified as White, Browns or Blacks from Rio de Janeiro and 212 unrelated Brazilian individuals self-identified as White or Blacks from São Paulo. The significance of association of SNP genotypes with self-assessed color was evaluated using partial regression analysis. After controlling for ancestry estimates as covariates, only four SNPs remained significantly associated with skin pigmentation: rs1426654 and rs2555364 within SLC24A5, rs16891982 at SLC45A2 and rs1042602 at TYR. These loci are known to be involved in melanin synthesis or transport of melanosomes. We found that neither genotypes of these SNPs, nor their combination with biogeographical ancestry in principal component analysis, could predict self-assessed color in Brazilians at an individual level. However, significant correlations did emerge at group level, demonstrating that even though elements other than skin, eye and hair pigmentation do influence self-assessed color in Brazilians, the sociological act of self-classification is still substantially dependent of genotype at these four SNPs.
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Affiliation(s)
- Danielle Fernandes Durso
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Sergio Paulo Bydlowski
- Laboratório de Genética e Hematologia Molecular, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Mara Helena Hutz
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Guilherme Suarez-Kurtz
- Coordenação de Pesquisa/Divisão de Farmacologia, Instituto Nacional do Câncer (INCA), Rio de Janeiro, RJ, Brazil
| | - Tiago R. Magalhães
- Laboratório de Genômica Clínica, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Sérgio Danilo Junho Pena
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
- Laboratório de Genômica Clínica, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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Basu Mallick C, Iliescu FM, Möls M, Hill S, Tamang R, Chaubey G, Goto R, Ho SYW, Gallego Romero I, Crivellaro F, Hudjashov G, Rai N, Metspalu M, Mascie-Taylor CGN, Pitchappan R, Singh L, Mirazon-Lahr M, Thangaraj K, Villems R, Kivisild T. The light skin allele of SLC24A5 in South Asians and Europeans shares identity by descent. PLoS Genet 2013; 9:e1003912. [PMID: 24244186 PMCID: PMC3820762 DOI: 10.1371/journal.pgen.1003912] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 09/07/2013] [Indexed: 11/18/2022] Open
Abstract
Skin pigmentation is one of the most variable phenotypic traits in humans. A non-synonymous substitution (rs1426654) in the third exon of SLC24A5 accounts for lighter skin in Europeans but not in East Asians. A previous genome-wide association study carried out in a heterogeneous sample of UK immigrants of South Asian descent suggested that this gene also contributes significantly to skin pigmentation variation among South Asians. In the present study, we have quantitatively assessed skin pigmentation for a largely homogeneous cohort of 1228 individuals from the Southern region of the Indian subcontinent. Our data confirm significant association of rs1426654 SNP with skin pigmentation, explaining about 27% of total phenotypic variation in the cohort studied. Our extensive survey of the polymorphism in 1573 individuals from 54 ethnic populations across the Indian subcontinent reveals wide presence of the derived-A allele, although the frequencies vary substantially among populations. We also show that the geospatial pattern of this allele is complex, but most importantly, reflects strong influence of language, geography and demographic history of the populations. Sequencing 11.74 kb of SLC24A5 in 95 individuals worldwide reveals that the rs1426654-A alleles in South Asian and West Eurasian populations are monophyletic and occur on the background of a common haplotype that is characterized by low genetic diversity. We date the coalescence of the light skin associated allele at 22–28 KYA. Both our sequence and genome-wide genotype data confirm that this gene has been a target for positive selection among Europeans. However, the latter also shows additional evidence of selection in populations of the Middle East, Central Asia, Pakistan and North India but not in South India. Human skin color is one of the most visible aspects of human diversity. The genetic basis of pigmentation in Europeans has been understood to some extent, but our knowledge about South Asians has been restricted to a handful of studies. It has been suggested that a single nucleotide difference in SLC24A5 accounts for 25–38% European-African pigmentation differences and correlates with lighter skin. This genetic variant has also been associated with skin color variation among South Asians living in the UK. Here, we report a study based on a homogenous cohort of South India. Our results confirm that SLC24A5 plays a key role in pigmentation diversity of South Asians. Country-wide screening of the variant reveals that the light skin associated allele is widespread in the Indian subcontinent and its complex patterning is shaped by a combination of processes involving selection and demographic history of the populations. By studying the variation of SLC24A5 sequences among a diverse set of individuals, we show that the light skin associated allele in South Asians is identical by descent to that found in Europeans. Our study also provides new insights into positive selection acting on the gene and the evolutionary history of light skin in humans.
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Affiliation(s)
- Chandana Basu Mallick
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Biocentre, Tartu, Estonia
- * E-mail: (CBM); (TK)
| | - Florin Mircea Iliescu
- Division of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Märt Möls
- Estonian Biocentre, Tartu, Estonia
- Institute of Mathematical Statistics, University of Tartu, Tartu, Estonia
| | - Sarah Hill
- Division of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Rakesh Tamang
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Rie Goto
- Division of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Simon Y. W. Ho
- School of Biological Sciences, University of Sydney, Sydney, Australia
| | - Irene Gallego Romero
- Division of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Federica Crivellaro
- Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge, United Kingdom
| | - Georgi Hudjashov
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Biocentre, Tartu, Estonia
| | - Niraj Rai
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Mait Metspalu
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Biocentre, Tartu, Estonia
| | | | - Ramasamy Pitchappan
- Chettinad Academy of Research and Education, Chettinad Health City, Chennai, India
| | - Lalji Singh
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Banaras Hindu University, Varanasi, India
| | - Marta Mirazon-Lahr
- Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge, United Kingdom
| | | | - Richard Villems
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Biocentre, Tartu, Estonia
- Estonian Academy of Sciences, Tallinn, Estonia
| | - Toomas Kivisild
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Biocentre, Tartu, Estonia
- Division of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (CBM); (TK)
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Molecular phylogeography of a human autosomal skin color locus under natural selection. G3-GENES GENOMES GENETICS 2013; 3:2059-67. [PMID: 24048645 PMCID: PMC3815065 DOI: 10.1534/g3.113.007484] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Divergent natural selection caused by differences in solar exposure has resulted in distinctive variations in skin color between human populations. The derived light skin color allele of the SLC24A5 gene, A111T, predominates in populations of Western Eurasian ancestry. To gain insight into when and where this mutation arose, we defined common haplotypes in the genomic region around SLC24A5 across diverse human populations and deduced phylogenetic relationships between them. Virtually all chromosomes carrying the A111T allele share a single 78-kb haplotype that we call C11, indicating that all instances of this mutation in human populations share a common origin. The C11 haplotype was most likely created by a crossover between two haplotypes, followed by the A111T mutation. The two parental precursor haplotypes are found from East Asia to the Americas but are nearly absent in Africa. The distributions of C11 and its parental haplotypes make it most likely that these two last steps occurred between the Middle East and the Indian subcontinent, with the A111T mutation occurring after the split between the ancestors of Europeans and East Asians.
