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Association between Variants in the OCA2-HERC2 Region and Blue Eye Colour in HERC2 rs12913832 AA and AG Individuals. Genes (Basel) 2023; 14:genes14030698. [PMID: 36980970 PMCID: PMC10048254 DOI: 10.3390/genes14030698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/01/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
The OCA2-HERC2 region is strongly associated with human pigmentation, especially eye colour. The HERC2 SNP rs12913832 is currently the best-known predictor for blue and brown eye colour. However, in a previous study we found that 43 of 166 Norwegians with the brown eye colour genotype rs12913832:AA or AG, did not have the expected brown eye colour. In this study, we carried out massively parallel sequencing of a ~500 kbp HERC2-OCA2 region in 94 rs12913832:AA and AG Norwegians (43 blue-eyed and 51 brown-eyed) to search for novel blue eye colour variants. The new candidate variants were subsequently typed in a Norwegian biobank population (total n = 519) for population specific association analysis. We identified five new variants, rs74409036:A, rs78544415:T, rs72714116:T, rs191109490:C and rs551217952:C, to be the most promising candidates for explaining blue eye colour in individuals with the rs12913832:AA and AG genotype. Additionally, we confirmed the association of the missense variants rs74653330:T and rs121918166:T with blue eye colour, and observed lighter skin colour in rs74653330:T individuals. In total, 37 (86%) of the 43 blue-eyed rs12913832:AA and AG Norwegians could potentially be explained by these seven variants, and we suggest including them in future prediction models.
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Experimental long-distance haplotyping of OCA2-HERC2 variants. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2022. [DOI: 10.1016/j.fsigss.2022.10.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Stålhammar G, Williams PA, Landelius T. The prognostic implication of latitude in uveal melanoma: a nationwide observational cohort study of all patients born in Sweden between 1947 and 1989. Discov Oncol 2022; 13:116. [PMID: 36310339 PMCID: PMC9618472 DOI: 10.1007/s12672-022-00584-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/17/2022] [Indexed: 04/17/2023] Open
Abstract
BACKGROUND The incidence of uveal melanoma increases with latitude. In this study, we examine the importance of latitude for uveal melanoma prognosis. METHODS All uveal melanoma patients born in Sweden between 1947 and 1990 were included (n = 745). The latitude of patients' birthplaces and home counties at the time of uveal melanoma diagnosis were collected. For all latitudes, data on sunlight and UV intensity parameters, temperature, daytime length variations, and socioeconomic factors were added. The prognostic implication of birthplace latitude and of moving > 1 degree of latitude was examined with multivariate Cox regressions and competing risk analyses. FINDINGS There were no significant differences in patient sex, age, tumor size, T-category, or BAP-1 immunoexpression between patients born in the south, central or northern regions of Sweden. Decreasing birthplace latitude was a predictor of uveal melanoma-related mortality in multivariate Cox regression. Patients that were born in southern regions or moved > 1 degree south between birth and diagnosis had higher incidence of uveal melanoma-related mortality in competing risk analysis. The sum of yearly sunshine hours, global sunlight radiation, average daily ultraviolet light intensity, average annual temperature, or net wealth were not predictors of uveal melanoma-related mortality. INTERPRETATION Latitude is a prognostic factor in uveal melanoma. This does not seem to be related to variations in patient or tumor characteristics at presentation, in management, in sunlight intensity, in ultraviolet light irradiance, in temperature, or in wealth. Future studies should examine if periodical changes in daylight hours or other factors could explain the prognostic implication.
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Affiliation(s)
- Gustav Stålhammar
- Department of Clinical Neuroscience, Division of Eye and Vision, St. Erik Eye Hospital, Karolinska Institutet, Eugeniavägen 12, 171 64, Stockholm, Sweden.
| | - Pete A Williams
- Department of Clinical Neuroscience, Division of Eye and Vision, St. Erik Eye Hospital, Karolinska Institutet, Eugeniavägen 12, 171 64, Stockholm, Sweden
| | - Tomas Landelius
- Swedish Meteorological and Hydrological Institute (SMHI), Norrköping, Sweden
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Association between copy number variations in the OCA2-HERC2 locus and human eye colour. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2022. [DOI: 10.1016/j.fsigss.2022.09.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Paparazzo E, Gozalishvili A, Lagani V, Geracitano S, Bauleo A, Falcone E, Passarino G, Montesanto A. A new approach to broaden the range of eye colour identifiable by IrisPlex in DNA phenotyping. Sci Rep 2022; 12:12803. [PMID: 35896692 PMCID: PMC9329466 DOI: 10.1038/s41598-022-17208-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/21/2022] [Indexed: 11/24/2022] Open
Abstract
IrisPlex system represents the most popular model for eye colour prediction. Based on six polymorphisms this model provides very accurate predictions that strongly depend on the definition of eye colour phenotypes. The aim of the present study was to introduce a new approach to improve eye colour prediction using the well-validated IrisPlex system. A sample of 238 individuals from a Southern Italian population was collected and for each of them a high-resolution image of eye was obtained. By quantifying eye colour variation into CIELAB space several clustering algorithms were applied for eye colour classification. Predictions with the IrisPlex model were obtained using eye colour categories defined by both visual inspection and clustering algorithms. IrisPlex system predicted blue and brown eye colour with high accuracy while it was inefficient in the prediction of intermediate eye colour. Clustering-based eye colour resulted in a significantly increased accuracy of the model especially for brown eyes. Our results confirm the validity of the IrisPlex system for forensic purposes. Although the quantitative approach here proposed for eye colour definition slightly improves its prediction accuracy, further research is still required to improve the model particularly for the intermediate eye colour prediction.
