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Gelmi MC, Jager MJ. Uveal melanoma: Current evidence on prognosis, treatment and potential developments. Asia Pac J Ophthalmol (Phila) 2024; 13:100060. [PMID: 38641203 DOI: 10.1016/j.apjo.2024.100060] [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: 03/26/2024] [Revised: 04/11/2024] [Accepted: 04/11/2024] [Indexed: 04/21/2024] Open
Abstract
Uveal Melanoma (UM) is a rare disease, yet it is the most common primary intraocular malignancy in adult patients. Despite continuous advancements and research, the risk of metastasis remains high. It is possible to stratify patients according to their risk of metastases using a variety of known risk factors. Even though there is no gold standard for the prognostication of patients with uveal melanoma, it is becoming increasingly clear that combining histo-pathological, patient-related and molecular prognostic markers allows a more accurate prediction of the metastatic risk than by using one parameter. Primary UM in the eye are treated very effectively with eye-sparing radiation-based techniques or enucleation. However, it is not yet possible to prevent or treat metastases with the current therapeutic options. Nonetheless, the efforts to find new therapeutic targets continue and progress is being made, especially in the field of targeted therapy, as exemplified by the anti-gp100 bispecific molecule Tebentafusp. This review delves into the history of uveal melanoma, its incidence, presentation and diagnosis, the known prognostic factors and the treatment options, both for the primary tumour and for metastases. We show that different populations may have different risks for developing UM, and that each country should evaluate their own patients.
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Affiliation(s)
- Maria Chiara Gelmi
- Department of Ophthalmology, Leiden University Medical Center, Leiden, the Netherlands
| | - Martine J Jager
- Department of Ophthalmology, Leiden University Medical Center, Leiden, the Netherlands.
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2
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Rahat MA, Akbar F, Rasool A, Ilyas M, Rakha A, Shams S, Jelani M, Bibi F, Shirah BH, Abdulkareem AA, Naseer MI, Israr M. Phenotypic Classification of Eye Colour and Developmental Validation of the Irisplex System on Population Living in Malakand Division, Pakistan. Biomedicines 2023; 11:biomedicines11041228. [PMID: 37189847 DOI: 10.3390/biomedicines11041228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 04/13/2023] [Accepted: 04/17/2023] [Indexed: 05/17/2023] Open
Abstract
The core objective of forensic DNA typing is developing DNA profiles from biological evidence for personal identification. The present study was designed to check the validation of the IrisPlex system and the Prevalence of eye colour in the Pakhtoon population residing within the Malakand Division. METHODS Eye colour digital photographs and buccal swab samples of 893 individuals of different age groups were collected. Multiplexed SNaPshot single base extension chemistry was used, and the genotypic results were analysed. Snapshot data were used for eye colour prediction through the IrisPlex and FROG-kb tool. RESULTS The results of the present study found brown eye colour to be the most prevalent eye colour in comparison to intermediate and blue coloured. Overall, individuals with brown-coloured eyes possess CT (46.84%) and TT (53.16%) genotypes. Blue eye-coloured individuals are solely of the CC genotype, while individuals of intermediate eye colour carry CT (45.15%) and CC (53.85%) genotypes in rs12913832 SNP in the HERC2 gene. It was also revealed that brown-coloured eyes individuals were dominant among all age groups followed by intermediate and blue. Statistical analysis between particular variables and eye colour showed a significant p-value (<0.05) for rs16891982 SNP in SLC45A2 gene, rs12913832 SNP in HERC2 gene, rs1393350 SNP in SLC45A2, districts and gender. The rest of the SNPs were non-significant with eye colour, respectively. The rs12896399 SNP and SNP rs1800407 were found significant with rs16891982 SNP. The result also demonstrated that the study group differs from the world population based on eye colour. The two eye colour prediction results were compared, and it was discovered that IrisPlex and FROG-Kb had similar higher prediction ratios for Brown and Blue eye colour. CONCLUSIONS The results of the current study revealed brown eye colour to be the most prevalent amongst members of the local population of Pakhtoon ethnicity in the Malakand Division of northern Pakistan. A set of contemporary human DNA samples with known phenotypes are used in this research to evaluate the custom panel's prediction accuracy. With the aid of this forensic test, DNA typing can be supplemented with details about the appearance of the person from whom the sample was taken in cases involving missing persons, ancient human remains, and trace samples. This study may be helpful for future population genetics and forensics studies.
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Affiliation(s)
- Murad Ali Rahat
- Centre for Biotechnology and Microbiology, University of Swat, Charbagh 19120, Pakistan
- Department of Forensic Sciences, University of Swat, Charbagh 19120, Pakistan
| | - Fazal Akbar
- Centre for Biotechnology and Microbiology, University of Swat, Charbagh 19120, Pakistan
| | - Akhtar Rasool
- Centre for Biotechnology and Microbiology, University of Swat, Charbagh 19120, Pakistan
| | - Muhammad Ilyas
- Centre for Omic Sciences, Islamia College University Peshawar, Peshawar 25120, Pakistan
| | - Allah Rakha
- Department of Forensic Sciences, University of Health Sciences, Lahore 54600, Pakistan
| | - Sulaiman Shams
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
| | - Musharraf Jelani
- Centre for Omic Sciences, Islamia College University Peshawar, Peshawar 25120, Pakistan
| | - Fehmida Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Bader H Shirah
- Department of Neuroscience, King Faisal Specialist Hospital & Research Centre, Jeddah 21589, Saudi Arabia
| | - Angham Abdulrhman Abdulkareem
- Faculty of Science, Department of Biochemistry, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Muhammad Imran Naseer
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Muhammad Israr
- Department of Forensic Sciences, University of Swat, Charbagh 19120, Pakistan
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3
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Fernandes B, Cavaco-Paulo A, Matamá T. A Comprehensive Review of Mammalian Pigmentation: Paving the Way for Innovative Hair Colour-Changing Cosmetics. BIOLOGY 2023; 12:biology12020290. [PMID: 36829566 PMCID: PMC9953601 DOI: 10.3390/biology12020290] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/26/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023]
Abstract
The natural colour of hair shafts is formed at the bulb of hair follicles, and it is coupled to the hair growth cycle. Three critical processes must happen for efficient pigmentation: (1) melanosome biogenesis in neural crest-derived melanocytes, (2) the biochemical synthesis of melanins (melanogenesis) inside melanosomes, and (3) the transfer of melanin granules to surrounding pre-cortical keratinocytes for their incorporation into nascent hair fibres. All these steps are under complex genetic control. The array of natural hair colour shades are ascribed to polymorphisms in several pigmentary genes. A myriad of factors acting via autocrine, paracrine, and endocrine mechanisms also contributes for hair colour diversity. Given the enormous social and cosmetic importance attributed to hair colour, hair dyeing is today a common practice. Nonetheless, the adverse effects of the long-term usage of such cosmetic procedures demand the development of new methods for colour change. In this context, case reports of hair lightening, darkening and repigmentation as a side-effect of the therapeutic usage of many drugs substantiate the possibility to tune hair colour by interfering with the biology of follicular pigmentary units. By scrutinizing mammalian pigmentation, this review pinpoints key targetable processes for the development of innovative cosmetics that can safely change the hair colour from the inside out.
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Affiliation(s)
- Bruno Fernandes
- CEB—Centre of Biological Engineering, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
| | - Artur Cavaco-Paulo
- CEB—Centre of Biological Engineering, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
- LABBELS—Associate Laboratory, 4710-057 Braga, Portugal
- Correspondence: (A.C.-P.); (T.M.); Tel.: +351-253-604-409 (A.C.-P.); +351-253-601-599 (T.M.)
| | - Teresa Matamá
- CEB—Centre of Biological Engineering, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
- LABBELS—Associate Laboratory, 4710-057 Braga, Portugal
- Correspondence: (A.C.-P.); (T.M.); Tel.: +351-253-604-409 (A.C.-P.); +351-253-601-599 (T.M.)
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Advancement in Human Face Prediction Using DNA. Genes (Basel) 2023; 14:genes14010136. [PMID: 36672878 PMCID: PMC9858985 DOI: 10.3390/genes14010136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 01/05/2023] Open
Abstract
The rapid improvements in identifying the genetic factors contributing to facial morphology have enabled the early identification of craniofacial syndromes. Similarly, this technology can be vital in forensic cases involving human identification from biological traces or human remains, especially when reference samples are not available in the deoxyribose nucleic acid (DNA) database. This review summarizes the currently used methods for predicting human phenotypes such as age, ancestry, pigmentation, and facial features based on genetic variations. To identify the facial features affected by DNA, various two-dimensional (2D)- and three-dimensional (3D)-scanning techniques and analysis tools are reviewed. A comparison between the scanning technologies is also presented in this review. Face-landmarking techniques and face-phenotyping algorithms are discussed in chronological order. Then, the latest approaches in genetic to 3D face shape analysis are emphasized. A systematic review of the current markers that passed the threshold of a genome-wide association (GWAS) of single nucleotide polymorphism (SNP)-face traits from the GWAS Catalog is also provided using the preferred reporting items for systematic reviews and meta-analyses (PRISMA), approach. Finally, the current challenges in forensic DNA phenotyping are analyzed and discussed.
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Demars J, Labrune Y, Iannuccelli N, Deshayes A, Leroux S, Gilbert H, Aymard P, Benitez F, Riquet J. A genome-wide epistatic network underlies the molecular architecture of continuous color variation of body extremities. Genomics 2022; 114:110361. [PMID: 35378242 DOI: 10.1016/j.ygeno.2022.110361] [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: 11/17/2021] [Revised: 03/22/2022] [Accepted: 03/29/2022] [Indexed: 01/14/2023]
Abstract
Deciphering the molecular architecture of coat coloration for a better understanding of the biological mechanisms underlying pigmentation still remains a challenge. We took advantage of a rabbit French experimental population in which both a pattern and a gradient of coloration from white to brown segregated within the himalayan phenotype. The whole experimental design was genotyped using the high density Affymetrix® AxiomOrcun™ SNP Array and phenotyped into 6 different groups ordered from the lighter to the darker. Genome-wide association analyses pinpointed an oligogenic determinism, under recessive and additive inheritance, involving genes already known in melanogenesis (ASIP, KIT, MC1R, TYR), and likely processed pseudogenes linked to ribosomal function, RPS20 and RPS14. We also identified (i) gene-gene interactions through ASIP:MC1R affecting light cream/beige phenotypes while KIT:RPS responsible of dark chocolate/brown colors and (ii) a genome-wide epistatic network involving several others coloration genes such as POT1 or HPS5. Finally, we determined the recessive inheritance of the English spotting phenotype likely involving a copy number variation affecting at least the end of the coding sequence of the KIT gene. Our analyses of coloration as a continuous trait allowed us to go beyond much of the established knowledge through the detection of additional genes and gene-gene interactions that may contribute to the molecular architecture of the coloration phenotype.