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Hudjashov G, Villems R, Kivisild T. Global patterns of diversity and selection in human tyrosinase gene. PLoS One 2013; 8:e74307. [PMID: 24040225 PMCID: PMC3770694 DOI: 10.1371/journal.pone.0074307] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 07/31/2013] [Indexed: 01/09/2023] Open
Abstract
Global variation in skin pigmentation is one of the most striking examples of environmental adaptation in humans. More than two hundred loci have been identified as candidate genes in model organisms and a few tens of these have been found to be significantly associated with human skin pigmentation in genome-wide association studies. However, the evolutionary history of different pigmentation genes is rather complex: some loci have been subjected to strong positive selection, while others evolved under the relaxation of functional constraints in low UV environment. Here we report the results of a global study of the human tyrosinase gene, which is one of the key enzymes in melanin production, to assess the role of its variation in the evolution of skin pigmentation differences among human populations. We observe a higher rate of non-synonymous polymorphisms in the European sample consistent with the relaxation of selective constraints. A similar pattern was previously observed in the MC1R gene and concurs with UV radiation-driven model of skin color evolution by which mutations leading to lower melanin levels and decreased photoprotection are subject to purifying selection at low latitudes while being tolerated or even favored at higher latitudes because they facilitate UV-dependent vitamin D production. Our coalescent date estimates suggest that the non-synonymous variants, which are frequent in Europe and North Africa, are recent and have emerged after the separation of East and West Eurasian populations.
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Affiliation(s)
- Georgi Hudjashov
- Evolutionary Biology Group, Estonian Biocentre, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- * E-mail:
| | - Richard Villems
- Evolutionary Biology Group, Estonian Biocentre, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Academy of Sciences, Tallinn, Estonia
| | - Toomas Kivisild
- Evolutionary Biology Group, Estonian Biocentre, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Division of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
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Schnetkamp PPM. The SLC24 gene family of Na⁺/Ca²⁺-K⁺ exchangers: from sight and smell to memory consolidation and skin pigmentation. Mol Aspects Med 2013; 34:455-64. [PMID: 23506883 DOI: 10.1016/j.mam.2012.07.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 03/09/2012] [Indexed: 01/28/2023]
Abstract
Members of the SLC24 gene family encode K(+)-dependent Na(+)/Ca(2+) exchangers (NCKX) that utilize both the inward Na(+) and outward K(+) gradients to extrude Ca(2+) from cells. There are five human SLC24 genes that play a role in biological process as diverse as vision in retinal rod and cone photoreceptors, olfaction, skin pigmentation and at least three of the five genes are also widely expressed in the brain. Here I review the functional, physiological and structural features of NCKX proteins that have emerged in the past few years.
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Affiliation(s)
- Paul P M Schnetkamp
- Department of Physiology & Pharmacology, Hotchkiss Brain Institute, Faculty of Medicine, University of Calgary, 3330 Hospital Dr. NW, Calgary, Canada AB T2N 4N1.
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Hart KL, Kimura SL, Mushailov V, Budimlija ZM, Prinz M, Wurmbach E. Improved eye- and skin-color prediction based on 8 SNPs. Croat Med J 2013; 54:248-56. [PMID: 23771755 PMCID: PMC3694299 DOI: 10.3325/cmj.2013.54.248] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Aim To improve the 7-plex system to predict eye and skin color by increasing precision and detailed phenotypic descriptions. Methods Analysis of an eighth single nucleotide polymorphism (SNP), rs12896399 (SLC24A4), showed a statistically significant association with human eye color (P = 0.007) but a rather poor strength of agreement (κ = 0.063). This SNP was added to the 7-plex system (rs12913832 at HERC2, rs1545397 at OCA2, rs16891982 at SLC45A2, rs1426654 at SLC24A5, rs885479 at MC1R, rs6119471 at ASIP, and rs12203592 at IRF4). Further, the instruction guidelines on the interpretation of genotypes were changed to create a new 8-plex system. This was based on the analysis of an 803-sample training set of various populations. The newly developed 8-plex system can predict the eye colors brown, green, and blue, and skin colors light, not dark, and not light. It is superior to the 7-plex system with its additional ability to predict blue eye and light skin color. Results The 8-plex system was tested on an additional 212 samples, the test set. Analysis showed that the number of positive descriptions for eye colors as being brown, green, or blue increased significantly (P = 6.98e-15, z-score: -7.786). The error rate for eye-color prediction was low, at approximately 5%, while the skin color prediction showed no error in the test set (1% in training set). Conclusions We can conclude that the new 8-plex system for the prediction of eye and skin color substantially enhances its former version.
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Affiliation(s)
- Katie L Hart
- Office of Chief Medical Examiner, Department of Forensic Biology, 421East 26th Street, Box 12-79, New York, NY 10016, USA
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Morice-Picard F, Lasseaux E, François S, Simon D, Rooryck C, Bieth E, Colin E, Bonneau D, Journel H, Walraedt S, Leroy BP, Meire F, Lacombe D, Arveiler B. SLC24A5 mutations are associated with non-syndromic oculocutaneous albinism. J Invest Dermatol 2013; 134:568-571. [PMID: 23985994 DOI: 10.1038/jid.2013.360] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Fanny Morice-Picard
- Maladies Rares: Génétique et Métabolisme (MRGM), University Bordeaux, Bordeaux, France; Service de Génétique Médicale, CHU de Bordeaux, Bordeaux, France
| | - Eulalie Lasseaux
- Service de Génétique Médicale, CHU de Bordeaux, Bordeaux, France
| | - Stéphane François
- Maladies Rares: Génétique et Métabolisme (MRGM), University Bordeaux, Bordeaux, France
| | - Delphine Simon
- Maladies Rares: Génétique et Métabolisme (MRGM), University Bordeaux, Bordeaux, France
| | - Caroline Rooryck
- Maladies Rares: Génétique et Métabolisme (MRGM), University Bordeaux, Bordeaux, France; Service de Génétique Médicale, CHU de Bordeaux, Bordeaux, France
| | - Eric Bieth
- Service de Génétique Médicale, CHU de Toulouse, Toulouse, France
| | - Estelle Colin
- Département de Biochimie et Génétique, LUNAM Université d'Angers, CHU Angers, Angers, France
| | - Dominique Bonneau
- Département de Biochimie et Génétique, LUNAM Université d'Angers, CHU Angers, Angers, France
| | - Hubert Journel
- Unité de Génétique Médicale, CH de Vannes, Vannes, France
| | - Sophie Walraedt
- Department of Ophthalmology, Ghent University Hospital & Ghent University, Ghent, Belgium
| | - Bart P Leroy
- Department of Ophthalmology, Ghent University Hospital & Ghent University, Ghent, Belgium; Center for Medical Genetics, Ghent University Hospital & Ghent University, Ghent, Belgium
| | - Francoise Meire
- Department of Pediatric Ophthalmology, Queen Fabiola Children's University Hospital, Brussels, Belgium
| | - Didier Lacombe
- Maladies Rares: Génétique et Métabolisme (MRGM), University Bordeaux, Bordeaux, France; Service de Génétique Médicale, CHU de Bordeaux, Bordeaux, France
| | - Benoit Arveiler
- Maladies Rares: Génétique et Métabolisme (MRGM), University Bordeaux, Bordeaux, France; Service de Génétique Médicale, CHU de Bordeaux, Bordeaux, France.