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Affiliation(s)
- Ersilia Paparazzo
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036, Rende, Italy
| | - Anzor Gozalishvili
- Toptal, LLC, 2810 N. Church St. #36879, Wilmington, DE, 19802-4447, USA.,Ivane Javakhishvili Tbilisi State University, 0162, Tbilisi, Georgia
| | - Vincenzo Lagani
- Institute of Chemical Biology, Ilia State University, 0162, Tbilisi, Georgia.,Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology KAUST, Thuwal, 23952, Saudi Arabia
| | - Silvana Geracitano
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036, Rende, Italy
| | - Alessia Bauleo
- BIOGENET, Medical and Forensic Genetics Laboratory, 87100, Cosenza, ASP, Italy
| | - Elena Falcone
- BIOGENET, Medical and Forensic Genetics Laboratory, 87100, Cosenza, ASP, Italy
| | - Giuseppe Passarino
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036, Rende, Italy
| | - Alberto Montesanto
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036, Rende, Italy.
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Balagué-Dobón L, Cáceres A, González JR. Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure. Brief Bioinform 2022; 23:6535682. [PMID: 35211719 PMCID: PMC8921734 DOI: 10.1093/bib/bbac043] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 12/12/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are the most abundant type of genomic variation and the most accessible to genotype in large cohorts. However, they individually explain a small proportion of phenotypic differences between individuals. Ancestry, collective SNP effects, structural variants, somatic mutations or even differences in historic recombination can potentially explain a high percentage of genomic divergence. These genetic differences can be infrequent or laborious to characterize; however, many of them leave distinctive marks on the SNPs across the genome allowing their study in large population samples. Consequently, several methods have been developed over the last decade to detect and analyze different genomic structures using SNP arrays, to complement genome-wide association studies and determine the contribution of these structures to explain the phenotypic differences between individuals. We present an up-to-date collection of available bioinformatics tools that can be used to extract relevant genomic information from SNP array data including population structure and ancestry; polygenic risk scores; identity-by-descent fragments; linkage disequilibrium; heritability and structural variants such as inversions, copy number variants, genetic mosaicisms and recombination histories. From a systematic review of recently published applications of the methods, we describe the main characteristics of R packages, command-line tools and desktop applications, both free and commercial, to help make the most of a large amount of publicly available SNP data.
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Further insight into the global variability of the OCA2-HERC2 locus for human pigmentation from multiallelic markers. Sci Rep 2021; 11:22530. [PMID: 34795370 PMCID: PMC8602267 DOI: 10.1038/s41598-021-01940-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 11/02/2021] [Indexed: 11/20/2022] Open
Abstract
The OCA2-HERC2 locus is responsible for the greatest proportion of eye color variation in humans. Numerous studies extensively described both functional SNPs and associated patterns of variation over this region. The goal of our study is to examine how these haplotype structures and allelic associations vary when highly variable markers such as microsatellites are used. Eleven microsatellites spanning 357 Kb of OCA2-HERC2 genes are analyzed in 3029 individuals from worldwide populations. We found that several markers display large differences in allele frequency (10% to 35% difference) among Europeans, East Asians and Africans. In Europe, the alleles showing increased frequency can also discriminate individuals with (IrisPlex) predicted blue and brown eyes. Distinct haplotypes are identified around the variants C and T of the functional SNP rs12913832 (associated to blue eyes), with linkage disequilibrium r2 values significant up to 237 Kb. The haplotype carrying the allele rs12913832 C has high frequency (76%) in blue eye predicted individuals (30% in brown eye predicted individuals), while the haplotype associated to the allele rs12913832 T is restricted to brown eye predicted individuals. Finally, homozygosity values reach levels of 91% near rs12913832. Odds ratios show values of 4.2, 7.4 and 10.4 for four markers around rs12913832 and 7.1 for their core haplotype. Hence, this study provides an example on the informativeness of multiallelic markers that, despite their current limited potential contribution to forensic eye color prediction, supports the use of microsatellites for identifying causing variants showing similar genetic features and history.
