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Liu J, Bitsue HK, Yang Z. Skin colour: A window into human phenotypic evolution and environmental adaptation. Mol Ecol 2024; 33:e17369. [PMID: 38713101 DOI: 10.1111/mec.17369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/13/2024] [Accepted: 04/17/2024] [Indexed: 05/08/2024]
Abstract
As modern humans ventured out of Africa and dispersed around the world, they faced novel environmental challenges that led to geographic adaptations including skin colour. Over the long history of human evolution, skin colour has changed dramatically, showing tremendous diversity across different geographical regions, for example, the majority of individuals from the expansive lands of Africa have darker skin, whereas the majority of people from Eurasia exhibit lighter skin. What adaptations did lighter skin confer upon modern humans as they migrated from Africa to Eurasia? What genetic mechanisms underlie the diversity of skin colour observed in different populations? In recent years, scientists have gradually gained a deeper understanding of the interactions between pigmentation gene and skin colour through population-based genomic studies of different groups around the world, particularly in East Asia and Africa. In this review, we summarize our current understanding of 26 skin colour-related pigmentation genes and 48 SNPs that influence skin colour. Important pigmentation genes across three major populations are described in detail: MFSD12, SLC24A5, PDPK1 and DDB1/CYB561A3/TMEM138 influence skin colour in African populations; OCA2, KITLG, SLC24A2, GNPAT and PAH are key to the evolution of skin pigmentation in East Asian populations; and SLC24A5, SLC45A2, TYR, TYRP1, ASIP, MC1R and IRF4 significantly contribute to the lightening of skin colour in European populations. We summarized recent findings in genomic studies of skin colour in populations that implicate diverse geographic environments, local adaptation among populations, gene flow and multi-gene interactions as factors influencing skin colour diversity.
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Affiliation(s)
- Jiuming Liu
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Habtom K Bitsue
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Zhaohui Yang
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
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2
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Brancato D, Coniglio E, Bruno F, Agostini V, Saccone S, Federico C. Forensic DNA Phenotyping: Genes and Genetic Variants for Eye Color Prediction. Genes (Basel) 2023; 14:1604. [PMID: 37628655 PMCID: PMC10454093 DOI: 10.3390/genes14081604] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/31/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
In recent decades, the use of genetic polymorphisms related to specific phenotypes, such as eye color, has greatly contributed to the development of the research field called forensic DNA phenotyping (FDP), enabling the investigators of crime cases to reduce the number of suspects, making their work faster and more precise. Eye color is a polygenic phenotype, and many genetic variants have been highlighted, with the major contributor being the HERC2-OCA2 locus, where many single nucleotide variations (SNPs) were identified. Interestingly, the HERC2-OCA2 locus, containing the intronic SNP rs12913832, the major eye color determinant, shows a high level of evolutionary conservation across many species of vertebrates. Currently, there are some genetic panels to predict eye color by genomic DNA analysis, even if the exact role of the SNP variants in the formation of eye color is still poorly understood, with a low level of predictivity in the so-called intermediate eye color. Many variants in OCA2, HERC2, and other genes lie in introns or correspond to synonymous variants, highlighting greater complexity in the mechanism of action of such genes than a simple missense variation. Here, we show the main genes involved in oculocutaneous pigmentation and their structural and functional features, as well as which genetic variants show the highest level of eye color predictivity in currently used FDP assays. Despite the great recent advances and impact of FDP in criminal cases, it is necessary to enhance scientific research to better understand the mechanism of action behind each genetic variant involved in eye color, with the goal of obtaining higher levels of prediction.
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Affiliation(s)
- Desiree Brancato
- Department Biological, Geological, Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (D.B.); (E.C.); (F.B.); (C.F.)
| | - Elvira Coniglio
- Department Biological, Geological, Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (D.B.); (E.C.); (F.B.); (C.F.)
| | - Francesca Bruno
- Department Biological, Geological, Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (D.B.); (E.C.); (F.B.); (C.F.)
| | - Vincenzo Agostini
- Department Science and Technical Innovation, University of Eastern Piedmont, Viale Teresa Michel 11, 15121 Alessandria, Italy;
| | - Salvatore Saccone
- Department Biological, Geological, Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (D.B.); (E.C.); (F.B.); (C.F.)
| | - Concetta Federico
- Department Biological, Geological, Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (D.B.); (E.C.); (F.B.); (C.F.)
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3
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Elkin J, Martin A, Courtier-Orgogozo V, Santos ME. Analysis of the genetic loci of pigment pattern evolution in vertebrates. Biol Rev Camb Philos Soc 2023; 98:1250-1277. [PMID: 37017088 DOI: 10.1111/brv.12952] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/08/2023] [Accepted: 03/14/2023] [Indexed: 04/06/2023]
Abstract
Vertebrate pigmentation patterns are amongst the best characterised model systems for studying the genetic basis of adaptive evolution. The wealth of available data on the genetic basis for pigmentation evolution allows for analysis of trends and quantitative testing of evolutionary hypotheses. We employed Gephebase, a database of genetic variants associated with natural and domesticated trait variation, to examine trends in how cis-regulatory and coding mutations contribute to vertebrate pigmentation phenotypes, as well as factors that favour one mutation type over the other. We found that studies with lower ascertainment bias identified higher proportions of cis-regulatory mutations, and that cis-regulatory mutations were more common amongst animals harbouring a higher number of pigment cell classes. We classified pigmentation traits firstly according to their physiological basis and secondly according to whether they affect colour or pattern, and identified that carotenoid-based pigmentation and variation in pattern boundaries are preferentially associated with cis-regulatory change. We also classified genes according to their developmental, cellular, and molecular functions. We found a greater proportion of cis-regulatory mutations in genes implicated in upstream developmental processes compared to those involved in downstream cellular functions, and that ligands were associated with a higher proportion of cis-regulatory mutations than their respective receptors. Based on these trends, we discuss future directions for research in vertebrate pigmentation evolution.
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Affiliation(s)
- Joel Elkin
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, 800 22nd St. NW, Suite 6000, Washington, DC, 20052, USA
| | | | - M Emília Santos
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
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4
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Fernandes B, Cavaco-Paulo A, Matamá T. A Comprehensive Review of Mammalian Pigmentation: Paving the Way for Innovative Hair Colour-Changing Cosmetics. BIOLOGY 2023; 12:biology12020290. [PMID: 36829566 PMCID: PMC9953601 DOI: 10.3390/biology12020290] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/26/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023]
Abstract
The natural colour of hair shafts is formed at the bulb of hair follicles, and it is coupled to the hair growth cycle. Three critical processes must happen for efficient pigmentation: (1) melanosome biogenesis in neural crest-derived melanocytes, (2) the biochemical synthesis of melanins (melanogenesis) inside melanosomes, and (3) the transfer of melanin granules to surrounding pre-cortical keratinocytes for their incorporation into nascent hair fibres. All these steps are under complex genetic control. The array of natural hair colour shades are ascribed to polymorphisms in several pigmentary genes. A myriad of factors acting via autocrine, paracrine, and endocrine mechanisms also contributes for hair colour diversity. Given the enormous social and cosmetic importance attributed to hair colour, hair dyeing is today a common practice. Nonetheless, the adverse effects of the long-term usage of such cosmetic procedures demand the development of new methods for colour change. In this context, case reports of hair lightening, darkening and repigmentation as a side-effect of the therapeutic usage of many drugs substantiate the possibility to tune hair colour by interfering with the biology of follicular pigmentary units. By scrutinizing mammalian pigmentation, this review pinpoints key targetable processes for the development of innovative cosmetics that can safely change the hair colour from the inside out.
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Affiliation(s)
- Bruno Fernandes
- CEB—Centre of Biological Engineering, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
| | - Artur Cavaco-Paulo
- CEB—Centre of Biological Engineering, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
- LABBELS—Associate Laboratory, 4710-057 Braga, Portugal
- Correspondence: (A.C.-P.); (T.M.); Tel.: +351-253-604-409 (A.C.-P.); +351-253-601-599 (T.M.)
| | - Teresa Matamá
- CEB—Centre of Biological Engineering, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
- LABBELS—Associate Laboratory, 4710-057 Braga, Portugal
- Correspondence: (A.C.-P.); (T.M.); Tel.: +351-253-604-409 (A.C.-P.); +351-253-601-599 (T.M.)
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5
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Lucock MD. The evolution of human skin pigmentation: A changing medley of vitamins, genetic variability, and UV radiation during human expansion. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 180:252-271. [PMID: 36790744 PMCID: PMC10083917 DOI: 10.1002/ajpa.24564] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/19/2022] [Accepted: 05/25/2022] [Indexed: 04/12/2023]
Abstract
This review examines putative, yet likely critical evolutionary pressures contributing to human skin pigmentation and subsequently, depigmentation phenotypes. To achieve this, it provides a synthesis of ideas that frame contemporary thinking, without limiting the narrative to pigmentation genes alone. It examines how geography and hence the quality and quantity of UV exposure, pigmentation genes, diet-related genes, vitamins, anti-oxidant nutrients, and cultural practices intersect and interact to facilitate the evolution of human skin color. The article has a strong focus on the vitamin D-folate evolutionary model, with updates on the latest biophysical research findings to support this paradigm. This model is examined within a broad canvas that takes human expansion out of Africa and genetic architecture into account. A thorough discourse on the biology of melanization is provided (includes relationship to BH4 and DNA damage repair), with the relevance of this to the UV sensitivity of folate and UV photosynthesis of vitamin D explained in detail, including the relevance of these vitamins to reproductive success. It explores whether we might be able to predict vitamin-related gene polymorphisms that pivot metabolism to the prevailing UVR exposome within the vitamin D-folate evolutionary hypothesis context. This is discussed in terms of a primary adaptive phenotype (pigmentation/depigmentation), a secondary adaptive phenotype (flexible metabolic phenotype based on vitamin-related gene polymorphism profile), and a tertiary adaptive strategy (dietary anti-oxidants to support the secondary adaptive phenotype). Finally, alternative evolutionary models for pigmentation are discussed, as are challenges to future research in this area.
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Affiliation(s)
- Mark D. Lucock
- School of Environmental & Life SciencesUniversity of NewcastleOurimbahNew South WalesAustralia
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6
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Sun D, Qi X, Wen H, Li C, Li J, Chen J, Tao Z, Zhu M, Zhang X, Li Y. The genetic basis and potential molecular mechanism of yellow-albino northern snakehead ( Channa argus). Open Biol 2023; 13:220235. [PMID: 36789536 PMCID: PMC9929503 DOI: 10.1098/rsob.220235] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
Body colour is an important economic trait for commercial fishes. Recently, a new colour morph displaying market-favoured yellow skin (termed as yellow-mutant, YM) of northern snakehead (Channa argus) was discovered in China. We confirmed that YM snakehead is an albino with complete loss of melanin in the skin and eyes by histological and ultrastructural observations, and inherited as a recessive Mendelian trait. By applying genomic analysis approaches, in combination with gene knockdown and rescue experiments, we suggested a non-sense mutation in slc45a2 (c.383G > A) is the causation for the YM snakehead. Notably, significantly higher levels of key melanogenesis genes (tyr, tyrp1, dct and pmel) and phospho-MITF protein were detected in YM snakehead than those in wild-type individuals, and the underlying mechanism was further investigated by comparative transcriptomic analysis. Results revealed that differential expressed genes involved in pathways like MAPK, WNT and calcium signalling were significantly induced in YM snakehead, which might account for the increased amount of melanogenesis elements, and presumably be stimulated by fibroblast-derived melanogenic factors in a paracrine manner. Our study clarified the genetic basis of colour variation in C. argus and provided the preliminary clue indicating the potential involvement of fibroblasts in pigmentation in fish.
