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Sigurðardóttir H, Ablondi M, Kristjansson T, Lindgren G, Eriksson S. Genetic diversity and signatures of selection in Icelandic horses and Exmoor ponies. BMC Genomics 2024; 25:772. [PMID: 39118059 PMCID: PMC11308356 DOI: 10.1186/s12864-024-10682-8] [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: 03/27/2024] [Accepted: 08/01/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND The Icelandic horse and Exmoor pony are ancient, native breeds, adapted to harsh environmental conditions and they have both undergone severe historic bottlenecks. However, in modern days, the selection pressures on these breeds differ substantially. The aim of this study was to assess genetic diversity in both breeds through expected (HE) and observed heterozygosity (HO) and effective population size (Ne). Furthermore, we aimed to identify runs of homozygosity (ROH) to estimate and compare genomic inbreeding and signatures of selection in the breeds. RESULTS HO was estimated at 0.34 and 0.33 in the Icelandic horse and Exmoor pony, respectively, aligning closely with HE of 0.34 for both breeds. Based on genomic data, the Ne for the last generation was calculated to be 125 individuals for Icelandic horses and 42 for Exmoor ponies. Genomic inbreeding coefficient (FROH) ranged from 0.08 to 0.20 for the Icelandic horse and 0.12 to 0.27 for the Exmoor pony, with the majority of inbreeding attributed to short ROHs in both breeds. Several ROH islands associated with performance were identified in the Icelandic horse, featuring target genes such as DMRT3, DOCK8, EDNRB, SLAIN1, and NEURL1. Shared ROH islands between both breeds were linked to metabolic processes (FOXO1), body size, and the immune system (CYRIB), while private ROH islands in Exmoor ponies were associated with coat colours (ASIP, TBX3, OCA2), immune system (LYG1, LYG2), and fertility (TEX14, SPO11, ADAM20). CONCLUSIONS Evaluations of genetic diversity and inbreeding reveal insights into the evolutionary trajectories of both breeds, highlighting the consequences of population bottlenecks. While the genetic diversity in the Icelandic horse is acceptable, a critically low genetic diversity was estimated for the Exmoor pony, which requires further validation. Identified signatures of selection highlight the differences in the use of the two breeds as well as their adaptive trait similarities. The results provide insight into genomic regions under selection pressure in a gaited performance horse breed and various adaptive traits in small-sized native horse breeds. This understanding contributes to preserving genetic diversity and population health in these equine populations.
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Affiliation(s)
- Heiðrún Sigurðardóttir
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, P.O. Box 7023, Uppsala, 75007, Sweden.
- Faculty of Agricultural Sciences, Agricultural University of Iceland, Hvanneyri, Borgarbyggð, 311, Iceland.
| | - Michela Ablondi
- Department of Veterinary Science, University of Parma, Parma, 43126, Italy
| | - Thorvaldur Kristjansson
- Faculty of Agricultural Sciences, Agricultural University of Iceland, Hvanneyri, Borgarbyggð, 311, Iceland
| | - Gabriella Lindgren
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, P.O. Box 7023, Uppsala, 75007, Sweden
- Center for Animal Breeding and Genetics, Department of Biosystems, KU Leuven, Leuven, 3001, Belgium
| | - Susanne Eriksson
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, P.O. Box 7023, Uppsala, 75007, Sweden
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Bjeloš M, Ćurić A, Bušić M, Rak B, Kuzmanović Elabjer B. Genotype-Phenotype Correlation Model for the Spectrum of TYR-Associated Albinism. Diagnostics (Basel) 2024; 14:1583. [PMID: 39125459 PMCID: PMC11311874 DOI: 10.3390/diagnostics14151583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Revised: 07/16/2024] [Accepted: 07/22/2024] [Indexed: 08/12/2024] Open
Abstract
We present two children aged 3 and 5 years who share identical TYR genotype, yet exhibit contrasting phenotypic manifestations in terms of eye, skin, and hair coloration. The patients are heterozygous for TYR c.1A>G, p. (Met1?), which is pathogenic, and homozygous for TYR c.1205G>A, p. (Arg402Gln), which is classified as a risk factor. The children manifested diminished visual acuity, nystagmus, and foveal hypoplasia. The first patient presented with hypopigmentation of the skin, hair, and ocular tissues, while the second patient presented with hypopigmentation of the skin, hair, retinal pigment epithelium, and choroid with dark brown irises. Furthermore, the brown-eyed subject presented astigmatic refractive error and both global and local stereopsis capabilities, contrasting with the presentation of hypermetropia, strabismus, and the absence of stereopsis in the blue-eyed individual. Herein, we propose a genotype-phenotype correlation model to elucidate the diverse clinical presentations stemming from biallelic and triallelic pathogenic variants in TYR, establishing a link between the residual tyrosinase activity and resultant phenotypes. According to our proposed model, the severity of TYR variants correlates with distinct albino phenotypes. Our findings propose the potential association between reduced pigmentation levels in ocular tissues and binocular functions, suggesting pigmentation as a possible independent variable influencing the onset of strabismus-an association unreported until now in the existing literature.
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Affiliation(s)
- Mirjana Bjeloš
- University Eye Department, Reference Center of the Ministry of Health of the Republic of Croatia for Inherited Retinal Dystrophies, Reference Center of the Ministry of Health of the Republic of Croatia for Pediatric Ophthalmology and Strabismus, University Hospital “Sveti Duh”, 10000 Zagreb, Croatia; (M.B.); (M.B.); (B.R.); (B.K.E.)
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Faculty of Dental Medicine and Health Osijek, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Ana Ćurić
- University Eye Department, Reference Center of the Ministry of Health of the Republic of Croatia for Inherited Retinal Dystrophies, Reference Center of the Ministry of Health of the Republic of Croatia for Pediatric Ophthalmology and Strabismus, University Hospital “Sveti Duh”, 10000 Zagreb, Croatia; (M.B.); (M.B.); (B.R.); (B.K.E.)
- Faculty of Dental Medicine and Health Osijek, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Mladen Bušić
- University Eye Department, Reference Center of the Ministry of Health of the Republic of Croatia for Inherited Retinal Dystrophies, Reference Center of the Ministry of Health of the Republic of Croatia for Pediatric Ophthalmology and Strabismus, University Hospital “Sveti Duh”, 10000 Zagreb, Croatia; (M.B.); (M.B.); (B.R.); (B.K.E.)
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Faculty of Dental Medicine and Health Osijek, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Benedict Rak
- University Eye Department, Reference Center of the Ministry of Health of the Republic of Croatia for Inherited Retinal Dystrophies, Reference Center of the Ministry of Health of the Republic of Croatia for Pediatric Ophthalmology and Strabismus, University Hospital “Sveti Duh”, 10000 Zagreb, Croatia; (M.B.); (M.B.); (B.R.); (B.K.E.)
| | - Biljana Kuzmanović Elabjer
- University Eye Department, Reference Center of the Ministry of Health of the Republic of Croatia for Inherited Retinal Dystrophies, Reference Center of the Ministry of Health of the Republic of Croatia for Pediatric Ophthalmology and Strabismus, University Hospital “Sveti Duh”, 10000 Zagreb, Croatia; (M.B.); (M.B.); (B.R.); (B.K.E.)
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Faculty of Dental Medicine and Health Osijek, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
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Bukayev A, Gorin I, Aidarov B, Darmenov A, Balanovska E, Zhabagin M. Predictive accuracy of genetic variants for eye color in a Kazakh population using the IrisPlex system. BMC Res Notes 2024; 17:187. [PMID: 38970104 PMCID: PMC11227171 DOI: 10.1186/s13104-024-06856-y] [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: 04/01/2024] [Accepted: 07/02/2024] [Indexed: 07/07/2024] Open
Abstract
OBJECTIVE This study assesses the accuracy of the IrisPlex system, a genetic eye color prediction tool for forensic analysis, in the Kazakh population. The study compares previously published genotypes of 515 Kazakh individuals from varied geographical and ethnohistorical contexts with phenotypic data on their eye color, introduced for the first time in this research. RESULTS The IrisPlex panel's effectiveness in predicting eye color in the Kazakh population was validated. It exhibited slightly lower accuracy than in Western European populations but was higher than in Siberian populations. The sensitivity was notably high for brown-eyed individuals (0.99), but further research is needed for blue and intermediate eye colors. This study establishes IrisPlex as a useful predictive tool in the Kazakh population and provides a basis for future investigations into the genetic basis of phenotypic variations in this diverse population.
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Affiliation(s)
- Alizhan Bukayev
- National Center for Biotechnology, Astana, 010000, Kazakhstan
| | - Igor Gorin
- Research Centre for Medical Genetics, Moscow, 115522, Russia
| | - Baglan Aidarov
- National Center for Biotechnology, Astana, 010000, Kazakhstan
| | - Akynkali Darmenov
- Karaganda Academy of the Ministry of Internal Affairs of the Republic of Kazakhstan named after Barimbek Beisenov, Karaganda, 100000, Kazakhstan
| | | | - Maxat Zhabagin
- National Center for Biotechnology, Astana, 010000, Kazakhstan.
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Brancato D, Bruno F, Coniglio E, Sturiale V, Saccone S, Federico C. The Chromatin Organization Close to SNP rs12913832, Involved in Eye Color Variation, Is Evolutionary Conserved in Vertebrates. Int J Mol Sci 2024; 25:6602. [PMID: 38928306 PMCID: PMC11204186 DOI: 10.3390/ijms25126602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 06/12/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
The most significant genetic influence on eye color pigmentation is attributed to the intronic SNP rs12913832 in the HERC2 gene, which interacts with the promoter region of the contiguous OCA2 gene. This interaction, through the formation of a chromatin loop, modulates the transcriptional activity of OCA2, directly affecting eye color pigmentation. Recent advancements in technology have elucidated the precise spatial organization of the genome within the cell nucleus, with chromatin architecture playing a pivotal role in regulating various genome functions. In this study, we investigated the organization of the chromatin close to the HERC2/OCA2 locus in human lymphocyte nuclei using fluorescence in situ hybridization (FISH) and high-throughput chromosome conformation capture (Hi-C) data. The 3 Mb of genomic DNA that belonged to the chromosomal region 15q12-q13.1 revealed the presence of three contiguous chromatin loops, which exhibited a different level of compaction depending on the presence of the A or G allele in the SNP rs12913832. Moreover, the analysis of the genomic organization of the genes has demonstrated that this chromosomal region is evolutionarily highly conserved, as evidenced by the analysis of syntenic regions in species from other Vertebrate classes. Thus, the role of rs12913832 variant is relevant not only in determining the transcriptional activation of the OCA2 gene but also in the chromatin compaction of a larger region, underscoring the critical role of chromatin organization in the proper regulation of the involved genes. It is crucial to consider the broader implications of this finding, especially regarding the potential regulatory role of similar polymorphisms located within intronic regions, which do not influence the same gene by modulating the splicing process, but they regulate the expression of adjacent genes. Therefore, caution should be exercised when utilizing whole-exome sequencing for diagnostic purposes, as intron sequences may provide valuable gene regulation information on the region where they reside. Thus, future research efforts should also be directed towards gaining a deeper understanding of the precise mechanisms underlying the role and mode of action of intronic SNPs in chromatin loop organization and transcriptional regulation.
