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Fine AG, Steinrücken M. A novel expectation-maximization approach to infer general diploid selection from time-series genetic data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.10.593575. [PMID: 38798346 PMCID: PMC11118272 DOI: 10.1101/2024.05.10.593575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Detecting and quantifying the strength of selection is a main objective in population genetics. Since selection acts over multiple generations, many approaches have been developed to detect and quantify selection using genetic data sampled at multiple points in time. Such time series genetic data is commonly analyzed using Hidden Markov Models, but in most cases, under the assumption of additive selection. However, many examples of genetic variation exhibiting non-additive mechanisms exist, making it critical to develop methods that can characterize selection in more general scenarios. Thus, we extend a previously introduced expectation-maximization algorithm for the inference of additive selection coefficients to the case of general diploid selection, in which heterozygote and homozygote fitnesses are parameterized independently. We furthermore introduce a framework to identify bespoke modes of diploid selection from given data, as well as a procedure for aggregating data across linked loci to increase power and robustness. Using extensive simulation studies, we find that our method accurately and efficiently estimates selection coefficients for different modes of diploid selection across a wide range of scenarios; however, power to classify the mode of selection is low unless selection is very strong. We apply our method to ancient DNA samples from Great Britain in the last 4,450 years, and detect evidence for selection in six genomic regions, including the well-characterized LCT locus. Our work is the first genome-wide scan characterizing signals of general diploid selection.
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Affiliation(s)
- Adam G Fine
- Department of Ecology and Evolution, University of Chicago
- Graduate Program in Biophysical Sciences, University of Chicago
| | - Matthias Steinrücken
- Department of Ecology and Evolution, University of Chicago
- Department of Human Genetics, University of Chicago
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2
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Fazzari V, Moo-Choy A, Panoyan MA, Abbatangelo CL, Polimanti R, Novroski NM, Wendt FR. Multi-ancestry tandem repeat association study of hair colour using exome-wide sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.24.581865. [PMID: 38464141 PMCID: PMC10925195 DOI: 10.1101/2024.02.24.581865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Hair colour variation is influenced by hundreds of positions across the human genome but this genetic contribution has only been narrowly explored. Genome-wide association studies identified single nucleotide polymorphisms (SNPs) influencing hair colour but the biology underlying these associations is challenging to interpret. We report 16 tandem repeats (TRs) with effects on different models of hair colour plus two TRs associated with hair colour in diverse ancestry groups. Several of these TRs expand or contract amino acid coding regions of their localized protein such that structure, and by extension function, may be altered. We also demonstrate that independent of SNP variation, these TRs can be used to great an additive polygenic score that predicts darker hair colour. This work adds to the growing body of evidence regarding TR influence on human traits with relatively large and independent effects relative to surrounding SNP variation.
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3
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Shuey MM, Lee KM, Keaton J, Khankari NK, Breeyear JH, Walker VM, Miller DR, Heberer KR, Reaven PD, Clarke SL, Lee J, Lynch JA, Vujkovic M, Edwards TL. A genetically supported drug repurposing pipeline for diabetes treatment using electronic health records. EBioMedicine 2023; 94:104674. [PMID: 37399599 PMCID: PMC10328805 DOI: 10.1016/j.ebiom.2023.104674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 07/05/2023] Open
Abstract
BACKGROUND The identification of new uses for existing drug therapies has the potential to identify treatments for comorbid conditions that have the added benefit of glycemic control while also providing a rapid, low-cost approach to drug (re)discovery. METHODS We developed and tested a genetically-informed drug-repurposing pipeline for diabetes management. This approach mapped genetically-predicted gene expression signals from the largest genome-wide association study for type 2 diabetes mellitus to drug targets using publicly available databases to identify drug-gene pairs. These drug-gene pairs were then validated using a two-step approach: 1) a self-controlled case-series (SCCS) using electronic health records from a discovery and replication population, and 2) Mendelian randomization (MR). FINDINGS After filtering on sample size, 20 candidate drug-gene pairs were validated and various medications demonstrated evidence of glycemic regulation including two anti-hypertensive classes: angiotensin-converting enzyme inhibitors as well as calcium channel blockers (CCBs). The CCBs demonstrated the strongest evidence of glycemic reduction in both validation approaches (SCCS HbA1c and glucose reduction: -0.11%, p = 0.01 and -0.85 mg/dL, p = 0.02, respectively; MR: OR = 0.84, 95% CI = 0.81, 0.87, p = 5.0 x 10-25). INTERPRETATION Our results support CCBs as a strong candidate medication for blood glucose reduction in addition to cardiovascular disease reduction. Further, these results support the adaptation of this approach for use in future drug-repurposing efforts for other conditions. FUNDING National Institutes of Health, Medical Research Council Integrative Epidemiology Unit at the University of Bristol, UK Medical Research Council, American Heart Association, and Department of Veterans Affairs (VA) Informatics and Computing Infrastructure and VA Cooperative Studies Program.