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Affiliation(s)
- Donglei Sun
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Fisheries College, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Xin Qi
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Fisheries College, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Haishen Wen
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Fisheries College, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Jianlong Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Fisheries College, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Jiwei Chen
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Fisheries College, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Zexin Tao
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Fisheries College, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Mingxin Zhu
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Fisheries College, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Xiaoyan Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Yun Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education (KLMME), Fisheries College, Ocean University of China, Qingdao 266003, People's Republic of China
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7
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Farré X, Blay N, Cortés B, Carreras A, Iraola-Guzmán S, de Cid R. Skin Phototype and Disease: A Comprehensive Genetic Approach to Pigmentary Traits Pleiotropy Using PRS in the GCAT Cohort. Genes (Basel) 2023; 14:149. [PMID: 36672889 PMCID: PMC9859115 DOI: 10.3390/genes14010149] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/22/2022] [Accepted: 12/26/2022] [Indexed: 01/09/2023] Open
Abstract
Human pigmentation has largely been associated with different disease prevalence among populations, but most of these studies are observational and inconclusive. Known to be genetically determined, pigmentary traits have largely been studied by Genome-Wide Association Study (GWAS), mostly in Caucasian ancestry cohorts from North Europe, identifying robustly, several loci involved in many of the pigmentary traits. Here, we conduct a detailed analysis by GWAS and Polygenic Risk Score (PRS) of 13 pigmentary-related traits in a South European cohort of Caucasian ancestry (n = 20,000). We observed fair phototype strongly associated with non-melanoma skin cancer and other dermatoses and confirmed by PRS-approach the shared genetic basis with skin and eye diseases, such as melanoma (OR = 0.95), non-melanoma skin cancer (OR = 0.93), basal cell carcinoma (OR = 0.97) and darker phototype with vitiligo (OR = 1.02), cataracts (OR = 1.04). Detailed genetic analyses revealed 37 risk loci associated with 10 out of 13 analyzed traits, and 16 genes significantly associated with at least two pigmentary traits. Some of them have been widely reported, such as MC1R, HERC2, OCA2, TYR, TYRP1, SLC45A2, and some novel candidate genes C1QTNF3, LINC02876, and C1QTNF3-AMACR have not been reported in the GWAS Catalog, with regulatory potential. These results highlight the importance of the assess phototype as a genetic proxy of skin functionality and disease when evaluating open mixed populations.
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Affiliation(s)
| | | | | | | | | | - Rafael de Cid
- Genomes for Life-GCAT Lab, Germans Trias i Pujol Research Institute (IGTP), 08916 Badalona, Spain
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8
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Guc Z, Guc H. Sunlight: Friend or foe? A natural source of vitamin D or a risk factor for cutaneous malignancy? TURKISH JOURNAL OF PLASTIC SURGERY 2022. [DOI: 10.4103/tjps.tjps_66_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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9
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A large Canadian cohort provides insights into the genetic architecture of human hair colour. Commun Biol 2021; 4:1253. [PMID: 34737440 PMCID: PMC8568909 DOI: 10.1038/s42003-021-02764-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 10/08/2021] [Indexed: 12/05/2022] Open
Abstract
Hair colour is a polygenic phenotype that results from differences in the amount and ratio of melanins located in the hair bulb. Genome-wide association studies (GWAS) have identified many loci involved in the pigmentation pathway affecting hair colour. However, most of the associated loci overlap non-protein coding regions and many of the molecular mechanisms underlying pigmentation variation are still not understood. Here, we conduct GWAS meta-analyses of hair colour in a Canadian cohort of 12,741 individuals of European ancestry. By performing fine-mapping analyses we identify candidate causal variants in pigmentation loci associated with blonde, red and brown hair colour. Additionally, we observe colocalization of several GWAS hits with expression and methylation quantitative trait loci (QTLs) of cultured melanocytes. Finally, transcriptome-wide association studies (TWAS) further nominate the expression of EDNRB and CDK10 as significantly associated with hair colour. Our results provide insights on the mechanisms regulating pigmentation biology in humans.
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10
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Li Y, Li WQ, Li T, Qureshi AA, Cho E. Eye color and the risk of skin cancer. Cancer Causes Control 2021; 33:109-116. [PMID: 34687387 DOI: 10.1007/s10552-021-01508-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 10/08/2021] [Indexed: 10/20/2022]
Abstract
Melanoma, basal cell carcinoma (BCC) and squamous cell carcinoma (SCC) are the most common skin cancers. The incidence rates of all three types of skin cancers have increased in the past three decades. Light pigmentary traits have been recognized as one of the host risk factors for skin cancer, but findings on associations between eye colors and risk of skin cancers have been inconsistent.We performed a prospective analysis to examine the association between eye colors and risk of skin cancers using the Health Professionals Follow-up Study (HPFS). Cox proportional hazard models were applied to estimate relative risks (RRs) and their 95% confidence intervals (CIs). Effect modifications due to hair color and skin reaction to sun were also examined.The HPFS included 35,662 males. During a median follow-up of 19 years (1988-2012), 445 melanoma, 1123 SCC, and 7198 BCC cases were documented. Compared to those whose eye colors were dark or brown, participants with hazel/green/medium and blue/light colors had a 24% (RR = 1.24, 95% CI: 1.06-1.45) and a 19% (RR = 1.19, 95% CI: 1.01-1.41) higher risk of SCC, respectively. Similarly, a higher risk of BCC was observed in participants with hazel/green/medium eye colors (RR = 1.16, 95% CI: 1.09-1.23) and blue/light eye colors (RR = 1.17, 95% CI: 1.10-1.25). We did not find significant associations between eye color and risk of melanoma. Lighter eye color was associated with increased risks of SCC and BCC among those with dark hair colors (p for interaction ≤ 0.02).In conclusion, in this large prospective study of men, we found that light eye colors were associated with higher risks of SCC and BCC, but not melanoma. Further studies are needed to confirm this association in other populations.
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Affiliation(s)
- Yueyao Li
- Department of Dermatology, The Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Wen-Qing Li
- Department of Dermatology, The Warren Alpert Medical School of Brown University, Providence, RI, USA.,Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Cancer Epidemiology, Peking University Cancer Hospital & Institute, Beijing, China.,Department of Epidemiology, Brown School of Public Health, Providence, RI, USA
| | - Tricia Li
- Department of Dermatology, The Warren Alpert Medical School of Brown University, Providence, RI, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Womens Hospital, Boston, MA, USA
| | - Abrar A Qureshi
- Department of Dermatology, The Warren Alpert Medical School of Brown University, Providence, RI, USA.,Department of Epidemiology, Brown School of Public Health, Providence, RI, USA
| | - Eunyoung Cho
- Department of Dermatology, The Warren Alpert Medical School of Brown University, Providence, RI, USA. .,Department of Epidemiology, Brown School of Public Health, Providence, RI, USA. .,Channing Division of Network Medicine, Department of Medicine, Brigham and Womens Hospital, Boston, MA, USA.
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11
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Lucock MD, Jones PR, Veysey M, Thota R, Garg M, Furst J, Martin C, Yates Z, Scarlett CJ, Jablonski NG, Chaplin G, Beckett EL. Biophysical evidence to support and extend the vitamin D-folate hypothesis as a paradigm for the evolution of human skin pigmentation. Am J Hum Biol 2021; 34:e23667. [PMID: 34418235 DOI: 10.1002/ajhb.23667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVE To test the "vitamin D-folate hypothesis for the evolution of human skin pigmentation." METHODS Total ozone mapping spectrometer (TOMS) satellite data were used to examine surface UV-irradiance in a large (n = 649) Australian cross-sectional study population. Genetic analysis was used to score vitamin D- and folate-related gene polymorphisms (n = 22), along with two pigmentation gene variants (IRF4-rs12203592/HERC2-rs12913832). Red cell folate and vitamin D3 were measured by immunoassay and HPLC, respectively. RESULTS Ultraviolet radiation (UVR) and pigmentation genes interact to modify blood vitamin levels; Light skin IRF4-TT genotype has greatest folate loss while light skin HERC2-GG genotype has greatest vitamin D3 synthesis (reflected in both TOMS and seasonal data). UV-wavelength exhibits a dose-response relationship in folate loss within light skin IRF4-TT genotype (305 > 310 > 324 > 380 nm). Significant vitamin D3 photosynthesis only occurs within light skin HERC2-GG genotype, and is maximal at 305 nm. Three dietary antioxidants (vitamins C, E, and β-carotene) interact with UVR and pigmentation genes preventing oxidative loss of labile reduced folate vitamers, with greatest benefit in light skin IRF4-TT subjects. The putative photosensitiser, riboflavin, did not sensitize red cell folate to UVR and actually afforded protection. Four genes (5xSNPs) influenced blood vitamin levels when stratified by pigmentation genotype; MTHFR-rs1801133/rs1801131, TS-rs34489327, CYP24A-rs17216707, and VDR-ApaI-rs7975232. Lightest IRF4-TT/darkest HERC2-AA genotype combination (greatest folate loss/lowest vitamin D3 synthesis) has 0% occurrence. The opposing, commonest (39%) compound genotype (darkest IRF4-CC/lightest HERC2-GG) permits least folate loss and greatest synthesis of vitamin D3 . CONCLUSION New biophysical evidence supports the vitamin D-folate hypothesis for evolution of skin pigmentation.