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Affiliation(s)
- Julie Demars
- GenPhySE, Université de Toulouse, INRAE, ENVT, Toulouse INP, F-31326 Castanet-Tolosan, France.
| | - Yann Labrune
- GenPhySE, Université de Toulouse, INRAE, ENVT, Toulouse INP, F-31326 Castanet-Tolosan, France.
| | - Nathalie Iannuccelli
- GenPhySE, Université de Toulouse, INRAE, ENVT, Toulouse INP, F-31326 Castanet-Tolosan, France.
| | - Alice Deshayes
- UMR967, CEA, INSERM, Institut de Radiobiologie Cellulaire et Moléculaire, Télomères et réparation du chromosome, F- 92265 Fontenay-aux-Roses, France.
| | - Sophie Leroux
- GenPhySE, Université de Toulouse, INRAE, ENVT, Toulouse INP, F-31326 Castanet-Tolosan, France.
| | - Hélène Gilbert
- GenPhySE, Université de Toulouse, INRAE, ENVT, Toulouse INP, F-31326 Castanet-Tolosan, France.
| | - Patrick Aymard
- GenPhySE, Université de Toulouse, INRAE, ENVT, Toulouse INP, F-31326 Castanet-Tolosan, France.
| | - Florence Benitez
- GenPhySE, Université de Toulouse, INRAE, ENVT, Toulouse INP, F-31326 Castanet-Tolosan, France.
| | - Juliette Riquet
- GenPhySE, Université de Toulouse, INRAE, ENVT, Toulouse INP, F-31326 Castanet-Tolosan, France.
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Tian C, Duan L, Fu C, He J, Dai J, Zhu G. Study on the Correlation Between Iris Characteristics and Schizophrenia. Neuropsychiatr Dis Treat 2022; 18:811-820. [PMID: 35431547 PMCID: PMC9005354 DOI: 10.2147/ndt.s361614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/01/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Recently, researchers have conducted many studies on the potential contribution of the retina and other eye structures on schizophrenia. This study aimed to evaluate differences in iris characteristics between patients with schizophrenia and healthy individuals so as to find more easily accessible and easily measurable biomarkers with a view to improving clinical assessments and furthering our understanding of the disease. METHODS Overall, 80 patients with schizophrenia and 52 healthy individuals were included in the case group and the control group, respectively. Iris images were collected from all subjects to compare differences in the structure and color of the iris. The Positive and Negative Symptom Scale (PANSS) and the Modified Overt Aggression Scale (MOAS) were used to evaluate the clinical symptoms and characteristics of 45 first-episode untreated schizophrenics, and analyzed correlations between iris characteristics and schizophrenia symptoms. RESULTS There were significant differences in iris crypts (P<0.05) and pigment spots (P<0.01) between the case and control group, but no significant difference was found in iris wrinkles (P<0.05). The logistic regression analysis demonstrated that the total iris crypts [odds ratio (OR) 1.166, 95% confidence interval (CI) 1.022-1.330] and total iris pigment spots (OR 1.815, 95% CI 1.186-2.775) increased the risk of suffering from schizophrenia. Furthermore, it was demonstrated that the number of iris crypts was positively associated with the MOAS score (r=0.474, P<0.01). Moreover, the number of the iris pigment spots (r=0.395, P<0.01) and wrinkles (r=0.309, P<0.05) were positively correlated with the subjects' negative symptom scores, respectively. CONCLUSION Iris crypts and pigment spots were identified as potential biomarkers for detecting schizophrenia. In patients with first-episode untreated schizophrenia, iris characteristics may help psychiatrists to identify the illness and its severity, and to detect characteristic clinical symptoms.
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Affiliation(s)
- Chunsheng Tian
- Department of Psychiatry, The First Affiliated Hospital of China Medical University, Shenyang, 110001, People's Republic of China.,Shenyang Mental Health Center, Shenyang, 110168, People's Republic of China
| | - Li Duan
- Department of Psychiatry, The First Affiliated Hospital of China Medical University, Shenyang, 110001, People's Republic of China.,School of Nursing, Chengde Medical University, Chengde, 067000, People's Republic of China
| | - Chunfeng Fu
- Department of Psychiatry, The First Affiliated Hospital of China Medical University, Shenyang, 110001, People's Republic of China
| | - Juan He
- Department of Psychiatry, The First Affiliated Hospital of China Medical University, Shenyang, 110001, People's Republic of China
| | - Jiali Dai
- Department of Psychiatry, The First Affiliated Hospital of China Medical University, Shenyang, 110001, People's Republic of China
| | - Gang Zhu
- Department of Psychiatry, The First Affiliated Hospital of China Medical University, Shenyang, 110001, People's Republic of China
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7
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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: 18] [Impact Index Per Article: 6.0] [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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8
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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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9
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Nascimento AV, Cardoso DF, Santos DJA, Romero ARS, Scalez DCB, Borquis RRA, Neto FRA, Gondro C, Tonhati H. Inbreeding coefficients and runs of homozygosity islands in Brazilian water buffalo. J Dairy Sci 2020; 104:1917-1927. [PMID: 33272579 DOI: 10.3168/jds.2020-18397] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 09/10/2020] [Indexed: 01/03/2023]
Abstract
Characterization of autozygosity is relevant to monitor genetic diversity and manage inbreeding levels in breeding programs. Identification of autozygosity hotspots can unravel genomic regions targeted by selection for economically important traits and can help identify candidate genes for selection. In this study, we estimated the inbreeding levels of a Brazilian population of Murrah buffalo undergoing selection for milk production traits, particularly milk yield. We also studied the distribution of runs of homozygosity (ROH) islands and identified putative genes and quantitative trait loci (QTL) under selection. We genotyped 422 Murrah buffalo for 51,611 SNP; 350 of these had ROH longer than 10 Mb, indicating the occurrence of inbreeding in the last 5 generations. The mean length of the ROH per animal was 4.28 ± 1.85 Mb. Inbreeding coefficients were calculated from the genomic relationship matrix, the pedigree, and the ROH, with estimates varying between 0.242 and 0.035. Inbreeding estimates from the pedigree had a low correlation with the genomic estimates, and estimates from the genomic relationship matrix were much higher than those from the pedigree or the ROH. Signatures of selection were identified in 6 genomic regions, located on chromosomes 1, 2, 3, 5, 16, and 18, encompassing a total of 190 genes and 174 QTL. Many of the genes (e.g., APRT and ACSF3) and QTL identified are related to milk production traits, such as milk yield, milk fat yield and percentage, and milk protein yield and percentage. Other genes are associated with reproduction and immune response traits as well as morphological aspects of the buffalo species. Inbreeding levels in this population are still low but are increasing due to selection and should be managed to avoid future losses due to inbreeding depression. The proximity of genes linked to milk production traits with genes associated with reproduction and immune system traits suggests the need to include these latter genes in the breeding program to avoid negatively affecting them due to selection for production traits.
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Affiliation(s)
- A V Nascimento
- Department of Animal Science, São Paulo State University (UNESP), Jaboticabal, 14884900, Brazil
| | - D F Cardoso
- Department of Animal Science, São Paulo State University (UNESP), Jaboticabal, 14884900, Brazil
| | - D J A Santos
- Department of Animal Science, University of Maryland, College Park 20742
| | - A R S Romero
- Department of Animal Science, São Paulo State University (UNESP), Jaboticabal, 14884900, Brazil
| | - D C B Scalez
- Department of Animal Science, São Paulo State University (UNESP), Jaboticabal, 14884900, Brazil
| | - R R A Borquis
- College of Agricultural Sciences, Federal University of Grande Dourados (UFGD), Dourados, 79804970, Brazil
| | - F R A Neto
- Goiano Federal Institute, Campus Rio Verde, Rio Verde, 75909120, Brazil
| | - C Gondro
- Department of Animal Science, Michigan State University, East Lansing 48824
| | - H Tonhati
- Department of Animal Science, São Paulo State University (UNESP), Jaboticabal, 14884900, Brazil.
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10
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Wu Z, Ioannidis NM, Zou J. Predicting target genes of non-coding regulatory variants with IRT. Bioinformatics 2020; 36:4440-4448. [PMID: 32330225 DOI: 10.1093/bioinformatics/btaa254] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/15/2020] [Accepted: 04/17/2020] [Indexed: 11/14/2022] Open
Abstract
SUMMARY Interpreting genetic variants of unknown significance (VUS) is essential in clinical applications of genome sequencing for diagnosis and personalized care. Non-coding variants remain particularly difficult to interpret, despite making up a large majority of trait associations identified in genome-wide association studies (GWAS) analyses. Predicting the regulatory effects of non-coding variants on candidate genes is a key step in evaluating their clinical significance. Here, we develop a machine-learning algorithm, Inference of Connected expression quantitative trait loci (eQTLs) (IRT), to predict the regulatory targets of non-coding variants identified in studies of eQTLs. We assemble datasets using eQTL results from the Genotype-Tissue Expression (GTEx) project and learn to separate positive and negative pairs based on annotations characterizing the variant, gene and the intermediate sequence. IRT achieves an area under the receiver operating characteristic curve (ROC-AUC) of 0.799 using random cross-validation, and 0.700 for a more stringent position-based cross-validation. Further evaluation on rare variants and experimentally validated regulatory variants shows a significant enrichment in IRT identifying the true target genes versus negative controls. In gene-ranking experiments, IRT achieves a top-1 accuracy of 50% and top-3 accuracy of 90%. Salient features, including GC-content, histone modifications and Hi-C interactions are further analyzed and visualized to illustrate their influences on predictions. IRT can be applied to any VUS of interest and each candidate nearby gene to output a score reflecting the likelihood of regulatory effect on the expression level. These scores can be used to prioritize variants and genes to assist in patient diagnosis and GWAS follow-up studies. AVAILABILITY AND IMPLEMENTATION Codes and data used in this work are available at https://github.com/miaecle/eQTL_Trees. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zhenqin Wu
- Department of Chemistry, Stanford University, CA 94305, USA.,Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, 94305 CA, USA
| | - Nilah M Ioannidis
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, 94305 CA, USA
| | - James Zou
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, 94305 CA, USA.,Chan-Zuckerberg Biohub, San Francisco, 94158 CA, USA
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Al-Rashedi NA, Mandal AM, ALObaidi LAH. Eye color prediction using the IrisPlex system: a limited pilot study in the Iraqi population. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2020. [DOI: 10.1186/s41935-020-00200-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Abstract
Background
Forensic DNA phenotyping has gained momentum in the recent past due to the prediction of externally visible characters (EVCs) from the biological sample. The most common phenotypes like eye, hair, and skin color are predicted from the biological samples using a web-based system called IrisPlex. Based on six genetic SNPs, the IrisPlex system is developed and validated for its prediction accuracy in diverse ethnic groups worldwide. In previous studies, this system proved to have significant prediction accuracy. The EVCs vary substantially based on different geographical locations. Hence, the objective of this study was to validate the accuracy of the IrisPlex system in predicting the eye colors in the Iraqi population.