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127
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Chabris CF, Lee JJ, Benjamin DJ, Beauchamp JP, Glaeser EL, Borst G, Pinker S, Laibson DI. Why it is hard to find genes associated with social science traits: theoretical and empirical considerations. Am J Public Health 2013; 103 Suppl 1:S152-66. [PMID: 23927501 DOI: 10.2105/ajph.2013.301327] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
OBJECTIVES We explain why traits of interest to behavioral scientists may have a genetic architecture featuring hundreds or thousands of loci with tiny individual effects rather than a few with large effects and why such an architecture makes it difficult to find robust associations between traits and genes. METHODS We conducted a genome-wide association study at 2 sites, Harvard University and Union College, measuring more than 100 physical and behavioral traits with a sample size typical of candidate gene studies. We evaluated predictions that alleles with large effect sizes would be rare and most traits of interest to social science are likely characterized by a lack of strong directional selection. We also carried out a theoretical analysis of the genetic architecture of traits based on R.A. Fisher's geometric model of natural selection and empirical analyses of the effects of selection bias and phenotype measurement stability on the results of genetic association studies. RESULTS Although we replicated several known genetic associations with physical traits, we found only 2 associations with behavioral traits that met the nominal genome-wide significance threshold, indicating that physical and behavioral traits are mainly affected by numerous genes with small effects. CONCLUSIONS The challenge for social science genomics is the likelihood that genes are connected to behavioral variation by lengthy, nonlinear, interactive causal chains, and unraveling these chains requires allying with personal genomics to take advantage of the potential for large sample sizes as well as continuing with traditional epidemiological studies.
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Affiliation(s)
- Christopher F Chabris
- Christopher F. Chabris is with the Department of Psychology, Union College, Schenectady, NY. James J. Lee, Gregoire Borst, and Steven Pinker are with the Department of Psychology, Harvard University, Cambridge, MA. Daniel J. Benjamin is with the Department of Economics, Cornell University, Ithaca, NY. Jonathan P. Beauchamp, Edward L. Glaeser, and David I. Laibson are with the Department of Economics, Harvard University
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128
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Lim JE, Oh B. Allelic frequencies of 20 visible phenotype variants in the korean population. Genomics Inform 2013; 11:93-6. [PMID: 23843775 PMCID: PMC3704932 DOI: 10.5808/gi.2013.11.2.93] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 05/21/2013] [Accepted: 05/23/2013] [Indexed: 11/20/2022] Open
Abstract
The prediction of externally visible characteristics from DNA has been studied for forensic genetics over the last few years. Externally visible characteristics include hair, skin, and eye color, height, and facial morphology, which have high heritability. Recent studies using genome-wide association analysis have identified genes and variations that correlate with human visible phenotypes and developed phenotype prediction programs. However, most prediction models were constructed and validated based on genotype and phenotype information on Europeans. Therefore, we need to validate prediction models in diverse ethnic populations. In this study, we selected potentially useful variations for forensic science that are associated with hair and eye color, iris pattern, and facial morphology, based on previous studies, and analyzed their frequencies in 1,920 Koreans. Among 20 single nucleotide polymorphisms (SNPs), 10 SNPs were polymorphic, 6 SNPs were very rare (minor allele frequency < 0.005), and 4 SNPs were monomorphic in the Korean population. Even though the usability of these SNPs should be verified by an association study in Koreans, this study provides 10 potential SNP markers for forensic science for externally visible characteristics in the Korean population.
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Affiliation(s)
- Ji Eun Lim
- Department of Biomedical Engineering, Kyung Hee University School of Medicine, Seoul 130-701, Korea
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129
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Xu X, Dong GX, Hu XS, Miao L, Zhang XL, Zhang DL, Yang HD, Zhang TY, Zou ZT, Zhang TT, Zhuang Y, Bhak J, Cho Y, Dai WT, Jiang TJ, Xie C, Li R, Luo SJ. The Genetic Basis of White Tigers. Curr Biol 2013; 23:1031-5. [DOI: 10.1016/j.cub.2013.04.054] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 03/19/2013] [Accepted: 04/18/2013] [Indexed: 10/26/2022]
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130
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Poetsch M, Wiegand A, Harder M, Blöhm R, Rakotomavo N, Freitag-Wolf S, von Wurmb-Schwark N. Determination of population origin: a comparison of autosomal SNPs, Y-chromosomal and mtDNA haplogroups using a Malagasy population as example. Eur J Hum Genet 2013; 21:1423-8. [PMID: 23612573 DOI: 10.1038/ejhg.2013.51] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 02/13/2013] [Accepted: 02/20/2013] [Indexed: 11/09/2022] Open
Abstract
Y-chromosomal and mitochondrial DNA (mtDNA) polymorphisms have been used for population studies for a long time. However, there is another possibility to define the origin of a population: autosomal single-nucleotide polymorphisms (SNPs) whose allele frequencies differ considerably in different populations. In an attempt to compare the usefulness of these approaches we studied a population from Madagascar using all the three mentioned approaches. Former investigations of Malagasy maternal (mtDNA) and paternal (Y chromosome) lineages have led to the assumption that the Malagasy are an admixed population with an African and Asian-Indonesian heritage. Our additional study demonstrated that more than two-third of the Malagasy investigated showed clearly a West African genotype regarding only the autosomal SNPs despite the fact that 64% had an Asian mtDNA and more than 70% demonstrated an Asian-Indonesian heritage in either mtDNA or Y-chromosomal haplogroup or both. Nonetheless, the admixture of the Malagasy could be confirmed. A clear African or Asian-Indonesian heritage according to all the three DNA approaches investigated was only found in 14% and 1% of male samples, respectively. Not even the European or Northern African influences, detected in 9% of males (Y-chromosomal analysis) and 11% of samples (autosomal SNPs) were consistent. No Malagasy in our samples showed a European or Northern African origin in both categories. So, the analysis of autosomal SNPs could confirm the admixed character of the Malagasy population, even if it pointed to a greater African influence as detectable by Y-chromosomal or mtDNA analysis.
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Affiliation(s)
- Micaela Poetsch
- Institute of Legal Medicine, University Hospital Essen, Essen, Germany
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131
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Liu F, Wen B, Kayser M. Colorful DNA polymorphisms in humans. Semin Cell Dev Biol 2013; 24:562-75. [PMID: 23587773 DOI: 10.1016/j.semcdb.2013.03.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 03/26/2013] [Indexed: 10/26/2022]
Abstract
In this review article we summarize current knowledge on how variation on the DNA level influences human pigmentation including color variation of iris, hair, and skin. We review recent progress in the field of human pigmentation genetics by focusing on the genes and DNA polymorphisms discovered to be involved in determining human pigmentation traits, their association with diseases particularly skin cancers, and their power to predict human eye, hair, and skin colors with potential utilization in forensic investigations.
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Affiliation(s)
- Fan Liu
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.