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Affiliation(s)
- Mark D Lucock
- School of Environmental and Life Sciences, University of Newcastle, Ourimbah, New South Wales, Australia
| | - Patrice R Jones
- School of Environmental and Life Sciences, University of Newcastle, Ourimbah, New South Wales, Australia
| | | | - Rohith Thota
- Nutraceuticals Research Group, University of Newcastle, Callaghan, New South Wales, Australia.,Metabolism and Nutrition, Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Manohar Garg
- Nutraceuticals Research Group, University of Newcastle, Callaghan, New South Wales, Australia
| | - John Furst
- Maths and Physical Sciences, University of Newcastle, Ourimbah, New South Wales, Australia
| | - Charlotte Martin
- School of Environmental and Life Sciences, University of Newcastle, Ourimbah, New South Wales, Australia
| | - Zoe Yates
- Biomedical Sciences and Pharmacy, University of Newcastle, Ourimbah, New South Wales, Australia
| | - Christopher J Scarlett
- School of Environmental and Life Sciences, University of Newcastle, Ourimbah, New South Wales, Australia
| | - Nina G Jablonski
- Anthropology Department, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - George Chaplin
- Anthropology Department, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Emma L Beckett
- School of Environmental and Life Sciences, University of Newcastle, Ourimbah, New South Wales, Australia
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12
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Batai K, Cui Z, Arora A, Shah-Williams E, Hernandez W, Ruden M, Hollowell CMP, Hooker SE, Bathina M, Murphy AB, Bonilla C, Kittles RA. Genetic loci associated with skin pigmentation in African Americans and their effects on vitamin D deficiency. PLoS Genet 2021; 17:e1009319. [PMID: 33600456 PMCID: PMC7891745 DOI: 10.1371/journal.pgen.1009319] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 12/21/2020] [Indexed: 01/08/2023] Open
Abstract
A recent genome-wide association study (GWAS) in African descent populations identified novel loci associated with skin pigmentation. However, how genomic variations affect skin pigmentation and how these skin pigmentation gene variants affect serum 25(OH) vitamin D variation has not been explored in African Americans (AAs). In order to further understand genetic factors that affect human skin pigmentation and serum 25(OH)D variation, we performed a GWAS for skin pigmentation with 395 AAs and a replication study with 681 AAs. Then, we tested if the identified variants are associated with serum 25(OH) D concentrations in a subset of AAs (n = 591). Skin pigmentation, Melanin Index (M-Index), was measured using a narrow-band reflectometer. Multiple regression analysis was performed to identify variants associated with M-Index and to assess their role in serum 25(OH)D variation adjusting for population stratification and relevant confounding variables. A variant near the SLC24A5 gene (rs2675345) showed the strongest signal of association with M-Index (P = 4.0 x 10-30 in the pooled dataset). Variants in SLC24A5, SLC45A2 and OCA2 together account for a large proportion of skin pigmentation variance (11%). The effects of these variants on M-Index was modified by sex (P for interaction = 0.009). However, West African Ancestry (WAA) also accounts for a large proportion of M-Index variance (23%). M-Index also varies among AAs with high WAA and high Genetic Score calculated from top variants associated with M-Index, suggesting that other unknown genomic factors related to WAA are likely contributing to skin pigmentation variation. M-Index was not associated with serum 25(OH)D concentrations, but the Genetic Score was significantly associated with vitamin D deficiency (serum 25(OH)D levels less than 12 ng/mL) (OR, 1.30; 95% CI, 1.04-1.64). The findings support the hypothesis suggesting that skin pigmentation evolved responding to increased demand for subcutaneous vitamin D synthesis in high latitude environments.
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Affiliation(s)
- Ken Batai
- Department of Urology, University of Arizona, Tucson, Arizona, United States of America
| | - Zuxi Cui
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Amit Arora
- Department of Epidemiology and Biostatistics, University of Arizona, Tucson, Arizona, United States of America
| | - Ebony Shah-Williams
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, Indiana United States of America
| | - Wenndy Hernandez
- Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Maria Ruden
- Department of Surgery, Cook County Health and Hospitals System, Chicago, Illinois, United States of America
| | - Courtney M. P. Hollowell
- Department of Surgery, Cook County Health and Hospitals System, Chicago, Illinois, United States of America
| | - Stanley E. Hooker
- Division of Health Equities, Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, California, United States of America
| | - Madhavi Bathina
- Division of Health Equities, Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, California, United States of America
| | - Adam B. Murphy
- Department of Urology, Northwestern University, Chicago, Illinois, United States of America
| | - Carolina Bonilla
- Departamento de Medicina Preventiva, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Rick A. Kittles
- Division of Health Equities, Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, California, United States of America
- * E-mail:
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13
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Huang X, Wang S, Jin L, He Y. Dissecting dynamics and differences of selective pressures in the evolution of human pigmentation. Biol Open 2021; 10:bio056523. [PMID: 33495209 PMCID: PMC7888712 DOI: 10.1242/bio.056523] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 12/21/2020] [Indexed: 01/05/2023] Open
Abstract
Human pigmentation is a highly diverse and complex trait among populations and has drawn particular attention from both academic and non-academic investigators for thousands of years. Previous studies detected selection signals in several human pigmentation genes, but few studies have integrated contribution from multiple genes to the evolution of human pigmentation. Moreover, none has quantified selective pressures on human pigmentation over epochs and between populations. Here, we dissect dynamics and differences of selective pressures during different periods and between distinct populations with new approaches. We use genotype data of 19 genes associated with human pigmentation from 17 publicly available datasets and obtain data for 2346 individuals of six representative population groups from across the world. Our results quantify the strength of natural selection on light pigmentation not only in modern Europeans (0.0259/generation) but also in proto-Eurasians (0.00650/generation). Our results also suggest that several derived alleles associated with human dark pigmentation may be under positive directional selection in some African populations. Our study provides the first attempt to quantitatively investigate the dynamics of selective pressures during different time periods in the evolution of human pigmentation.This article has an associated First Person interview with the first author of the article.
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Affiliation(s)
- Xin Huang
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Society Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Sijia Wang
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Society Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Li Jin
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Society Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yungang He
- Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
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14
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Lucock M. Vitamin-related phenotypic adaptation to exposomal factors: The folate-vitamin D-exposome triad. Mol Aspects Med 2021; 87:100944. [PMID: 33551238 DOI: 10.1016/j.mam.2021.100944] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/02/2021] [Accepted: 01/25/2021] [Indexed: 12/16/2022]
Abstract
The biological role of two key vitamins, folic acid and vitamin D is so fundamental to life processes, it follows that their UV sensitivity, dietary abundance (both key exposomal factors) and variability in dependent genes will modify their functional efficacy, particularly in the context of maintaining the integrity and function of genome and epigenome. This article therefore examines folate and vitamin D-related phenotypic adaptation to environmental factors which vary across the human life cycle as well as over an evolutionary time-scale. Molecular mechanisms, key nutrigenomic factors, phenotypic maladaptation and evolutionary models are discussed.
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Affiliation(s)
- Mark Lucock
- School of Environmental & Life Sciences, University of Newcastle, PO Box 127, Brush Rd, Ourimbah, NSW, 2258, Australia.
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15
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Norton HL. The color of normal: How a Eurocentric focus erases pigmentation complexity. Am J Hum Biol 2020; 33:e23554. [PMID: 33337560 DOI: 10.1002/ajhb.23554] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/03/2020] [Accepted: 12/06/2020] [Indexed: 11/06/2022] Open
Abstract
OBJECTIVES Skin pigmentation is both a highly variable and highly visible human phenotypic trait. Investigations into the biology and origins of this variation have been the focus of research in the fields of dermatology, anthropology, and forensic science, among others. This manuscript explores how much of what we know about the biology, genetics, and evolutionary origins of pigmentation has been strongly influenced by investigations and applications that focus on lighter skin. METHODS I reviewed literature from the fields of dermatology, anthropology and evolutionary genetics, and forensic science to assess how perceptions of lighter skin as the "normal" state in humans can shape the ways that knowledge is gathered and applied in these fields. RESULTS This normalization of lighter skin has impacted common tools used in dermatology and shaped the framework of dermatological education. A strong Eurocentric bias has shaped our understanding of the genetic architecture of pigmentary traits, which influences the ways in we understand the evolutionary processes leading to modern pigmentation diversity. Finally, I discuss how these biases in pigmentation genetics work in combination with phenotypic systems that privilege predicting lighter pigmentation variation to impede accurate prediction of intermediate phenotypes, particularly in individuals with ancestry from multiple populations. This can lead to a disproportionate targeting of already over-policed populations with darker skin. CONCLUSIONS Potential changes to how we conceptualize clinical and basic pigmentation research may help to reduce existing health disparities and improve understanding of pigmentation genetic architecture and how this knowledge is applied in forensic contexts.
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Affiliation(s)
- Heather L Norton
- Department of Anthropology, University of Cincinnati, Cincinnati, Ohio, USA
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16
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Bâlteanu VA, Cardoso TF, Amills M, Luigi-Sierra MG, Egerszegi I, Anton I, Zsolnai A. Red and blond Mangalitza pigs display a signature of divergent directional selection in the SLC45A2 gene. Anim Genet 2020; 52:66-77. [PMID: 33316088 DOI: 10.1111/age.13031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2020] [Indexed: 12/11/2022]
Abstract
The Mangalitza lard-type pig breed is well known for its fat appearance and curly hair, and it is mainly distributed in Eastern Europe. Four main lines were created in the nineteenth century by artificial selection: Blond Mangalitza, Black Mangalitza, Swallow-Belly Mangalitza and Red Mangalitza. The Swallow-Belly line has a black coat combined with yellow-blond throat and underbelly. In the current work, we aimed to investigate if the colourations of Mangalitza pigs are genetically determined by one or a few loci whose frequencies have been modified by artificial selection. The results of selection scans, with HapFLK and BayeScan, and of a GWAS for coat colour highlighted the existence of one region on SSC16 (18-20 Mb) with potential effects on hair pigmentation (Red vs. Blond contrast). The analysis of the gene content of this region allowed us to detect the solute carrier family 45 member 2 (SLC45A2) locus as a candidate gene for this trait. The polymorphism of the SLC45A2 locus has been associated with reduced levels or the absence of melanin in several mammalian species. The genotyping of four missense polymorphisms evidenced that rs341599992:G > A and rs693695020:G > A SNPs are strongly but not fully associated with the red and blond coat colours of Mangalitza pigs, a result that was confirmed by performing a haplotype association test. The near fixation of alternative SLC45A2 genotypes in Red and Blond Mangalitza pigs provides a compelling example of the consequences of a divergent directional selection for coat colour in a domestic species.
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Affiliation(s)
- V A Bâlteanu
- Institute of Life Sciences, University of Agricultural Sciences and Veterinary Medicine, Calea Mănăştur 3-5, Cluj-Napoca, 400372, Romania
| | - T F Cardoso
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, 08193, Spain.,CAPES Foundation, Ministry of Education of Brazil, Brasilia, 7004020, Brazil
| | - M Amills
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, 08193, Spain.,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - M G Luigi-Sierra
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, 08193, Spain
| | - I Egerszegi
- Szent István University, Páter Károly u. 1, Gödöllő, 2100, Hungary
| | - I Anton
- NARIC-Research Institute for Animal Breeding, Nutrition and Meat Science, Gesztenyés u. 1, Herceghalom, 2053, Hungary
| | - A Zsolnai
- NARIC-Research Institute for Animal Breeding, Nutrition and Meat Science, Gesztenyés u. 1, Herceghalom, 2053, Hungary
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17
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Browning SR, Browning BL. Probabilistic Estimation of Identity by Descent Segment Endpoints and Detection of Recent Selection. Am J Hum Genet 2020; 107:895-910. [PMID: 33053335 PMCID: PMC7553009 DOI: 10.1016/j.ajhg.2020.09.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/25/2020] [Indexed: 12/18/2022] Open
Abstract
Most methods for fast detection of identity by descent (IBD) segments report identity by state segments without any quantification of the uncertainty in the endpoints and lengths of the IBD segments. We present a method for determining the posterior probability distribution of IBD segment endpoints. Our approach accounts for genotype errors, recent mutations, and gene conversions which disrupt DNA sequence identity within IBD segments, and it can be applied to large cohorts with whole-genome sequence or SNP array data. We find that our method's estimates of uncertainty are well calibrated for homogeneous samples. We quantify endpoint uncertainty for 77.7 billion IBD segments from 408,883 individuals of white British ancestry in the UK Biobank, and we use these IBD segments to find regions showing evidence of recent natural selection. We show that many spurious selection signals are eliminated by the use of unbiased estimates of IBD segment endpoints and a pedigree-based genetic map. Eleven of the twelve regions with the greatest evidence for recent selection in our scan have been identified as selected in previous analyses using different approaches. Our computationally efficient method for quantifying IBD segment endpoint uncertainty is implemented in the open source ibd-ends software package.