Methods
Six genetic single-nucleotide polymorphisms SNPs (HERC2-rs12913832, OCA2- rs1800407, SLC24A4-rs12896399, SLC45A2- rs16891982, TYR-rs1393350, and IRF4- rs12203592) in 58 Iraqi subjects were performed using Sequenom MassARRAY Genotyping. According to Liu et al., a predicted probability of 0.7 was considered as the threshold.
Results
Participants in this study of brown color were observed in 44.83%, intermediate in 43.1%, and blue in 12.07%. Completely predictive accuracy is obtained in 1; we observed the AUC at threshold 0.7 was 0.91 for brown, 0.79 for blue, and 0.60 for intermediate eye color. The sensitivity was 42.85% for blue, 0% for intermediate eye color, and 100% for brown-colored eye. Specificity was 100% for blue, 100% for intermediate, and 78.13% for brown eye color.
Conclusion
Hence, it was concluded that the prediction accuracy of the IrisPlex system for blue and brown color eye in the Iraqi population is significant in the studied population size. However, a pivotal study with larger sample size is required to represent the prediction accuracy of the IrisPlex system in the whole Iraqi population.
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12
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García-Cano J, Martinez-Martinez A, Sala-Gaston J, Pedrazza L, Rosa JL. HERCing: Structural and Functional Relevance of the Large HERC Ubiquitin Ligases. Front Physiol 2019; 10:1014. [PMID: 31447701 PMCID: PMC6692442 DOI: 10.3389/fphys.2019.01014] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 07/23/2019] [Indexed: 12/12/2022] Open
Abstract
Homologous to the E6AP carboxyl terminus (HECT) and regulator of chromosome condensation 1 (RCC1)-like domain-containing proteins (HERCs) belong to the superfamily of ubiquitin ligases. HERC proteins are divided into two subfamilies, Large and Small HERCs. Despite their similarities in terms of both structure and domains, these subfamilies are evolutionarily very distant and result from a convergence phenomenon rather than from a common origin. Large HERC genes, HERC1 and HERC2, are present in most metazoan taxa. They encode very large proteins (approximately 5,000 amino acid residues in a single polypeptide chain) that contain more than one RCC1-like domain as a structural characteristic. Accumulating evidences show that these unusually large proteins play key roles in a wide range of cellular functions which include neurodevelopment, DNA damage repair, and cell proliferation. To better understand the origin, evolution, and function of the Large HERC family, this minireview provides with an integrated overview of their structure and function and details their physiological implications. This study also highlights and discusses how dysregulation of these proteins is associated with severe human diseases such as neurological disorders and cancer.
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Affiliation(s)
- Jesús García-Cano
- Ubiquitylation and Cell Signalling Lab, IDIBELL, Departament de Ciències Fisiològiques, Universitat de Barcelona, Barcelona, Spain
| | - Arturo Martinez-Martinez
- Ubiquitylation and Cell Signalling Lab, IDIBELL, Departament de Ciències Fisiològiques, Universitat de Barcelona, Barcelona, Spain
| | - Joan Sala-Gaston
- Ubiquitylation and Cell Signalling Lab, IDIBELL, Departament de Ciències Fisiològiques, Universitat de Barcelona, Barcelona, Spain
| | - Leonardo Pedrazza
- Ubiquitylation and Cell Signalling Lab, IDIBELL, Departament de Ciències Fisiològiques, Universitat de Barcelona, Barcelona, Spain
| | - Jose Luis Rosa
- Ubiquitylation and Cell Signalling Lab, IDIBELL, Departament de Ciències Fisiològiques, Universitat de Barcelona, Barcelona, Spain
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Lona-Durazo F, Hernandez-Pacheco N, Fan S, Zhang T, Choi J, Kovacs MA, Loftus SK, Le P, Edwards M, Fortes-Lima CA, Eng C, Huntsman S, Hu D, Gómez-Cabezas EJ, Marín-Padrón LC, Grauholm J, Mors O, Burchard EG, Norton HL, Pavan WJ, Brown KM, Tishkoff S, Pino-Yanes M, Beleza S, Marcheco-Teruel B, Parra EJ. Meta-analysis of GWA studies provides new insights on the genetic architecture of skin pigmentation in recently admixed populations. BMC Genet 2019; 20:59. [PMID: 31315583 PMCID: PMC6637524 DOI: 10.1186/s12863-019-0765-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/08/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Association studies in recently admixed populations are extremely useful to identify the genetic architecture of pigmentation, due to their high genotypic and phenotypic variation. However, to date only four Genome-Wide Association Studies (GWAS) have been carried out in these populations. RESULTS We present a GWAS of skin pigmentation in an admixed sample from Cuba (N = 762). Additionally, we conducted a meta-analysis including the Cuban sample, and admixed samples from Cape Verde, Puerto Rico and African-Americans from San Francisco. This meta-analysis is one of the largest efforts so far to characterize the genetic basis of skin pigmentation in admixed populations (N = 2,104). We identified five genome-wide significant regions in the meta-analysis, and explored if the markers observed in these regions are associated with the expression of relevant pigmentary genes in human melanocyte cultures. In three of the regions identified in the meta-analysis (SLC24A5, SLC45A2, and GRM5/TYR), the association seems to be driven by non-synonymous variants (rs1426654, rs16891982, and rs1042602, respectively). The rs16891982 polymorphism is strongly associated with the expression of the SLC45A2 gene. In the GRM5/TYR region, in addition to the rs1042602 non-synonymous SNP located on the TYR gene, variants located in the nearby GRM5 gene have an independent effect on pigmentation, possibly through regulation of gene expression of the TYR gene. We also replicated an association recently described near the MFSD12 gene on chromosome 19 (lead variant rs112332856). Additionally, our analyses support the presence of multiple signals in the OCA2/HERC2/APBA2 region on chromosome 15. A clear causal candidate is the HERC2 intronic variant rs12913832, which has a profound influence on OCA2 expression. This variant has pleiotropic effects on eye, hair, and skin pigmentation. However, conditional and haplotype-based analyses indicate the presence of other variants with independent effects on melanin levels in OCA2 and APBA2. Finally, a follow-up of genome-wide signals identified in a recent GWAS for tanning response indicates that there is a substantial overlap in the genetic factors influencing skin pigmentation and tanning response. CONCLUSIONS Our meta-analysis of skin pigmentation GWAS in recently admixed populations provides new insights about the genetic architecture of this complex trait.
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Affiliation(s)
- Frida Lona-Durazo
- Department of Anthropology, University of Toronto at Mississauga, Health Sciences Complex, room 352, Mississauga, Ontario, L5L 1C6, Canada
| | - Natalia Hernandez-Pacheco
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Shaohua Fan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Tongwu Zhang
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, USA
| | - Jiyeon Choi
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, USA
| | - Michael A Kovacs
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, USA
| | - Stacie K Loftus
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, USA
| | - Phuong Le
- Department of Anthropology, University of Toronto at Mississauga, Health Sciences Complex, room 352, Mississauga, Ontario, L5L 1C6, Canada
| | - Melissa Edwards
- Department of Anthropology, University of Toronto at Mississauga, Health Sciences Complex, room 352, Mississauga, Ontario, L5L 1C6, Canada
| | - Cesar A Fortes-Lima
- Evolutionary Anthropology Team, Laboratory Eco-Anthropology and Ethno-Biology UMR7206, CNRS-MNHN-University Paris Diderot, Musée de l'Homme, Paris, France.,Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Celeste Eng
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Scott Huntsman
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Donglei Hu
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | | | | | - Jonas Grauholm
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Ole Mors
- Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus University, Aarhus, Denmark.,Psychiatric Department, Aarhus University Hospital, Aarhus, Denmark
| | - Esteban G Burchard
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Heather L Norton
- Department of Anthropology, University of Cincinnati, Cincinnati, USA
| | - William J Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, USA
| | - Kevin M Brown
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, USA
| | - Sarah Tishkoff
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.,Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Maria Pino-Yanes
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, La Laguna, Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Sandra Beleza
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, UK
| | | | - Esteban J Parra
- Department of Anthropology, University of Toronto at Mississauga, Health Sciences Complex, room 352, Mississauga, Ontario, L5L 1C6, Canada.