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132
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Beleza S, Johnson NA, Candille SI, Absher DM, Coram MA, Lopes J, Campos J, Araújo II, Anderson TM, Vilhjálmsson BJ, Nordborg M, Correia e Silva A, Shriver MD, Rocha J, Barsh GS, Tang H. Genetic architecture of skin and eye color in an African-European admixed population. PLoS Genet 2013; 9:e1003372. [PMID: 23555287 PMCID: PMC3605137 DOI: 10.1371/journal.pgen.1003372] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 01/22/2013] [Indexed: 11/18/2022] Open
Abstract
Variation in human skin and eye color is substantial and especially apparent in admixed populations, yet the underlying genetic architecture is poorly understood because most genome-wide studies are based on individuals of European ancestry. We study pigmentary variation in 699 individuals from Cape Verde, where extensive West African/European admixture has given rise to a broad range in trait values and genomic ancestry proportions. We develop and apply a new approach for measuring eye color, and identify two major loci (HERC2[OCA2] P = 2.3×10−62, SLC24A5 P = 9.6×10−9) that account for both blue versus brown eye color and varying intensities of brown eye color. We identify four major loci (SLC24A5 P = 5.4×10−27, TYR P = 1.1×10−9, APBA2[OCA2] P = 1.5×10−8, SLC45A2 P = 6×10−9) for skin color that together account for 35% of the total variance, but the genetic component with the largest effect (∼44%) is average genomic ancestry. Our results suggest that adjacent cis-acting regulatory loci for OCA2 explain the relationship between skin and eye color, and point to an underlying genetic architecture in which several genes of moderate effect act together with many genes of small effect to explain ∼70% of the estimated heritability. Differences in skin and eye color are some of the most obvious traits that underlie human diversity, yet most of our knowledge regarding the genetic basis for these traits is based on the limited range of variation represented by individuals of European ancestry. We have studied a unique population in Cape Verde, an archipelago located off the West African coast, in which extensive mixing between individuals of Portuguese and West African ancestry has given rise to a broad range of phenotypes and ancestral genome proportions. Our results help to explain how genes work together to control the full range of pigmentary phenotypic diversity, provide new insight into the evolution of these traits, and provide a model for understanding other types of quantitative variation in admixed populations.
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Affiliation(s)
- Sandra Beleza
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- * E-mail: (SB); (GSB)
| | - Nicholas A. Johnson
- Department of Statistics, Stanford University, Stanford, California, United States of America
| | - Sophie I. Candille
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Devin M. Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Marc A. Coram
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jailson Lopes
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), Vairão, Portugal
- Universidade de Cabo Verde (Uni-CV), Praia, Santiago, Cabo Verde
| | - Joana Campos
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | | | - Tovi M. Anderson
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | | | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria
| | | | - Mark D. Shriver
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Jorge Rocha
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Gregory S. Barsh
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
- * E-mail: (SB); (GSB)
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
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Scheetz TE, Fingert JH, Wang K, Kuehn MH, Knudtson KL, Alward WLM, Boldt HC, Russell SR, Folk JC, Casavant TL, Braun TA, Clark AF, Stone EM, Sheffield VC. A genome-wide association study for primary open angle glaucoma and macular degeneration reveals novel Loci. PLoS One 2013; 8:e58657. [PMID: 23536807 PMCID: PMC3594156 DOI: 10.1371/journal.pone.0058657] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 02/07/2013] [Indexed: 11/22/2022] Open
Abstract
Glaucoma and age-related macular degeneration (AMD) are the two leading causes of visual loss in the United States. We utilized a novel study design to perform a genome-wide association for both primary open angle glaucoma (POAG) and AMD. This study design utilized a two-stage process for hypothesis generation and validation, in which each disease cohort was utilized as a control for the other. A total of 400 POAG patients and 400 AMD patients were ascertained and genotyped at 500,000 loci. This study identified a novel association of complement component 7 (C7) to POAG. Additionally, an association of central corneal thickness, a known risk factor for POAG, was found to be associated with ribophorin II (RPN2). Linked monogenic loci for POAG and AMD were also evaluated for evidence of association, none of which were found to be significantly associated. However, several yielded putative associations requiring validation. Our data suggest that POAG is more genetically complex than AMD, with no common risk alleles of large effect.
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Affiliation(s)
- Todd E Scheetz
- Department of Ophthalmology and Visual Sciences, The University of Iowa, Iowa City, Iowa, United States of America
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Wei AH, Zang DJ, Zhang Z, Liu XZ, He X, Yang L, Wang Y, Zhou ZY, Zhang MR, Dai LL, Yang XM, Li W. Exome sequencing identifies SLC24A5 as a candidate gene for nonsyndromic oculocutaneous albinism. J Invest Dermatol 2013; 133:1834-40. [PMID: 23364476 DOI: 10.1038/jid.2013.49] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Oculocutaneous albinism (OCA) is a heterogeneous and autosomal recessive disorder with hypopigmentation in the eye, hair, and skin color. Four genes, TYR, OCA2, TYRP1, and SLC45A2, have been identified as causative genes for nonsyndromic OCA1-4, respectively. The genetic identity of OCA5 locus on 4q24 is unknown. Additional unknown OCA genes may exist as at least 5% of OCA patients have not been characterized during mutational screening in several populations. We used exome sequencing with a family-based recessive mutation model to determine that SLC24A5 is a previously unreported candidate gene for nonsyndromic OCA, which we designate as OCA6. Two deleterious mutations in this patient, c.591G>A and c.1361insT, were identified. We found apparent increase of immature melanosomes and less mature melanosomes in the patient's skin melanocytes. However, no defects in the platelet dense granules were observed, excluding typical Hermansky-Pudlak syndrome (HPS), a well-known syndromic OCA. Moreover, the SLC24A5 protein was reduced in steady-state levels in mouse HPS mutants with deficiencies in BLOC-1 and BLOC-2. Our results suggest that SLC24A5 is a previously unreported nonsyndromic OCA candidate gene and that the SLC24A5 transporter is transported into mature melanosomes by HPS protein complexes.
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Affiliation(s)
- Ai-Hua Wei
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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135
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Vasseur E, Quintana-Murci L. The impact of natural selection on health and disease: uses of the population genetics approach in humans. Evol Appl 2013; 6:596-607. [PMID: 23789027 PMCID: PMC3684741 DOI: 10.1111/eva.12045] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 12/13/2012] [Indexed: 01/09/2023] Open
Abstract
Investigations of the legacy of natural selection in the human genome have proved particularly informative, pinpointing functionally important regions that have participated in our genetic adaptation to the environment. Furthermore, genetic dissection of the intensity and type of selection acting on human genes can be used to predict involvement in different forms and severities of human diseases. We review here the progress made in population genetics studies toward understanding the effects of selection, in its different forms and intensities, on human genome diversity. We discuss some outstanding, robust examples of genes and biological functions subject to strong dietary, climatic and pathogen selection pressures. We also explore the possible relationship between cancer and natural selection, a topic that has been largely neglected because cancer is generally seen as a late-onset disease. Finally, we discuss how the present-day incidence of some diseases of modern societies may represent a by-product of past adaptation to other selective forces and changes in lifestyle. This perspective thus illustrates the value of adopting a population genetics approach in delineating the biological mechanisms that have played a major evolutionary role in the way humans have genetically adapted to different environments and lifestyles over time.