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Affiliation(s)
| | | | | | | | - Salvatore Saccone
- Department Biological, Geological and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy; (D.B.); (F.B.); (E.C.); (V.S.); (C.F.)
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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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Becher D, Jmel H, Kheriji N, Sarno S, Kefi R. Genetic landscape of forensic DNA phenotyping markers among Mediterranean populations. Forensic Sci Int 2024; 354:111906. [PMID: 38128201 DOI: 10.1016/j.forsciint.2023.111906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/02/2023] [Indexed: 12/23/2023]
Abstract
Forensic DNA Phenotyping can reveal the appearance of an unknown individual by predicting the External Visible Characteristics (EVC) from DNA obtained at the crime scene. Our aim is to characterize the genetic landscape of Human identification markers responsible for EVC among Mediterranean populations compared to other worldwide groups. We conducted an exhaustive search for genes involved in EVC variation. Then, variants located on these genes were extracted from public genotypic data of Mediterranean, American, African and East Asiatic populations. The genetic landscape of these Human identification markers, their allelic distribution and admixture analyses, were determined using plink, R and ADMIXTURE softwares. Our results showed that the Mediterranean populations appear close to the Mexican populations and distinguished from sub Saharan African populations living in the USA and from East Asiatic populations. We highlighted a total of 103454 common variants shared between the studied populations and among them, 25 common variants associated with EVC. Interestingly, genotype frequencies results showed that the rs17646946, rs13016869, rs977588, rs1805008 and rs2240751 variants located respectively in the TCHH, PRKCE, OCA2, MC1R and MFSD12 genes are significantly different between the Mediterranean and Asiatic populations. The genotype frequencies of the variants rs977589 and rs7179994 located in the OCA2 gene, and of rs12913832 and rs2240751 located respectively in HERC2 and MFSD12 genes are significantly different between the Mediterranean and American populations. Our work generates a large number of EVC variants that could be a valuable resource for future studies in the forensic field.
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Affiliation(s)
- Dorra Becher
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, BP 74, 13 Place Pasteur, Tunis 1002, Tunisia; Directorate of Technical and Scientific Police, Sub-Directorate of Forensic and Scientific Laboratories, Tunis,Tunisia; University of Carthage, National Institute of Applied Science and Technology, Tunis, Tunisia
| | - Haifa Jmel
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, BP 74, 13 Place Pasteur, Tunis 1002, Tunisia; Genetic Typing Service, Institut Pasteur de Tunis, BP 74, 13 Place Pasteur, Tunis 1002, Tunisia; University of Tunis El Manar, 2092 El Manar I, Tunis, Tunisia
| | - Nadia Kheriji
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, BP 74, 13 Place Pasteur, Tunis 1002, Tunisia; University of Tunis El Manar, 2092 El Manar I, Tunis, Tunisia
| | - Stefania Sarno
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Rym Kefi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, BP 74, 13 Place Pasteur, Tunis 1002, Tunisia; Genetic Typing Service, Institut Pasteur de Tunis, BP 74, 13 Place Pasteur, Tunis 1002, Tunisia; University of Tunis El Manar, 2092 El Manar I, Tunis, Tunisia.
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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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Association between Variants in the OCA2-HERC2 Region and Blue Eye Colour in HERC2 rs12913832 AA and AG Individuals. Genes (Basel) 2023; 14:genes14030698. [PMID: 36980970 PMCID: PMC10048254 DOI: 10.3390/genes14030698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/01/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
The OCA2-HERC2 region is strongly associated with human pigmentation, especially eye colour. The HERC2 SNP rs12913832 is currently the best-known predictor for blue and brown eye colour. However, in a previous study we found that 43 of 166 Norwegians with the brown eye colour genotype rs12913832:AA or AG, did not have the expected brown eye colour. In this study, we carried out massively parallel sequencing of a ~500 kbp HERC2-OCA2 region in 94 rs12913832:AA and AG Norwegians (43 blue-eyed and 51 brown-eyed) to search for novel blue eye colour variants. The new candidate variants were subsequently typed in a Norwegian biobank population (total n = 519) for population specific association analysis. We identified five new variants, rs74409036:A, rs78544415:T, rs72714116:T, rs191109490:C and rs551217952:C, to be the most promising candidates for explaining blue eye colour in individuals with the rs12913832:AA and AG genotype. Additionally, we confirmed the association of the missense variants rs74653330:T and rs121918166:T with blue eye colour, and observed lighter skin colour in rs74653330:T individuals. In total, 37 (86%) of the 43 blue-eyed rs12913832:AA and AG Norwegians could potentially be explained by these seven variants, and we suggest including them in future prediction models.
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Hohl DM, González R, Di Santo Meztler GP, Patiño-Rico J, Dejean C, Avena S, Gutiérrez MDLÁ, Catanesi CI. Applicability of the IrisPlex system for eye color prediction in an admixed population from Argentina. Ann Hum Genet 2022; 86:297-327. [PMID: 35946314 DOI: 10.1111/ahg.12480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 11/29/2022]
Abstract
Eye color prediction based on an individual's genetic information is of interest in the field of forensic genetics. In recent years, researchers have studied different genes and markers associated with this externally visible characteristic and have developed methods for its prediction. The IrisPlex represents a validated tool for homogeneous populations, though its applicability in populations of mixed ancestry is limited, mainly regarding the prediction of intermediate eye colors. With the aim of validating the applicability of this system in an admixed population from Argentina (n = 302), we analyzed the six single nucleotide variants used in that multiplex for eye color and four additional SNPs, and evaluated its prediction ability. We also performed a genotype-phenotype association analysis. This system proved to be useful when dealing with the extreme ends of the eye color spectrum (blue and brown) but presented difficulties in determining the intermediate phenotypes (green), which were found in a large proportion of our population. We concluded that these genetic tools should be used with caution in admixed populations and that more studies are required in order to improve the prediction of intermediate phenotypes.
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Affiliation(s)
- Diana María Hohl
- Laboratorio de Diversidad Genética, Instituto Multidisciplinario de Biología Celular IMBICE (CONICET-UNLP-CIC), La Plata, Buenos Aires, Argentina
| | - Rebeca González
- Laboratorio de Diversidad Genética, Instituto Multidisciplinario de Biología Celular IMBICE (CONICET-UNLP-CIC), La Plata, Buenos Aires, Argentina
| | - Gabriela Paula Di Santo Meztler
- Centro de Investigación de Proteínas Vegetales (CIPROVE-Centro Asociado CICPBA-UNLP), Depto. de Cs. Biológicas, Facultad de Cs. Exactas, Universidad Nacional de La Plata (UNLP), La Plata, Buenos Aires, Argentina
| | - Jessica Patiño-Rico
- Centro de Ciencias Naturales, Ambientales y Antropológicas, Universidad Maimónides, Buenos Aires, Argentina
| | - Cristina Dejean
- Centro de Ciencias Naturales, Ambientales y Antropológicas, Universidad Maimónides, Buenos Aires, Argentina.,Universidad de Buenos Aires, Facultad de Filosofía y Letras, Instituto de Ciencias Antropológicas (ICA), Sección Antropología Biológica, Buenos Aires, Argentina
| | - Sergio Avena
- Centro de Ciencias Naturales, Ambientales y Antropológicas, Universidad Maimónides, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas CONICET, Buenos Aires, Argentina
| | - María De Los Ángeles Gutiérrez
- Centro de Investigaciones del Medioambiente CIM, Facultad de Ciencias Exactas-CONICET, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Cecilia Inés Catanesi
- Laboratorio de Diversidad Genética, Instituto Multidisciplinario de Biología Celular IMBICE (CONICET-UNLP-CIC), La Plata, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas CONICET, Buenos Aires, Argentina.,Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
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'Guess who'? An Italian multicentric study on pigmentation traits prevalence in endometriosis localizations. Eur J Obstet Gynecol Reprod Biol 2022; 274:5-12. [PMID: 35561567 DOI: 10.1016/j.ejogrb.2022.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/27/2022] [Accepted: 05/01/2022] [Indexed: 11/23/2022]
Abstract
OBJECTIVES Previous evidence seems to support the more common presence of certain pigmentation types in women with endometriosis. The aim of this study was to assess the association of certain somatic phenotypes with specific localizations of the disease. The genetic makeup of those somatic traits may will help in better define the disease pathogenesis. STUDY DESIGN Multicentric, retrospective study of women aged 18 to 45 with histologically confirmed endometriosis. 575 patients were recruited at eleven different Italian endometriosis clinics from March 2015 to January 2021. Data regarding clinical and surgical features were recorded following the self-administered endometriosis patient questionnaire and the surgical standard of reports approved by the World Endometriosis Research Foundation (WERF). Pigmentation types/somatic phenotypes frequencies among endometriosis localizations were reported. A logistic regression analysis was performed to determine somatic types independently associated with disease' localizations. RESULTS Having green eyes increased by ∼4 folds (OR 3.7; 95% CI: 1.42-9.61; p = 0.007) the risk of having a ureteral nodule, whereas brown/black eyes decreased this risk (OR 0.34; 95% CI: 0.13-0.87; p = 0.025). Consistently, the combination of green eyes and blonde/light brown hairs increased the odds of ureteral endometriosis by more than 5 folds (OR 5.40; 95%CI: 2.02-14.49; p = 0.001), even after correction for anthropometric confounders (aOR 5.85; 95% CI: 2.13-16.09; p < 0.001). CONCLUSIONS The association between endometriosis and pigmentary traits has been herein confirmed, with the novel finding of the possible predisposition of ureteral endometriosis in patients with green eyes and blonde/light brown hairs. Further investigation on the genetic makeup of somatic traits may provide new inroads also into the molecular aspects of endometriosis leading to a better understanding of this complex disease.