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14
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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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15
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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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16
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Kukla-Bartoszek M, Pośpiech E, Spólnicka M, Karłowska-Pik J, Strapagiel D, Żądzińska E, Rosset I, Sobalska-Kwapis M, Słomka M, Walsh S, Kayser M, Sitek A, Branicki W. Investigating the impact of age-depended hair colour darkening during childhood on DNA-based hair colour prediction with the HIrisPlex system. Forensic Sci Int Genet 2018; 36:26-33. [DOI: 10.1016/j.fsigen.2018.06.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 05/12/2018] [Accepted: 06/06/2018] [Indexed: 12/14/2022]
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17
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Klaassen H, Wang Y, Adamski K, Rohner N, Kowalko JE. CRISPR mutagenesis confirms the role of oca2 in melanin pigmentation in Astyanax mexicanus. Dev Biol 2018; 441:313-318. [DOI: 10.1016/j.ydbio.2018.03.014] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 03/08/2018] [Accepted: 03/14/2018] [Indexed: 01/02/2023]
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18
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Pośpiech E, Chen Y, Kukla-Bartoszek M, Breslin K, Aliferi A, Andersen JD, Ballard D, Chaitanya L, Freire-Aradas A, van der Gaag KJ, Girón-Santamaría L, Gross TE, Gysi M, Huber G, Mosquera-Miguel A, Muralidharan C, Skowron M, Carracedo Á, Haas C, Morling N, Parson W, Phillips C, Schneider PM, Sijen T, Syndercombe-Court D, Vennemann M, Wu S, Xu S, Jin L, Wang S, Zhu G, Martin NG, Medland SE, Branicki W, Walsh S, Liu F, Kayser M. Towards broadening Forensic DNA Phenotyping beyond pigmentation: Improving the prediction of head hair shape from DNA. Forensic Sci Int Genet 2018; 37:241-251. [PMID: 30268682 DOI: 10.1016/j.fsigen.2018.08.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 07/18/2018] [Accepted: 08/27/2018] [Indexed: 10/28/2022]
Abstract
Human head hair shape, commonly classified as straight, wavy, curly or frizzy, is an attractive target for Forensic DNA Phenotyping and other applications of human appearance prediction from DNA such as in paleogenetics. The genetic knowledge underlying head hair shape variation was recently improved by the outcome of a series of genome-wide association and replication studies in a total of 26,964 subjects, highlighting 12 loci of which 8 were novel and introducing a prediction model for Europeans based on 14 SNPs. In the present study, we evaluated the capacity of DNA-based head hair shape prediction by investigating an extended set of candidate SNP predictors and by using an independent set of samples for model validation. Prediction model building was carried out in 9674 subjects (6068 from Europe, 2899 from Asia and 707 of admixed European and Asian ancestries), used previously, by considering a novel list of 90 candidate SNPs. For model validation, genotype and phenotype data were newly collected in 2415 independent subjects (2138 Europeans and 277 non-Europeans) by applying two targeted massively parallel sequencing platforms, Ion Torrent PGM and MiSeq, or the MassARRAY platform. A binomial model was developed to predict straight vs. non-straight hair based on 32 SNPs from 26 genetic loci we identified as significantly contributing to the model. This model achieved prediction accuracies, expressed as AUC, of 0.664 in Europeans and 0.789 in non-Europeans; the statistically significant difference was explained mostly by the effect of one EDAR SNP in non-Europeans. Considering sex and age, in addition to the SNPs, slightly and insignificantly increased the prediction accuracies (AUC of 0.680 and 0.800, respectively). Based on the sample size and candidate DNA markers investigated, this study provides the most robust, validated, and accurate statistical prediction models and SNP predictor marker sets currently available for predicting head hair shape from DNA, providing the next step towards broadening Forensic DNA Phenotyping beyond pigmentation traits.
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Affiliation(s)
- Ewelina Pośpiech
- Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Gronostajowa st. 9, 30-387, Kraków, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa st. 7A, 30-387, Kraków, Poland
| | - Yan Chen
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beichen West Road 1-104, Chaoyang, Beijing, 100101, PR China; University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan, Beijing, 100049, PR China
| | - Magdalena Kukla-Bartoszek
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa st. 7, 30-387, Kraków, Poland
| | - Krystal Breslin
- Department of Biology, Indiana University Purdue University Indianapolis (IUPUI), IN, USA
| | - Anastasia Aliferi
- King's Forensics, Faculty of Life Sciences and Medicine, King's College London, 150 Stamford Street, London, United Kingdom
| | - Jeppe D Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, DK-2100, Copenhagen, Denmark
| | - David Ballard
- King's Forensics, Faculty of Life Sciences and Medicine, King's College London, 150 Stamford Street, London, United Kingdom
| | - Lakshmi Chaitanya
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, Netherlands
| | - Ana Freire-Aradas
- Institute of Legal Medicine, Medical Faculty, University of Cologne, Melatengürtel 60/62, D-50823, Cologne, Germany; Forensic Genetics Unit, Institute of Forensic Sciences, R/ San Francisco s/n, Faculty of Medicine, 15782, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Kristiaan J van der Gaag
- Division of Biological Traces, Netherlands Forensic Institute, P.O. Box 24044, 2490 AA, The Hague, The Netherlands
| | - Lorena Girón-Santamaría
- Forensic Genetics Unit, Institute of Forensic Sciences, R/ San Francisco s/n, Faculty of Medicine, 15782, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Theresa E Gross
- Institute of Legal Medicine, Medical Faculty, University of Cologne, Melatengürtel 60/62, D-50823, Cologne, Germany
| | - Mario Gysi
- Zurich Institute of Forensic Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Gabriela Huber
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstrasse 44, 6020, Innsbruck, Austria
| | - Ana Mosquera-Miguel
- Forensic Genetics Unit, Institute of Forensic Sciences, R/ San Francisco s/n, Faculty of Medicine, 15782, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Charanya Muralidharan
- Department of Biology, Indiana University Purdue University Indianapolis (IUPUI), IN, USA
| | - Małgorzata Skowron
- Department of Dermatology, Collegium Medicum of the Jagiellonian University, Skawińska st. 8, 31-066, Kraków, Poland
| | - Ángel Carracedo
- Forensic Genetics Unit, Institute of Forensic Sciences, R/ San Francisco s/n, Faculty of Medicine, 15782, University of Santiago de Compostela, Santiago de Compostela, Spain; Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, KSA, Saudi Arabia
| | - Cordula Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, DK-2100, Copenhagen, Denmark
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstrasse 44, 6020, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, 13 Thomas Building, University Park, PA, 16802, USA
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, R/ San Francisco s/n, Faculty of Medicine, 15782, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Peter M Schneider
- Institute of Legal Medicine, Medical Faculty, University of Cologne, Melatengürtel 60/62, D-50823, Cologne, Germany
| | - Titia Sijen
- Division of Biological Traces, Netherlands Forensic Institute, P.O. Box 24044, 2490 AA, The Hague, The Netherlands
| | - Denise Syndercombe-Court
- King's Forensics, Faculty of Life Sciences and Medicine, King's College London, 150 Stamford Street, London, United Kingdom
| | - Marielle Vennemann
- Institute of Legal Medicine, University of Münster, Röntgenstr. 23, 48149, Münster, Germany
| | - Sijie Wu
- University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan, Beijing, 100049, PR China; Chinese Academy of Sciences Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road Shanghai, 200031, PR China
| | - Shuhua Xu
- University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan, Beijing, 100049, PR China; Chinese Academy of Sciences Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road Shanghai, 200031, PR 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, 2005 Song Hu Road Shanghai, 200438, PR China; School of Life Science and Technology, Shanghai-Tech University, 393 Middle Huaxia Road, Pudong, Shanghai, 201210, PR China
| | - Li Jin
- Chinese Academy of Sciences Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road Shanghai, 200031, PR 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, 2005 Song Hu Road Shanghai, 200438, PR China
| | - Sijia Wang
- University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan, Beijing, 100049, PR China; Chinese Academy of Sciences Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road Shanghai, 200031, PR 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, 2005 Song Hu Road Shanghai, 200438, PR China
| | - Ghu Zhu
- Queensland Institute of Medical Research, Royal Brisbane Hospital, QLD 4029, Brisbane, Australia
| | - Nick G Martin
- Queensland Institute of Medical Research, Royal Brisbane Hospital, QLD 4029, Brisbane, Australia
| | - Sarah E Medland
- Queensland Institute of Medical Research, Royal Brisbane Hospital, QLD 4029, Brisbane, Australia
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa st. 7A, 30-387, Kraków, Poland
| | - Susan Walsh
- Department of Biology, Indiana University Purdue University Indianapolis (IUPUI), IN, USA
| | - Fan Liu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beichen West Road 1-104, Chaoyang, Beijing, 100101, PR China; University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan, Beijing, 100049, PR China; Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, Netherlands
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, Netherlands.
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19
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Hernando B, Sanz-Page E, Pitarch G, Mahiques L, Valcuende-Cavero F, Martinez-Cadenas C. Genetic variants associated with skin photosensitivity in a southern European population from Spain. PHOTODERMATOLOGY PHOTOIMMUNOLOGY & PHOTOMEDICINE 2018; 34:415-422. [PMID: 29974532 DOI: 10.1111/phpp.12412] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/04/2018] [Accepted: 06/29/2018] [Indexed: 12/18/2022]
Abstract
BACKGROUND/PURPOSE Recent GWAS studies, mostly performed in populations of North European origin, have identified the genetic loci associated with pigmentation, sun sensitivity, freckling and skin cancer susceptibility. Here, we aimed at addressing the genetic determinants of sunlight sensitivity in Spain, a southern European population. METHODS Nine SNPs located in 8 pigmentation-related genes (IRF4, TYR, ASP, HERC2, OCA2, BNC2, SLC24A4 and SLC45A2) were genotyped in 456 Spaniards. Additionally, the complete sequence of the MC1R gene was obtained, testing each nonsynonymous mutation supported by the classification as R or r alleles. A standardised questionnaire was used to collect demographic characteristics, pigmentation and sun sensitivity traits, as well as sun exposure habits. RESULTS MC1R R alleles and IRF4 rs12203592 were significantly associated with sunlight sensitivity at the Bonferroni-corrected level (P-value < 4.54 × 10-3 ). Genetic variants in SLC45A2 (rs16891982) and HERC2 (rs12913832) were also found to be significantly associated with skin photosensitivity in our Spanish sample. Interaction analysis using the MDR method revealed epistatic effects when these four variants were considered together. CONCLUSION MC1R, IRF4, HERC2 and SLC45A2 play a significant role in skin sensitivity to sunlight in the Spanish population. Moreover, interaction among these four loci seems to modulate the ability of the skin to respond to UV radiation.