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Diepenbroek M, Bayer B, Anslinger K. Pushing the Boundaries: Forensic DNA Phenotyping Challenged by Single-Cell Sequencing. Genes (Basel) 2021; 12:genes12091362. [PMID: 34573344 PMCID: PMC8466929 DOI: 10.3390/genes12091362] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/24/2021] [Accepted: 08/27/2021] [Indexed: 12/26/2022] Open
Abstract
Single-cell sequencing is a fast developing and very promising field; however, it is not commonly used in forensics. The main motivation behind introducing this technology into forensics is to improve mixture deconvolution, especially when a trace consists of the same cell type. Successful studies demonstrate the ability to analyze a mixture by separating single cells and obtaining CE-based STR profiles. This indicates a potential use of the method in other forensic investigations, like forensic DNA phenotyping, in which using mixed traces is not fully recommended. For this study, we collected single-source autopsy blood from which the white cells were first stained and later separated with the DEPArray™ N×T System. Groups of 20, 10, and 5 cells, as well as 20 single cells, were collected and submitted for DNA extraction. Libraries were prepared using the Ion AmpliSeq™ PhenoTrivium Panel, which includes both phenotype (HIrisPlex-S: eye, hair, and skin color) and ancestry-associated SNP-markers. Prior to sequencing, half of the single-cell-based libraries were additionally amplified and purified in order to improve the library concentrations. Ancestry and phenotype analysis resulted in nearly full consensus profiles resulting in correct predictions not only for the cells groups but also for the ten re-amplified single-cell libraries. Our results suggest that sequencing of single cells can be a promising tool used to deconvolute mixed traces submitted for forensic DNA phenotyping.
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Kukla-Bartoszek M, Teisseyre P, Pośpiech E, Karłowska-Pik J, Zieliński P, Woźniak A, Boroń M, Dąbrowski M, Zubańska M, Jarosz A, Płoski R, Grzybowski T, Spólnicka M, Mielniczuk J, Branicki W. Searching for improvements in predicting human eye colour from DNA. Int J Legal Med 2021; 135:2175-2187. [PMID: 34259936 PMCID: PMC8523394 DOI: 10.1007/s00414-021-02645-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/17/2021] [Indexed: 01/29/2023]
Abstract
Increasing understanding of human genome variability allows for better use of the predictive potential of DNA. An obvious direct application is the prediction of the physical phenotypes. Significant success has been achieved, especially in predicting pigmentation characteristics, but the inference of some phenotypes is still challenging. In search of further improvements in predicting human eye colour, we conducted whole-exome (enriched in regulome) sequencing of 150 Polish samples to discover new markers. For this, we adopted quantitative characterization of eye colour phenotypes using high-resolution photographic images of the iris in combination with DIAT software analysis. An independent set of 849 samples was used for subsequent predictive modelling. Newly identified candidates and 114 additional literature-based selected SNPs, previously associated with pigmentation, and advanced machine learning algorithms were used. Whole-exome sequencing analysis found 27 previously unreported candidate SNP markers for eye colour. The highest overall prediction accuracies were achieved with LASSO-regularized and BIC-based selected regression models. A new candidate variant, rs2253104, located in the ARFIP2 gene and identified with the HyperLasso method, revealed predictive potential and was included in the best-performing regression models. Advanced machine learning approaches showed a significant increase in sensitivity of intermediate eye colour prediction (up to 39%) compared to 0% obtained for the original IrisPlex model. We identified a new potential predictor of eye colour and evaluated several widely used advanced machine learning algorithms in predictive analysis of this trait. Our results provide useful hints for developing future predictive models for eye colour in forensic and anthropological studies.
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Affiliation(s)
- Magdalena Kukla-Bartoszek
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland. .,Malopolska Centre of Biotechnology of the Jagiellonian University, Kraków, Poland.
| | - Paweł Teisseyre
- Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland.,Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Ewelina Pośpiech
- Malopolska Centre of Biotechnology of the Jagiellonian University, Kraków, Poland
| | - Joanna Karłowska-Pik
- Faculty of Mathematics and Computer Science, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Piotr Zieliński
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Anna Woźniak
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - Michał Boroń
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - Michał Dąbrowski
- Laboratory of Bioinformatics, Neurobiology Centre, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Magdalena Zubańska
- Faculty of Law and Administration, Department of Criminology and Forensic Sciences, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland.,Unit of Forensic Sciences, Faculty of Internal Security, Police Academy, Szczytno, Poland
| | - Agata Jarosz
- Malopolska Centre of Biotechnology of the Jagiellonian University, Kraków, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Warsaw Medical University, Warsaw, Poland
| | - Tomasz Grzybowski
- Division of Molecular and Forensic Genetics, Department of Forensic Medicine, Nicolaus Copernicus University in Toruń, Collegium Medicum in Bydgoszcz, Bydgoszcz, Poland
| | | | - Jan Mielniczuk
- Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland.,Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology of the Jagiellonian University, Kraków, Poland. .,Central Forensic Laboratory of the Police, Warsaw, Poland.
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