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Mackey DA. What colour are your eyes? Teaching the genetics of eye colour & colour vision. Edridge Green Lecture RCOphth Annual Congress Glasgow May 2019. Eye (Lond) 2022; 36:704-715. [PMID: 34426658 PMCID: PMC8956647 DOI: 10.1038/s41433-021-01749-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/31/2021] [Accepted: 08/06/2021] [Indexed: 02/07/2023] Open
Abstract
Eye colour and colour perception are excellent examples to use when teaching genetics as they encompass not simply the basic Mendelian genetics of dominant, recessive and X-linked disorders, but also many of the new concepts such as non-allelic diseases, polygenic disease, phenocopies, genome-wide association study (GWAS), founder effects, gene-environment interaction, evolutionary drivers for variations, copy number variation, insertions deletions, methylation and gene inactivation. Beyond genetics, colour perception touches on concepts involving optics, physics, physiology and psychology and can capture the imagination of the population, as we saw with social media trend of "#the dress". Television shows such as Game of Thrones focused attention on the eye colour of characters, as well as their Dire-wolves and Dragons. These themes in popular culture can be leveraged as tools to teach and engage everyone in genetics, which is now a key component in all eye diseases. As the explosion of data from genomics, big data and artificial intelligence transforms medicine, ophthalmologists need to be genetically literate. Genetics is relevant, not just for Inherited Retinal Diseases and congenital abnormalities but also for the leading causes of blindness: age-related macular degeneration, glaucoma, myopia, diabetic retinopathy and cataract. Genetics should be part of the armamentarium of every practicing ophthalmologist. We need to ask every patient about their family history. In the near future, patients will attend eye clinics with genetic results showing they are at high risk of certain eye diseases and ophthalmologists will need to know how to screen, follow and treat these patients.
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Affiliation(s)
- David A. Mackey
- grid.1012.20000 0004 1936 7910Lions Eye Institute, University of Western Australia, Perth, WA Australia ,grid.1009.80000 0004 1936 826XSchool of Medicine, University of Tasmania, Hobart, Tas Australia
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12
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Pan Y, Zhang C, Lu Y, Ning Z, Lu D, Gao Y, Zhao X, Yang Y, Guan Y, Mamatyusupu D, Xu S. Genomic diversity and post-admixture adaptation in the Uyghurs. Natl Sci Rev 2022; 9:nwab124. [PMID: 35350227 PMCID: PMC8953455 DOI: 10.1093/nsr/nwab124] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/30/2021] [Accepted: 06/07/2021] [Indexed: 11/17/2022] Open
Abstract
Population admixture results in genome-wide combinations of genetic variants derived from different ancestral populations of distinct ancestry, thus providing a unique opportunity for understanding the genetic determinants of phenotypic variation in humans. Here, we used whole-genome sequencing of 92 individuals with high coverage (30–60×) to systematically investigate genomic diversity in the Uyghurs living in Xinjiang, China (XJU), an admixed population of both European-like and East-Asian-like ancestry. The XJU population shows greater genetic diversity, especially a higher proportion of rare variants, compared with their ancestral source populations, corresponding to greater phenotypic diversity of XJU. Admixture-induced functional variants in EDAR were associated with the diversity of facial morphology in XJU. Interestingly, the interaction of functional variants between SLC24A5 and OCA2 likely influences the diversity of skin pigmentation. Notably, selection has seemingly been relaxed or canceled in several genes with significantly biased ancestry, such as HERC2–OCA2. Moreover, signatures of post-admixture adaptation in XJU were identified, including genes related to metabolism (e.g. CYP2D6), digestion (e.g. COL11A1), olfactory perception (e.g. ANO2) and immunity (e.g. HLA). Our results demonstrated population admixture as a driving force, locally or globally, in shaping human genetic and phenotypic diversity as well as in adaptive evolution.
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Affiliation(s)
- Yuwen Pan
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031, China
| | - Chao Zhang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031, China
| | - Yan Lu
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University , Shanghai 200438, China
| | - Zhilin Ning
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031, China
| | - Dongsheng Lu
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031, China
| | - Yang Gao
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University , Shanghai 201210, China
| | - Xiaohan Zhao
- Human Phenome Institute, Fudan University , Shanghai 201203, China
| | - Yajun Yang
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University , Shanghai 200438, China
| | - Yaqun Guan
- Department of Biochemistry and Molecular Biology, Preclinical Medicine College, Xinjiang Medical University , Urumqi 830011, China
| | - Dolikun Mamatyusupu
- College of the Life Sciences and Technology, Xinjiang University , Urumqi 830046, China
| | - Shuhua Xu
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai 200031, China
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University , Shanghai 200438, China
- School of Life Science and Technology, ShanghaiTech University , Shanghai 201210, China
- Human Phenome Institute, Fudan University , Shanghai 201203, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences , Kunming 650223, China
- Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University , Zhengzhou 450052, China
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13
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Pośpiech E, Teisseyre P, Mielniczuk J, Branicki W. Predicting Physical Appearance from DNA Data-Towards Genomic Solutions. Genes (Basel) 2022; 13:genes13010121. [PMID: 35052461 PMCID: PMC8774670 DOI: 10.3390/genes13010121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 02/04/2023] Open
Abstract
The idea of forensic DNA intelligence is to extract from genomic data any information that can help guide the investigation. The clues to the externally visible phenotype are of particular practical importance. The high heritability of the physical phenotype suggests that genetic data can be easily predicted, but this has only become possible with less polygenic traits. The forensic community has developed DNA-based predictive tools by employing a limited number of the most important markers analysed with targeted massive parallel sequencing. The complexity of the genetics of many other appearance phenotypes requires big data coupled with sophisticated machine learning methods to develop accurate genomic predictors. A significant challenge in developing universal genomic predictive methods will be the collection of sufficiently large data sets. These should be created using whole-genome sequencing technology to enable the identification of rare DNA variants implicated in phenotype determination. It is worth noting that the correctness of the forensic sketch generated from the DNA data depends on the inclusion of an age factor. This, however, can be predicted by analysing epigenetic data. An important limitation preventing whole-genome approaches from being commonly used in forensics is the slow progress in the development and implementation of high-throughput, low DNA input sequencing technologies. The example of palaeoanthropology suggests that such methods may possibly be developed in forensics.
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Affiliation(s)
- Ewelina Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland;
| | - Paweł Teisseyre
- Institute of Computer Science, Polish Academy of Sciences, 01-248 Warsaw, Poland; (P.T.); (J.M.)
- Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland
| | - Jan Mielniczuk
- Institute of Computer Science, Polish Academy of Sciences, 01-248 Warsaw, Poland; (P.T.); (J.M.)
- Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland;
- Central Forensic Laboratory of the Police, 00-583 Warsaw, Poland
- Correspondence: ; Tel.: +48-126-645-024
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14
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Wierenga APA, Brouwer NJ, Gelmi MC, Verdijk RM, Stern MH, Bas Z, Malkani K, van Duinen SG, Ganguly A, Kroes WGM, Marinkovic M, Luyten GPM, Shields CL, Jager MJ. Chromosome 3 and 8q aberrations in Uveal Melanoma show greater impact on survival in patients with light iris versus dark iris color. Ophthalmology 2021; 129:421-430. [PMID: 34780841 DOI: 10.1016/j.ophtha.2021.11.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 11/01/2021] [Accepted: 11/05/2021] [Indexed: 10/19/2022] Open
Abstract
PURPOSE Individuals with gray, blue, or green iris have a higher chance of developing uveal melanoma (UM) than those with brown eyes. We wondered whether iris pigmentation might not only be related to predisposition to UM, but also to its behavior and therefore compared clinical, histopathologic, and genetic characteristics of UM between eyes with different iris colors. DESIGN We determined iris color in a large cohort of patients who had undergone an enucleation for UM. Clinical and histopathological tumor characteristics, chromosome status, and survival were compared between three groups, based on iris color. PARTICIPANTS 412 patients with choroidal/ciliary body UM, who had undergone primary enucleation at the Leiden University Medical Center (LUMC), Leiden, The Netherlands, between 1993 and 2019, divided into three groups, based on iris color (gray/blue, green/hazel, and brown). Validation cohort: 934 choroidal/ciliary body UM patients treated at Wills Eye Hospital (WEH), Philadelphia, United States. METHODS Comparison of clinical, histopathologic, and genetic characteristics of UM in patients with different iris colors. MAIN OUTCOME MEASURES Melanoma-related survival in UM patients, divided over three iris color groups, in relation to the tumor's chromosome 3 and 8q status. RESULTS Moderate and heavy tumor pigmentation was especially seen in eyes with brown iris (p < 0.001). Survival did not differ between patients with different iris colors (p = 0.28). However, in patients with a light iris, copy number changes in chromosome 3 and 8q had a greater influence on survival than in patients with a dark iris. Similarly, chromosome 3 and chromosome 8q status affected survival more among patients with lightly-pigmented tumors than in patients with heavily-pigmented tumors. The WEH cohort similarly showed a greater influence of chromosome aberrations in light-eyed individuals. CONCLUSIONS While iris color by itself did not relate to survival of UM patients, chromosome 3 and 8q aberrations had a much larger influence on survival in patients with light iris compared to those with brown iris. This suggests a synergistic effect of iris pigmentation and chromosome status in the regulation of oncogenic behavior of UM. Iris color should be taken into consideration when calculating the risk for developing metastases.
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Affiliation(s)
- Annemijn P A Wierenga
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Niels J Brouwer
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Maria Chiara Gelmi
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Robert M Verdijk
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands; Department of Pathology, Section Ophthalmic Pathology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Marc-Henri Stern
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue, Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris, France
| | - Zeynep Bas
- Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, PA, USA
| | - Kabir Malkani
- Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, PA, USA
| | - Sjoerd G van Duinen
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Arupa Ganguly
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA. USA
| | - Wilma G M Kroes
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marina Marinkovic
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Gregorius P M Luyten
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Carol L Shields
- Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, PA, USA
| | - Martine J Jager
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands.