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Affiliation(s)
- Estelle Vasseur
- Institut Pasteur, Unit of Human Evolutionary Genetics 75015, Paris, France ; Centre National de la Recherche Scientifique, URA 3012 75015, Paris, France ; Centre National de la Recherche Scientifique, UMR 5174, Evolution et Diversité Biologique 31062, Toulouse, France ; Université de Toulouse 31062, Toulouse, France
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136
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Ozerov M, Vasemägi A, Wennevik V, Niemelä E, Prusov S, Kent M, Vähä JP. Cost-effective genome-wide estimation of allele frequencies from pooled DNA in Atlantic salmon (Salmo salar L.). BMC Genomics 2013; 14:12. [PMID: 23324082 PMCID: PMC3575319 DOI: 10.1186/1471-2164-14-12] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 01/02/2013] [Indexed: 12/13/2022] Open
Abstract
Background New sequencing technologies have tremendously increased the number of known molecular markers (single nucleotide polymorphisms; SNPs) in a variety of species. Concurrently, improvements to genotyping technology have now made it possible to efficiently genotype large numbers of genome-wide distributed SNPs enabling genome wide association studies (GWAS). However, genotyping significant numbers of individuals with large number of SNPs remains prohibitively expensive for many research groups. A possible solution to this problem is to determine allele frequencies from pooled DNA samples, such ‘allelotyping’ has been presented as a cost-effective alternative to individual genotyping and has become popular in human GWAS. In this article we have tested the effectiveness of DNA pooling to obtain accurate allele frequency estimates for Atlantic salmon (Salmo salar L.) populations using an Illumina SNP-chip. Results In total, 56 Atlantic salmon DNA pools from 14 populations were analyzed on an Atlantic salmon SNP-chip containing probes for 5568 SNP markers, 3928 of which were bi-allelic. We developed an efficient quality control filter which enables exclusion of loci showing high error rate and minor allele frequency (MAF) close to zero. After applying multiple quality control filters we obtained allele frequency estimates for 3631 bi-allelic loci. We observed high concordance (r > 0.99) between allele frequency estimates derived from individual genotyping and DNA pools. Our results also indicate that even relatively small DNA pools (35 individuals) can provide accurate allele frequency estimates for a given sample. Conclusions Despite of higher level of variation associated with array replicates compared to pool construction, we suggest that both sources of variation should be taken into account. This study demonstrates that DNA pooling allows fast and high-throughput determination of allele frequencies in Atlantic salmon enabling cost-efficient identification of informative markers for discrimination of populations at various geographical scales, as well as identification of loci controlling ecologically and economically important traits.
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Affiliation(s)
- Mikhail Ozerov
- Kevo Subarctic Research Institute, University of Turku, Turku 20014, Finland
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137
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Holliday EG, Smith AV, Cornes BK, Buitendijk GHS, Jensen RA, Sim X, Aspelund T, Aung T, Baird PN, Boerwinkle E, Cheng CY, van Duijn CM, Eiriksdottir G, Gudnason V, Harris T, Hewitt AW, Inouye M, Jonasson F, Klein BEK, Launer L, Li X, Liew G, Lumley T, McElduff P, McKnight B, Mitchell P, Psaty BM, Rochtchina E, Rotter JI, Scott RJ, Tay W, Taylor K, Teo YY, Uitterlinden AG, Viswanathan A, Xie S, Vingerling JR, Klaver CCW, Tai ES, Siscovick D, Klein R, Cotch MF, Wong TY, Attia J, Wang JJ. Insights into the genetic architecture of early stage age-related macular degeneration: a genome-wide association study meta-analysis. PLoS One 2013; 8:e53830. [PMID: 23326517 PMCID: PMC3543264 DOI: 10.1371/journal.pone.0053830] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 12/03/2012] [Indexed: 12/16/2022] Open
Abstract
Genetic factors explain a majority of risk variance for age-related macular degeneration (AMD). While genome-wide association studies (GWAS) for late AMD implicate genes in complement, inflammatory and lipid pathways, the genetic architecture of early AMD has been relatively under studied. We conducted a GWAS meta-analysis of early AMD, including 4,089 individuals with prevalent signs of early AMD (soft drusen and/or retinal pigment epithelial changes) and 20,453 individuals without these signs. For various published late AMD risk loci, we also compared effect sizes between early and late AMD using an additional 484 individuals with prevalent late AMD. GWAS meta-analysis confirmed previously reported association of variants at the complement factor H (CFH) (peak P = 1.5×10−31) and age-related maculopathy susceptibility 2 (ARMS2) (P = 4.3×10−24) loci, and suggested Apolipoprotein E (ApoE) polymorphisms (rs2075650; P = 1.1×10−6) associated with early AMD. Other possible loci that did not reach GWAS significance included variants in the zinc finger protein gene GLI3 (rs2049622; P = 8.9×10−6) and upstream of GLI2 (rs6721654; P = 6.5×10−6), encoding retinal Sonic hedgehog signalling regulators, and in the tyrosinase (TYR) gene (rs621313; P = 3.5×10−6), involved in melanin biosynthesis. For a range of published, late AMD risk loci, estimated effect sizes were significantly lower for early than late AMD. This study confirms the involvement of multiple established AMD risk variants in early AMD, but suggests weaker genetic effects on the risk of early AMD relative to late AMD. Several biological processes were suggested to be potentially specific for early AMD, including pathways regulating RPE cell melanin content and signalling pathways potentially involved in retinal regeneration, generating hypotheses for further investigation.
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Affiliation(s)
- Elizabeth G Holliday
- Centre for Clinical Epidemiology and Biostatistics, and School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales, Australia.
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NCKX5, a natural regulator of human skin colour variation, regulates the expression of key pigment genes MC1R and alpha-MSH and alters cholesterol homeostasis in normal human melanocytes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 961:95-107. [PMID: 23224873 DOI: 10.1007/978-1-4614-4756-6_9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Natural human skin colour is determined both by environmental exposure to ultraviolet light and through inherited genetic variation in a very limited number of genes. Variation of a non-synonymous single-nucleotide polymorphism (nsSNP; rs1426654) in the gene (SLC24A5) encoding the NCKX5 protein is associated with differences in constitutive skin colour in South Asians. The nsSNP encodes the substitution of alanine for threonine at residue 111 (A111T) near a transmembrane region required for exchanger activity, a region which is highly conserved across different species and between NCKX family members. We have shown that NCKX5 is located at the trans-Golgi network of melanocytes and functions as a potassium-dependent sodium-calcium exchanger. When heterologously expressed, the 111T variant of NCKX5 shows significantly lower exchanger activity than the A111 variant. We have postulated that lower exchanger activity causes the reduced melanogenesis and lighter skin in Thr111-positive individuals. We used gene expression microarrays with qPCR replication and validation to assess the impact of siRNA-mediated knockdown of SLC24A5 on the transcriptome of cultured normal human melanocytes (NHM). Very few genes associated with melanogenesis were altered at the transcript level except for MC1R, suggesting that SLC24A5 interacts with at least one well-characterized melanogenic signalling pathway. More surprisingly, the expression of a number of cholesterol homeostatic genes was altered after SLC24A5 knockdown, and the total cholesterol content of NHM was increased. Cholesterol has previously been identified as a potential melanogenic regulator, and our data imply that NCKX5 exchanger function influences natural variation in skin pigmentation via a novel, unknown mechanism affecting cellular sterol levels.