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Affiliation(s)
- Megan M Shuey
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kyung Min Lee
- VA Informatics and Computer Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT, USA
| | - Jacob Keaton
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA; Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nikhil K Khankari
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joseph H Breeyear
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA; Nashville VA Medical Center, Nashville, TN, USA
| | - Venexia M Walker
- Medical Research Council, Integrative Epidemiology Unit, University of Bristol, Bristol, UK; Bristol Medical School, UK; Population Health Sciences, University of Bristol, Bristol, UK; Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Donald R Miller
- Center for Healthcare Organization and Implementation Research, Bedford VA Healthcare System, Bedford, MA, USA; Center for Population Health, Department of Biomedical and Nutritional Sciences, University of Massachusetts, Lowell, MA, USA
| | - Kent R Heberer
- VA Palo Alto Health Care System, Palo Alto, CA, USA; Departments of Medicine and Endocrinology, Stanford University School of Medicine, Stanford, CA, USA
| | - Peter D Reaven
- Phoenix VA Health Care System, Phoenix, AZ, USA; College of Medicine, University of Arizona, Phoenix, AZ, USA
| | - Shoa L Clarke
- Departments of Medicine and Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jennifer Lee
- VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Julie A Lynch
- VA Informatics and Computer Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT, USA; School of Medicine, University of Utah, Salt Lake City, UT, USA
| | - Marijana Vujkovic
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA; Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| | - Todd L Edwards
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA; Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Nashville VA Medical Center, Nashville, TN, USA.
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Kayser M, Branicki W, Parson W, Phillips C. Recent advances in Forensic DNA Phenotyping of appearance, ancestry and age. Forensic Sci Int Genet 2023; 65:102870. [PMID: 37084623 DOI: 10.1016/j.fsigen.2023.102870] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/04/2023] [Indexed: 04/09/2023]
Abstract
Forensic DNA Phenotyping (FDP) comprises the prediction of a person's externally visible characteristics regarding appearance, biogeographic ancestry and age from DNA of crime scene samples, to provide investigative leads to help find unknown perpetrators that cannot be identified with forensic STR-profiling. In recent years, FDP has advanced considerably in all of its three components, which we summarize in this review article. Appearance prediction from DNA has broadened beyond eye, hair and skin color to additionally comprise other traits such as eyebrow color, freckles, hair structure, hair loss in men, and tall stature. Biogeographic ancestry inference from DNA has progressed from continental ancestry to sub-continental ancestry detection and the resolving of co-ancestry patterns in genetically admixed individuals. Age estimation from DNA has widened beyond blood to more somatic tissues such as saliva and bones as well as new markers and tools for semen. Technological progress has allowed forensically suitable DNA technology with largely increased multiplex capacity for the simultaneous analysis of hundreds of DNA predictors with targeted massively parallel sequencing (MPS). Forensically validated MPS-based FDP tools for predicting from crime scene DNA i) several appearance traits, ii) multi-regional ancestry, iii) several appearance traits together with multi-regional ancestry, and iv) age from different tissue types, are already available. Despite recent advances that will likely increase the impact of FDP in criminal casework in the near future, moving reliable appearance, ancestry and age prediction from crime scene DNA to the level of detail and accuracy police investigators may desire, requires further intensified scientific research together with technical developments and forensic validations as well as the necessary funding.
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Affiliation(s)
- Manfred Kayser
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Wojciech Branicki
- Institute of Zoology and Biomedical Research, Jagiellonian University, Kraków, Poland,; Institute of Forensic Research, Kraków, Poland
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, PA, USA
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
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Farré X, Blay N, Cortés B, Carreras A, Iraola-Guzmán S, de Cid R. Skin Phototype and Disease: A Comprehensive Genetic Approach to Pigmentary Traits Pleiotropy Using PRS in the GCAT Cohort. Genes (Basel) 2023; 14:149. [PMID: 36672889 PMCID: PMC9859115 DOI: 10.3390/genes14010149] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/22/2022] [Accepted: 12/26/2022] [Indexed: 01/09/2023] Open
Abstract
Human pigmentation has largely been associated with different disease prevalence among populations, but most of these studies are observational and inconclusive. Known to be genetically determined, pigmentary traits have largely been studied by Genome-Wide Association Study (GWAS), mostly in Caucasian ancestry cohorts from North Europe, identifying robustly, several loci involved in many of the pigmentary traits. Here, we conduct a detailed analysis by GWAS and Polygenic Risk Score (PRS) of 13 pigmentary-related traits in a South European cohort of Caucasian ancestry (n = 20,000). We observed fair phototype strongly associated with non-melanoma skin cancer and other dermatoses and confirmed by PRS-approach the shared genetic basis with skin and eye diseases, such as melanoma (OR = 0.95), non-melanoma skin cancer (OR = 0.93), basal cell carcinoma (OR = 0.97) and darker phototype with vitiligo (OR = 1.02), cataracts (OR = 1.04). Detailed genetic analyses revealed 37 risk loci associated with 10 out of 13 analyzed traits, and 16 genes significantly associated with at least two pigmentary traits. Some of them have been widely reported, such as MC1R, HERC2, OCA2, TYR, TYRP1, SLC45A2, and some novel candidate genes C1QTNF3, LINC02876, and C1QTNF3-AMACR have not been reported in the GWAS Catalog, with regulatory potential. These results highlight the importance of the assess phototype as a genetic proxy of skin functionality and disease when evaluating open mixed populations.