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15
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Silva LDFD, Lima ASB, Dall’Oglio CF, Hallal RJ. Heterocromia de íris: uma revisão das condições que podem afetar a pigmentação iridiana. REVISTA BRASILEIRA DE OFTALMOLOGIA 2021. [DOI: 10.37039/1982.8551.20210050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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16
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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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17
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Koirala M, Shashikala HBM, Jeffries J, Wu B, Loftus SK, Zippin JH, Alexov E. Computational Investigation of the pH Dependence of Stability of Melanosome Proteins: Implication for Melanosome formation and Disease. Int J Mol Sci 2021; 22:ijms22158273. [PMID: 34361043 PMCID: PMC8347052 DOI: 10.3390/ijms22158273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 11/16/2022] Open
Abstract
Intravesicular pH plays a crucial role in melanosome maturation and function. Melanosomal pH changes during maturation from very acidic in the early stages to neutral in late stages. Neutral pH is critical for providing optimal conditions for the rate-limiting, pH-sensitive melanin-synthesizing enzyme tyrosinase (TYR). This dramatic change in pH is thought to result from the activity of several proteins that control melanosomal pH. Here, we computationally investigated the pH-dependent stability of several melanosomal membrane proteins and compared them to the pH dependence of the stability of TYR. We confirmed that the pH optimum of TYR is neutral, and we also found that proteins that are negative regulators of melanosomal pH are predicted to function optimally at neutral pH. In contrast, positive pH regulators were predicted to have an acidic pH optimum. We propose a competitive mechanism among positive and negative regulators that results in pH equilibrium. Our findings are consistent with previous work that demonstrated a correlation between the pH optima of stability and activity, and they are consistent with the expected activity of positive and negative regulators of melanosomal pH. Furthermore, our data suggest that disease-causing variants impact the pH dependence of melanosomal proteins; this is particularly prominent for the OCA2 protein. In conclusion, melanosomal pH appears to affect the activity of multiple melanosomal proteins.
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Affiliation(s)
- Mahesh Koirala
- Department of Physics, Clemson University, Clemson, SC 29634, USA; (M.K.); (H.B.M.S.); (J.J.); (B.W.)
| | - H. B. Mihiri Shashikala
- Department of Physics, Clemson University, Clemson, SC 29634, USA; (M.K.); (H.B.M.S.); (J.J.); (B.W.)
| | - Jacob Jeffries
- Department of Physics, Clemson University, Clemson, SC 29634, USA; (M.K.); (H.B.M.S.); (J.J.); (B.W.)
| | - Bohua Wu
- Department of Physics, Clemson University, Clemson, SC 29634, USA; (M.K.); (H.B.M.S.); (J.J.); (B.W.)
| | - Stacie K. Loftus
- Genetic Disease Research Branch, National Human Genome Research Branch, National Institutes of Health, Bethesda, MD 22066, USA;
| | - Jonathan H. Zippin
- Department of Dermatology, Weill Cornell Medical College, New York, NY 10021, USA;
| | - Emil Alexov
- Department of Physics, Clemson University, Clemson, SC 29634, USA; (M.K.); (H.B.M.S.); (J.J.); (B.W.)
- Correspondence:
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18
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Loftus SK, Lundh L, Watkins-Chow DE, Baxter LL, Pairo-Castineira E, Nisc Comparative Sequencing Program, Jackson IJ, Oetting WS, Pavan WJ, Adams DR. A custom capture sequence approach for oculocutaneous albinism identifies structural variant alleles at the OCA2 locus. Hum Mutat 2021; 42:1239-1253. [PMID: 34246199 DOI: 10.1002/humu.24257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/02/2021] [Accepted: 06/24/2021] [Indexed: 11/09/2022]
Abstract
Oculocutaneous albinism (OCA) is a heritable disorder of pigment production that manifests as hypopigmentation and altered eye development. Exon sequencing of known OCA genes is unsuccessful in producing a complete molecular diagnosis for a significant number of affected individuals. We sequenced the DNA of individuals with OCA using short-read custom capture sequencing that targeted coding, intronic, and noncoding regulatory regions of known OCA genes, and genome-wide association study-associated pigmentation loci. We identified an OCA2 complex structural variant (CxSV), defined by a 143 kb inverted segment reintroduced in intron 1, upstream of the native location. The corresponding CxSV junctions were observed in 11/390 probands screened. The 143 kb CxSV presents in one family as a copy number variant duplication for the 143 kb region. In the remaining 10/11 families, the 143 kb CxSV acquired an additional 184 kb deletion across the same region, restoring exons 3-19 of OCA2 to a copy-number neutral state. Allele-associated haplotype analysis found rare SNVs rs374519281 and rs139696407 are linked with the 143 kb CxSV in both OCA2 alleles. For individuals in which customary molecular evaluation does not reveal a biallelic OCA diagnosis, we recommend preliminary screening for these haplotype-associated rare variants, followed by junction-specific validation for the OCA2 143 kb CxSV.
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Affiliation(s)
- Stacie K Loftus
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Linnea Lundh
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Dawn E Watkins-Chow
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Laura L Baxter
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Erola Pairo-Castineira
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, UK.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | | | - Ian J Jackson
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, UK.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - William S Oetting
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, Minnesota, USA
| | - William J Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - David R Adams
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
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19
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Gene Discovery Using Twins. Twin Res Hum Genet 2021; 23:90-93. [PMID: 32638676 DOI: 10.1017/thg.2020.38] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
One of Nick's key early achievements at QIMR was to establish a twin study on melanoma risk factors. The Brisbane Twin Nevus Study (BTNS) had an initial focus on nevus (mole) count in adolescents but, reflecting Nick's broad interests, expanded in scope enormously over the decades. In the skin cancer arena, BTNS was essential to genetic discoveries in melanoma, eye color and pigmentation. Later studies amassed data on thousands of phenotypes, ranging from molecular phenotypes such as gene expression to studies where gene mapping findings in adolescents turned out to have translational potential in late-onset diseases. Nick's twin data have formed the basis for an enormous range of discoveries, with Nick and his colleagues continuing to capitalize on these data.
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20
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Feng Y, McQuillan MA, Tishkoff SA. Evolutionary genetics of skin pigmentation in African populations. Hum Mol Genet 2021; 30:R88-R97. [PMID: 33438000 PMCID: PMC8117430 DOI: 10.1093/hmg/ddab007] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/07/2021] [Accepted: 01/07/2021] [Indexed: 12/14/2022] Open
Abstract
Skin color is a highly heritable human trait, and global variation in skin pigmentation has been shaped by natural selection, migration and admixture. Ethnically diverse African populations harbor extremely high levels of genetic and phenotypic diversity, and skin pigmentation varies widely across Africa. Recent genome-wide genetic studies of skin pigmentation in African populations have advanced our understanding of pigmentation biology and human evolutionary history. For example, novel roles in skin pigmentation for loci near MFSD12 and DDB1 have recently been identified in African populations. However, due to an underrepresentation of Africans in human genetic studies, there is still much to learn about the evolutionary genetics of skin pigmentation. Here, we summarize recent progress in skin pigmentation genetics in Africans and discuss the importance of including more ethnically diverse African populations in future genetic studies. In addition, we discuss methods for functional validation of adaptive variants related to skin pigmentation.
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Affiliation(s)
- Yuanqing Feng
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael A McQuillan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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21
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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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22
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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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23
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Fang S, Lu J, Zhou X, Wang Y, Ross MI, Gershenwald JE, Cormier JN, Wargo J, Sui D, Amos CI, Lee JE. Functional annotation of melanoma risk loci identifies novel susceptibility genes. Carcinogenesis 2020; 41:452-457. [PMID: 31630191 DOI: 10.1093/carcin/bgz173] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/23/2019] [Accepted: 10/15/2019] [Indexed: 12/27/2022] Open
Abstract
Genome-wide association study (GWAS)-identified single-nucleotide polymorphisms (SNPs) are tag SNPs located in both transcribed and non-coding regulatory DNA regions, rather than representing causal or functional variants for disease. To identify functional variants or genes for melanoma susceptibility, we used functional mapping and annotation (FUMA) to perform functional annotation of the summary statistics of 2541 significant melanoma risk SNPs (P < 5 × 10-8) identified by GWAS. The original GWAS melanoma study included 15 990 cases and 26 409 controls, representing the largest international meta-analysis of melanoma susceptibility. We prioritized 330 unique genes, including those in immune cytokine signaling pathways, from 19 loci through positional, expression quantitative trait locus, and chromatin interaction mapping. In comparison, only 38 melanoma-related genes were identified in the original meta-analysis. In addition to the well-known melanoma susceptibility genes confirmed in the meta-analysis (MC1R, CDKN2A, TERT, OCA2 and ARNT/SETDB1), we also identified additional novel genes using FUMA to map SNPs to genes. Through chromatin interaction mapping, we prioritized IFNA7, IFNA10, IFNA16, IFNA17, IFNA14, IFNA6, IFNA21, IFNA4, IFNE and IFNA5; these 10 most significant genes are all involved in immune system and cytokine signaling pathways. In the gene analysis, we identified 72 genes with a P < 2.5 × 10-6. The genes associated with melanoma risk were DEF8 (P = 1.09 × 10-57), DBNDD1 (P = 2.19 × 10-42), SPATA33 (P = 3.54 × 10-38) and MC1R (P = 1.04 × 10-36). In summary, this study identifies novel putative melanoma susceptibility genes and provides a guide for further experimental validation of functional variants and disease-related genes.