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Affiliation(s)
- Sharon R Browning
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA.
| | - Brian L Browning
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA; Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
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18
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Rayner JE, Duffy DL, Smit DJ, Jagirdar K, Lee KJ, De’Ambrosis B, Smithers BM, McMeniman EK, McInerney-Leo AM, Schaider H, Stark MS, Soyer HP, Sturm RA. Germline and somatic albinism variants in amelanotic/hypomelanotic melanoma: Increased carriage of TYR and OCA2 variants. PLoS One 2020; 15:e0238529. [PMID: 32966289 PMCID: PMC7510969 DOI: 10.1371/journal.pone.0238529] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 08/18/2020] [Indexed: 12/30/2022] Open
Abstract
Amelanotic/hypomelanotic melanoma is a clinicopathologic subtype with absent or minimal melanin. This study assessed previously reported coding variants in albinism genes (TYR, OCA2, TYRP1, SLC45A2, SLC24A5, LRMDA) and common intronic, regulatory variants of OCA2 in individuals with amelanotic/hypomelanotic melanoma, pigmented melanoma cases and controls. Exome sequencing was available for 28 individuals with amelanotic/hypomelanotic melanoma and 303 individuals with pigmented melanoma, which were compared to whole exome data from 1144 Australian controls. Microarray genotyping was available for a further 17 amelanotic/hypomelanotic melanoma, 86 pigmented melanoma, 147 melanoma cases (pigmentation unknown) and 652 unaffected controls. Rare deleterious variants in TYR/OCA1 were more common in amelanotic/hypomelanotic melanoma cases than pigmented melanoma cases (set mixed model association tests P = 0.0088). The OCA2 hypomorphic allele p.V443I was more common in melanoma cases (1.8%) than controls (1.0%, X2 P = 0.02), and more so in amelanotic/hypomelanotic melanoma (4.4%, X2 P = 0.007). No amelanotic/hypomelanotic melanoma cases carried an eye and skin darkening haplotype of OCA2 (including rs7174027), present in 7.1% of pigmented melanoma cases (P = 0.0005) and 9.4% controls. Variants in TYR and OCA2 may play a role in amelanotic/hypomelanotic melanoma susceptibility. We suggest that somatic loss of function at these loci could contribute to the loss of tumor pigmentation, consistent with this we found a higher rate of somatic mutation in TYR/OCA2 in amelanotic/hypomelanotic melanoma vs pigmented melanoma samples (28.6% vs 3.0%; P = 0.021) from The Cancer Genome Atlas Skin Cutaneous Melanoma collection.
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Affiliation(s)
- Jenna E. Rayner
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
| | - David L. Duffy
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
- QIMR Berghofer Medical Research Institute, Brisbane, Qld, Australia
| | - Darren J. Smit
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
| | - Kasturee Jagirdar
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
| | - Katie J. Lee
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
| | - Brian De’Ambrosis
- Dermatology Department, Princess Alexandra Hospital, Brisbane, Qld, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Qld, Australia
- South East Dermatology, Annerley, Brisbane, Qld, Australia
| | - B. Mark Smithers
- Queensland Melanoma Project, School of Medicine, The University of Queensland, Brisbane, Qld, Australia
| | - Erin K. McMeniman
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
- Dermatology Department, Princess Alexandra Hospital, Brisbane, Qld, Australia
| | - Aideen M. McInerney-Leo
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
| | - Helmut Schaider
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
| | - Mitchell S. Stark
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
| | - H. Peter Soyer
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
- Dermatology Department, Princess Alexandra Hospital, Brisbane, Qld, Australia
| | - Richard A. Sturm
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
- * E-mail:
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19
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Association between brown eye colour in rs12913832:GG individuals and SNPs in TYR, TYRP1, and SLC24A4. PLoS One 2020; 15:e0239131. [PMID: 32915910 PMCID: PMC7485777 DOI: 10.1371/journal.pone.0239131] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 08/31/2020] [Indexed: 01/04/2023] Open
Abstract
The genotype of a single SNP, rs12913832, is the primary predictor of blue and brown eye colours. The genotypes rs12913832:AA and rs12913832:GA are most often observed in individuals with brown eye colours, whereas rs12913832:GG is most often observed in individuals with blue eye colours. However, approximately 3% of Europeans with the rs12913832:GG genotype have brown eye colours. The purpose of the study presented here was to identify variants that explain brown eye colour formation in individuals with the rs12913832:GG genotype. Genes and regulatory regions surrounding SLC24A4, TYRP1, SLC24A5, IRF4, TYR, and SLC45A2, as well as the upstream region of OCA2 within the HERC2 gene were sequenced in a study comprising 40 individuals with the rs12913832:GG genotype. Of these, 24 individuals were considered to have blue eye colours and 16 individuals were considered to have brown eye colours. We identified 211 variants within the SLC24A4, TYRP1, IRF4, and TYR target regions associated with eye colour. Based on in silico analyses of predicted variant effects we recognized four variants, TYRP1 rs35866166:C, TYRP1 rs62538956:C, SLC24A4 rs1289469:C, and TYR rs1126809:G, to be the most promising candidates for explanation of brown eye colour in individuals with the rs12913832:GG genotype. Of the 16 individuals with brown eye colours, 14 individuals had four alleles, whereas the alleles were rare in the blue eyed individuals. rs35866166, rs62538956, and rs1289469 were for the first time found to be associated with pigmentary traits, whilst rs1126809 was previously found to be associated with pigmentary variation. To improve prediction of eye colours we suggest that future eye colour prediction models should include rs35866166, rs62538956, rs1289469, and rs1126809.
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20
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Böhme I, Schönherr R, Eberle J, Bosserhoff AK. Membrane Transporters and Channels in Melanoma. Rev Physiol Biochem Pharmacol 2020; 181:269-374. [PMID: 32737752 DOI: 10.1007/112_2020_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent research has revealed that ion channels and transporters can be important players in tumor development, progression, and therapy resistance in melanoma. For example, members of the ABC family were shown to support cancer stemness-like features in melanoma cells, while several members of the TRP channel family were reported to act as tumor suppressors.Also, many transporter proteins support tumor cell viability and thus suppress apoptosis induction by anticancer therapy. Due to the high number of ion channels and transporters and the resulting high complexity of the field, progress in understanding is often focused on single molecules and is in total rather slow. In this review, we aim at giving an overview about a broad subset of ion transporters, also illustrating some aspects of the field, which have not been addressed in detail in melanoma. In context with the other chapters in this special issue on "Transportome Malfunctions in the Cancer Spectrum," a comparison between melanoma and these tumors will be possible.
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Affiliation(s)
- Ines Böhme
- Institute of Biochemistry, Emil Fischer Center, Friedrich-Alexander-University of Erlangen-Nürnberg, Erlangen, Germany
| | - Roland Schönherr
- Institute of Biochemistry and Biophysics, Friedrich Schiller University Jena and Jena University Hospital, Jena, Germany
| | - Jürgen Eberle
- Department of Dermatology, Venerology and Allergology, Skin Cancer Center Charité, University Medical Center Charité, Berlin, Germany
| | - Anja Katrin Bosserhoff
- Institute of Biochemistry, Emil Fischer Center, Friedrich-Alexander-University of Erlangen-Nürnberg, Erlangen, Germany. .,Comprehensive Cancer Center (CCC) Erlangen-EMN, Erlangen, Germany.
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21
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Andersen JD, Meyer OS, Simão F, Jannuzzi J, Carvalho E, Andersen MM, Pereira V, Børsting C, Morling N, Gusmão L. Skin pigmentation and genetic variants in an admixed Brazilian population of primarily European ancestry. Int J Legal Med 2020; 134:1569-1579. [PMID: 32385594 DOI: 10.1007/s00414-020-02307-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 04/22/2020] [Indexed: 01/16/2023]
Abstract
Although many genes have been shown to be associated with human pigmentary traits and forensic prediction assays exist (e.g. HIrisPlex-S), the genetic knowledge about skin colour remains incomplete. The highly admixed Brazilian population is an interesting study population for investigation of the complex genotype-phenotype architecture of human skin colour because of its large variation. Here, we compared variants in 22 pigmentary genes with quantitative skin pigmentation levels on the buttock, arm, and forehead areas of 266 genetically admixed Brazilian individuals. The genetic ancestry of each individual was estimated by typing 46 AIM-InDels. The mean proportion of genetic ancestry was 68.8% European, 20.8% Sub-Saharan African, and 10.4% Native American. A high correlation (adjusted R2 = 0.65, p < 0.05) was observed between nine SNPs and quantitative skin pigmentation using multiple linear regression analysis. The correlations were notably smaller between skin pigmentation and biogeographic ancestry (adjusted R2 = 0.45, p < 0.05), or markers in the leading forensic skin colour prediction system, the HIrisPlex-S (adjusted R2 = 0.54, p < 0.05). Four of the nine SNPs, OCA2 rs1448484 (rank 2), APBA2 rs4424881 (rank 4), MFSD12 rs10424065 (rank 8), and TYRP1 1408799 (rank 9) were not investigated as part of the HIrisPlex-S selection process, and therefore not included in the HIrisPlex-S model. Our results indicate that these SNPs account for a substantial part of the skin colour variation in individuals of admixed ancestry. Hence, we suggest that these SNPs are considered when developing future skin colour prediction models.
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Affiliation(s)
- Jeppe D Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100, Copenhagen, Denmark.
| | - Olivia S Meyer
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | - Filipa Simão
- DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Juliana Jannuzzi
- DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Elizeu Carvalho
- DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Mikkel M Andersen
- Department of Mathematical Sciences, Aalborg University, DK-9000, Aalborg, Denmark
| | - Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
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22
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Yang Z, Shi H, Ma P, Zhao S, Kong Q, Bian T, Gong C, Zhao Q, Liu Y, Qi X, Zhang X, Han Y, Liu J, Li Q, Chen H, Su B. Darwinian Positive Selection on the Pleiotropic Effects of KITLG Explain Skin Pigmentation and Winter Temperature Adaptation in Eurasians. Mol Biol Evol 2020; 35:2272-2283. [PMID: 29961894 DOI: 10.1093/molbev/msy136] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Human skin color diversity is considered an adaptation to environmental conditions such as UV radiation. Investigations into the genetic bases of such adaptation have identified a group of pigmentation genes contributing to skin color diversity in African and non-African populations. Here, we present a population analysis of the pigmentation gene KITLG with previously reported signal of Darwinian positive selection in both European and East Asian populations. We demonstrated that there had been recurrent selective events in the upstream and the downstream regions of KITLG in Eurasian populations. More importantly, besides the expected selection on the KITLG variants favoring light skin in coping with the weak UV radiation at high latitude, we observed a KITLG variant showing adaptation to winter temperature. In particular, compared with UV radiation, winter temperature showed a much stronger correlation with the prevalence of the presumably adaptive KITLG allele in Asian populations. This observation was further supported by the in vitro functional test at low temperature. Consequently, the pleiotropic effects of KITLG, that is, pigmentation and thermogenesis were both targeted by natural selection that acted on different KITLG sequence variants, contributing to the adaptation of Eurasians to both UV radiation and winter temperature at high latitude areas.