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Affiliation(s)
| | | | | | | | | | - Rafael de Cid
- Genomes for Life-GCAT Lab, Germans Trias i Pujol Research Institute (IGTP), 08916 Badalona, Spain
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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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Kataria S, Dabas P, Saraswathy KN, Sachdeva MP, Jain S. Investigating the morphology and genetics of scalp and facial hair characteristics for phenotype prediction. Sci Justice 2023; 63:135-148. [PMID: 36631178 DOI: 10.1016/j.scijus.2022.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Microscopic traits and ultrastructure of hair such as cross-sectional shape, pigmentation, curvature, and internal structure help determine the level of variations between and across human populations. Apart from cosmetics and anthropological applications, such as determining species, somatic origin (body area), and biogeographic ancestry, the evidential value of hair has increased with rapid progression in the area of forensic DNA phenotyping (FDP). Individuals differ in the features of their scalp hair (greying, shape, colour, balding, thickness, and density) and facial hair (eyebrow thickness, monobrow, and beard thickness) features. Scalp and facial hair characteristics are genetically controlled and lead to visible inter-individual variations within and among populations of various ethnic origins. Hence, these characteristics can be exploited and made more inclusive in FDP, thereby leading to more comprehensive, accurate, and robust prediction models for forensic purposes. The present article focuses on understanding the genetics of scalp and facial hair characteristics with the goal to develop a more inclusive approach to better understand hair biology by integrating hair microscopy with genetics for genotype-phenotype correlation research.
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Affiliation(s)
- Suraj Kataria
- Department of Anthropology, University of Delhi, India.
| | - Prashita Dabas
- Amity Institute of Forensic Sciences, Amity University, Noida, Uttar Pradesh, India.
| | | | - M P Sachdeva
- Department of Anthropology, University of Delhi, India.
| | - Sonal Jain
- Department of Anthropology, University of Delhi, India.
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Simcoe MJ, Shah A, Fan B, Choquet H, Weisschuh N, Waseem NH, Jiang C, Melles RB, Ritch R, Mahroo OA, Wissinger B, Jorgenson E, Wiggs JL, Garway-Heath DF, Hysi PG, Hammond CJ. Genome-Wide Association Study Identifies Two Common Loci Associated with Pigment Dispersion Syndrome/Pigmentary Glaucoma and Implicates Myopia in its Development. Ophthalmology 2022; 129:626-636. [PMID: 35031440 DOI: 10.1016/j.ophtha.2022.01.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 01/03/2022] [Accepted: 01/05/2022] [Indexed: 11/27/2022] Open
Abstract
PURPOSE To identify genetic variants associated with pigment dispersion syndrome (PDS) and pigmentary glaucoma (PG) in unrelated patients and to further understand the genetic and potentially causal relationships between PDS and associated risk factors. DESIGN A 2-stage genome-wide association meta-analysis with replication and subsequent in silico analyses including Mendelian randomization. PARTICIPANTS A total of 574 cases with PG or PDS and 52 627 controls of European descent. METHODS Genome-wide association analyses were performed in 4 cohorts and meta-analyzed in 3 stages: (1) a discovery meta-analysis was performed in 3 cohorts, (2) replication was performed in the fourth cohort, and (3) all 4 cohorts were meta-analyzed to increase statistical power. Two-sample Mendelian randomization was used to determine whether refractive error and intraocular pressure exert causal effects over PDS. MAIN OUTCOME MEASURES The association of genetic variants with PDS and whether myopia exerts causal effects over PDS. RESULTS Significant association was present at 2 novel loci for PDS/PG. These loci and follow-up analyses implicate the genes gamma secretase activator protein (GSAP) (lead single nucleotide polymorphism [SNP]: rs9641220, P = 6.0×10-10) and glutamate metabotropic receptor 5 (GRM5)/TYR (lead SNP: rs661177, P = 3.9×10-9) as important factors in disease risk. Mendelian randomization showed significant evidence that negative refractive error (myopia) exerts a direct causal effect over PDS (P = 8.86×10-7). CONCLUSIONS Common SNPs relating to the GSAP and GRM5/TYR genes are associated risk factors for the development of PDS and PG. Although myopia is a known risk factor, this study uses genetic data to demonstrate that myopia is, in part, a cause of PDS and PG.
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Affiliation(s)
- Mark J Simcoe
- Department of Ophthalmology, Kings College London, London, United Kingdom; Department of Twins Research and Genetic Epidemiology, Kings College London, London, United Kingdom; Institute of Ophthalmology, University College London, London, United Kingdom
| | - Ameet Shah
- Department of Ophthalmology, Royal Free Hospital NHS Foundation Trust, Pond Street, London, United Kingdom
| | - Baojian Fan
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts
| | - Hélène Choquet
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Nicole Weisschuh
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Naushin H Waseem
- Institute of Ophthalmology, University College London, London, United Kingdom
| | - Chen Jiang
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Ronald B Melles
- Kaiser Permanente Northern California, Department of Ophthalmology, Redwood City, California
| | - Robert Ritch
- Einhorn Clinical Research Center, New York Eye and Ear Infirmary of Mount Sinai, New York, New York
| | - Omar A Mahroo
- Department of Ophthalmology, Kings College London, London, United Kingdom; Department of Twins Research and Genetic Epidemiology, Kings College London, London, United Kingdom; Institute of Ophthalmology, University College London, London, United Kingdom
| | - Bernd Wissinger
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Janey L Wiggs
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts
| | - David F Garway-Heath
- National Institute for Health Research Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, United Kingdom
| | - Pirro G Hysi
- Department of Ophthalmology, Kings College London, London, United Kingdom; Department of Twins Research and Genetic Epidemiology, Kings College London, London, United Kingdom
| | - Christopher J Hammond
- Department of Ophthalmology, Kings College London, London, United Kingdom; Department of Twins Research and Genetic Epidemiology, Kings College London, London, United Kingdom.