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Affiliation(s)
- Barbara Hernando
- Department of Medicine, Jaume I University of Castellon, Castellon, Spain
| | - Elena Sanz-Page
- Department of Medicine, Jaume I University of Castellon, Castellon, Spain
| | - Gerard Pitarch
- Department of Dermatology, Castellon University General Hospital, Castellon, Spain
| | - Laura Mahiques
- Department of Dermatology, Castellon University General Hospital, Castellon, Spain
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20
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Is Eye Color Related to Dental Injection Pain? A Prospective, Randomized, Single-blind Study. J Endod 2018; 44:734-737. [DOI: 10.1016/j.joen.2018.01.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/12/2018] [Accepted: 01/19/2018] [Indexed: 01/20/2023]
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21
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Zar MS, Shahid AA, Shahzad MS, Shin KJ, Lee HY, Lee SS, Israr M, Wiegand P, Kulstein G. Forensic SNP Genotyping with SNaPshot: Development of a Novel In-house SBE Multiplex SNP Assay,. J Forensic Sci 2018; 63:1824-1829. [DOI: 10.1111/1556-4029.13783] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 02/12/2018] [Accepted: 02/28/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Mian Sahib Zar
- Center for Synthetic Biology Engineering Research (CSynBER); Shenzhen Institute of Advanced Technology; Chinese Academy of Sciences; 1068 Xuevuan Avenue Shenzhen University Town, Shenzhen China
- National Lab and CAS Center of Excellence for Biomacromolecules; Institute of Biophysics; Chinese Academy of Sciences; Beijing 100101 China
- Department of Forensic Sciences; University of Health Sciences; Lahore Pakistan
- Centre of Excellence in Molecular Biology (CEMB); University of the Punjab; Lahore Pakistan
- Department of Forensic Medicine; Yonsei University College of Medicine; Seoul South Korea
| | - Ahmad Ali Shahid
- Centre of Excellence in Molecular Biology (CEMB); University of the Punjab; Lahore Pakistan
| | - Muhammad Saqib Shahzad
- Centre of Excellence in Molecular Biology (CEMB); University of the Punjab; Lahore Pakistan
| | - Kyoung-Jin Shin
- Department of Forensic Medicine; Yonsei University College of Medicine; Seoul South Korea
| | - Hwan Young Lee
- Department of Forensic Medicine; Yonsei University College of Medicine; Seoul South Korea
| | - Sang-Seob Lee
- Section of Forensic Odontology; Medical Examiner's Office; National Forensic Service; 10 Ipchun-ro Wonju Gangwon-do Republic of Korea
| | - Muhammad Israr
- Department of Forensic Studies; University of Swat; Swat Khyber Pakhtunkhwa Pakistan
| | - Peter Wiegand
- Institute of Legal Medicine; Ulm University; Medical Center; Albert-Einstein-Allee 23; Ulm Germany 89081
| | - Galina Kulstein
- Institute of Legal Medicine; Ulm University; Medical Center; Albert-Einstein-Allee 23; Ulm Germany 89081
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22
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Sarkar A, Nandineni MR. Association of common genetic variants with human skin color variation in Indian populations. Am J Hum Biol 2017; 30. [PMID: 28984396 DOI: 10.1002/ajhb.23068] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 08/21/2017] [Accepted: 09/21/2017] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES Human skin color is one of the most conspicuously variable physical traits that has attracted the attention of physical anthropologists, social scientists and human geneticists. Although several studies have established the underlying genes and their variants affecting human skin color, they were mostly confined to Europeans and Africans and similar studies in Indian populations have been scanty. Studying the association between candidate genetic variants and skin color will help to validate previous findings and to better understand the molecular mechanism of skin color variation. METHODS In this study, 22 candidate SNPs from 12 genes were tested for association with skin color in 299 unrelated samples sourced from nine geographical locations in India. RESULTS Our study establishes the association of 9 SNPs with the phenotype in Indian populations and could explain ∼31% of the variance in skin color. Haplotype analysis of chromosome 15 revealed a significant association of alleles G, A and C of SNPs rs1426654, rs11070627, and rs12913316, respectively, to the phenotype, and accounted for 17% of the variance. Latitude of the sampling location was also a significant factor, contributing to ∼19% of the variation observed in the samples. CONCLUSIONS These observations support the findings that rs1426654 and rs4775730 located in SLC24A5, and rs11070627 and rs12913316 located in MYEF2 and CTXN2 genes respectively, are major contributors toward skin pigmentation and would aid in further unraveling the genotype-phenotype association in Indian populations. These findings can be utilized in forensic DNA applications for criminal investigations.
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Affiliation(s)
- Anujit Sarkar
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, Telangana, 500001, India.,Graduate studies, Manipal University, Manipal, 576104, India
| | - Madhusudan R Nandineni
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, Telangana, 500001, India.,Laboratory of DNA Fingerprinting Services, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, Telangana, 500001, India
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23
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Robinson JK, Penedo FJ, Hay JL, Jablonski NG. Recognizing Latinos' range of skin pigment and phototypes to enhance skin cancer prevention. Pigment Cell Melanoma Res 2017; 30:488-492. [PMID: 28504868 DOI: 10.1111/pcmr.12598] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/08/2017] [Indexed: 11/26/2022]
Abstract
Latinos in the United States may have the mistaken assumption that their natural pigmentation protects them from developing skin cancer that, effectively, serves as a barrier to Latinos receiving education in primary and secondary prevention of skin cancer. Latino adults of Mexican or Puerto Rican heritage attending community health fairs in the greater Chicago area responded to a culturally informed and sensitive measure for sunburn and tan, which was previously adapted to capture skin irritation with tenderness from the sun occurring in darker skin types (n = 350). By self-reported responses and spectrophotometry assessment of constitutive pigmentation, adapted Fitzpatrick skin types (FST) ranged from skin type I-IV in the Mexican American participants and from II to V in the Puerto Rican participants. The objectively measured proportion of adapted FST II skin type was greater than commonly perceived and demonstrated that many Latinos do indeed have sun-sensitive skin.
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Affiliation(s)
- June K Robinson
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Frank J Penedo
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Jennifer L Hay
- Department of Psychiatry & Behavioral Sciences, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Nina G Jablonski
- Stellenbosch Institute for Advanced Study, The Pennsylvania State University, University Park, PA, USA
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24
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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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25
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Identification of a novel locus associated with skin colour in African-admixed populations. Sci Rep 2017; 7:44548. [PMID: 28300201 PMCID: PMC5353593 DOI: 10.1038/srep44548] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/23/2017] [Indexed: 11/30/2022] Open
Abstract
Skin pigmentation is a complex trait that varies largely among populations. Most genome-wide association studies of this trait have been performed in Europeans and Asians. We aimed to uncover genes influencing skin colour in African-admixed individuals. We performed a genome-wide association study of melanin levels in 285 Hispanic/Latino individuals from Puerto Rico, analyzing 14 million genetic variants. A total of 82 variants with p-value ≤1 × 10−5 were followed up in 373 African Americans. Fourteen single nucleotide polymorphisms were replicated, of which nine were associated with skin colour at genome-wide significance in a meta-analysis across the two studies. These results validated the association of two previously known skin pigmentation genes, SLC24A5 (minimum p = 2.62 × 10−14, rs1426654) and SLC45A2 (minimum p = 9.71 × 10−10, rs16891982), and revealed the intergenic region of BEND7 and PRPF18 as a novel locus associated with this trait (minimum p = 4.58 × 10−9, rs6602666). The most significant variant within this region is common among African-descent populations but not among Europeans or Native Americans. Our findings support the advantages of analyzing African-admixed populations to discover new genes influencing skin pigmentation.
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26
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Wollstein A, Walsh S, Liu F, Chakravarthy U, Rahu M, Seland JH, Soubrane G, Tomazzoli L, Topouzis F, Vingerling JR, Vioque J, Böhringer S, Fletcher AE, Kayser M. Novel quantitative pigmentation phenotyping enhances genetic association, epistasis, and prediction of human eye colour. Sci Rep 2017; 7:43359. [PMID: 28240252 PMCID: PMC5327401 DOI: 10.1038/srep43359] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/23/2017] [Indexed: 11/09/2022] Open
Abstract
Success of genetic association and the prediction of phenotypic traits from DNA are known to depend on the accuracy of phenotype characterization, amongst other parameters. To overcome limitations in the characterization of human iris pigmentation, we introduce a fully automated approach that specifies the areal proportions proposed to represent differing pigmentation types, such as pheomelanin, eumelanin, and non-pigmented areas within the iris. We demonstrate the utility of this approach using high-resolution digital eye imagery and genotype data from 12 selected SNPs from over 3000 European samples of seven populations that are part of the EUREYE study. In comparison to previous quantification approaches, (1) we achieved an overall improvement in eye colour phenotyping, which provides a better separation of manually defined eye colour categories. (2) Single nucleotide polymorphisms (SNPs) known to be involved in human eye colour variation showed stronger associations with our approach. (3) We found new and confirmed previously noted SNP-SNP interactions. (4) We increased SNP-based prediction accuracy of quantitative eye colour. Our findings exemplify that precise quantification using the perceived biological basis of pigmentation leads to enhanced genetic association and prediction of eye colour. We expect our approach to deliver new pigmentation genes when applied to genome-wide association testing.
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Affiliation(s)
- Andreas Wollstein
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands.,Section of Evolutionary Biology, Department of Biology II, University of Munich LMU, Planegg-Martinsried, Germany
| | - Susan Walsh
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Fan Liu
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.,Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Usha Chakravarthy
- Centre for Vision and Vascular Science, The Queen's University Belfast, Belfast, United Kingdom
| | - Mati Rahu
- Department of Epidemiology and Biostatistics, National Institute for Health Development, Tallinn, Estonia
| | - Johan H Seland
- Department of Ophthalmology, University of Bergen, School of Medicine, Bergen, Norway
| | - Gisèle Soubrane
- Clinique Ophthalmologique, Universitaire De Creteil, Paris, France
| | | | - Fotis Topouzis
- Department of Ophthalmology, Aristotle University of Thessaloniki, School of Medicine, Thessaloniki, Greece
| | - Johannes R Vingerling
- Department of Ophthalmology, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Jesus Vioque
- Dpto. Salud Publica Universidad Miguel Hernandez, Alicante, El Centro de Investigacion Biomedica en Red de Epidemiologıa y Salud Publica (CIBERESP), Elche, Spain
| | - Stefan Böhringer
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
| | - Astrid E Fletcher
- Faculty of Epidemiology &Population Health, London School of Hygiene &Tropical Medicine, London, United Kingdom
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
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27
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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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28
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Key FM, Fu Q, Romagné F, Lachmann M, Andrés AM. Human adaptation and population differentiation in the light of ancient genomes. Nat Commun 2016; 7:10775. [PMID: 26988143 PMCID: PMC4802047 DOI: 10.1038/ncomms10775] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 01/18/2016] [Indexed: 01/24/2023] Open
Abstract
The influence of positive selection sweeps in human evolution is increasingly debated, although our ability to detect them is hampered by inherent uncertainties in the timing of past events. Ancient genomes provide snapshots of allele frequencies in the past and can help address this question. We combine modern and ancient genomic data in a simple statistic (DAnc) to time allele frequency changes, and investigate the role of drift and adaptation in population differentiation. Only 30% of the most strongly differentiated alleles between Africans and Eurasians changed in frequency during the colonization of Eurasia, but in Europe these alleles are enriched in genic and putatively functional alleles to an extent only compatible with local adaptation. Adaptive alleles—especially those associated with pigmentation—are mostly of hunter-gatherer origin, although lactose persistence arose in a haplotype present in farmers. These results provide evidence for a role of local adaptation in human population differentiation. Detecting the targets of positive selection in the human genome is challenging. Here, the authors combine modern and ancient genomes to show that alleles strongly differentiated between Africans and Europeans mediated local adaptation in European populations, and were mostly contributed by ancient hunter-gatherers.