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Affiliation(s)
- Shenying Fang
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jiachun Lu
- The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, School of Public Health, Guangzhou Medical University, Guangzhou, China
| | - Xinke Zhou
- The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yuling Wang
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Merrick I Ross
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jeffrey E Gershenwald
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Janice N Cormier
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dawen Sui
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Jeffrey E Lee
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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24
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Skin Pigmentation Differences between Mongolian, Korean, and Uzbekistan Ancient Human DNA Samples. BIOMED RESEARCH INTERNATIONAL 2020; 2020:2585324. [PMID: 33083459 PMCID: PMC7559177 DOI: 10.1155/2020/2585324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 06/23/2020] [Accepted: 07/10/2020] [Indexed: 11/17/2022]
Abstract
Background This study reports the use of real-time PCR to identify the SNP rs1545397 in the intron region on the OCA2 gene from ancient and degraded DNA isolated from ancient human bones from Mongolia, Korea, and Uzbekistan. This SNP is a marker for skin pigmentation. LightCycler-based probes (HybProbes) were designed. A LightCycler (version 2.0) system was used for the real-time PCR. Results The results of the real-time PCRs of three different genotypes of SNP rs1545397 were compared with those of the direct sequencing. Melting curve analysis was used for genotype determination. Three genotypes were distinguished: the homozygous T (T/T) SNP type formed a distinct melting peak at 53.3 ± 0.14°C, the homozygous A (A/A) SNP type formed a distinct melting peak at 57.8 ± 0.12°C, and the heterozygous A/T SNP type formed two distinct melting peaks at 53.3 ± 0.17°C and 57.8 ± 0.15°C. Mongolian aDNA samples tested in this study carried all three types of the SNP (A/T, A/A, and T/T) with no distinctly predominant type observed. In contrast, Korean aDNA samples carried the Asian genotype (T/T), while the Uzbekistan aDNA samples carried the European genotype (A/A) more often than the Asian genotype (T/T). Conclusions Human Mongolian aDNA samples had A/T, A/A, and T/T SNP rs1545397 with no distinct predominant genotype. When combined with the archeological and aDNA studies of other coupling morphologies with aDNA, our results infer that Mongolia's prehistoric population had considerable heterogeneity of skin color and morphological traits and that in the Neolithic period, a Eurasian or mixed population inhabited the western part of Mongolia.
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25
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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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26
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Kidd KK, Pakstis AJ, Donnelly MP, Bulbul O, Cherni L, Gurkan C, Kang L, Li H, Yun L, Paschou P, Meiklejohn KA, Haigh E, Speed WC. The distinctive geographic patterns of common pigmentation variants at the OCA2 gene. Sci Rep 2020; 10:15433. [PMID: 32963319 PMCID: PMC7508881 DOI: 10.1038/s41598-020-72262-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 08/17/2020] [Indexed: 11/25/2022] Open
Abstract
Oculocutaneous Albinism type 2 (OCA2) is a gene of great interest because of genetic variation affecting normal pigmentation variation in humans. The diverse geographic patterns for variant frequencies at OCA2 have been evident but have not been systematically investigated, especially outside of Europe. Here we examine population genetic variation in and near the OCA2 gene from a worldwide perspective. The very different patterns of genetic variation found across world regions suggest strong selection effects may have been at work over time. For example, analyses involving the variants that affect pigmentation of the iris argue that the derived allele of the rs1800407 single nucleotide polymorphism, which produces a hypomorphic protein, may have contributed to the previously demonstrated positive selection in Europe for the enhancer variant responsible for light eye color. More study is needed on the relationships of the genetic variation at OCA2 to variation in pigmentation in areas beyond Europe.
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Affiliation(s)
- Kenneth K Kidd
- Professor Emeritus, Department of Genetics, Yale University School of Medicine, P.O. Box 208005, New Haven, CT, 06520-8005, USA.
| | - Andrew J Pakstis
- Professor Emeritus, Department of Genetics, Yale University School of Medicine, P.O. Box 208005, New Haven, CT, 06520-8005, USA
| | - Michael P Donnelly
- Professor Emeritus, Department of Genetics, Yale University School of Medicine, P.O. Box 208005, New Haven, CT, 06520-8005, USA.,Biological and Environmental Sciences, Troy University, Dothan, AL, 36303, USA
| | - Ozlem Bulbul
- Institute of Forensic Science, Istanbul University-Cerrahpasa, Istanbul, 34500, Turkey
| | - Lotfi Cherni
- Laboratory of Genetics, Immunology and Human Pathologies, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia.,Higher Institute of Biotechnology of Monastir, Monastir University, 5000, Monastir, Tunisia
| | - Cemal Gurkan
- Turkish Cypriot DNA Laboratory, Committee on Missing Persons in Cyprus Turkish Cypriot Member Office, Nicosia, North Cyprus), Turkey.,Dr. Fazıl Küçük Faculty of Medicine, Eastern Mediterranean University, Famagusta (North Cyprus), Turkey
| | - Longli Kang
- Key Laboratory forMolecular GeneticMechanisms and Intervention Research On High Altitude Disease of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, 712082, Shaanxi, China.,Key Laboratory of High Altitude Environment and Genes Related To Disease of Tibet Ministry of Education, School of Medicine, Xizang Minzu University, Xianyang, 712082, Shaanxi, China
| | - Hui Li
- MOE State Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Libing Yun
- Institute of Forensic Medicine, West China College of Preclinical and Forensic Medicine, Sichuan University, No.16. Section 3. RenMin Nan Road, Chengdu, 610041, Sichuan, China
| | - Peristera Paschou
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Kelly A Meiklejohn
- Department of Population Health and Pathobiology, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - Eva Haigh
- Professor Emeritus, Department of Genetics, Yale University School of Medicine, P.O. Box 208005, New Haven, CT, 06520-8005, USA
| | - William C Speed
- Professor Emeritus, Department of Genetics, Yale University School of Medicine, P.O. Box 208005, New Haven, CT, 06520-8005, USA
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27
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Balanovska E, Lukianova E, Kagazezheva J, Maurer A, Leybova N, Agdzhoyan A, Gorin I, Petrushenko V, Zhabagin M, Pylev V, Kostryukova E, Balanovsky O. Optimizing the genetic prediction of the eye and hair color for North Eurasian populations. BMC Genomics 2020; 21:527. [PMID: 32912208 PMCID: PMC7488246 DOI: 10.1186/s12864-020-06923-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 07/17/2020] [Indexed: 01/05/2023] Open
Abstract
Background Predicting the eye and hair color from genotype became an established and widely used tool in forensic genetics, as well as in studies of ancient human populations. However, the accuracy of this tool has been verified on the West and Central Europeans only, while populations from border regions between Europe and Asia (like Caucasus and Ural) also carry the light pigmentation phenotypes. Results We phenotyped 286 samples collected across North Eurasia, genotyped them by the standard HIrisPlex-S markers and found that predictive power in Caucasus/Ural/West Siberian populations is reasonable but lower than that in West Europeans. As these populations have genetic ancestries different from that of West Europeans, we hypothesized they may carry a somewhat different allele spectrum. Thus, for all samples we performed the exome sequencing additionally enriched with the 53 genes and intergenic regions known to be associated with the eye/hair color. Our association analysis replicated the importance of the key previously known SNPs but also identified five new markers whose eye color prediction power for the studied populations is compatible with the two major previously well-known SNPs. Four out of these five SNPs lie within the HERС2 gene and the fifth in the intergenic region. These SNPs are found at high frequencies in most studied populations. The released dataset of exomes from Russian populations can be further used for population genetic and medical genetic studies. Conclusions This study demonstrated that precision of the established systems for eye/hair color prediction from a genotype is slightly lower for the populations from the border regions between Europe and Asia that for the West Europeans. However, this precision can be improved if some newly revealed predictive SNPs are added into the panel. We discuss that the replication of these pigmentation-associated SNPs on the independent North Eurasian sample is needed in the future studies.
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Affiliation(s)
- Elena Balanovska
- Research Centre for Medical Genetics, Moscow, Russia.,Biobank of North Eurasia, Moscow, Russia
| | | | - Janet Kagazezheva
- Research Centre for Medical Genetics, Moscow, Russia.,Vavilov Institute of General Genetics, Moscow, Russia.,Krasnodar State Medical University, Krasnodar, Russia
| | - Andrey Maurer
- Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow, Russia
| | - Natalia Leybova
- Institute of Ethnology and Anthropology of Russian Academy of Sciences, Moscow, Russia
| | - Anastasiya Agdzhoyan
- Research Centre for Medical Genetics, Moscow, Russia.,Vavilov Institute of General Genetics, Moscow, Russia
| | - Igor Gorin
- Vavilov Institute of General Genetics, Moscow, Russia.,Moscow Institute of Physics and Technology, Moscow, Russia
| | - Valeria Petrushenko
- Vavilov Institute of General Genetics, Moscow, Russia.,Moscow Institute of Physics and Technology, Moscow, Russia
| | - Maxat Zhabagin
- National Center for Biotechnology, Nursultan, Kazakhstan
| | | | - Elena Kostryukova
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russia
| | - Oleg Balanovsky
- Research Centre for Medical Genetics, Moscow, Russia. .,Biobank of North Eurasia, Moscow, Russia. .,Vavilov Institute of General Genetics, Moscow, Russia.
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28
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McInerney-Leo AM, West J, Meiser B, West M, Brown MA, Duncan E. Causal Attributions in an Australian Aboriginal Family With Marfan Syndrome: A Qualitative Study. Front Genet 2020; 11:461. [PMID: 32457804 PMCID: PMC7221064 DOI: 10.3389/fgene.2020.00461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 04/14/2020] [Indexed: 12/02/2022] Open
Abstract
Causal attributions are important determinants of how health threats are processed and affect health-related behaviors. To date, there has been no research on causal attributions in genetic conditions in Aboriginal Australians. Forty members of a large Aboriginal Australian family with Marfan syndrome (MFS) were invited to participate in an ethically approved study exploring causal attributions, including perceived causes of phenotypic variability within the family. Eighteen individuals consented to conduct semi-structured qualitative interviews, which were recorded, transcribed verbatim and analyzed thematically. Most participants knew that MFS was genetic, but there were diverse theories about inheritance, including beliefs that it skipped generations, was affected by birth order and/or gender, and that it co-occurred with inheritance of blue eyes within this family. The mutation was thought to have been inherited from British settlers and initially triggered by disease or diet. Factors believed to modify disease severity included other genes and lifestyle factors, particularly alcohol and substance abuse and stress. Generally, this family did not endorse “blaming” chance or a higher power for phenotypic variability, though some felt that the spirits or a deity may have played a role. In conclusion, although participants knew MFS was a genetic condition, many speculated about the role of non-genetic causes in initiating the original mutation; and the gene-environment interaction was thought to affect severity. This study demonstrates a successful approach for exploring causal attributions in other genetic conditions in First Australians.