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Bonilla C, Mejia-Lancheros C. The Skin We Live in: Pigmentation Traits and Tanning Behaviour in British Young Adults, an Observational and Genetically-Informed Study. Genes (Basel) 2022; 13:896. [PMID: 35627282 PMCID: PMC9140533 DOI: 10.3390/genes13050896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 02/04/2023] Open
Abstract
Skin cancer incidence has been increasing worldwide, representing a particularly high burden for populations of European ancestry. Outdoor and indoor tanning using ultraviolet (UV) radiation devices are major risk factors for skin cancer. While tanning behaviours can be modified by targeted interventions to reduce skin cancer rates, there is insufficient evidence on the motivations for tanning preferences and their relationship with pigmentation phenotypes. The present observational and genetically-informed study investigates motives for tanning and the role that pigmentation phenotypes play on outdoor and indoor tanning behaviour in British young adults. This study included 3722 participants from the Avon Longitudinal Study of Parents and Children in South West England, with data on pigmentation features, tanning ability and preferences, and SNP genotypes. Liking to tan and outdoor tanning were strongly influenced by pigmentary traits and tanning ability. However, the association of these phenotypes with UV indoor tanning was weaker. Our results provide evidence to support the implementation of skin cancer preventative interventions that consider individual biological characteristics and motives for undergoing outdoor and indoor tanning.
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Affiliation(s)
- Carolina Bonilla
- Departamento de Medicina Preventiva, Faculdade de Medicina, Universidade de São Paulo, São Paulo CEP 01246-903, Brazil
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Cilia Mejia-Lancheros
- MAP Centre for Urban Health Solutions, Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON M5B 1W8, Canada;
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Pośpiech E, Teisseyre P, Mielniczuk J, Branicki W. Predicting Physical Appearance from DNA Data-Towards Genomic Solutions. Genes (Basel) 2022; 13:genes13010121. [PMID: 35052461 PMCID: PMC8774670 DOI: 10.3390/genes13010121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 02/04/2023] Open
Abstract
The idea of forensic DNA intelligence is to extract from genomic data any information that can help guide the investigation. The clues to the externally visible phenotype are of particular practical importance. The high heritability of the physical phenotype suggests that genetic data can be easily predicted, but this has only become possible with less polygenic traits. The forensic community has developed DNA-based predictive tools by employing a limited number of the most important markers analysed with targeted massive parallel sequencing. The complexity of the genetics of many other appearance phenotypes requires big data coupled with sophisticated machine learning methods to develop accurate genomic predictors. A significant challenge in developing universal genomic predictive methods will be the collection of sufficiently large data sets. These should be created using whole-genome sequencing technology to enable the identification of rare DNA variants implicated in phenotype determination. It is worth noting that the correctness of the forensic sketch generated from the DNA data depends on the inclusion of an age factor. This, however, can be predicted by analysing epigenetic data. An important limitation preventing whole-genome approaches from being commonly used in forensics is the slow progress in the development and implementation of high-throughput, low DNA input sequencing technologies. The example of palaeoanthropology suggests that such methods may possibly be developed in forensics.
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Affiliation(s)
- Ewelina Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland;
| | - Paweł Teisseyre
- Institute of Computer Science, Polish Academy of Sciences, 01-248 Warsaw, Poland; (P.T.); (J.M.)
- Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland
| | - Jan Mielniczuk
- Institute of Computer Science, Polish Academy of Sciences, 01-248 Warsaw, Poland; (P.T.); (J.M.)
- Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland;
- Central Forensic Laboratory of the Police, 00-583 Warsaw, Poland
- Correspondence: ; Tel.: +48-126-645-024
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11
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Mathieson I, Terhorst J. Direct detection of natural selection in Bronze Age Britain. Genome Res 2022; 32:2057-2067. [PMID: 36316157 PMCID: PMC9808619 DOI: 10.1101/gr.276862.122] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 08/29/2022] [Indexed: 11/04/2022]
Abstract
We developed a novel method for efficiently estimating time-varying selection coefficients from genome-wide ancient DNA data. In simulations, our method accurately recovers selective trajectories and is robust to misspecification of population size. We applied it to a large data set of ancient and present-day human genomes from Britain and identified seven loci with genome-wide significant evidence of selection in the past 4500 yr. Almost all of them can be related to increased vitamin D or calcium levels, suggesting strong selective pressure on these or related phenotypes. However, the strength of selection on individual loci varied substantially over time, suggesting that cultural or environmental factors moderated the genetic response. Of 28 complex anthropometric and metabolic traits, skin pigmentation was the only one with significant evidence of polygenic selection, further underscoring the importance of phenotypes related to vitamin D. Our approach illustrates the power of ancient DNA to characterize selection in human populations and illuminates the recent evolutionary history of Britain.