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Affiliation(s)
- Zhaohui Yang
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Yunnan Provincial Academy of Science and Technology, Kunming, China
| | - Hong Shi
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China.,Yunnan Provincial Academy of Science and Technology, Kunming, China
| | - Pengcheng Ma
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Shilei Zhao
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Qinghong Kong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Tianhao Bian
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China.,Yunnan Provincial Academy of Science and Technology, Kunming, China
| | - Chao Gong
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China.,Yunnan Provincial Academy of Science and Technology, Kunming, China
| | - Qi Zhao
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China.,Yunnan Provincial Academy of Science and Technology, Kunming, China
| | - Yuan Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xuebin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xiaoming Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yinglun Han
- College of Life Science, Liaoning Normal University, Dalian, China
| | - Jiewei Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Qingwei Li
- College of Life Science, Liaoning Normal University, Dalian, China
| | - Hua Chen
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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23
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Glueck C, Wilson JA. RETRACTED: Is photoshop with Qualitative Image Analysis a valid technique for measuring hair morphology? A test using wires of known dimensions. JOURNAL OF VERTEBRATE BIOLOGY 2019. [DOI: 10.25225/fozo.012.2019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Christopher Glueck
- Department of Biology, University of Nebraska at Omaha, 6001 Dodge Street, Omaha, NE 68182-0040, USA; e-mail:
| | - James A. Wilson
- Department of Biology, University of Nebraska at Omaha, 6001 Dodge Street, Omaha, NE 68182-0040, USA; e-mail:
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24
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The Evolutionary History of Human Skin Pigmentation. J Mol Evol 2019; 88:77-87. [PMID: 31363820 DOI: 10.1007/s00239-019-09902-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 07/16/2019] [Indexed: 02/07/2023]
Abstract
Skin pigmentation is a complex, conspicuous, highly variable human trait that exhibits a remarkable correlation with latitude. The evolutionary history and genetic basis of skin color variation has been the subject of intense research in the last years. This article reviews the major hypotheses explaining skin color diversity and explores the implications of recent findings about the genes associated with skin pigmentation for understanding the evolutionary forces that have shaped the current patterns of skin color variation. A major aspect of these findings is that the genetic basis of skin color is less simple than previously thought and that geographic variation in skin pigmentation was influenced by the concerted action of different types of natural selection, rather than just by selective sweeps in a few key genes.
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25
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Abstract
Human skin and hair color are visible traits that can vary dramatically within and across ethnic populations. The genetic makeup of these traits-including polymorphisms in the enzymes and signaling proteins involved in melanogenesis, and the vital role of ion transport mechanisms operating during the maturation and distribution of the melanosome-has provided new insights into the regulation of pigmentation. A large number of novel loci involved in the process have been recently discovered through four large-scale genome-wide association studies in Europeans, two large genetic studies of skin color in Africans, one study in Latin Americans, and functional testing in animal models. The responsible polymorphisms within these pigmentation genes appear at different population frequencies, can be used as ancestry-informative markers, and provide insight into the evolutionary selective forces that have acted to create this human diversity.
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Affiliation(s)
- William J Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
| | - Richard A Sturm
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Queensland 4102, Australia;
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26
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Evaluation of the classification method using ancestry SNP markers for ethnic group. COMMUNICATIONS FOR STATISTICAL APPLICATIONS AND METHODS 2019. [DOI: 10.29220/csam.2019.26.1.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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27
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Quillen EE, Norton HL, Parra EJ, Lona-Durazo F, Ang KC, Illiescu FM, Pearson LN, Shriver MD, Lasisi T, Gokcumen O, Starr I, Lin YL, Martin AR, Jablonski NG. Shades of complexity: New perspectives on the evolution and genetic architecture of human skin. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 168 Suppl 67:4-26. [PMID: 30408154 DOI: 10.1002/ajpa.23737] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/17/2018] [Accepted: 09/20/2018] [Indexed: 02/06/2023]
Abstract
Like many highly variable human traits, more than a dozen genes are known to contribute to the full range of skin color. However, the historical bias in favor of genetic studies in European and European-derived populations has blinded us to the magnitude of pigmentation's complexity. As deliberate efforts are being made to better characterize diverse global populations and new sequencing technologies, better measurement tools, functional assessments, predictive modeling, and ancient DNA analyses become more widely accessible, we are beginning to appreciate how limited our understanding of the genetic bases of human skin color have been. Novel variants in genes not previously linked to pigmentation have been identified and evidence is mounting that there are hundreds more variants yet to be found. Even for genes that have been exhaustively characterized in European populations like MC1R, OCA2, and SLC24A5, research in previously understudied groups is leading to a new appreciation of the degree to which genetic diversity, epistatic interactions, pleiotropy, admixture, global and local adaptation, and cultural practices operate in population-specific ways to shape the genetic architecture of skin color. Furthermore, we are coming to terms with how factors like tanning response and barrier function may also have influenced selection on skin throughout human history. By examining how our knowledge of pigmentation genetics has shifted in the last decade, we can better appreciate how far we have come in understanding human diversity and the still long road ahead for understanding many complex human traits.
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Affiliation(s)
- Ellen E Quillen
- Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina.,Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Heather L Norton
- Department of Anthropology, University of Cincinnati, Cincinnati, Ohio
| | - Esteban J Parra
- Department of Anthropology, University of Toronto - Mississauga, Mississauga, Ontario, Canada
| | - Frida Lona-Durazo
- Department of Anthropology, University of Toronto - Mississauga, Mississauga, Ontario, Canada
| | - Khai C Ang
- Department of Pathology and Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, Pennsylvania
| | - Florin Mircea Illiescu
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom.,Centro de Estudios Interculturales e Indígenas - CIIR, P. Universidad Católica de Chile, Santiago, Chile
| | - Laurel N Pearson
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| | - Mark D Shriver
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| | - Tina Lasisi
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| | - Omer Gokcumen
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York
| | - Izzy Starr
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York
| | - Yen-Lung Lin
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York
| | - Alicia R Martin
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Nina G Jablonski
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
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28
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Bradbury C, Köttgen A, Staubach F. Off-target phenotypes in forensic DNA phenotyping and biogeographic ancestry inference: A resource. Forensic Sci Int Genet 2018; 38:93-104. [PMID: 30391626 DOI: 10.1016/j.fsigen.2018.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/27/2018] [Accepted: 10/13/2018] [Indexed: 01/04/2023]
Abstract
With recent advances in DNA sequencing technologies it has become feasible and cost effective to genotype larger marker sets for forensic purposes. Two technologies that make use of the larger marker sets have come into focus in forensic research and applications; inference of biogeographic ancestry (BGA) and forensic DNA phenotyping (FDP). These methods hold the promise to reveal information about a yet unknown perpetrator from a DNA sample. In contrast, DNA-profiling, that is a standard practice in case work, relies on matching DNA-profiles between crime scene material and suspects on a database of DNA-profiles. Markers for DNA-profiling were developed under the premise to reveal as little additional information about the human source of the profile as possible, the rationale being that personal privacy rights have to be balanced against the public interest in solving a crime. The same argument holds for markers used in BGA and FDP; these markers might also reveal information on off-target phenotypes (OTPs), that go beyond BGA and the phenotypes targeted in FDP. In particular, health related OTPs might shift the balance between privacy protection and public interest. However, to our knowledge, there is currently no convenient resource available to incorporate knowledge on OTPs in BGA and FDP assay design and application. In order to provide such a resource, we performed a systematic search for OTPs associated with a comprehensive set of markers (1766 SNPs) used or suggested to be used for BGA inference and FDP. In this set, we identified a relatively small number of 27 SNPs (1.53%) that convey information on diverse health related OTPs such as cancer risk, induced asthma, or risk of alcoholism. Some of these SNPs are commonly used for FDP and BGA across different marker sets. We conclude that the effects of SNP markers used in FDP and BGA on OTPs are currently limited, with few exceptions that should be considered in a balanced decision on assay design and application.
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Affiliation(s)
- Cedric Bradbury
- University College Freiburg, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Dept. of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Fabian Staubach
- Institute of Biology I, Dept. of Evolutionary Biology and Ecology, Albert-Ludwigs-University Freiburg, Freiburg, Germany.
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29
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Okamura K, Hayashi M, Nakajima O, Kono M, Abe Y, Hozumi Y, Suzuki T. A 4‐bp deletion promoter variant (rs984225803) is associated with mild
OCA
4 among Japanese patients. Pigment Cell Melanoma Res 2018; 32:79-84. [DOI: 10.1111/pcmr.12727] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 06/11/2018] [Accepted: 07/13/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Ken Okamura
- Department of DermatologyFaculty of MedicineYamagata University Yamagata Japan
| | - Masahiro Hayashi
- Department of DermatologyFaculty of MedicineYamagata University Yamagata Japan
| | - Osamu Nakajima
- Faculty of MedicineResearch Center for Molecular GeneticsInstitute for Promotion of Medical Science ResearchYamagata University Yamagata Japan
| | - Michihiro Kono
- Department of DermatologyNagoya University Graduate School of Medicine Nagoya Japan
| | - Yuko Abe
- Department of DermatologyFaculty of MedicineYamagata University Yamagata Japan
| | - Yutaka Hozumi
- Department of DermatologyFaculty of MedicineYamagata University Yamagata Japan
| | - Tamio Suzuki
- Department of DermatologyFaculty of MedicineYamagata University Yamagata Japan
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30
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Evaluation of the Relationship between Alopecia Areata and Viral Antigen Exposure. Am J Clin Dermatol 2018; 19:119-126. [PMID: 28801732 DOI: 10.1007/s40257-017-0312-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Alopecia areata (AA) is an autoimmune disease characterized by non-scarring alopecia with T-cell infiltration at the affected hair follicle. OBJECTIVE Our aim was to study the potential link between hepatitis B virus (HBV) antigen exposure and AA. METHODS Two pediatric patients with AA following hepatitis B vaccination were identified in a general dermatology clinic. A bioinformatics analysis and an electronic medical record (EMR) database query were performed at the University of Rochester Medical Center to identify patients with AA, coexisting viral infections, vaccinations, or interferon (IFN) therapy in order to determine if the presence of AA and these conditions was higher than in AA patients without these associated conditions or therapy. RESULTS An increased frequency of AA among those who received the HBV surface protein antigen [odds ratio (OR) 2.7, p < 0.0001] was identified, and an independent analysis revealed an increased frequency of AA in those receiving IFN-β treatment (OR 8.1, p < 0.05). One potential antigenic target identified was SLC45A2, a melanosomal transport protein important in skin and hair pigmentation. The longest potential vaccine peptide fragment match (8-mer) was to a segment of natural killer (NK) cell inhibitory receptors, KIR3DL2 and KIR3DL1. Predictive modeling of major histocompatibility complex (MHC)-peptide binding demonstrated potential binding of this peptide to MHC relevant to AA. LIMITATIONS The results will need to be verified in additional patient databases allowing analysis of temporal relationships, and with molecular experiments of the identified antigens. CONCLUSIONS Our data confirm associations between viral infection and IFN treatment with AA. It establishes that the hepatitis B surface protein antigen has shared epitopes with human killer immunoglobulin-like receptors.