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139
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Rodriguez-Flores JL, Fuller J, Hackett NR, Salit J, Malek JA, Al-Dous E, Chouchane L, Zirie M, Jayoussi A, Mahmoud MA, Crystal RG, Mezey JG. Exome sequencing of only seven Qataris identifies potentially deleterious variants in the Qatari population. PLoS One 2012; 7:e47614. [PMID: 23139751 PMCID: PMC3490971 DOI: 10.1371/journal.pone.0047614] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 09/19/2012] [Indexed: 01/30/2023] Open
Abstract
The Qatari population, located at the Arabian migration crossroads of African and Eurasia, is comprised of Bedouin, Persian and African genetic subgroups. By deep exome sequencing of only 7 Qataris, including individuals in each subgroup, we identified 2,750 nonsynonymous SNPs predicted to be deleterious, many of which are linked to human health, or are in genes linked to human health. Many of these SNPs were at significantly elevated deleterious allele frequency in Qataris compared to other populations worldwide. Despite the small sample size, SNP allele frequency was highly correlated with a larger Qatari sample. Together, the data demonstrate that exome sequencing of only a small number of individuals can reveal genetic variations with potential health consequences in understudied populations.
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Affiliation(s)
- Juan L. Rodriguez-Flores
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Jennifer Fuller
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Neil R. Hackett
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Jacqueline Salit
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Joel A. Malek
- Department of Genetic Medicine, Weill Cornell Medical College – Qatar, Doha, Qatar
| | - Eman Al-Dous
- Department of Genetic Medicine, Weill Cornell Medical College – Qatar, Doha, Qatar
| | - Lotfi Chouchane
- Department of Genetic Medicine, Weill Cornell Medical College – Qatar, Doha, Qatar
| | - Mahmoud Zirie
- Hamad Medical Corporation, Doha, Qatar
- Department of Medicine, Weill Cornell Medical College – Qatar, Doha, Qatar
| | | | - Mai A. Mahmoud
- Department of Medicine, Weill Cornell Medical College – Qatar, Doha, Qatar
| | - Ronald G. Crystal
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
- Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Jason G. Mezey
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
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140
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Genome-wide association studies of quantitatively measured skin, hair, and eye pigmentation in four European populations. PLoS One 2012; 7:e48294. [PMID: 23118974 PMCID: PMC3485197 DOI: 10.1371/journal.pone.0048294] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 09/25/2012] [Indexed: 12/21/2022] Open
Abstract
Pigmentation of the skin, hair, and eyes varies both within and between human populations. Identifying the genes and alleles underlying this variation has been the goal of many candidate gene and several genome-wide association studies (GWAS). Most GWAS for pigmentary traits to date have been based on subjective phenotypes using categorical scales. But skin, hair, and eye pigmentation vary continuously. Here, we seek to characterize quantitative variation in these traits objectively and accurately and to determine their genetic basis. Objective and quantitative measures of skin, hair, and eye color were made using reflectance or digital spectroscopy in Europeans from Ireland, Poland, Italy, and Portugal. A GWAS was conducted for the three quantitative pigmentation phenotypes in 176 women across 313,763 SNP loci, and replication of the most significant associations was attempted in a sample of 294 European men and women from the same countries. We find that the pigmentation phenotypes are highly stratified along axes of European genetic differentiation. The country of sampling explains approximately 35% of the variation in skin pigmentation, 31% of the variation in hair pigmentation, and 40% of the variation in eye pigmentation. All three quantitative phenotypes are correlated with each other. In our two-stage association study, we reproduce the association of rs1667394 at the OCA2/HERC2 locus with eye color but we do not identify new genetic determinants of skin and hair pigmentation supporting the lack of major genes affecting skin and hair color variation within Europe and suggesting that not only careful phenotyping but also larger cohorts are required to understand the genetic architecture of these complex quantitative traits. Interestingly, we also see that in each of these four populations, men are more lightly pigmented in the unexposed skin of the inner arm than women, a fact that is underappreciated and may vary across the world.
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141
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Comprehensive candidate gene study highlights UGT1A and BNC2 as new genes determining continuous skin color variation in Europeans. Hum Genet 2012; 132:147-58. [PMID: 23052946 DOI: 10.1007/s00439-012-1232-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 09/18/2012] [Indexed: 01/09/2023]
Abstract
Natural variation in human skin pigmentation is primarily due to genetic causes rooted in recent evolutionary history. Genetic variants associated with human skin pigmentation confer risk of skin cancer and may provide useful information in forensic investigations. Almost all previous gene-mapping studies of human skin pigmentation were based on categorical skin color information known to oversimplify the continuous nature of human skin coloration. We digitally quantified skin color into hue and saturation dimensions for 5,860 Dutch Europeans based on high-resolution skin photographs. We then tested an extensive list of 14,185 single nucleotide polymorphisms in 281 candidate genes potentially involved in human skin pigmentation for association with quantitative skin color phenotypes. Confirmatory association was revealed for several known skin color genes including HERC2, MC1R, IRF4, TYR, OCA2, and ASIP. We identified two new skin color genes: genetic variants in UGT1A were significantly associated with hue and variants in BNC2 were significantly associated with saturation. Overall, digital quantification of human skin color allowed detecting new skin color genes. The variants identified in this study may also contribute to the risk of skin cancer. Our findings are also important for predicting skin color in forensic investigations.
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142
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Tsetskhladze ZR, Canfield VA, Ang KC, Wentzel SM, Reid KP, Berg AS, Johnson SL, Kawakami K, Cheng KC. Functional assessment of human coding mutations affecting skin pigmentation using zebrafish. PLoS One 2012; 7:e47398. [PMID: 23071798 PMCID: PMC3468441 DOI: 10.1371/journal.pone.0047398] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 09/12/2012] [Indexed: 11/19/2022] Open
Abstract
A major challenge in personalized medicine is the lack of a standard way to define the functional significance of the numerous nonsynonymous, single nucleotide coding variants that are present in each human individual. To begin to address this problem, we have used pigmentation as a model polygenic trait, three common human polymorphisms thought to influence pigmentation, and the zebrafish as a model system. The approach is based on the rescue of embryonic zebrafish mutant phenotypes by “humanized” zebrafish orthologous mRNA. Two hypomorphic polymorphisms, L374F in SLC45A2, and A111T in SLC24A5, have been linked to lighter skin color in Europeans. The phenotypic effect of a second coding polymorphism in SLC45A2, E272K, is unclear. None of these polymorphisms had been tested in the context of a model organism. We have confirmed that zebrafish albino fish are mutant in slc45a2; wild-type slc45a2 mRNA rescued the albino mutant phenotype. Introduction of the L374F polymorphism into albino or the A111T polymorphism into slc24a5 (golden) abolished mRNA rescue of the respective mutant phenotypes, consistent with their known contributions to European skin color. In contrast, the E272K polymorphism had no effect on phenotypic rescue. The experimental conclusion that E272K is unlikely to affect pigmentation is consistent with a lack of correlation between this polymorphism and quantitatively measured skin color in 59 East Asian humans. A survey of mutations causing human oculocutaneous albinism yielded 257 missense mutations, 82% of which are theoretically testable in zebrafish. The developed approach may be extended to other model systems and may potentially contribute to our understanding the functional relationships between DNA sequence variation, human biology, and disease.