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Affiliation(s)
- Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jonathan Terhorst
- Department of Statistics, University of Michigan, Ann Arbor, Michigan 48109, USA
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12
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Venkataraman GR, DeBoever C, Tanigawa Y, Aguirre M, Ioannidis AG, Mostafavi H, Spencer CCA, Poterba T, Bustamante CD, Daly MJ, Pirinen M, Rivas MA. Bayesian model comparison for rare-variant association studies. Am J Hum Genet 2021; 108:2354-2367. [PMID: 34822764 PMCID: PMC8715195 DOI: 10.1016/j.ajhg.2021.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 11/02/2021] [Indexed: 12/12/2022] Open
Abstract
Whole-genome sequencing studies applied to large populations or biobanks with extensive phenotyping raise new analytic challenges. The need to consider many variants at a locus or group of genes simultaneously and the potential to study many correlated phenotypes with shared genetic architecture provide opportunities for discovery not addressed by the traditional one variant, one phenotype association study. Here, we introduce a Bayesian model comparison approach called MRP (multiple rare variants and phenotypes) for rare-variant association studies that considers correlation, scale, and direction of genetic effects across a group of genetic variants, phenotypes, and studies, requiring only summary statistic data. We apply our method to exome sequencing data (n = 184,698) across 2,019 traits from the UK Biobank, aggregating signals in genes. MRP demonstrates an ability to recover signals such as associations between PCSK9 and LDL cholesterol levels. We additionally find MRP effective in conducting meta-analyses in exome data. Non-biomarker findings include associations between MC1R and red hair color and skin color, IL17RA and monocyte count, and IQGAP2 and mean platelet volume. Finally, we apply MRP in a multi-phenotype setting; after clustering the 35 biomarker phenotypes based on genetic correlation estimates, we find that joint analysis of these phenotypes results in substantial power gains for gene-trait associations, such as in TNFRSF13B in one of the clusters containing diabetes- and lipid-related traits. Overall, we show that the MRP model comparison approach improves upon useful features from widely used meta-analysis approaches for rare-variant association analyses and prioritizes protective modifiers of disease risk.
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Affiliation(s)
| | - Christopher DeBoever
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Yosuke Tanigawa
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Matthew Aguirre
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | | | | | | | - Timothy Poterba
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carlos D Bustamante
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Mark J Daly
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Matti Pirinen
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland; Department of Public Health, University of Helsinki, Helsinki 00014, Finland; Department of Mathematics and Statistics, University of Helsinki, Helsinki 00014, Finland.
| | - Manuel A Rivas
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA.
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13
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A large Canadian cohort provides insights into the genetic architecture of human hair colour. Commun Biol 2021; 4:1253. [PMID: 34737440 PMCID: PMC8568909 DOI: 10.1038/s42003-021-02764-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 10/08/2021] [Indexed: 12/05/2022] Open
Abstract
Hair colour is a polygenic phenotype that results from differences in the amount and ratio of melanins located in the hair bulb. Genome-wide association studies (GWAS) have identified many loci involved in the pigmentation pathway affecting hair colour. However, most of the associated loci overlap non-protein coding regions and many of the molecular mechanisms underlying pigmentation variation are still not understood. Here, we conduct GWAS meta-analyses of hair colour in a Canadian cohort of 12,741 individuals of European ancestry. By performing fine-mapping analyses we identify candidate causal variants in pigmentation loci associated with blonde, red and brown hair colour. Additionally, we observe colocalization of several GWAS hits with expression and methylation quantitative trait loci (QTLs) of cultured melanocytes. Finally, transcriptome-wide association studies (TWAS) further nominate the expression of EDNRB and CDK10 as significantly associated with hair colour. Our results provide insights on the mechanisms regulating pigmentation biology in humans.
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14
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A Genome-Wide Scan on Individual Typology Angle Found Variants at SLC24A2 Associated with Skin Color Variation in Chinese Populations. J Invest Dermatol 2021; 142:1223-1227.e14. [PMID: 34570997 DOI: 10.1016/j.jid.2021.07.186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 07/01/2021] [Accepted: 07/09/2021] [Indexed: 11/21/2022]
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15
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GenNet framework: interpretable deep learning for predicting phenotypes from genetic data. Commun Biol 2021; 4:1094. [PMID: 34535759 PMCID: PMC8448759 DOI: 10.1038/s42003-021-02622-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 08/26/2021] [Indexed: 12/31/2022] Open
Abstract
Applying deep learning in population genomics is challenging because of computational issues and lack of interpretable models. Here, we propose GenNet, a novel open-source deep learning framework for predicting phenotypes from genetic variants. In this framework, interpretable and memory-efficient neural network architectures are constructed by embedding biologically knowledge from public databases, resulting in neural networks that contain only biologically plausible connections. We applied the framework to seventeen phenotypes and found well-replicated genes such as HERC2 and OCA2 for hair and eye color, and novel genes such as ZNF773 and PCNT for schizophrenia. Additionally, the framework identified ubiquitin mediated proteolysis, endocrine system and viral infectious diseases as most predictive biological pathways for schizophrenia. GenNet is a freely available, end-to-end deep learning framework that allows researchers to develop and use interpretable neural networks to obtain novel insights into the genetic architecture of complex traits and diseases. van Hilten and colleagues present GenNet, a deep-learning framework for predicting phenotype from genetic data. This framework generates interpretable neural networks that provide insight into the genetic basis of complex traits and diseases.