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31
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Szpak M, Mezzavilla M, Ayub Q, Chen Y, Xue Y, Tyler-Smith C. FineMAV: prioritizing candidate genetic variants driving local adaptations in human populations. Genome Biol 2018; 19:5. [PMID: 29343290 PMCID: PMC5771147 DOI: 10.1186/s13059-017-1380-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 12/12/2017] [Indexed: 12/30/2022] Open
Abstract
We present a new method, Fine-Mapping of Adaptive Variation (FineMAV), which combines population differentiation, derived allele frequency, and molecular functionality to prioritize positively selected candidate variants for functional follow-up. We calibrate and test FineMAV using eight experimentally validated "gold standard" positively selected variants and simulations. FineMAV has good sensitivity and a low false discovery rate. Applying FineMAV to the 1000 Genomes Project Phase 3 SNP dataset, we report many novel selected variants, including ones in TGM3 and PRSS53 associated with hair phenotypes that we validate using available independent data. FineMAV is widely applicable to sequence data from both human and other species.
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Affiliation(s)
- Michał Szpak
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
| | - Massimo Mezzavilla
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
- Division of Experimental Genetics, Sidra Medical and Research Center, Doha, Qatar
| | - Qasim Ayub
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
- Present Address: Genomics Facility, School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Darul Ehsan Malaysia
| | - Yuan Chen
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
| | - Yali Xue
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
| | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA UK
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32
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Ombra MN, Paliogiannis P, Doneddu V, Sini MC, Colombino M, Rozzo C, Stanganelli I, Tanda F, Cossu A, Palmieri G. Vitamin D status and risk for malignant cutaneous melanoma: recent advances. Eur J Cancer Prev 2017; 26:532-541. [PMID: 28125434 PMCID: PMC5627529 DOI: 10.1097/cej.0000000000000334] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 12/07/2016] [Indexed: 01/08/2023]
Abstract
Cutaneous malignant melanoma, whose incidence is increasing steadily worldwide, is the result of complex interactions between individual genetic factors and environmental risk factors. Ultraviolet radiation represents the most important environmental risk factor for the development of skin cancers, including melanoma. Sun exposure and early sunburn during childhood are the principal causes of cutaneous melanoma insurgence in adults, with double the risk relative to a nonexposed population. Consequently, ultraviolet protection has long been recognized as an important measure to prevent such a malignancy. Biological and epidemiological data suggest that vitamin D status could affect the risk of cancer and play a role in cancer prevention by exerting antiproliferative effects. Solar radiations are critical for vitamin D synthesis in humans; however, uncontrolled and intensive sun exposure is dangerous to skin health and may contribute toward the development of cutaneous malignant melanoma. An optimum balance between sun protection and exposure is thus advocated. Additional research is required to confirm the preventive role of vitamin D in melanoma incidence or a positive influence on patient outcome.
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Affiliation(s)
- Maria N. Ombra
- Institute of Food Sciences, National Research Council (CNR), Avellino
| | | | - Valentina Doneddu
- Department of Surgical, Microsurgical and Medical Sciences, University of Sassari
| | - Maria C. Sini
- Institute of Biomolecular Chemistry, National Research Council (CNR), Cancer Genetics Unit, Sassari
| | - Maria Colombino
- Institute of Biomolecular Chemistry, National Research Council (CNR), Cancer Genetics Unit, Sassari
| | - Carla Rozzo
- Institute of Biomolecular Chemistry, National Research Council (CNR), Cancer Genetics Unit, Sassari
| | - Ignazio Stanganelli
- Romagna Scientific Institute for the Study and Cure of Tumors, Skin Cancer Unit, Meldola, Italy
| | - Francesco Tanda
- Department of Surgical, Microsurgical and Medical Sciences, University of Sassari
| | - Antonio Cossu
- Department of Surgical, Microsurgical and Medical Sciences, University of Sassari
| | - Giuseppe Palmieri
- Institute of Biomolecular Chemistry, National Research Council (CNR), Cancer Genetics Unit, Sassari
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33
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Genome-Wide Association Shows that Pigmentation Genes Play a Role in Skin Aging. J Invest Dermatol 2017; 137:1887-1894. [DOI: 10.1016/j.jid.2017.04.026] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 04/05/2017] [Accepted: 04/24/2017] [Indexed: 01/27/2023]
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34
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Fábos B, Farkas K, Tóth L, Sulák A, Tripolszki K, Tihanyi M, Németh R, Vas K, Csoma Z, Kemény L, Széll M, Nagy N. Delineating the genetic heterogeneity of OCA in Hungarian patients. Eur J Med Res 2017. [PMID: 28629449 PMCID: PMC5477306 DOI: 10.1186/s40001-017-0262-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Oculocutaneous albinism (OCA) is a clinically and genetically heterogenic group of pigmentation abnormalities characterized by variable hair, skin, and ocular hypopigmentation. Six known genes and a locus on human chromosome 4q24 have been implicated in the etiology of isolated OCA forms (OCA 1-7). METHODS The most frequent OCA types among Caucasians are OCA1, OCA2, and OCA4. We aimed to investigate genes responsible for the development of these OCA forms in Hungarian OCA patients (n = 13). Mutation screening and polymorphism analysis were performed by direct sequencing on TYR, OCA2, SLC45A2 genes. RESULTS Although the clinical features of the investigated Hungarian OCA patients were identical, the molecular genetic data suggested OCA1 subtype in eight cases and OCA4 subtype in two cases. The molecular diagnosis was not clearly identifiable in three cases. In four patients, two different heterozygous known pathogenic or predicted to be pathogenic mutations were present. Seven patients had only one pathogenic mutation, which was associated with non-pathogenic variants in six cases. In two patients no pathogenic mutation was identified. CONCLUSIONS Our results suggest that the concomitant screening of the non-pathogenic variants-which alone do not cause the development of OCA, but might have clinical significance in association with a pathogenic variant-is important. Our results also show significant variation in the disease spectrum compared to other populations. These data also confirm that the concomitant analysis of OCA genes is critical, providing new insights to the phenotypic diversity of OCA and expanding the mutation spectrum of OCA genes in Hungarian patients.
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Affiliation(s)
- Beáta Fábos
- Mór Kaposi Teaching Hospital of the Somogy County, Kaposvár, Hungary
| | - Katalin Farkas
- MTA-SZTE Dermatological Research Group, University of Szeged, Szeged, Hungary
| | - Lola Tóth
- Department of Medical Genetics, University of Szeged, 4 Somogyi Bela Street, 6720, Szeged, Hungary
| | - Adrienn Sulák
- Department of Medical Genetics, University of Szeged, 4 Somogyi Bela Street, 6720, Szeged, Hungary
| | - Kornélia Tripolszki
- Department of Medical Genetics, University of Szeged, 4 Somogyi Bela Street, 6720, Szeged, Hungary
| | - Mariann Tihanyi
- Genetic Laboratory, Hospital of Zala County, Zalaegerszeg, Hungary
| | - Réka Németh
- Department of Dermatology and Allergology, University of Szeged, Szeged, Hungary
| | - Krisztina Vas
- Department of Dermatology and Allergology, University of Szeged, Szeged, Hungary
| | - Zsanett Csoma
- Department of Dermatology and Allergology, University of Szeged, Szeged, Hungary
| | - Lajos Kemény
- MTA-SZTE Dermatological Research Group, University of Szeged, Szeged, Hungary.,Department of Dermatology and Allergology, University of Szeged, Szeged, Hungary
| | - Márta Széll
- MTA-SZTE Dermatological Research Group, University of Szeged, Szeged, Hungary.,Department of Medical Genetics, University of Szeged, 4 Somogyi Bela Street, 6720, Szeged, Hungary
| | - Nikoletta Nagy
- MTA-SZTE Dermatological Research Group, University of Szeged, Szeged, Hungary. .,Department of Medical Genetics, University of Szeged, 4 Somogyi Bela Street, 6720, Szeged, Hungary. .,Department of Dermatology and Allergology, University of Szeged, Szeged, Hungary.
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35
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Park J, Talukder AH, Lim SA, Kim K, Pan K, Melendez B, Bradley SD, Jackson KR, Khalili JS, Wang J, Creasy C, Pan BF, Woodman SE, Bernatchez C, Hawke D, Hwu P, Lee KM, Roszik J, Lizée G, Yee C. SLC45A2: A Melanoma Antigen with High Tumor Selectivity and Reduced Potential for Autoimmune Toxicity. Cancer Immunol Res 2017. [PMID: 28630054 DOI: 10.1158/2326-6066.cir-17-0051] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Cytotoxic T lymphocyte (CTL)-based immunotherapies have had remarkable success at generating objective clinical responses in patients with advanced metastatic melanoma. Although the melanocyte differentiation antigens (MDA) MART-1, PMEL, and tyrosinase were among the first melanoma tumor-associated antigens identified and targeted with immunotherapy, expression within normal melanocytes of the eye and inner ear can elicit serious autoimmune side effects, thus limiting their clinical potential as CTL targets. Using a tandem mass spectrometry (MS) approach to analyze the immunopeptidomes of 55 melanoma patient-derived cell lines, we identified a number of shared HLA class I-bound peptides derived from the melanocyte-specific transporter protein SLC45A2. Antigen-specific CTLs generated against HLA-A*0201- and HLA-A*2402-restricted SLC45A2 peptides effectively killed a majority of HLA-matched cutaneous, uveal, and mucosal melanoma cell lines tested (18/25). CTLs specific for SLC45A2 showed significantly reduced recognition of HLA-matched primary melanocytes that were, conversely, robustly killed by MART1- and PMEL-specific T cells. Transcriptome analysis revealed that SLC45A2 mRNA expression in normal melanocytes was less than 2% that of other MDAs, therefore providing a more favorable melanoma-to-melanocyte expression ratio. Expression of SLC45A2 and CTL sensitivity could be further upregulated in BRAF(V600E)-mutant melanoma cells upon treatment with BRAF or MEK inhibitors, similarly to other MDAs. Taken together, our study demonstrates the feasibility of using tandem MS as a means of discovering shared immunogenic tumor-associated epitopes and identifies SLC45A2 as a promising immunotherapeutic target for melanoma with high tumor selectivity and reduced potential for autoimmune toxicity. Cancer Immunol Res; 5(8); 618-29. ©2017 AACR.