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Affiliation(s)
- Aideen M McInerney-Leo
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Jennifer West
- Prince Charles Hospital Clinical Unit, School of Clinical Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Bettina Meiser
- Prince of Wales Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Malcolm West
- Prince Charles Hospital Clinical Unit, School of Clinical Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Matthew A Brown
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia.,Guy's and St Thomas' NHS Foundation Trust and King's College London NIHR Biomedical Research Centre, London, United Kingdom
| | - Emma Duncan
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia.,Department of Endocrinology, James Mayne Building, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
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29
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Miller M, Vitale D, Kahn PC, Rost B, Bromberg Y. funtrp: identifying protein positions for variation driven functional tuning. Nucleic Acids Res 2020; 47:e142. [PMID: 31584091 PMCID: PMC6868392 DOI: 10.1093/nar/gkz818] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/05/2019] [Accepted: 09/12/2019] [Indexed: 12/12/2022] Open
Abstract
Evaluating the impact of non-synonymous genetic variants is essential for uncovering disease associations and mechanisms of evolution. An in-depth understanding of sequence changes is also fundamental for synthetic protein design and stability assessments. However, the variant effect predictor performance gain observed in recent years has not kept up with the increased complexity of new methods. One likely reason for this might be that most approaches use similar sets of gene and protein features for modeling variant effects, often emphasizing sequence conservation. While high levels of conservation highlight residues essential for protein activity, much of the variation observable in vivo is arguably weaker in its impact, thus requiring evaluation at a higher level of resolution. Here, we describe functionNeutral/Toggle/Rheostatpredictor (funtrp), a novel computational method that categorizes protein positions based on the position-specific expected range of mutational impacts: Neutral (weak/no effects), Rheostat (function-tuning positions), or Toggle (on/off switches). We show that position types do not correlate strongly with familiar protein features such as conservation or protein disorder. We also find that position type distribution varies across different protein functions. Finally, we demonstrate that position types can improve performance of existing variant effect predictors and suggest a way forward for the development of new ones.
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Affiliation(s)
- Maximilian Miller
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ 08901, USA
| | - Daniel Vitale
- Columbian College of Arts and Sciences Data Science Program Corcoran Hall, 725 21st Street NW, Washington, DC 20052, USA
| | - Peter C Kahn
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ 08901, USA
| | - Burkhard Rost
- Department for Bioinformatics and Computational Biology, Technische Universität München, Boltzmannstr. 3, 85748 Garching/Munich, Germany.,Institute for Advanced Study at Technische Universität München (TUM-IAS), Lichtenbergstraße 2a 85748 Garching/Munich, Germany
| | - Yana Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ 08901, USA.,Institute for Advanced Study at Technische Universität München (TUM-IAS), Lichtenbergstraße 2a 85748 Garching/Munich, Germany.,Department of Genetics, Rutgers University, Human Genetics Institute, Life Sciences Building, 145 Bevier Road, Piscataway, NJ 08854, USA
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30
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Sarin KY, Lin Y, Daneshjou R, Ziyatdinov A, Thorleifsson G, Rubin A, Pardo LM, Wu W, Khavari PA, Uitterlinden A, Nijsten T, Toland AE, Olafsson JH, Sigurgeirsson B, Thorisdottir K, Jorgensen E, Whittemore AS, Kraft P, Stacey SN, Stefansson K, Asgari MM, Han J. Genome-wide meta-analysis identifies eight new susceptibility loci for cutaneous squamous cell carcinoma. Nat Commun 2020; 11:820. [PMID: 32041948 PMCID: PMC7010741 DOI: 10.1038/s41467-020-14594-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 01/20/2020] [Indexed: 02/06/2023] Open
Abstract
Cutaneous squamous cell carcinoma (SCC) is one of the most common cancers in the United States. Previous genome-wide association studies (GWAS) have identified 14 single nucleotide polymorphisms (SNPs) associated with cutaneous SCC. Here, we report the largest cutaneous SCC meta-analysis to date, representing six international cohorts and totaling 19,149 SCC cases and 680,049 controls. We discover eight novel loci associated with SCC, confirm all previously associated loci, and perform fine mapping of causal variants. The novel SNPs occur within skin-specific regulatory elements and implicate loci involved in cancer development, immune regulation, and keratinocyte differentiation in SCC susceptibility. The authors perform a meta-analysis of cutaneous squamous cell carcinoma, identifying causal variants within skin-specific regulatory elements.
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Affiliation(s)
- Kavita Y Sarin
- Department of Dermatology, Stanford University School of Medicine, 450 Broadway St, C-229, Redwood City, CA, 94305, USA.
| | - Yuan Lin
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Melvin & Bren Simon Cancer Center, Indiana University, 1050 Wishard Blvd, Indianapolis, IN, 46202, USA
| | - Roxana Daneshjou
- Department of Dermatology, Stanford University School of Medicine, 450 Broadway St, C-229, Redwood City, CA, 94305, USA
| | - Andrey Ziyatdinov
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | | | - Adam Rubin
- Department of Dermatology, Stanford University School of Medicine, 450 Broadway St, C-229, Redwood City, CA, 94305, USA
| | - Luba M Pardo
- Department of Dermatology, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015, GD, Rotterdam, The Netherlands
| | - Wenting Wu
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Melvin & Bren Simon Cancer Center, Indiana University, 1050 Wishard Blvd, Indianapolis, IN, 46202, USA
| | - Paul A Khavari
- Department of Dermatology, Stanford University School of Medicine, 450 Broadway St, C-229, Redwood City, CA, 94305, USA
| | - Andre Uitterlinden
- Department of Internal Medicine, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015, GD, Rotterdam, The Netherlands
| | - Tamar Nijsten
- Department of Dermatology, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015, GD, Rotterdam, The Netherlands
| | - Amanda E Toland
- Departments of Cancer Biology and Genetics and Department of Internal Medicine, Division of Human Genetics, Comprehensive Cancer Center, Ohio State University, 460W. 12th Ave, Columbus, OH, 43420, USA
| | - Jon H Olafsson
- Landspitali-University Hospital, Skaftahild 24, 105, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, 101, Reykjavik, Iceland
| | - Bardur Sigurgeirsson
- Landspitali-University Hospital, Skaftahild 24, 105, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, 101, Reykjavik, Iceland
| | - Kristin Thorisdottir
- Landspitali-University Hospital, Skaftahild 24, 105, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, 101, Reykjavik, Iceland
| | - Eric Jorgensen
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Alice S Whittemore
- Departments of Epidemiology and Population Health and of Biomedical Data Sciences, Stanford University School of Medicine Redwood Bldg, T204, Stanford, 94305, CA, USA
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Simon N Stacey
- deCODE genetics/Amgen Inc., Sturlugata 8, 101, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen Inc., Sturlugata 8, 101, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, 101, Reykjavik, Iceland
| | - Maryam M Asgari
- Department of Dermatology, Massachusetts General Hospital, 50 Staniford Street, Suite 270, 02114, Boston, MA, USA
| | - Jiali Han
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Melvin & Bren Simon Cancer Center, Indiana University, 1050 Wishard Blvd, Indianapolis, IN, 46202, USA.
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31
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Louhelainen J, Miller D. Forensic Investigation of a Shawl Linked to the "Jack the Ripper" Murders. J Forensic Sci 2020; 65:295-303. [PMID: 30859587 DOI: 10.1111/1556-4029.14038] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 02/05/2019] [Accepted: 02/06/2019] [Indexed: 11/28/2022]
Abstract
A set of historic murders, known as the "Jack the Ripper murders," started in London in August 1888. The killer's identity has remained a mystery to date. Here, we describe the investigation of, to our knowledge, the only remaining physical evidence linked to these murders, recovered from one of the victims at the scene of the crime. We applied novel, minimally destructive techniques for sample recovery from forensically relevant stains on the evidence and separated single cells linked to the suspect, followed by phenotypic analysis. The mtDNA profiles of both the victim and the suspect matched the corresponding reference samples, fortifying the link of the evidence to the crime scene. Genomic DNA from single cells recovered from the evidence was amplified, and the phenotypic information acquired matched the only witness statement regarded as reliable. To our knowledge, this is the most advanced study to date regarding this case.
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Affiliation(s)
- Jari Louhelainen
- Pharmacy and Biomolecular Sciences, James Parsons Building Byrom Street, Room 10.06, Liverpool, L3 3AF, UK
| | - David Miller
- Reproduction and Early Development Group, Institute of Genetics, Health and Therapeutics, University of Leeds, Clarendon Way, Leeds, LS2 9JT, UK
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32
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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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33
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Zaorska K, Zawierucha P, Nowicki M. Prediction of skin color, tanning and freckling from DNA in Polish population: linear regression, random forest and neural network approaches. Hum Genet 2019; 138:635-647. [PMID: 30980179 PMCID: PMC6554257 DOI: 10.1007/s00439-019-02012-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/08/2019] [Indexed: 12/16/2022]
Abstract
Predicting phenotypes from DNA has recently become extensively studied field in forensic research and is referred to as Forensic DNA Phenotyping. Systems based on single nucleotide polymorphisms for accurate prediction of iris, hair and skin color in global population, independent of bio-geographical ancestry, have recently been introduced. Here, we analyzed 14 SNPs for distinct skin pigmentation traits in a homogeneous cohort of 222 Polish subjects. We compared three different algorithms: General Linear Model based on logistic regression, Random Forest and Neural Network in 18 developed prediction models. We demonstrate Random Forest to be the most accurate algorithm for 3- and 4-category estimations (total of 58.3% correct calls for skin color prediction, 47.2% for tanning prediction, 50% for freckling prediction). Binomial Logistic Regression was the best approach in 2-category estimations (total of 69.4% correct calls, AUC = 0.673 for tanning prediction; total of 52.8% correct calls, AUC = 0.537 for freckling prediction). Our study confirms the association of rs12913832 (HERC2) with all three skin pigmentation traits, but also variants associated solely with certain pigmentation traits, namely rs6058017 and rs4911414 (ASIP) with skin sensitivity to sun and tanning abilities, rs12203592 (IRF4) with freckling and rs4778241 and rs4778138 (OCA2) with skin color and tanning. Finally, we assessed significant differences in allele frequencies in comparison with CEU data and our study provides a starting point for the development of prediction models for homogeneous populations with less internal differentiation than in the global predictive testing.