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16
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Boer CG, Hatzikotoulas K, Southam L, Stefánsdóttir L, Zhang Y, Coutinho de Almeida R, Wu TT, Zheng J, Hartley A, Teder-Laving M, Skogholt AH, Terao C, Zengini E, Alexiadis G, Barysenka A, Bjornsdottir G, Gabrielsen ME, Gilly A, Ingvarsson T, Johnsen MB, Jonsson H, Kloppenburg M, Luetge A, Lund SH, Mägi R, Mangino M, Nelissen RRGHH, Shivakumar M, Steinberg J, Takuwa H, Thomas LF, Tuerlings M, Babis GC, Cheung JPY, Kang JH, Kraft P, Lietman SA, Samartzis D, Slagboom PE, Stefansson K, Thorsteinsdottir U, Tobias JH, Uitterlinden AG, Winsvold B, Zwart JA, Davey Smith G, Sham PC, Thorleifsson G, Gaunt TR, Morris AP, Valdes AM, Tsezou A, Cheah KSE, Ikegawa S, Hveem K, Esko T, Wilkinson JM, Meulenbelt I, Lee MTM, van Meurs JBJ, Styrkársdóttir U, Zeggini E. Deciphering osteoarthritis genetics across 826,690 individuals from 9 populations. Cell 2021; 184:4784-4818.e17. [PMID: 34450027 PMCID: PMC8459317 DOI: 10.1016/j.cell.2021.07.038] [Citation(s) in RCA: 159] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 03/26/2021] [Accepted: 07/30/2021] [Indexed: 12/19/2022]
Abstract
Osteoarthritis affects over 300 million people worldwide. Here, we conduct a genome-wide association study meta-analysis across 826,690 individuals (177,517 with osteoarthritis) and identify 100 independently associated risk variants across 11 osteoarthritis phenotypes, 52 of which have not been associated with the disease before. We report thumb and spine osteoarthritis risk variants and identify differences in genetic effects between weight-bearing and non-weight-bearing joints. We identify sex-specific and early age-at-onset osteoarthritis risk loci. We integrate functional genomics data from primary patient tissues (including articular cartilage, subchondral bone, and osteophytic cartilage) and identify high-confidence effector genes. We provide evidence for genetic correlation with phenotypes related to pain, the main disease symptom, and identify likely causal genes linked to neuronal processes. Our results provide insights into key molecular players in disease processes and highlight attractive drug targets to accelerate translation.
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Affiliation(s)
- Cindy G Boer
- Department of Internal Medicine, Erasmus MC, Medical Center, 3015CN Rotterdam, the Netherlands
| | - Konstantinos Hatzikotoulas
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Lorraine Southam
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | | | - Yanfei Zhang
- Genomic Medicine Institute, Geisinger Health System, Danville, PA 17822, USA
| | - Rodrigo Coutinho de Almeida
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Postzone S05-P Leiden University Medical Center, 2333ZC Leiden, the Netherlands
| | - Tian T Wu
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Jie Zheng
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - April Hartley
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; Musculoskeletal Research Unit, Translation Health Sciences, Bristol Medical School, University of Bristol, Southmead Hospital, Bristol BS10 5NB, UK
| | - Maris Teder-Laving
- Estonian Genome Center, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Anne Heidi Skogholt
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan
| | - Eleni Zengini
- 4(th) Psychiatric Department, Dromokaiteio Psychiatric Hospital, 12461 Athens, Greece
| | - George Alexiadis
- 1(st) Department of Orthopaedics, KAT General Hospital, 14561 Athens, Greece
| | - Andrei Barysenka
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | | | - Maiken E Gabrielsen
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Arthur Gilly
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Thorvaldur Ingvarsson
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland; Department of Orthopedic Surgery, Akureyri Hospital, 600 Akureyri, Iceland
| | - Marianne B Johnsen
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7491 Trondheim, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0316 Oslo, Norway; Research and Communication Unit for Musculoskeletal Health (FORMI), Department of Research, Innovation and Education, Division of Clinical Neuroscience, Oslo University Hospital, 0424 Oslo, Norway
| | - Helgi Jonsson
- Department of Medicine, Landspitali The National University Hospital of Iceland, 108 Reykjavik, Iceland; Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Margreet Kloppenburg
- Departments of Rheumatology and Clinical Epidemiology, Leiden University Medical Center, 9600, 23OORC Leiden, the Netherlands
| | - Almut Luetge
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | | | - Reedik Mägi
- Estonian Genome Center, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, Kings College London, London SE1 7EH, UK
| | - Rob R G H H Nelissen
- Department of Orthopaedics, Leiden University Medical Center, 9600, 23OORC Leiden, the Netherlands
| | - Manu Shivakumar
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Julia Steinberg
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Daffodil Centre, The University of Sydney, a joint venture with Cancer Council NSW, Sydney, NSW 1340, Australia
| | - Hiroshi Takuwa
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan; Department of Orthopedic Surgery, Shimane University, Shimane 693-8501, Japan
| | - Laurent F Thomas
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7491 Trondheim, Norway; Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway; BioCore-Bioinformatics Core Facility, Norwegian University of Science and Technology, 7491 Trondheim, Norway; Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, 7030 Trondheim, Norway
| | - Margo Tuerlings
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Postzone S05-P Leiden University Medical Center, 2333ZC Leiden, the Netherlands
| | - George C Babis
- 2(nd) Department of Orthopaedics, National and Kapodistrian University of Athens, Medical School, Nea Ionia General Hospital Konstantopouleio, 14233 Athens, Greece
| | - Jason Pui Yin Cheung
- Department of Orthopaedics and Traumatology, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Jae Hee Kang
- Department of Medicine, Brigham and Women's Hospital, 181 Longwood Ave, Boston, MA 02115, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
| | - Steven A Lietman
- Musculoskeletal Institute, Geisinger Health System, Danville, PA 17822, USA
| | - Dino Samartzis