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Affiliation(s)
- Felix M Key
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Qiaomei Fu
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China.,Department of Genetics, Harvard Medical School, Boston 02115, Massachusetts, USA
| | - Frédéric Romagné
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Michael Lachmann
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Santa Fe Institute, Santa Fe, New Mexico 87501, USA
| | - Aida M Andrés
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
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29
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Asgari MM, Wang W, Ioannidis NM, Itnyre J, Hoffmann T, Jorgenson E, Whittemore AS. Identification of Susceptibility Loci for Cutaneous Squamous Cell Carcinoma. J Invest Dermatol 2016; 136:930-937. [PMID: 26829030 DOI: 10.1016/j.jid.2016.01.013] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/04/2016] [Accepted: 01/06/2016] [Indexed: 12/20/2022]
Abstract
We report a genome-wide association study of cutaneous squamous cell carcinoma conducted among non-Hispanic white members of the Kaiser Permanente Northern California health care system. The study includes a genome-wide screen of 61,457 members (6,891 cases and 54,566 controls) genotyped on the Affymetrix Axiom European array and a replication phase involving an independent set of 6,410 additional members (810 cases and 5,600 controls). Combined analysis of screening and replication phases identified 10 loci containing single-nucleotide polymorphisms (SNPs) with P-values < 5 × 10(-8). Six loci contain genes in the pigmentation pathway; SNPs at these loci appear to modulate squamous cell carcinoma risk independently of the pigmentation phenotypes. Another locus contains HLA class II genes studied in relation to elevated squamous cell carcinoma risk following immunosuppression. SNPs at the remaining three loci include an intronic SNP in FOXP1 at locus 3p13, an intergenic SNP at 3q28 near TP63, and an intergenic SNP at 9p22 near BNC2. These findings provide insights into the genetic factors accounting for inherited squamous cell carcinoma susceptibility.
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Affiliation(s)
- Maryam M Asgari
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts, USA; Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
| | - Wei Wang
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, California, USA
| | - Nilah M Ioannidis
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, California, USA; Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Jacqueline Itnyre
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, California, USA
| | - Thomas Hoffmann
- Department of Epidemiology and Biostatistics and Institute for Human Genetics, University of California, San Francisco, California, USA
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
| | - Alice S Whittemore
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, California, USA.
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30
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31
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Huang T, Shu Y, Cai YD. Genetic differences among ethnic groups. BMC Genomics 2015; 16:1093. [PMID: 26690364 PMCID: PMC4687076 DOI: 10.1186/s12864-015-2328-0] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 12/15/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Many differences between different ethnic groups have been observed, such as skin color, eye color, height, susceptibility to some diseases, and response to certain drugs. However, the genetic bases of such differences have been under-investigated. Since the HapMap project, large-scale genotype data from Caucasian, African and Asian population samples have been available. The project found that these populations were located in different areas of the PCA (Principal Component Analysis) plot. However, as an unsupervised method, PCA does not measure the differences in each single nucleotide polymorphism (SNP) among populations. RESULTS We applied an advanced mutual information-based feature selection method to detect associations between SNP status and ethnic groups using the latest HapMap Phase 3 release version 3, which included more sub-populations. A total of 299 SNPs were identified, and they can accurately predicted the ethnicity of all HapMap populations. The 10-fold cross validation accuracy of the SMO (sequential minimal optimization) model on training dataset was 0.901, and the accuracy on independent test dataset was 0.895. CONCLUSIONS In-depth functional analysis of these SNPs and their nearby genes revealed the genetic bases of skin and eye color differences among populations.
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Affiliation(s)
- Tao Huang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, P. R. China.
| | - Yang Shu
- Sate Key Laboratory of Biotherapy, Sichuan University, Sichuan, 610041, P. R. China.
| | - Yu-Dong Cai
- College of Life Science, Shanghai University, Shanghai, 200444, P. R. China.
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32
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Testing for Ancient Selection Using Cross-population Allele Frequency Differentiation. Genetics 2015; 202:733-50. [PMID: 26596347 DOI: 10.1534/genetics.115.178095] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 11/18/2015] [Indexed: 12/18/2022] Open
Abstract
A powerful way to detect selection in a population is by modeling local allele frequency changes in a particular region of the genome under scenarios of selection and neutrality and finding which model is most compatible with the data. A previous method based on a cross-population composite likelihood ratio (XP-CLR) uses an outgroup population to detect departures from neutrality that could be compatible with hard or soft sweeps, at linked sites near a beneficial allele. However, this method is most sensitive to recent selection and may miss selective events that happened a long time ago. To overcome this, we developed an extension of XP-CLR that jointly models the behavior of a selected allele in a three-population tree. Our method - called "3-population composite likelihood ratio" (3P-CLR) - outperforms XP-CLR when testing for selection that occurred before two populations split from each other and can distinguish between those events and events that occurred specifically in each of the populations after the split. We applied our new test to population genomic data from the 1000 Genomes Project, to search for selective sweeps that occurred before the split of Yoruba and Eurasians, but after their split from Neanderthals, and that could have led to the spread of modern-human-specific phenotypes. We also searched for sweep events that occurred in East Asians, Europeans, and the ancestors of both populations, after their split from Yoruba. In both cases, we are able to confirm a number of regions identified by previous methods and find several new candidates for selection in recent and ancient times. For some of these, we also find suggestive functional mutations that may have driven the selective events.
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33
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Nakagome S, Alkorta-Aranburu G, Amato R, Howie B, Peter BM, Hudson RR, Di Rienzo A. Estimating the Ages of Selection Signals from Different Epochs in Human History. Mol Biol Evol 2015; 33:657-69. [PMID: 26545921 DOI: 10.1093/molbev/msv256] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genetic variation harbors signatures of natural selection driven by selective pressures that are often unknown. Estimating the ages of selection signals may allow reconstructing the history of environmental changes that shaped human phenotypes and diseases. We have developed an approximate Bayesian computation (ABC) approach to estimate allele ages under a model of selection on new mutations and under demographic models appropriate for human populations. We have applied it to two resequencing data sets: An ultra-high depth data set from a relatively small sample of unrelated individuals and a lower depth data set in a larger sample with transmission information. In addition to evaluating the accuracy of our method based on simulations, for each SNP, we assessed the consistency between the posterior probabilities estimated by the ABC approach and the ancient DNA record, finding good agreement between the two types of data and methods. Applying this ABC approach to data for eight single nucleotide polymorphisms (SNPs), we were able to rule out an onset of selection prior to the dispersal out-of-Africa for three of them and more recent than the spread of agriculture for an additional three SNPs.
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Affiliation(s)
| | | | - Roberto Amato
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, United Kingdom
| | - Bryan Howie
- Department of Human Genetics, University of Chicago
| | | | - Richard R Hudson
- Department of Human Genetics, University of Chicago Department of Ecology and Evolution, University of Chicago
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López S, García I, Smith I, Sevilla A, Izagirre N, de la Rúa C, Alonso S. Discovery of copy number variants by multiplex amplifiable probe hybridization (MAPH) in candidate pigmentation genes. Ann Hum Biol 2015; 42:485-93. [DOI: 10.3109/03014460.2014.965202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Forensic DNA Phenotyping: Predicting human appearance from crime scene material for investigative purposes. Forensic Sci Int Genet 2015; 18:33-48. [DOI: 10.1016/j.fsigen.2015.02.003] [Citation(s) in RCA: 227] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 01/29/2015] [Accepted: 02/11/2015] [Indexed: 01/17/2023]
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Dario P, Mouriño H, Oliveira AR, Lucas I, Ribeiro T, Porto MJ, Costa Santos J, Dias D, Corte Real F. Assessment of IrisPlex-based multiplex for eye and skin color prediction with application to a Portuguese population. Int J Legal Med 2015; 129:1191-200. [PMID: 26289415 DOI: 10.1007/s00414-015-1248-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 08/12/2015] [Indexed: 11/26/2022]
Abstract
DNA phenotyping research is one of the most emergent areas of forensic genetics. Predictions of externally visible characteristics are possible through analysis of single nucleotide polymorphisms. These tools can provide police with "intelligence" in cases where there are no obvious suspects and unknown biological samples found at the crime scene do not result in any criminal DNA database hits. IrisPlex, an eye color prediction assay, revealed high prediction rates for blue and brown eye color in European populations. However, this is less predictive in some non-European populations, probably due to admixing. When compared to other European countries, Portugal has a relatively admixed population, resulting from a genetic influx derived from its proximity to and historical relations with numerous African territories. The aim of this work was to evaluate the utility of IrisPlex in the Portuguese population. Furthermore, the possibility of supplementing this multiplex with additional markers to also achieve skin color prediction within this population was evaluated. For that, IrisPlex was augmented with additional SNP loci. Eye and skin color prediction was estimated using the multinomial logistic regression and binomial logistic regression models, respectively. The results demonstrated eye color prediction accuracies of the IrisPlex system of 90 and 60% for brown and blue eye color, respectively, and 77% for intermediate eye color, after allele frequency adjustment. With regard to skin color, it was possible to achieve a prediction accuracy of 93%. In the future, phenotypic determination multiplexes must include additional loci to permit skin color prediction as presented in this study as this can be an advantageous tool for forensic investigation.
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Affiliation(s)
- Paulo Dario
- INMLCF - National Institute of Legal Medicine and Forensic Sciences, Largo da Sé Nova, 3000-213, Coimbra, Portugal.
- Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016, Lisboa, Portugal.
- CENCIFOR - Forensic Sciences Centre, Largo da Sé Nova, 3000-213, Coimbra, Portugal.