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Affiliation(s)
- Zurab R. Tsetskhladze
- Jake Gittlen Cancer Research Foundation, Penn State Hershey College of Medicine, Hershey, Pennsylvania, United States of America
- Division of Experimental Pathology, Department of Pathology, Penn State Hershey College of Medicine, Hershey, Pennsylvania, United States of America
- * E-mail: (ZRT); (KCC)
| | - Victor A. Canfield
- Department of Pharmacology, Penn State Hershey College of Medicine, Hershey, Pennsylvania, United States of America
| | - Khai C. Ang
- Jake Gittlen Cancer Research Foundation, Penn State Hershey College of Medicine, Hershey, Pennsylvania, United States of America
- Division of Experimental Pathology, Department of Pathology, Penn State Hershey College of Medicine, Hershey, Pennsylvania, United States of America
| | - Steven M. Wentzel
- Jake Gittlen Cancer Research Foundation, Penn State Hershey College of Medicine, Hershey, Pennsylvania, United States of America
- Division of Experimental Pathology, Department of Pathology, Penn State Hershey College of Medicine, Hershey, Pennsylvania, United States of America
| | - Katherine P. Reid
- Jake Gittlen Cancer Research Foundation, Penn State Hershey College of Medicine, Hershey, Pennsylvania, United States of America
- Division of Experimental Pathology, Department of Pathology, Penn State Hershey College of Medicine, Hershey, Pennsylvania, United States of America
| | - Arthur S. Berg
- Department of Public Health Sciences, Penn State Hershey College of Medicine, Hershey, Pennsylvania, United States of America
| | - Stephen L. Johnson
- Department of Genetics, Washington University Medical School, St. Louis, Missouri, United States of America
| | - Koichi Kawakami
- Division of Molecular and Developmental Biology, National Institute of Genetics, Department of Genetics, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka, Japan
| | - Keith C. Cheng
- Jake Gittlen Cancer Research Foundation, Penn State Hershey College of Medicine, Hershey, Pennsylvania, United States of America
- Division of Experimental Pathology, Department of Pathology, Penn State Hershey College of Medicine, Hershey, Pennsylvania, United States of America
- * E-mail: (ZRT); (KCC)
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143
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Abstract
Genome-wide association studies and comparative genomics have established major loci and specific polymorphisms affecting human skin, hair and eye color. Environmental changes have had an impact on selected pigmentation genes as populations have expanded into different regions of the globe.
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Affiliation(s)
- Richard A Sturm
- Institute for Molecular Bioscience, Melanogenix Group, The University of Queensland, Brisbane, Qld 4072, Australia.
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144
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Molecular basis of albinism in India: evaluation of seven potential candidate genes and some new findings. Gene 2012; 511:470-4. [PMID: 23010199 DOI: 10.1016/j.gene.2012.09.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Revised: 09/06/2012] [Accepted: 09/06/2012] [Indexed: 11/21/2022]
Abstract
Albinism represents a group of genetic disorders with a broad spectrum of hypopigmentary phenotypes dependent on the genetic background of the patients. Oculocutaneous albinism (OCA) patients have little or no pigment in their eyes, skin and hair, whereas ocular albinism (OA) primarily presents the ocular symptoms, and the skin and hair color may vary from near normal to very fair. Mutations in genes directly or indirectly regulating melanin production are responsible for different forms of albinism with overlapping clinical features. In this study, 27 albinistic individuals from 24 families were screened for causal variants by a PCR-sequencing based approach. TYR, OCA2, TYRP1, SLC45A2, SLC24A5, TYRP2 and SILV were selected as candidate genes. We identified 5 TYR and 3 OCA2 mutations, majority in homozygous state, in 8 unrelated patients including a case of autosomal recessive ocular albinism (AROA). A homozygous 4-nucleotide novel insertion in SLC24A5 was detected in a person showing with extreme cutaneous hypopigmentation. A potential causal variant was identified in the TYRP2 gene in a single patient. Haplotype analyses in the patients carrying homozygous mutations in the classical OCA genes suggested founder effect. This is the first report of an Indian AROA patient harboring a mutation in OCA2. Our results also reveal for the first time that mutations in SLC24A5 could contribute to extreme hypopigmentation in humans.
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145
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Beleza S, Santos AM, McEvoy B, Alves I, Martinho C, Cameron E, Shriver MD, Parra EJ, Rocha J. The timing of pigmentation lightening in Europeans. Mol Biol Evol 2012; 30:24-35. [PMID: 22923467 DOI: 10.1093/molbev/mss207] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The inverse correlation between skin pigmentation and latitude observed in human populations is thought to have been shaped by selective pressures favoring lighter skin to facilitate vitamin D synthesis in regions far from the equator. Several candidate genes for skin pigmentation have been shown to exhibit patterns of polymorphism that overlap the geospatial variation in skin color. However, little work has focused on estimating the time frame over which skin pigmentation has changed and on the intensity of selection acting on different pigmentation genes. To provide a temporal framework for the evolution of lighter pigmentation, we used forward Monte Carlo simulations coupled with a rejection sampling algorithm to estimate the time of onset of selective sweeps and selection coefficients at four genes associated with this trait in Europeans: KITLG, TYRP1, SLC24A5, and SLC45A2. Using compound haplotype systems consisting of rapidly evolving microsatellites linked to one single-nucleotide polymorphism in each gene, we estimate that the onset of the sweep shared by Europeans and East Asians at KITLG occurred approximately 30,000 years ago, after the out-of-Africa migration, whereas the selective sweeps for the European-specific alleles at TYRP1, SLC24A5, and SLC45A2 started much later, within the last 11,000-19,000 years, well after the first migrations of modern humans into Europe. We suggest that these patterns were influenced by recent increases in size of human populations, which favored the accumulation of advantageous variants at different loci.
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Affiliation(s)
- Sandra Beleza
- IPATIMUP, Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal.
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146
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Poetsch M, Blöhm R, Harder M, Inoue H, von Wurmb-Schwark N, Freitag-Wolf S. Prediction of people's origin from degraded DNA--presentation of SNP assays and calculation of probability. Int J Legal Med 2012; 127:347-57. [PMID: 22918435 DOI: 10.1007/s00414-012-0728-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 06/12/2012] [Indexed: 11/26/2022]
Abstract
The characterization of externally visible traits by DNA analysis is already an important tool when investigating ancient skeletal remains and may gain similar importance in future forensic DNA analysis. This, however, depends on the different legal regulations in the different countries. Besides eye or hair color, the population origin can provide crucial information in criminal prosecution. In this study, we present the analysis of 16 single-nucleotide polymorphisms (SNPs) combined to two robust SNaPshot assays with a detection threshold of 25-pg DNA. This assay was applied to 891 people from seven different populations (West Africa, North Africa, Turkey, Near East, Balkan states, North Europe, and Japan) with a thorough statistical evaluation. The prediction model was validated by an additional 125 individuals predominantly with an ancestry from those same regions. The specificity of these SNPs for the prediction of all population origins is very high (>90 %), but the sensitivity varied greatly (more than 90 % for West Africa, but only 25 % for the Near East). We could identify West Africans with a certainty of 100 %, and people from North Africa, the Balkan states, or North Europe nearly with the same reliability while determination of Turks or people from the Near East was rather difficult. In conclusion, the two SNaPshot assays are a powerful and reliable tool for the identification of people with an ancestry in one of the above listed populations, even from degraded DNA.