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Affiliation(s)
- Katarzyna Zaorska
- Department of Histology and Embryology, University of Medical Sciences, 60-781, Poznan, Poland.
| | - Piotr Zawierucha
- Department of Anatomy, University of Medical Sciences, 60-781, Poznan, Poland
| | - Michał Nowicki
- Department of Histology and Embryology, University of Medical Sciences, 60-781, Poznan, Poland
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34
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Katsara MA, Nothnagel M. True colors: A literature review on the spatial distribution of eye and hair pigmentation. Forensic Sci Int Genet 2019; 39:109-118. [DOI: 10.1016/j.fsigen.2019.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 12/11/2018] [Accepted: 01/01/2019] [Indexed: 10/27/2022]
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35
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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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36
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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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37
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Eye color prediction using single nucleotide polymorphisms in Saudi population. Saudi J Biol Sci 2018; 26:1607-1612. [PMID: 31762634 PMCID: PMC6864217 DOI: 10.1016/j.sjbs.2018.09.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/27/2018] [Accepted: 09/27/2018] [Indexed: 01/18/2023] Open
Abstract
Background DNA prediction of eye color represent one application of the externally visible characteristics (EVC), which attained growing interest in the field of DNA forensic phenotyping. This is mainly due to its ability to narrow the pool of suspects without the need to compare any retrieved DNA material from the crime scene to a reference DNA. Several methods and multiplex genetic panel were proposed with variable prediction accuracy between different populations. However, such panel was not previously tested in the Saudi population, nor any populations of the Middle East and North Africa origin. Method A panel of eleven single nucleotide polymorphisms (SNPs) was tested for their association with three eye colors (brown, hazel, and intermediate) in 80 volunteer Saudi individuals. SNPs and haplotype association test with eye colors were performed to identify the top significant SNPs with the three eye colors. Also, multinomial logistic regression was used to construct the prediction model using a training set of 60 subjects, and a validation set of 20 subjects. The goodness of fit parameter of the model to correctly predicts each eye color as compared to the other was performed. Results Eye color was significantly associated with rs12913832, rs7170852, and rs916977 that are located within HERC2. SNP rs12913832 was the top significant SNP (p-value = 1.78E−15) that accounted for the association in this region, as the other SNPs were not significant after adjusting for rs12913832. A prediction model containing five SNPs showed high prediction accuracy with Area Under the receiver operating characteristic Curves (AUC) equals to 0.95 and 0.83 for brown and intermediate eye colors, respectively. However, the model’s performance was very low for predicting the hazel eye color with AUC equals 0.75. Discussion Despite the small sample size of our study, we reported very significant SNP associations with eye color. Our model to predict eye colors based on DNA material showed high accuracy for brown and intermediate eye colors. The eye color prediction-model underperformed for the hazel eye colors, suggesting that larger sample size, as well as more comprehensive set of SNPs, could improve the model-prediction accuracy.
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38
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Chaitanya L, Breslin K, Zuñiga S, Wirken L, Pośpiech E, Kukla-Bartoszek M, Sijen T, Knijff PD, Liu F, Branicki W, Kayser M, Walsh S. The HIrisPlex-S system for eye, hair and skin colour prediction from DNA: Introduction and forensic developmental validation. Forensic Sci Int Genet 2018; 35:123-135. [DOI: 10.1016/j.fsigen.2018.04.004] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 03/05/2018] [Accepted: 04/06/2018] [Indexed: 11/29/2022]
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39
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Laino AM, Berry EG, Jagirdar K, Lee KJ, Duffy DL, Soyer HP, Sturm RA. Iris pigmented lesions as a marker of cutaneous melanoma risk: an Australian case-control study. Br J Dermatol 2018; 178:1119-1127. [PMID: 29315480 DOI: 10.1111/bjd.16323] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/27/2017] [Indexed: 02/04/2023]
Abstract
BACKGROUND Iris naevi and iris freckles have a frequency of 4% and 50% in the European population, respectively. They are associated with dysplastic naevi, but few studies have examined their link to cutaneous melanoma. OBJECTIVES To assess whether iris pigmented lesions are a predictive indicator for cutaneous melanoma. METHODS This is a melanoma case-control study of 1254 European-background Australians. Sun exposure and melanoma history, a saliva sample for DNA analysis and eye photographs taken with a digital camera were collected from 1117 participants. Iris images were assessed by up to four trained observers for the number of iris pigmented lesions. The data were analysed for correlations between iris pigmented lesions and melanoma history. RESULTS Case participants over the age of 40 had similar numbers of iris pigmented lesions to age matched controls (mean 5·7 vs. 5·2, P = 0·02), but in younger case and control participants there was a greater difference (mean 3·96 vs. 2·19, P = 0·004). A logistic regression adjusted for age, sex, skin, hair and eye colour, skin freckling and naevus count found that the presence of three or more iris pigmented lesions increases the melanoma risk 1·45-fold [95% confidence interval (CI) 1·07-1·95]. HERC2/OCA2 rs12913832 and IRF4 rs12203592 influenced both eye colour and the number of iris pigmented lesions. On the HERC2/OCA2 A/A and A/G genotype background there was an increasing proportion of blue eye colour when carrying the IRF4 T allele (P = 3 × 10-4 ) and a higher number of iris pigmented lesions with the IRF4 T/T homozygote (P = 3 × 10-9 ). CONCLUSIONS Iris pigmented lesion count provides additional predictive information for melanoma risk above that from conventional risk factors.
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Affiliation(s)
- A M Laino
- Dermatology Research Centre, The University of Queensland, UQ Diamantina Institute, Translational Research Institute, Brisbane, 4102, Australia
| | - E G Berry
- Dermatology Research Centre, The University of Queensland, UQ Diamantina Institute, Translational Research Institute, Brisbane, 4102, Australia.,Department of Dermatology, Emory University School of Medicine, Atlanta, 30309, GA, U.S.A
| | - K Jagirdar
- Dermatology Research Centre, The University of Queensland, UQ Diamantina Institute, Translational Research Institute, Brisbane, 4102, Australia
| | - K J Lee
- Dermatology Research Centre, The University of Queensland, UQ Diamantina Institute, Translational Research Institute, Brisbane, 4102, Australia
| | - D L Duffy
- Dermatology Research Centre, The University of Queensland, UQ Diamantina Institute, Translational Research Institute, Brisbane, 4102, Australia.,QIMR Berghofer Medical Research Institute, Brisbane, 4006, Australia
| | - H P Soyer
- Dermatology Research Centre, The University of Queensland, UQ Diamantina Institute, Translational Research Institute, Brisbane, 4102, Australia.,Department of Dermatology, Princess Alexandra Hospital, Brisbane, 4102, Australia
| | - R A Sturm
- Dermatology Research Centre, The University of Queensland, UQ Diamantina Institute, Translational Research Institute, Brisbane, 4102, Australia
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40
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Molecular Genetics of Pigment Dispersion Syndrome and Pigmentary Glaucoma: New Insights into Mechanisms. J Ophthalmol 2018; 2018:5926906. [PMID: 29780638 PMCID: PMC5892222 DOI: 10.1155/2018/5926906] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 02/22/2018] [Indexed: 12/20/2022] Open
Abstract
We explore the ideas and advances surrounding the genetic basis of pigment dispersion syndrome (PDS) and pigmentary glaucoma (PG). As PG is the leading cause of nontraumatic blindness in young adults and current tailored interventions have proven ineffective, a better understanding of the underlying causes of PDS, PG, and their relationship is essential. Despite PDS being a subclinical disease, a large proportion of patients progress to PG with associated vision loss. Decades of research have supported a genetic component both for PDS and conversion to PG. We review the body of evidence supporting a genetic basis in humans and animal models and reevaluate classical mechanisms of PDS/PG considering this new evidence.
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41
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Hohl DM, Bezus B, Ratowiecki J, Catanesi CI. Genetic and phenotypic variability of iris color in Buenos Aires population. Genet Mol Biol 2018; 41:50-58. [PMID: 29658972 PMCID: PMC5901501 DOI: 10.1590/1678-4685-gmb-2017-0175] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 08/31/2017] [Indexed: 11/21/2022] Open
Abstract
The aim of this work was to describe the phenotypic and genotypic variability related to iris color for the population of Buenos Aires province (Argentina), and to assess the usefulness of current methods of analysis for this country. We studied five Single Nucleotide Polymorphisms (SNPs) included in the IrisPlex kit, in 118 individuals, and we quantified eye color with Digital Iris Analysis Tool. The markers fit Hardy-Weinberg equilibrium for the whole sample, but not for rs12913832 within the group of brown eyes (LR=8.429; p=0.004). We found a remarkable association of HERC2 rs12913832 GG with blue color (p < 0.01) but the other markers did not show any association with iris color. The results for the Buenos Aires population differ from those of other populations of the world for these polymorphisms (p < 0,01). The differences we found might respond to the admixed ethnic composition of Argentina; therefore, methods of analysis used in European populations should be carefully applied when studying the population of Argentina. These findings reaffirm the importance of this investigation in the Argentinian population for people identification based on iris color.