- CESAM - Centre for Environmental and Marine Studies, Edifício C2, Campo Grande, 1749-016, Lisboa, Portugal.
| | - Helena Mouriño
- Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016, Lisboa, Portugal
| | - Ana Rita Oliveira
- Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016, Lisboa, Portugal
- CESAM - Centre for Environmental and Marine Studies, Edifício C2, Campo Grande, 1749-016, Lisboa, Portugal
| | - Isabel Lucas
- INMLCF - National Institute of Legal Medicine and Forensic Sciences, Largo da Sé Nova, 3000-213, Coimbra, Portugal
| | - Teresa Ribeiro
- INMLCF - National Institute of Legal Medicine and Forensic Sciences, Largo da Sé Nova, 3000-213, Coimbra, Portugal
- CENCIFOR - Forensic Sciences Centre, Largo da Sé Nova, 3000-213, Coimbra, Portugal
| | - Maria João Porto
- INMLCF - National Institute of Legal Medicine and Forensic Sciences, Largo da Sé Nova, 3000-213, Coimbra, Portugal
- CENCIFOR - Forensic Sciences Centre, Largo da Sé Nova, 3000-213, Coimbra, Portugal
| | - Jorge Costa Santos
- INMLCF - National Institute of Legal Medicine and Forensic Sciences, Largo da Sé Nova, 3000-213, Coimbra, Portugal
- CENCIFOR - Forensic Sciences Centre, Largo da Sé Nova, 3000-213, Coimbra, Portugal
- Faculty of Medicine, University of Lisbon, Av. Professor Egas Moniz, 1649-028, Lisboa, Portugal
| | - Deodália Dias
- Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016, Lisboa, Portugal
- CESAM - Centre for Environmental and Marine Studies, Edifício C2, Campo Grande, 1749-016, Lisboa, Portugal
| | - Francisco Corte Real
- INMLCF - National Institute of Legal Medicine and Forensic Sciences, Largo da Sé Nova, 3000-213, Coimbra, Portugal
- CENCIFOR - Forensic Sciences Centre, Largo da Sé Nova, 3000-213, Coimbra, Portugal
- Faculty of Medicine, University of Coimbra, Rua Larga, 3004-504, Coimbra, Portugal
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Caliebe A, Harder M, Schuett R, Krawczak M, Nebel A, von Wurmb-Schwark N. The more the merrier? How a few SNPs predict pigmentation phenotypes in the Northern German population. Eur J Hum Genet 2015; 24:739-47. [PMID: 26286644 DOI: 10.1038/ejhg.2015.167] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 04/01/2015] [Accepted: 06/07/2015] [Indexed: 01/24/2023] Open
Abstract
Human pigmentation traits are of great interest to many research areas, from ancient DNA analysis to forensic science. We developed a gene-based predictive model for pigmentation phenotypes in a realistic target population for forensic case work from Northern Germany and compared our model with those brought forth by previous studies of genetically more heterogeneous populations. In doing so, we aimed at answering the following research questions: (1) do existing models allow good prediction of high-quality phenotypes in a genetically similar albeit more homogeneous population? (2) Would a model specifically set up for the more homogeneous population perform notably better than existing models? (3) Can the number of markers included in existing models be reduced without compromising their predictive capability in the more homogenous population? We investigated the association between eye, hair and skin colour and 12 candidate single-nucleotide polymorphisms (SNPs) from six genes. Our study comprised two samples of 300 and 100 individuals from Northern Germany. SNP rs12913832 in HERC2 was found to be strongly associated with blue eye colour (odds ratio=40.0, P<1.2 × 10(-4)) and to yield moderate predictive power (AUC: 77%; sensitivity: 90%, specificity: 63%, both at a 0.5 threshold for blue eye colour probability). SNP associations with hair and skin colour were weaker and genotypes less predictive. A comparison with two recently published sets of markers to predict eye and hair colour revealed that the consideration of additional SNPs with weak-to-moderate effect increased the predictive power for eye colour, but not for hair colour.
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Affiliation(s)
- Amke Caliebe
- Institute of Medical Informatics and Statistics, Christian-Albrechts University Kiel, Kiel, Germany
| | - Melanie Harder
- Institute of Legal Medicine, Christian-Albrechts University Kiel, Kiel, Germany
| | - Rebecca Schuett
- Institute of Legal Medicine, Christian-Albrechts University Kiel, Kiel, Germany
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian-Albrechts University Kiel, Kiel, Germany
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Christian-Albrechts University Kiel, Kiel, Germany
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Voskoboinik L, Ayers SB, LeFebvre AK, Darvasi A. SNP-microarrays can accurately identify the presence of an individual in complex forensic DNA mixtures. Forensic Sci Int Genet 2015; 16:208-215. [DOI: 10.1016/j.fsigen.2015.01.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 12/02/2014] [Accepted: 01/27/2015] [Indexed: 11/27/2022]
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Visser M, Kayser M, Grosveld F, Palstra RJ. Genetic variation in regulatory DNA elements: the case of OCA2 transcriptional regulation. Pigment Cell Melanoma Res 2014; 27:169-77. [PMID: 24387780 DOI: 10.1111/pcmr.12210] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 12/20/2013] [Indexed: 12/16/2022]
Abstract
Mutations within the OCA2 gene or the complete absence of the OCA2 protein leads to oculocutaneous albinism type 2. The OCA2 protein plays a central role in melanosome biogenesis, and it is a strong determinant of the eumelanin content in melanocytes. Transcript levels of the OCA2 gene are strongly correlated with pigmentation intensities. Recent studies demonstrated that the transcriptional level of OCA2 is to a large extent determined by the noncoding SNP rs12913832 located 21.5 kb upstream of the OCA2 gene promoter. In this review, we discuss current hypotheses and the available data on the mechanism of OCA2 transcriptional regulation and how this is influenced by genetic variation. Finally, we will explore how future epigenetic studies can be used to advance our insight into the functional biology that connects genetic variation to human pigmentation.
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Affiliation(s)
- Mijke Visser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
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Sanfilippo PG, Wilkinson CH, Ruddle JB, Zhu G, Martin NG, Hewitt AW, Mackey DA. Don't it make your brown eyes blue? A comparison of iris colour across latitude in Australian twins. Clin Exp Optom 2014; 98:172-6. [PMID: 25251541 DOI: 10.1111/cxo.12209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 06/05/2014] [Accepted: 06/21/2014] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The aim was to determine whether latitudinal (Queensland versus Tasmania) variation in reported disease frequency in Australia may be biased by differences in population. METHODS A retrospective analysis was conducted from data of two large Australian twin studies (n = 1,835) having undertaken ophthalmic examination, namely, Twins Eye Study in Tasmania (TEST) and the Brisbane Adolescent Twins Study (BATS). Ordinal logistic regression was used to compute odds ratios and predicted probabilities for each category of eye colour by state. RESULTS Tasmanian residence was associated with lower odds of darker iris colour (odds ratio 0.77, 95% CI [0.63-0.95]) signifying that participants living in Tasmania (TAS) are less likely to have darker-coloured irides than those residing in Queensland (QLD). For individuals living in Tasmania the predicted probability (TAS versus QLD) of having light blue eyes was greater (16.7 versus 13.3 per cent), approximately the same for green eyes and less for brown/dark brown-coloured eyes (6.2 versus 7.9 per cent). CONCLUSIONS We found a general trend of individuals living in the southern states (TAS/VIC) of Australia having lighter-coloured irides compared to those living in the north (QLD). This finding has potential implications for all epidemiological research conducted to explore differences in UV-associated disease frequency in Australia, as population heterogeneity may confound the estimates obtained.
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Affiliation(s)
- Paul G Sanfilippo
- Lions Eye Institute, Centre for Ophthalmology and Visual Science, University of Western Australia, Perth, Australia; Centre for Eye Research Australia, University of Melbourne, Department of Ophthalmology, Royal Victorian Eye and Ear Hospital, Melbourne, Australia.
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Kosiniak-Kamysz A, Marczakiewicz-Lustig A, Marcińska M, Skowron M, Wojas-Pelc A, Pośpiech E, Branicki W. Increased risk of developing cutaneous malignant melanoma is associated with variation in pigmentation genes and VDR, and may involve epistatic effects. Melanoma Res 2014; 24:388-96. [PMID: 24926819 DOI: 10.1097/cmr.0000000000000095] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cutaneous malignant melanoma (CMM) is a malicious human skin cancer that primarily affects individuals with light pigmentation and heavy sun exposure, but also has a known familial association. Multiple genes and polymorphisms have been reported as low-penetrance susceptibility loci for CMM. Here, we examined 33 candidate polymorphisms located in 11 pigmentation genes and the vitamin D receptor gene (VDR) in a population of 130 cutaneous melanoma patients and 707 healthy controls. The genotypes obtained were evaluated for main association effects and potential gene-gene interactions. MC1R, TYR, VDR and SLC45A2 genes were found to be associated with CMM in our population. The results obtained for major function MC1R mutations were the most significant [with odds ratio (OR)=1.787, confidence interval (CI)=1.320-2.419 and P=1.715(-4)], followed by TYR (rs1393350) (with OR=1.569, CI=1.162-2.118, P=0.003), VDR (GCCC haplotype in rs2238136-rs4516035-rs7139166-rs11568820 block) (with OR=5.653, CI=1.794-17.811, P=0.003) and SLC45A2 (rs16891982) (with OR=0.238, CI=0.057-0.987, P=0.048). The study also detected significant intermolecular epistatic effects between MC1R and TYR, SLC45A2 and VDR, HERC2 and VDR, OCA2 and TPCN2, as well as intramolecular interactions between variants within the genes MC1R and VDR. In the final multivariate logistic regression model for CMM development, only the gene-gene interactions discovered remained significant, showing that epistasis may be an important factor in the risk of melanoma.
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Affiliation(s)
- Agnieszka Kosiniak-Kamysz
- aDepartment of Dermatology, Collegium Medicum of the Jagiellonian University bDepartment of Analytical Biochemistry, Jagiellonian University Medical College cDepartment of Genetics and Evolution, Institute of Zoology, Jagiellonian University dSection of Forensic Genetics, Institute of Forensic Research, Kraków, Poland
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Cuba: exploring the history of admixture and the genetic basis of pigmentation using autosomal and uniparental markers. PLoS Genet 2014; 10:e1004488. [PMID: 25058410 PMCID: PMC4109857 DOI: 10.1371/journal.pgen.1004488] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 05/20/2014] [Indexed: 11/19/2022] Open
Abstract
We carried out an admixture analysis of a sample comprising 1,019 individuals from all the provinces of Cuba. We used a panel of 128 autosomal Ancestry Informative Markers (AIMs) to estimate the admixture proportions. We also characterized a number of haplogroup diagnostic markers in the mtDNA and Y-chromosome in order to evaluate admixture using uniparental markers. Finally, we analyzed the association of 16 single nucleotide polymorphisms (SNPs) with quantitative estimates of skin pigmentation. In the total sample, the average European, African and Native American contributions as estimated from autosomal AIMs were 72%, 20% and 8%, respectively. The Eastern provinces of Cuba showed relatively higher African and Native American contributions than the Western provinces. In particular, the highest proportion of African ancestry was observed in the provinces of Guantánamo (40%) and Santiago de Cuba (39%), and the highest proportion of Native American ancestry in Granma (15%), Holguín (12%) and Las Tunas (12%). We found evidence of substantial population stratification in the current Cuban population, emphasizing the need to control for the effects of population stratification in association studies including individuals from Cuba. The results of the analyses of uniparental markers were concordant with those observed in the autosomes. These geographic patterns in admixture proportions are fully consistent with historical and archaeological information. Additionally, we identified a sex-biased pattern in the process of gene flow, with a substantially higher European contribution from the paternal side, and higher Native American and African contributions from the maternal side. This sex-biased contribution was particularly evident for Native American ancestry. Finally, we observed that SNPs located in the genes SLC24A5 and SLC45A2 are strongly associated with melanin levels in the sample.