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Affiliation(s)
- Jungsun Park
- Center for Cancer Immunology Research, Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Amjad H Talukder
- Center for Cancer Immunology Research, Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Seon A Lim
- Department of Biochemistry and Molecular Biology, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kwanghee Kim
- Center for Cancer Immunology Research, Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ke Pan
- Center for Cancer Immunology Research, Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Brenda Melendez
- Center for Cancer Immunology Research, Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sherille D Bradley
- Center for Cancer Immunology Research, Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kyle R Jackson
- Center for Cancer Immunology Research, Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jahan S Khalili
- Center for Cancer Immunology Research, Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Junmei Wang
- Center for Cancer Immunology Research, Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Caitlin Creasy
- Center for Cancer Immunology Research, Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bih-Fang Pan
- Department of Systems Biology, MD Anderson Cancer Center, Houston, Texas
| | - Scott E Woodman
- Center for Cancer Immunology Research, Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chantale Bernatchez
- Center for Cancer Immunology Research, Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David Hawke
- Department of Systems Biology, MD Anderson Cancer Center, Houston, Texas
| | - Patrick Hwu
- Center for Cancer Immunology Research, Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kyung-Mi Lee
- Department of Biochemistry and Molecular Biology, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jason Roszik
- Center for Cancer Immunology Research, Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gregory Lizée
- Center for Cancer Immunology Research, Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas. .,Departments of Melanoma Medical Oncology and Immunology, MD Anderson Cancer Center, Houston, Texas
| | - Cassian Yee
- Center for Cancer Immunology Research, Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas. .,Departments of Melanoma Medical Oncology and Immunology, MD Anderson Cancer Center, Houston, Texas
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36
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Walsh S, Chaitanya L, Breslin K, Muralidharan C, Bronikowska A, Pospiech E, Koller J, Kovatsi L, Wollstein A, Branicki W, Liu F, Kayser M. Global skin colour prediction from DNA. Hum Genet 2017; 136:847-863. [PMID: 28500464 PMCID: PMC5487854 DOI: 10.1007/s00439-017-1808-5] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 05/03/2017] [Indexed: 12/14/2022]
Abstract
Human skin colour is highly heritable and externally visible with relevance in medical, forensic, and anthropological genetics. Although eye and hair colour can already be predicted with high accuracies from small sets of carefully selected DNA markers, knowledge about the genetic predictability of skin colour is limited. Here, we investigate the skin colour predictive value of 77 single-nucleotide polymorphisms (SNPs) from 37 genetic loci previously associated with human pigmentation using 2025 individuals from 31 global populations. We identified a minimal set of 36 highly informative skin colour predictive SNPs and developed a statistical prediction model capable of skin colour prediction on a global scale. Average cross-validated prediction accuracies expressed as area under the receiver-operating characteristic curve (AUC) ± standard deviation were 0.97 ± 0.02 for Light, 0.83 ± 0.11 for Dark, and 0.96 ± 0.03 for Dark-Black. When using a 5-category, this resulted in 0.74 ± 0.05 for Very Pale, 0.72 ± 0.03 for Pale, 0.73 ± 0.03 for Intermediate, 0.87±0.1 for Dark, and 0.97 ± 0.03 for Dark-Black. A comparative analysis in 194 independent samples from 17 populations demonstrated that our model outperformed a previously proposed 10-SNP-classifier approach with AUCs rising from 0.79 to 0.82 for White, comparable at the intermediate level of 0.63 and 0.62, respectively, and a large increase from 0.64 to 0.92 for Black. Overall, this study demonstrates that the chosen DNA markers and prediction model, particularly the 5-category level; allow skin colour predictions within and between continental regions for the first time, which will serve as a valuable resource for future applications in forensic and anthropologic genetics.
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Affiliation(s)
- Susan Walsh
- Department of Biology, Indiana University Purdue University Indianapolis (IUPUI), Indianapolis, IN, USA.
| | - Lakshmi Chaitanya
- Department of Genetic Identification, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Krystal Breslin
- Department of Biology, Indiana University Purdue University Indianapolis (IUPUI), Indianapolis, IN, USA
| | - Charanya Muralidharan
- Department of Biology, Indiana University Purdue University Indianapolis (IUPUI), Indianapolis, IN, USA
| | - Agnieszka Bronikowska
- Department of Dermatology, Collegium Medicum of the Jagiellonian University, Kraków, Poland
| | - Ewelina Pospiech
- Faculty of Biology and Earth Sciences, Institute of Zoology, Jagiellonian University, Kraków, Poland
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Julia Koller
- Department of Genetic Identification, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Leda Kovatsi
- Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Andreas Wollstein
- Section of Evolutionary Biology, Department of Biology II, University of Munich LMU, Planegg-Martinsried, Germany
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - Fan Liu
- Department of Genetic Identification, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands.
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Siewierska-Górska A, Sitek A, Żądzińska E, Bartosz G, Strapagiel D. Association of five SNPs with human hair colour in the Polish population. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2017; 68:134-144. [DOI: 10.1016/j.jchb.2017.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 11/12/2016] [Indexed: 01/23/2023]
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Haplotypes from the SLC45A2 gene are associated with the presence of freckles and eye, hair and skin pigmentation in Brazil. Leg Med (Tokyo) 2017; 25:43-51. [DOI: 10.1016/j.legalmed.2016.12.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 12/05/2016] [Accepted: 12/30/2016] [Indexed: 01/28/2023]
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Wollstein A, Walsh S, Liu F, Chakravarthy U, Rahu M, Seland JH, Soubrane G, Tomazzoli L, Topouzis F, Vingerling JR, Vioque J, Böhringer S, Fletcher AE, Kayser M. Novel quantitative pigmentation phenotyping enhances genetic association, epistasis, and prediction of human eye colour. Sci Rep 2017; 7:43359. [PMID: 28240252 PMCID: PMC5327401 DOI: 10.1038/srep43359] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/23/2017] [Indexed: 11/09/2022] Open
Abstract
Success of genetic association and the prediction of phenotypic traits from DNA are known to depend on the accuracy of phenotype characterization, amongst other parameters. To overcome limitations in the characterization of human iris pigmentation, we introduce a fully automated approach that specifies the areal proportions proposed to represent differing pigmentation types, such as pheomelanin, eumelanin, and non-pigmented areas within the iris. We demonstrate the utility of this approach using high-resolution digital eye imagery and genotype data from 12 selected SNPs from over 3000 European samples of seven populations that are part of the EUREYE study. In comparison to previous quantification approaches, (1) we achieved an overall improvement in eye colour phenotyping, which provides a better separation of manually defined eye colour categories. (2) Single nucleotide polymorphisms (SNPs) known to be involved in human eye colour variation showed stronger associations with our approach. (3) We found new and confirmed previously noted SNP-SNP interactions. (4) We increased SNP-based prediction accuracy of quantitative eye colour. Our findings exemplify that precise quantification using the perceived biological basis of pigmentation leads to enhanced genetic association and prediction of eye colour. We expect our approach to deliver new pigmentation genes when applied to genome-wide association testing.
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Affiliation(s)
- Andreas Wollstein
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands.,Section of Evolutionary Biology, Department of Biology II, University of Munich LMU, Planegg-Martinsried, Germany
| | - Susan Walsh
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Fan Liu
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.,Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Usha Chakravarthy
- Centre for Vision and Vascular Science, The Queen's University Belfast, Belfast, United Kingdom
| | - Mati Rahu
- Department of Epidemiology and Biostatistics, National Institute for Health Development, Tallinn, Estonia
| | - Johan H Seland
- Department of Ophthalmology, University of Bergen, School of Medicine, Bergen, Norway
| | - Gisèle Soubrane
- Clinique Ophthalmologique, Universitaire De Creteil, Paris, France
| | | | - Fotis Topouzis
- Department of Ophthalmology, Aristotle University of Thessaloniki, School of Medicine, Thessaloniki, Greece
| | - Johannes R Vingerling
- Department of Ophthalmology, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Jesus Vioque
- Dpto. Salud Publica Universidad Miguel Hernandez, Alicante, El Centro de Investigacion Biomedica en Red de Epidemiologıa y Salud Publica (CIBERESP), Elche, Spain
| | - Stefan Böhringer
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
| | - Astrid E Fletcher
- Faculty of Epidemiology &Population Health, London School of Hygiene &Tropical Medicine, London, United Kingdom
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
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Lucock M, Beckett E, Martin C, Jones P, Furst J, Yates Z, Jablonski NG, Chaplin G, Veysey M. UV‐associated decline in systemic folate: implications for human nutrigenetics, health, and evolutionary processes. Am J Hum Biol 2016; 29. [DOI: 10.1002/ajhb.22929] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/13/2016] [Accepted: 09/25/2016] [Indexed: 12/15/2022] Open
Affiliation(s)
- Mark Lucock
- School of Environmental and Life SciencesUniversity of NewcastlePO Box 127, Brush RdOurimbah NSW2258 Australia
| | - Emma Beckett
- School of Environmental and Life SciencesUniversity of NewcastlePO Box 127, Brush RdOurimbah NSW2258 Australia
| | - Charlotte Martin
- School of Environmental and Life SciencesUniversity of NewcastlePO Box 127, Brush RdOurimbah NSW2258 Australia
| | - Patrice Jones
- School of Environmental and Life SciencesUniversity of NewcastlePO Box 127, Brush RdOurimbah NSW2258 Australia
| | - John Furst
- School of Maths and Physical SciencesUniversity of NewcastlePO Box 127, Brush RdOurimbah NSW2258 Australia
| | - Zoe Yates
- School of Biomedical Sciences and PharmacyUniversity of NewcastlePO Box 127, Brush RdOurimbah NSW2258 Australia
| | - Nina G. Jablonski
- Anthropology DepartmentThe Pennsylvania State University409 Carpenter BuildingUniversity Park Pennsylvania16802
| | - George Chaplin
- Anthropology DepartmentThe Pennsylvania State University409 Carpenter BuildingUniversity Park Pennsylvania16802
| | - Martin Veysey
- School of Medicine and Public Health, University of Newcastle, NSW, 2308, Australia and, Central Coast Local Health DistrictTeaching and Research Unit, Gosford HospitalGosford NSW2250PO Box 361 Australia
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Key FM, Fu Q, Romagné F, Lachmann M, Andrés AM. Human adaptation and population differentiation in the light of ancient genomes. Nat Commun 2016; 7:10775. [PMID: 26988143 PMCID: PMC4802047 DOI: 10.1038/ncomms10775] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 01/18/2016] [Indexed: 01/24/2023] Open
Abstract
The influence of positive selection sweeps in human evolution is increasingly debated, although our ability to detect them is hampered by inherent uncertainties in the timing of past events. Ancient genomes provide snapshots of allele frequencies in the past and can help address this question. We combine modern and ancient genomic data in a simple statistic (DAnc) to time allele frequency changes, and investigate the role of drift and adaptation in population differentiation. Only 30% of the most strongly differentiated alleles between Africans and Eurasians changed in frequency during the colonization of Eurasia, but in Europe these alleles are enriched in genic and putatively functional alleles to an extent only compatible with local adaptation. Adaptive alleles—especially those associated with pigmentation—are mostly of hunter-gatherer origin, although lactose persistence arose in a haplotype present in farmers. These results provide evidence for a role of local adaptation in human population differentiation. Detecting the targets of positive selection in the human genome is challenging. Here, the authors combine modern and ancient genomes to show that alleles strongly differentiated between Africans and Europeans mediated local adaptation in European populations, and were mostly contributed by ancient hunter-gatherers.