- Department of Orthopaedics and Traumatology, The University of Hong Kong, Pokfulam, Hong Kong, China; Department of Orthopaedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA
| | - P Eline Slagboom
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Postzone S05-P Leiden University Medical Center, 2333ZC Leiden, the Netherlands
| | - Kari Stefansson
- deCODE Genetics/Amgen Inc., 102 Reykjavik, Iceland; Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen Inc., 102 Reykjavik, Iceland; Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Jonathan H Tobias
- Musculoskeletal Research Unit, Translation Health Sciences, Bristol Medical School, University of Bristol, Southmead Hospital, Bristol BS10 5NB, UK; MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus MC, Medical Center, 3015CN Rotterdam, the Netherlands
| | - Bendik Winsvold
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7491 Trondheim, Norway; Department of Research, Innovation and Education, Division of Clinical Neuroscience, Oslo University Hospital and University of Oslo, 0450 Oslo, Norway; Department of Neurology, Oslo University Hospital, 0424 Oslo, Norway
| | - John-Anker Zwart
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7491 Trondheim, Norway; Department of Research, Innovation and Education, Division of Clinical Neuroscience, Oslo University Hospital and University of Oslo, 0450 Oslo, Norway
| | - George Davey Smith
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Pak Chung Sham
- Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | | | - Tom R Gaunt
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, University of Manchester, Manchester M13 9LJ, UK
| | - Ana M Valdes
- Faculty of Medicine and Health Sciences, School of Medicine, University of Nottingham, Nottingham, Nottinghamshire NG5 1PB, UK
| | - Aspasia Tsezou
- Laboratory of Cytogenetics and Molecular Genetics, Faculty of Medicine, University of Thessaly, Larissa 411 10, Greece
| | - Kathryn S E Cheah
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Shiro Ikegawa
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7491 Trondheim, Norway; HUNT Research Center, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7600 Levanger, Norway
| | - Tõnu Esko
- Estonian Genome Center, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - J Mark Wilkinson
- Department of Oncology and Metabolism and Healthy Lifespan Institute, University of Sheffield, Sheffield S10 2RX, UK
| | - Ingrid Meulenbelt
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Postzone S05-P Leiden University Medical Center, 2333ZC Leiden, the Netherlands
| | - Ming Ta Michael Lee
- Genomic Medicine Institute, Geisinger Health System, Danville, PA 17822, USA; Institute of Biomedical Sciences, Academia Sinica, 115 Taipei, Taiwan
| | - Joyce B J van Meurs
- Department of Internal Medicine, Erasmus MC, Medical Center, 3015CN Rotterdam, the Netherlands
| | | | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; TUM School of Medicine, Technical University of Munich and Klinikum Rechts der Isar, 81675 Munich, Germany.
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17
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Zhang T, Choi J, Dilshat R, Einarsdóttir BÓ, Kovacs MA, Xu M, Malasky M, Chowdhury S, Jones K, Bishop DT, Goldstein AM, Iles MM, Landi MT, Law MH, Shi J, Steingrímsson E, Brown KM. Cell-type-specific meQTLs extend melanoma GWAS annotation beyond eQTLs and inform melanocyte gene-regulatory mechanisms. Am J Hum Genet 2021; 108:1631-1646. [PMID: 34293285 PMCID: PMC8456160 DOI: 10.1016/j.ajhg.2021.06.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 06/23/2021] [Indexed: 01/09/2023] Open
Abstract
Although expression quantitative trait loci (eQTLs) have been powerful in identifying susceptibility genes from genome-wide association study (GWAS) findings, most trait-associated loci are not explained by eQTLs alone. Alternative QTLs, including DNA methylation QTLs (meQTLs), are emerging, but cell-type-specific meQTLs using cells of disease origin have been lacking. Here, we established an meQTL dataset by using primary melanocytes from 106 individuals and identified 1,497,502 significant cis-meQTLs. Multi-QTL colocalization with meQTLs, eQTLs, and mRNA splice-junction QTLs from the same individuals together with imputed methylome-wide and transcriptome-wide association studies identified candidate susceptibility genes at 63% of melanoma GWAS loci. Among the three molecular QTLs, meQTLs were the single largest contributor. To compare melanocyte meQTLs with those from malignant melanomas, we performed meQTL analysis on skin cutaneous melanomas from The Cancer Genome Atlas (n = 444). A substantial proportion of meQTL probes (45.9%) in primary melanocytes is preserved in melanomas, while a smaller fraction of eQTL genes is preserved (12.7%). Integration of melanocyte multi-QTLs and melanoma meQTLs identified candidate susceptibility genes at 72% of melanoma GWAS loci. Beyond GWAS annotation, meQTL-eQTL colocalization in melanocytes suggested that 841 unique genes potentially share a causal variant with a nearby methylation probe in melanocytes. Finally, melanocyte trans-meQTLs identified a hotspot for rs12203592, a cis-eQTL of a transcription factor, IRF4, with 131 candidate target CpGs. Motif enrichment and IRF4 ChIP-seq analysis demonstrated that these target CpGs are enriched in IRF4 binding sites, suggesting an IRF4-mediated regulatory network. Our study highlights the utility of cell-type-specific meQTLs.
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Affiliation(s)
- Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ramile Dilshat
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Berglind Ósk Einarsdóttir
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Michael A Kovacs
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Mai Xu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael Malasky
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Salma Chowdhury
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - D Timothy Bishop
- Leeds Institute for Data Analytics, School of Medicine, University of Leeds, Leeds LS9 7TF, UK
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Mark M Iles
- Leeds Institute for Data Analytics, School of Medicine, University of Leeds, Leeds LS9 7TF, UK
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Matthew H Law
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD 4059, Australia
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Eiríkur Steingrímsson
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Kevin M Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA.