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Affiliation(s)
- Micaela Poetsch
- Institute of Legal Medicine, University Hospital Essen, Hufelandstr. 55, 45122, Essen, Germany.
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147
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Paik SH, Kim HJ, Son HY, Lee S, Im SW, Ju YS, Yeon JH, Jo SJ, Eun HC, Seo JS, Kwon OS, Kim JI. Gene mapping study for constitutive skin color in an isolated Mongolian population. Exp Mol Med 2012; 44:241-9. [PMID: 22198297 PMCID: PMC3317488 DOI: 10.3858/emm.2012.44.3.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
To elucidate the genes responsible for constitutive human skin color, we measured the extent of skin pigmentation in the buttock, representative of lifelong non-sun-exposed skin, and conducted a gene mapping study on skin color in an isolated Mongolian population composed of 344 individuals from 59 families who lived in Dashbalbar, Mongolia. The heritability of constitutive skin color was 0.82, indicating significant genetic association on this trait. Through the linkage analysis using 1,039 short tandem repeat (STR) microsatellite markers, we identified a novel genomic region regulating constitutive skin color on 11q24.2 with an logarithm of odds (LOD) score of 3.39. In addition, we also found other candidate regions on 17q23.2, 6q25.1, and 13q33.2 (LOD ≥ 2). Family-based association tests on these regions with suggestive linkage peaks revealed ten and two significant single nucleotide polymorphisms (SNPs) on the linkage regions of chromosome 11 and 17, respectively. We were able to discover four possible candidate genes that would be implicated to regulate human skin color: ETS1, UBASH3B, ASAM, and CLTC.
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Affiliation(s)
- Seung Hwan Paik
- Department of Dermatology Seoul National University College of Medicine, Seoul 110-799, Korea
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148
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Pagani L, Kivisild T, Tarekegn A, Ekong R, Plaster C, Gallego Romero I, Ayub Q, Mehdi S, Thomas M, Luiselli D, Bekele E, Bradman N, Balding D, Tyler-Smith C. Ethiopian genetic diversity reveals linguistic stratification and complex influences on the Ethiopian gene pool. Am J Hum Genet 2012; 91:83-96. [PMID: 22726845 DOI: 10.1016/j.ajhg.2012.05.015] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 05/03/2012] [Accepted: 05/21/2012] [Indexed: 12/30/2022] Open
Abstract
Humans and their ancestors have traversed the Ethiopian landscape for millions of years, and present-day Ethiopians show great cultural, linguistic, and historical diversity, which makes them essential for understanding African variability and human origins. We genotyped 235 individuals from ten Ethiopian and two neighboring (South Sudanese and Somali) populations on an Illumina Omni 1M chip. Genotypes were compared with published data from several African and non-African populations. Principal-component and STRUCTURE-like analyses confirmed substantial genetic diversity both within and between populations, and revealed a match between genetic data and linguistic affiliation. Using comparisons with African and non-African reference samples in 40-SNP genomic windows, we identified "African" and "non-African" haplotypic components for each Ethiopian individual. The non-African component, which includes the SLC24A5 allele associated with light skin pigmentation in Europeans, may represent gene flow into Africa, which we estimate to have occurred ~3 thousand years ago (kya). The non-African component was found to be more similar to populations inhabiting the Levant rather than the Arabian Peninsula, but the principal route for the expansion out of Africa ~60 kya remains unresolved. Linkage-disequilibrium decay with genomic distance was less rapid in both the whole genome and the African component than in southern African samples, suggesting a less ancient history for Ethiopian populations.
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149
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Jaworek TJ, Kausar T, Bell SM, Tariq N, Maqsood MI, Sohail A, Ali M, Iqbal F, Rasool S, Riazuddin S, Shaikh RS, Ahmed ZM. Molecular genetic studies and delineation of the oculocutaneous albinism phenotype in the Pakistani population. Orphanet J Rare Dis 2012; 7:44. [PMID: 22734612 PMCID: PMC3537634 DOI: 10.1186/1750-1172-7-44] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 04/30/2012] [Indexed: 02/01/2023] Open
Abstract
Background Oculocutaneous albinism (OCA) is caused by a group of genetically heterogeneous inherited defects that result in the loss of pigmentation in the eyes, skin and hair. Mutations in the TYR, OCA2, TYRP1 and SLC45A2 genes have been shown to cause isolated OCA. No comprehensive analysis has been conducted to study the spectrum of OCA alleles prevailing in Pakistani albino populations. Methods We enrolled 40 large Pakistani families and screened them for OCA genes and a candidate gene, SLC24A5. Protein function effects were evaluated using in silico prediction algorithms and ex vivo studies in human melanocytes. The effects of splice-site mutations were determined using an exon-trapping assay. Results Screening of the TYR gene revealed four known (p.Arg299His, p.Pro406Leu, p.Gly419Arg, p.Arg278*) and three novel mutations (p.Pro21Leu, p.Cys35Arg, p.Tyr411His) in ten families. Ex vivo studies revealed the retention of an EGFP-tagged mutant (p.Pro21Leu, p.Cys35Arg or p.Tyr411His) tyrosinase in the endoplasmic reticulum (ER) at 37°C, but a significant fraction of p.Cys35Arg and p.Tyr411His left the ER in cells grown at a permissive temperature (31°C). Three novel (p.Asp486Tyr, p.Leu527Arg, c.1045-15 T > G) and two known mutations (p.Pro743Leu, p.Ala787Thr) of OCA2 were found in fourteen families. Exon-trapping assays with a construct containing a novel c.1045-15 T > G mutation revealed an error in splicing. No mutation in TYRP1, SLC45A2, and SLC24A5 was found in the remaining 16 families. Clinical evaluation of the families segregating either TYR or OCA2 mutations showed nystagmus, photophobia, and loss of pigmentation in the skin or hair follicles. Most of the affected individuals had grayish-blue colored eyes. Conclusions Our results show that ten and fourteen families harbored mutations in the TYR and OCA2 genes, respectively. Our findings, along with the results of previous studies, indicate that the p.Cys35Arg, p.Arg278* and p.Gly419Arg alleles of TYR and the p.Asp486Tyr and c.1045-15 T > G alleles of OCA2 are the most common causes of OCA in Pakistani families. To the best of our knowledge, this study represents the first documentation of OCA2 alleles in the Pakistani population. A significant proportion of our cohort did not have mutations in known OCA genes. Overall, our study contributes to the development of genetic testing protocols and genetic counseling for OCA in Pakistani families.
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Affiliation(s)
- Thomas J Jaworek
- Division of Pediatric Ophthalmology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH 45229, USA
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150
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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] [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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