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Affiliation(s)
- Diana María Hohl
- Laboratorio de Diversidad Genética, Instituto Multidisciplinario de Biología Celular IMBICE (CONICET-UNLP-CIC), La Plata, Buenos Aires, Argentina.,Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Brenda Bezus
- Laboratorio de Diversidad Genética, Instituto Multidisciplinario de Biología Celular IMBICE (CONICET-UNLP-CIC), La Plata, Buenos Aires, Argentina
| | - Julia Ratowiecki
- Centro de Estudios Médicos e Investigaciones Clínicas CEMIC CONICET, Buenos Aires, Argentina
| | - Cecilia Inés Catanesi
- Laboratorio de Diversidad Genética, Instituto Multidisciplinario de Biología Celular IMBICE (CONICET-UNLP-CIC), La Plata, Buenos Aires, Argentina.,Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
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42
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Martin AR, Lin M, Granka JM, Myrick JW, Liu X, Sockell A, Atkinson EG, Werely CJ, Möller M, Sandhu MS, Kingsley DM, Hoal EG, Liu X, Daly MJ, Feldman MW, Gignoux CR, Bustamante CD, Henn BM. An Unexpectedly Complex Architecture for Skin Pigmentation in Africans. Cell 2017; 171:1340-1353.e14. [PMID: 29195075 PMCID: PMC5884124 DOI: 10.1016/j.cell.2017.11.015] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 08/13/2017] [Accepted: 11/08/2017] [Indexed: 01/17/2023]
Abstract
Approximately 15 genes have been directly associated with skin pigmentation variation in humans, leading to its characterization as a relatively simple trait. However, by assembling a global survey of quantitative skin pigmentation phenotypes, we demonstrate that pigmentation is more complex than previously assumed, with genetic architecture varying by latitude. We investigate polygenicity in the KhoeSan populations indigenous to southern Africa who have considerably lighter skin than equatorial Africans. We demonstrate that skin pigmentation is highly heritable, but known pigmentation loci explain only a small fraction of the variance. Rather, baseline skin pigmentation is a complex, polygenic trait in the KhoeSan. Despite this, we identify canonical and non-canonical skin pigmentation loci, including near SLC24A5, TYRP1, SMARCA2/VLDLR, and SNX13, using a genome-wide association approach complemented by targeted resequencing. By considering diverse, under-studied African populations, we show how the architecture of skin pigmentation can vary across humans subject to different local evolutionary pressures.
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Affiliation(s)
- Alicia R Martin
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02141, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA 02141, USA.
| | - Meng Lin
- Department of Ecology and Evolution, SUNY Stony Brook, NY 11794, USA
| | - Julie M Granka
- Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Justin W Myrick
- Department of Ecology and Evolution, SUNY Stony Brook, NY 11794, USA
| | | | - Alexandra Sockell
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | | | - Cedric J Werely
- SA MRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Marlo Möller
- SA MRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | | | - David M Kingsley
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Eileen G Hoal
- SA MRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Xiao Liu
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02141, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA 02141, USA
| | - Marcus W Feldman
- Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA
| | | | | | - Brenna M Henn
- Department of Ecology and Evolution, SUNY Stony Brook, NY 11794, USA.
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43
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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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Andrade ES, Fracasso NC, Strazza Júnior PS, Simões AL, Mendes-Junior CT. Associations of OCA2 - HERC2 SNPs and haplotypes with human pigmentation characteristics in the Brazilian population. Leg Med (Tokyo) 2017; 24:78-83. [DOI: 10.1016/j.legalmed.2016.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 11/24/2016] [Accepted: 12/14/2016] [Indexed: 10/20/2022]
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Ludwig CA, Callaway NF, Fredrick DR, Blumenkranz MS, Moshfeghi DM. What colour are newborns' eyes? Prevalence of iris colour in the Newborn Eye Screening Test (NEST) study. Acta Ophthalmol 2016; 94:485-8. [PMID: 27061128 DOI: 10.1111/aos.13006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 01/07/2016] [Indexed: 11/25/2022]
Abstract
PURPOSE This study aims to assess the birth prevalence of iris colour among newborns in a prospective, healthy, full-term newborn cohort. METHODS The Newborn Eye Screening Test (NEST) study is a prospective cohort study conducted at Lucile Packard Children's Hospital at Stanford University School of Medicine. A paediatric vitreoretinal specialist (DMM) reviewed images sent to the Byers Eye Institute telemedicine reading centre and recorded eye colour for every infant screened. Variables were graphed to assess for normality, and frequencies per subject were reported for eye colour, sex, ethnicity and race. RESULTS Among 192 subjects screened in the first year of the NEST study with external images of appropriate quality for visualization of the irides, the birth prevalence of iris colour was 63.0% brown, 20.8% blue, 5.7% green/hazel, 9.9% indeterminate and 0.5% partial heterochromia. The study population was derived from a quaternary care children's hospital. We report the birth prevalence of iris colour among full-term newborns in a diverse prospective cohort. CONCLUSION The study demonstrates a broad range of iris colour prevalence at birth with a predominance of brown iris coloration. Future studies with the NEST cohort will assess the change in iris colour over time and whether the frequencies of eye colour change as the child ages.
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Affiliation(s)
- Cassie A Ludwig
- Byers Eye Institute, Stanford University School of Medicine, Palo Alto, California, USA
| | - Natalia F Callaway
- Byers Eye Institute, Stanford University School of Medicine, Palo Alto, California, USA
| | - Douglas R Fredrick
- Byers Eye Institute, Stanford University School of Medicine, Palo Alto, California, USA
| | - Mark S Blumenkranz
- Byers Eye Institute, Stanford University School of Medicine, Palo Alto, California, USA
| | - Darius M Moshfeghi
- Byers Eye Institute, Stanford University School of Medicine, Palo Alto, California, USA
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Pośpiech E, Karłowska-Pik J, Ziemkiewicz B, Kukla M, Skowron M, Wojas-Pelc A, Branicki W. Further evidence for population specific differences in the effect of DNA markers and gender on eye colour prediction in forensics. Int J Legal Med 2016; 130:923-934. [PMID: 27221533 PMCID: PMC4912978 DOI: 10.1007/s00414-016-1388-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/09/2016] [Indexed: 11/30/2022]
Abstract
The genetics of eye colour has been extensively studied over the past few years, and the identified polymorphisms have been applied with marked success in the field of Forensic DNA Phenotyping. A picture that arises from evaluation of the currently available eye colour prediction markers shows that only the analysis of HERC2-OCA2 complex has similar effectiveness in different populations, while the predictive potential of other loci may vary significantly. Moreover, the role of gender in the explanation of human eye colour variation should not be neglected in some populations. In the present study, we re-investigated the data for 1020 Polish individuals and using neural networks and logistic regression methods explored predictive capacity of IrisPlex SNPs and gender in this population sample. In general, neural networks provided higher prediction accuracy comparing to logistic regression (AUC increase by 0.02–0.06). Four out of six IrisPlex SNPs were associated with eye colour in the studied population. HERC2 rs12913832, OCA2 rs1800407 and SLC24A4 rs12896399 were found to be the most important eye colour predictors (p < 0.007) while the effect of rs16891982 in SLC45A2 was less significant. Gender was found to be significantly associated with eye colour with males having ~1.5 higher odds for blue eye colour comparing to females (p = 0.002) and was ranked as the third most important factor in blue/non-blue eye colour determination. However, the implementation of gender into the developed prediction models had marginal and ambiguous impact on the overall accuracy of prediction confirming that the effect of gender on eye colour in this population is small. Our study indicated the advantage of neural networks in prediction modeling in forensics and provided additional evidence for population specific differences in the predictive importance of the IrisPlex SNPs and gender.
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Affiliation(s)
- Ewelina Pośpiech
- Institute of Zoology, Faculty of Biology and Earth Sciences, Jagiellonian University, Kraków, Poland. .,Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland.
| | - Joanna Karłowska-Pik
- Faculty of Mathematics and Computer Science, Nicolaus Copernicus University, Toruń, Poland
| | - Bartosz Ziemkiewicz
- Faculty of Mathematics and Computer Science, Nicolaus Copernicus University, Toruń, Poland
| | - Magdalena Kukla
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Małgorzata Skowron
- Department of Dermatology, Collegium Medicum of the Jagiellonian University, Kraków, Poland
| | - Anna Wojas-Pelc
- Department of Dermatology, Collegium Medicum of the Jagiellonian University, Kraków, Poland
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
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Andersen JD, Pietroni C, Johansen P, Andersen MM, Pereira V, Børsting C, Morling N. Importance of nonsynonymous OCA2 variants in human eye color prediction. Mol Genet Genomic Med 2016; 4:420-30. [PMID: 27468418 PMCID: PMC4947861 DOI: 10.1002/mgg3.213] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 02/09/2016] [Accepted: 02/12/2016] [Indexed: 11/24/2022] Open
Abstract
Background The color of the eyes is one of the most prominent phenotypes in humans and it is often used to describe the appearance of an individual. The intensity of pigmentation in the iris is strongly associated with one single‐nucleotide polymorphism (SNP), rs12913832:A>G that is located in the promotor region of OCA2 (OMIM #611409). Nevertheless, many eye colors cannot be explained by only considering rs12913832:A>G. Methods In this study, we searched for additional variants in OCA2 to explain human eye color by sequencing a 500 kbp region, encompassing OCA2 and its promotor region. Results We identified three nonsynonymous OCA2 variants as important for eye color, including rs1800407:G>A (p.Arg419Gln) and two variants, rs74653330:A>T (p.Ala481Thr) and rs121918166:G>A (p.Val443Ile), not previously described as important for eye color variation. It was shown that estimated haplotypes consisting of four variants (rs12913832:A>G, rs1800407:G>A (p.Arg419Gln), rs74653330:A>T (p.Ala481Thr), and rs121918166:G>A (p.Val443Ile)) explained 75.6% (adjusted R2 = 0.76) of normal eye color variation, whereas rs12913832:A>G alone explained 68.8% (adjusted R2 = 0.69). Moreover, rs74653330:A>T (p.Ala481Thr) and rs121918166:G>A (p.Val443Ile) had a measurable effect on quantitative skin color (P = 0.008). Conclusion Our data showed that rs74653330:A>T (p.Ala481Thr) and rs121918166:G>A (p.Val443Ile) have a measurable effect on normal pigmentation variation.
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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
| | - Carlotta Pietroni
- Section of Forensic Genetics Department of Forensic Medicine Faculty of Health and Medical Sciences University of Copenhagen DK-2100 Copenhagen Denmark
| | - Peter Johansen
- Section of Forensic Genetics Department of Forensic Medicine Faculty of Health and Medical Sciences University of Copenhagen DK-2100 Copenhagen Denmark
| | - 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
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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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Botezatu A, Puiu M, Cucu N, Diaconu CC, Badiu C, Arsene C, Iancu IV, Plesa A, Anton G. Comparative molecular approaches in Prader–Willi syndrome diagnosis. Gene 2016; 575:353-8. [DOI: 10.1016/j.gene.2015.08.058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 07/27/2015] [Accepted: 08/17/2015] [Indexed: 12/01/2022]
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