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43
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Pośpiech E, Wojas-Pelc A, Walsh S, Liu F, Maeda H, Ishikawa T, Skowron M, Kayser M, Branicki W. The common occurrence of epistasis in the determination of human pigmentation and its impact on DNA-based pigmentation phenotype prediction. Forensic Sci Int Genet 2014; 11:64-72. [DOI: 10.1016/j.fsigen.2014.01.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 01/30/2014] [Accepted: 01/31/2014] [Indexed: 01/19/2023]
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Pietroni C, Andersen JD, Johansen P, Andersen MM, Harder S, Paulsen R, Børsting C, Morling N. The effect of gender on eye colour variation in European populations and an evaluation of the IrisPlex prediction model. Forensic Sci Int Genet 2014; 11:1-6. [DOI: 10.1016/j.fsigen.2014.02.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 01/29/2014] [Accepted: 02/02/2014] [Indexed: 11/25/2022]
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Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the last 5,000 y. Proc Natl Acad Sci U S A 2014; 111:4832-7. [PMID: 24616518 DOI: 10.1073/pnas.1316513111] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Pigmentation is a polygenic trait encompassing some of the most visible phenotypic variation observed in humans. Here we present direct estimates of selection acting on functional alleles in three key genes known to be involved in human pigmentation pathways--HERC2, SLC45A2, and TYR--using allele frequency estimates from Eneolithic, Bronze Age, and modern Eastern European samples and forward simulations. Neutrality was overwhelmingly rejected for all alleles studied, with point estimates of selection ranging from around 2-10% per generation. Our results provide direct evidence that strong selection favoring lighter skin, hair, and eye pigmentation has been operating in European populations over the last 5,000 y.
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46
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Durso DF, Bydlowski SP, Hutz MH, Suarez-Kurtz G, Magalhães TR, Junho Pena SD. Association of genetic variants with self-assessed color categories in Brazilians. PLoS One 2014; 9:e83926. [PMID: 24416183 PMCID: PMC3885524 DOI: 10.1371/journal.pone.0083926] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 11/09/2013] [Indexed: 01/07/2023] Open
Abstract
The Brazilian population was formed by extensive admixture of three different ancestral roots: Amerindians, Europeans and Africans. Our previous work has shown that at an individual level, ancestry, as estimated using molecular markers, was a poor predictor of color in Brazilians. We now investigate if SNPs known to be associated with human skin pigmentation can be used to predict color in Brazilians. For that, we studied the association of fifteen SNPs, previously known to be linked with skin color, in 243 unrelated Brazilian individuals self-identified as White, Browns or Blacks from Rio de Janeiro and 212 unrelated Brazilian individuals self-identified as White or Blacks from São Paulo. The significance of association of SNP genotypes with self-assessed color was evaluated using partial regression analysis. After controlling for ancestry estimates as covariates, only four SNPs remained significantly associated with skin pigmentation: rs1426654 and rs2555364 within SLC24A5, rs16891982 at SLC45A2 and rs1042602 at TYR. These loci are known to be involved in melanin synthesis or transport of melanosomes. We found that neither genotypes of these SNPs, nor their combination with biogeographical ancestry in principal component analysis, could predict self-assessed color in Brazilians at an individual level. However, significant correlations did emerge at group level, demonstrating that even though elements other than skin, eye and hair pigmentation do influence self-assessed color in Brazilians, the sociological act of self-classification is still substantially dependent of genotype at these four SNPs.
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Affiliation(s)
- Danielle Fernandes Durso
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Sergio Paulo Bydlowski
- Laboratório de Genética e Hematologia Molecular, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Mara Helena Hutz
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Guilherme Suarez-Kurtz
- Coordenação de Pesquisa/Divisão de Farmacologia, Instituto Nacional do Câncer (INCA), Rio de Janeiro, RJ, Brazil
| | - Tiago R. Magalhães
- Laboratório de Genômica Clínica, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Sérgio Danilo Junho Pena
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
- Laboratório de Genômica Clínica, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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Dembinski GM, Picard CJ. Evaluation of the IrisPlex DNA-based eye color prediction assay in a United States population. Forensic Sci Int Genet 2013; 9:111-7. [PMID: 24528589 DOI: 10.1016/j.fsigen.2013.12.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 08/27/2013] [Accepted: 12/04/2013] [Indexed: 12/21/2022]
Abstract
DNA phenotyping is a rapidly developing area of research in forensic biology. Externally visible characteristics (EVCs) can be determined based on genotype data, specifically based on single nucleotide polymorphisms (SNPs). These SNPs are chosen based on their association with genes related to the phenotypic expression of interest, with known examples in eye, hair, and skin color traits. DNA phenotyping has forensic importance when unknown biological samples at a crime scene do not result in a criminal database hit; a phenotypic profile of the sample can therefore be used to develop investigational leads. IrisPlex, an eye color prediction assay, has previously shown high prediction rates for blue and brown eye color in a Dutch European population. The objective of this work was to evaluate its utility in a North American population. We evaluated six SNPs included in the IrisPlex assay in population sample collected from a USA college campus. We used a quantitative method of eye color classification based on (RGB) color components of digital photographs of the eye taken from each study volunteer so that each eye was placed in one of three eye color categories: brown, intermediate, or blue. Objective color classification was shown to correlate with basic human visual determination making it a feasible option for use in future prediction assay development. Using these samples and various models, the maximum prediction accuracies of the IrisPlex system after allele frequency adjustment was 58% and 95% brown and blue eye color predictions, respectively, and 11% for intermediate eye colors. Future developments should include incorporation of additional informative SNPs, specifically related to the intermediate eye color, and we recommend the use of a Bayesian approach as a prediction model as likelihood ratios can be determined for reporting purposes.
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Affiliation(s)
- Gina M Dembinski
- Department of Biology and Forensic and Investigative Sciences Program, Indiana University-Purdue University Indianapolis, 723 W. Michigan Street, Indianapolis, IN 46202, USA.
| | - Christine J Picard
- Department of Biology and Forensic and Investigative Sciences Program, Indiana University-Purdue University Indianapolis, 723 W. Michigan Street, Indianapolis, IN 46202, USA.
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Kastelic V, Pośpiech E, Draus-Barini J, Branicki W, Drobnič K. Prediction of eye color in the Slovenian population using the IrisPlex SNPs. Croat Med J 2013; 54:381-6. [PMID: 23986280 PMCID: PMC3760663 DOI: 10.3325/cmj.2013.54.381] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
AIM To evaluate the accuracy of eye color prediction based on six IrisPlex single nucleotide polymorphisms (SNP) in a Slovenian population sample. METHODS Six IrisPlex predictor SNPs (HERC2 - rs12913832, OCA2 - rs1800407, SLC45A2 - rs16891982 and TYR - rs1393350, SLC24A4 - rs12896399, and IRF4 - rs12203592) of 105 individuals were analyzed using single base extension approach and SNaPshot chemistry. The IrisPlex multinomial regression prediction model was used to infer eye color probabilities. The accuracy of the IrisPlex was assessed through the calculation of sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and the area under the receiver characteristic operating curves (AUC). RESULTS Blue eye color was observed in 44.7%, brown in 29.6%, and intermediate in 25.7% participants. Prediction accuracy expressed by the AUC was 0.966 for blue, 0.913 for brown, and 0.796 for intermediate eye color. Sensitivity was 93.6% for blue, 58.1% for brown, and 0% for intermediate eye color. Specificity was 93.1% for blue, 89.2% for brown, and 100% for intermediate eye color. PPV was 91.7% for blue and 69.2% for brown color. NPV was 94.7% for blue and 83.5% for brown eye color. These values indicate prediction accuracy comparable to that established in other studies. CONCLUSION Blue and brown eye color can be reliably predicted from DNA samples using only six polymorphisms, while intermediate eye color defies prediction, indicating that more research is needed to genetically predict the whole variation of eye color in humans.
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Affiliation(s)
- Vanja Kastelic
- Vanja Kastelic, National Forensic Laboratory, General Police Directorate, Police, Ministry of the Interior, Vodovodna 95a, 1000 Ljubljana, Slovenia,
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Martinez-Cadenas C, Peña-Chilet M, Llorca-Cardeñosa MJ, Cervera R, Ibarrola-Villava M, Ribas G. Gender and eye colour prediction discrepancies: A reply to criticisms. Forensic Sci Int Genet 2013; 9:e7-9. [PMID: 24216441 DOI: 10.1016/j.fsigen.2013.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 09/30/2013] [Accepted: 10/05/2013] [Indexed: 01/16/2023]
Affiliation(s)
| | - Maria Peña-Chilet
- Medical Oncology and Haematology Unit, Health Research Institute - INCLIVA, Valencia, Spain
| | | | - Raimundo Cervera
- Medical Oncology and Haematology Unit, Health Research Institute - INCLIVA, Valencia, Spain
| | | | - Gloria Ribas
- Medical Oncology and Haematology Unit, Health Research Institute - INCLIVA, Valencia, Spain.
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50
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Rojek A, Niedziela M. Adrenal function and MC1R gene analysis in a prepubertal girl with generalized hyperpigmentation: case report. Arch Med Sci 2013; 9:761-4. [PMID: 24049543 PMCID: PMC3776169 DOI: 10.5114/aoms.2012.32791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 08/27/2011] [Accepted: 10/17/2011] [Indexed: 11/17/2022] Open
Affiliation(s)
- Aleksandra Rojek
- Department of Paediatric Endocrinology and Rheumatology, Molecular Endocrinology Laboratory, Poznan University of Medical Sciences, Poland
| | - Marek Niedziela
- Department of Paediatric Endocrinology and Rheumatology, Poznan University of Medical Sciences, Poland
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