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Affiliation(s)
- Felix M Key
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Qiaomei Fu
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China.,Department of Genetics, Harvard Medical School, Boston 02115, Massachusetts, USA
| | - Frédéric Romagné
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Michael Lachmann
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Santa Fe Institute, Santa Fe, New Mexico 87501, USA
| | - Aida M Andrés
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
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42
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Lasisi T, Ito S, Wakamatsu K, Shaw CN. Quantifying variation in human scalp hair fiber shape and pigmentation. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 160:341-52. [DOI: 10.1002/ajpa.22971] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 02/10/2016] [Accepted: 02/12/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Tina Lasisi
- Department of Archaeology and Anthropology, PAVE Research Group; University of Cambridge; UK
- Department of Anthropology; Pennsylvania State University, University Park; PA 16802
| | - Shosuke Ito
- Department of Chemistry; Fujita Health University School of Health Sciences; Toyoake Aichi Japan
| | - Kazumasa Wakamatsu
- Department of Chemistry; Fujita Health University School of Health Sciences; Toyoake Aichi Japan
| | - Colin N. Shaw
- Department of Archaeology and Anthropology, PAVE Research Group; University of Cambridge; UK
- Department of Archaeology and Anthropology; McDonald Institute for Archaeological Research, University of Cambridge; UK
- Department of Zoology, Cambridge BioTomography Centre; University of Cambridge; UK
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43
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Yang Z, Zhong H, Chen J, Zhang X, Zhang H, Luo X, Xu S, Chen H, Lu D, Han Y, Li J, Fu L, Qi X, Peng Y, Xiang K, Lin Q, Guo Y, Li M, Cao X, Zhang Y, Liao S, Peng Y, Zhang L, Guo X, Dong S, Liang F, Wang J, Willden A, Seang Aun H, Serey B, Sovannary T, Bunnath L, Samnom H, Mardon G, Li Q, Meng A, Shi H, Su B. A Genetic Mechanism for Convergent Skin Lightening during Recent Human Evolution. Mol Biol Evol 2016; 33:1177-87. [PMID: 26744415 PMCID: PMC4839214 DOI: 10.1093/molbev/msw003] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Skin lightening among Eurasians is thought to have been a convergence occurring independently in Europe and East Asia as an adaptation to high latitude environments. Among Europeans, several genes responsible for such lightening have been found, but the information available for East Asians is much more limited. Here, a genome-wide comparison between dark-skinned Africans and Austro-Asiatic speaking aborigines and light-skinned northern Han Chinese identified the pigmentation gene OCA2, showing unusually deep allelic divergence between these groups. An amino acid substitution (His615Arg) of OCA2 prevalent in most East Asian populations—but absent in Africans and Europeans—was significantly associated with skin lightening among northern Han Chinese. Further transgenic and targeted gene modification analyses of zebrafish and mouse both exhibited the phenotypic effect of the OCA2 variant manifesting decreased melanin production. These results indicate that OCA2 plays an important role in the convergent skin lightening of East Asians during recent human evolution.
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Affiliation(s)
- Zhaohui Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Hua Zhong
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX
| | - Jing Chen
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Xiaoming Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Hui Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xin Luo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Shuhua Xu
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hua Chen
- Center for Computational Genomics, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Dongsheng Lu
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yinglun Han
- College of Life Science, Liaoning Normal University, Dalian, China
| | - Jinkun Li
- Department of Urology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Lijie Fu
- Department of Urology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xuebin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yi Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Kun Xiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Qiang Lin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yan Guo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ming Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xiangyu Cao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yanfeng Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Shiyu Liao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yingmei Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Lin Zhang
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Xiaosen Guo
- BGI-Shenzhen, Shenzhen, China Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Jun Wang
- BGI-Shenzhen, Shenzhen, China Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Andrew Willden
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Hong Seang Aun
- Geography and Land Management, Royal University of Phnom Penh, Phnom Penh, Kingdom of Cambodia
| | - Bun Serey
- Geography and Land Management, Royal University of Phnom Penh, Phnom Penh, Kingdom of Cambodia
| | - Tuot Sovannary
- Geography and Land Management, Royal University of Phnom Penh, Phnom Penh, Kingdom of Cambodia
| | - Long Bunnath
- Geography and Land Management, Royal University of Phnom Penh, Phnom Penh, Kingdom of Cambodia
| | - Ham Samnom
- Capacity Development Facilitator for Handicap International Federation and Freelance Researcher, Battambang, Kingdom of Cambodia
| | - Graeme Mardon
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX
| | - Qingwei Li
- College of Life Science, Liaoning Normal University, Dalian, China
| | - Anming Meng
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Hong Shi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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Walsh S, Kayser M. A Practical Guide to the HIrisPlex System: Simultaneous Prediction of Eye and Hair Color from DNA. Methods Mol Biol 2016; 1420:213-231. [PMID: 27259743 DOI: 10.1007/978-1-4939-3597-0_17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The HIrisPlex system, which consists of two parts, allows the simultaneous prediction of eye and hair color from DNA, e.g., samples extracted from crime scene evidence. The first part is a highly sensitive multiplex genotyping assay consisting of 24 DNA markers using SNaPshot™ chemistry, for analysis on all Capillary Electrophoresis machines. The second part consists of statistical models that respectively establish eye and hair color prediction probabilities from complete and incomplete genotype profiles using parameters generated from large genotype and phenotype databases. This combined prediction tool constitutes the online system freely available to users. Here we provide a practical guide on how to use the HIrisPlex system for forensic and other DNA applications.
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Affiliation(s)
- Susan Walsh
- Department of Biology, Indiana University-Purdue University Indianapolis (IUPUI), 723 W. Michigan St., SL 350, Indianapolis, IN, 46202, USA.
| | - Manfred Kayser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, 3000 CB, Rotterdam, The Netherlands
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45
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Edwards M, Cha D, Krithika S, Johnson M, Cook G, Parra EJ. Iris pigmentation as a quantitative trait: variation in populations of European, East Asian and South Asian ancestry and association with candidate gene polymorphisms. Pigment Cell Melanoma Res 2015; 29:141-62. [DOI: 10.1111/pcmr.12435] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 11/02/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Melissa Edwards
- Department of Anthropology University of Toronto Mississauga Mississauga ON Canada
| | - David Cha
- Department of Anthropology University of Toronto Mississauga Mississauga ON Canada
| | - S. Krithika
- Department of Anthropology University of Toronto Mississauga Mississauga ON Canada
| | - Monique Johnson
- Department of Anthropology University of Toronto Mississauga Mississauga ON Canada
| | - Gillian Cook
- Department of Anthropology University of Toronto Mississauga Mississauga ON Canada
| | - Esteban J. Parra
- Department of Anthropology University of Toronto Mississauga Mississauga ON Canada
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Nakagome S, Alkorta-Aranburu G, Amato R, Howie B, Peter BM, Hudson RR, Di Rienzo A. Estimating the Ages of Selection Signals from Different Epochs in Human History. Mol Biol Evol 2015; 33:657-69. [PMID: 26545921 DOI: 10.1093/molbev/msv256] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genetic variation harbors signatures of natural selection driven by selective pressures that are often unknown. Estimating the ages of selection signals may allow reconstructing the history of environmental changes that shaped human phenotypes and diseases. We have developed an approximate Bayesian computation (ABC) approach to estimate allele ages under a model of selection on new mutations and under demographic models appropriate for human populations. We have applied it to two resequencing data sets: An ultra-high depth data set from a relatively small sample of unrelated individuals and a lower depth data set in a larger sample with transmission information. In addition to evaluating the accuracy of our method based on simulations, for each SNP, we assessed the consistency between the posterior probabilities estimated by the ABC approach and the ancient DNA record, finding good agreement between the two types of data and methods. Applying this ABC approach to data for eight single nucleotide polymorphisms (SNPs), we were able to rule out an onset of selection prior to the dispersal out-of-Africa for three of them and more recent than the spread of agriculture for an additional three SNPs.
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Affiliation(s)
| | | | - Roberto Amato
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, United Kingdom
| | - Bryan Howie
- Department of Human Genetics, University of Chicago
| | | | - Richard R Hudson
- Department of Human Genetics, University of Chicago Department of Ecology and Evolution, University of Chicago
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47
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López S, García I, Smith I, Sevilla A, Izagirre N, de la Rúa C, Alonso S. Discovery of copy number variants by multiplex amplifiable probe hybridization (MAPH) in candidate pigmentation genes. Ann Hum Biol 2015; 42:485-93. [DOI: 10.3109/03014460.2014.965202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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48
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Norton HL, Edwards M, Krithika S, Johnson M, Werren EA, Parra EJ. Quantitative assessment of skin, hair, and iris variation in a diverse sample of individuals and associated genetic variation. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 160:570-81. [PMID: 27435525 DOI: 10.1002/ajpa.22861] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 07/27/2015] [Accepted: 08/25/2015] [Indexed: 11/06/2022]
Abstract
OBJECTIVES The main goals of this study are to 1) quantitatively measure skin, hair, and iris pigmentation in a diverse sample of individuals, 2) describe variation within and between these samples, and 3) demonstrate how quantitative measures can facilitate genotype-phenotype association tests. MATERIALS AND METHODS We quantitatively characterize skin, hair, and iris pigmentation using the Melanin (M) Index (skin) and CIELab values (hair) in 1,450 individuals who self-identify as African American, East Asian, European, Hispanic, or South Asian. We also quantify iris pigmentation in a subset of these individuals using CIELab values from high-resolution iris photographs. We compare mean skin M index and hair and iris CIELab values among populations using ANOVA and MANOVA respectively and test for genotype-phenotype associations in the European sample. RESULTS All five populations are significantly different for skin (P <2 × 10(-16) ) and hair color (P <2 × 10(-16) ). Our quantitative analysis of iris and hair pigmentation reinforces the continuous, rather than discrete, nature of these traits. We confirm the association of three loci (rs16891982, rs12203592, and rs12913832) with skin pigmentation and four loci (rs12913832, rs12203592, rs12896399, and rs16891982) with hair pigmentation. Interestingly, the derived rs12203592 T allele located within the IRF4 gene is associated with lighter skin but darker hair color. DISCUSSION The quantitative methods used here provide a fine-scale assessment of pigmentation phenotype and facilitate genotype-phenotype associations, even with relatively small sample sizes. This represents an important expansion of current investigations into pigmentation phenotype and associated genetic variation by including non-European and admixed populations. Am J Phys Anthropol 160:570-581, 2016. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Heather L Norton
- Department of Anthropology, University of Cincinnati, Cincinnati, OH, 45238
| | - Melissa Edwards
- Department of Anthropology, University of Toronto Mississauga, Toronto, ON, Canada
| | - S Krithika
- Department of Anthropology, University of Toronto Mississauga, Toronto, ON, Canada
| | - Monique Johnson
- Department of Anthropology, University of Toronto Mississauga, Toronto, ON, Canada
| | - Elizabeth A Werren
- Department of Anthropology, University of Cincinnati, Cincinnati, OH, 45238
| | - Esteban J Parra
- Department of Anthropology, University of Toronto Mississauga, Toronto, ON, Canada
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Adrion JR, Hahn MW, Cooper BS. Revisiting classic clines in Drosophila melanogaster in the age of genomics. Trends Genet 2015; 31:434-44. [PMID: 26072452 PMCID: PMC4526433 DOI: 10.1016/j.tig.2015.05.006] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 05/11/2015] [Accepted: 05/12/2015] [Indexed: 12/16/2022]
Abstract
Adaptation to spatially varying environments has been studied for decades, but advances in sequencing technology are now enabling researchers to investigate the landscape of genetic variation underlying this adaptation genome wide. In this review we highlight some of the decades-long research on local adaptation in Drosophila melanogaster from well-studied clines in North America and Australia. We explore the evidence for parallel adaptation and identify commonalities in the genes responding to clinal selection across continents as well as discussing instances where patterns differ among clines. We also investigate recent studies utilizing whole-genome data to identify clines in D. melanogaster and several other systems. Although connecting segregating genomic variation to variation in phenotypes and fitness remains challenging, clinal genomics is poised to increase our understanding of local adaptation and the selective pressures that drive the extensive phenotypic diversity observed in nature.
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Affiliation(s)
- Jeffrey R Adrion
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN 47405, USA; School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
| | - Brandon S Cooper
- Center for Population Biology, University of California, Davis, CA 95616, USA; Department of Evolution and Ecology, University of California, Davis, CA 95616, USA.
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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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