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18
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Wang F, Luo Q, Chen Y, Liu Y, Xu K, Adhikari K, Cai X, Liu J, Li Y, Liu X, Ramirez-Aristeguieta LM, Yuan Z, Zhou Y, Li FF, Jiang B, Jin L, Ruiz-Linares A, Yang Z, Liu F, Wang S. A Genome-Wide Scan on Individual Typology Angle Found Variants at SLC24A2 Associated with Skin Color Variation in Chinese Populations. J Invest Dermatol 2021. [DOI: https://doi.org/10.1016/j.jid.2021.07.186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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19
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Sanderson E, Richardson TG, Hemani G, Davey Smith G. The use of negative control outcomes in Mendelian randomization to detect potential population stratification. Int J Epidemiol 2021; 50:1350-1361. [PMID: 33570130 PMCID: PMC8407870 DOI: 10.1093/ije/dyaa288] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2021] [Indexed: 12/14/2022] Open
Abstract
A key assumption of Mendelian randomization (MR) analysis is that there is no association between the genetic variants used as instruments and the outcome other than through the exposure of interest. One way in which this assumption can be violated is through population stratification, which can introduce confounding of the relationship between the genetic variants and the outcome and so induce an association between them. Negative control outcomes are increasingly used to detect unobserved confounding in observational epidemiological studies. Here we consider the use of negative control outcomes in MR studies to detect confounding of the genetic variants and the exposure or outcome. As a negative control outcome in an MR study, we propose the use of phenotypes which are determined before the exposure and outcome but which are likely to be subject to the same confounding as the exposure or outcome of interest. We illustrate our method with a two-sample MR analysis of a preselected set of exposures on self-reported tanning ability and hair colour. Our results show that, of the 33 exposures considered, genome-wide association studies (GWAS) of adiposity and education-related traits are likely to be subject to population stratification that is not controlled for through adjustment, and so any MR study including these traits may be subject to bias that cannot be identified through standard pleiotropy robust methods. Negative control outcomes should therefore be used regularly in MR studies to detect potential population stratification in the data used.
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Affiliation(s)
- Eleanor Sanderson
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Tom G Richardson
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - George Davey Smith
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
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20
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Allouche J, Rachmin I, Adhikari K, Pardo LM, Lee JH, McConnell AM, Kato S, Fan S, Kawakami A, Suita Y, Wakamatsu K, Igras V, Zhang J, Navarro PP, Lugo CM, Noonan HR, Christie KA, Itin K, Mujahid N, Lo JA, Won CH, Evans CL, Weng QY, Wang H, Osseiran S, Lovas A, Németh I, Cozzio A, Navarini AA, Hsiao JJ, Nguyen N, Kemény LV, Iliopoulos O, Berking C, Ruzicka T, Gonzalez-José R, Bortolini MC, Canizales-Quinteros S, Acuna-Alonso V, Gallo C, Poletti G, Bedoya G, Rothhammer F, Ito S, Schiaffino MV, Chao LH, Kleinstiver BP, Tishkoff S, Zon LI, Nijsten T, Ruiz-Linares A, Fisher DE, Roider E. NNT mediates redox-dependent pigmentation via a UVB- and MITF-independent mechanism. Cell 2021; 184:4268-4283.e20. [PMID: 34233163 PMCID: PMC8349839 DOI: 10.1016/j.cell.2021.06.022] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 03/09/2021] [Accepted: 06/15/2021] [Indexed: 12/26/2022]
Abstract
Ultraviolet (UV) light and incompletely understood genetic and epigenetic variations determine skin color. Here we describe an UV- and microphthalmia-associated transcription factor (MITF)-independent mechanism of skin pigmentation. Targeting the mitochondrial redox-regulating enzyme nicotinamide nucleotide transhydrogenase (NNT) resulted in cellular redox changes that affect tyrosinase degradation. These changes regulate melanosome maturation and, consequently, eumelanin levels and pigmentation. Topical application of small-molecule inhibitors yielded skin darkening in human skin, and mice with decreased NNT function displayed increased pigmentation. Additionally, genetic modification of NNT in zebrafish alters melanocytic pigmentation. Analysis of four diverse human cohorts revealed significant associations of skin color, tanning, and sun protection use with various single-nucleotide polymorphisms within NNT. NNT levels were independent of UVB irradiation and redox modulation. Individuals with postinflammatory hyperpigmentation or lentigines displayed decreased skin NNT levels, suggesting an NNT-driven, redox-dependent pigmentation mechanism that can be targeted with NNT-modifying topical drugs for medical and cosmetic purposes.
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Affiliation(s)
- Jennifer Allouche
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Inbal Rachmin
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Kaustubh Adhikari
- School of Mathematics and Statistics, The Open University, Milton Keynes, MK7 6AA, UK; Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Luba M Pardo
- Department of Dermatology, Erasmus Medical Center, 3015 Rotterdam, the Netherlands
| | - Ju Hee Lee
- Department of Dermatology and Cutaneous Biology Research Institute, Yonsei University College of Medicine, 03722 Seoul, Korea
| | - Alicia M McConnell
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and the Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Shinichiro Kato
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA; Department of Immunology, Center for 5D Cell Dynamics, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Shaohua Fan
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Fudan University, 200438 Shanghai, China
| | - Akinori Kawakami
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Yusuke Suita
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Kazumasa Wakamatsu
- Institute for Melanin Chemistry, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Vivien Igras
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Jianming Zhang
- National Research Center for Translational Medicine (Shanghai), State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025 Shanghai, China
| | - Paula P Navarro
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Camila Makhlouta Lugo
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Haley R Noonan
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and the Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Kathleen A Christie
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Kaspar Itin
- Department of Dermatology, University Hospital of Basel, 4031 Basel, Switzerland
| | - Nisma Mujahid
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA; Boston University School of Medicine, Boston, MA 02118, USA; University of Utah, Department of Dermatology, Salt Lake City, UT 84132, USA
| | - Jennifer A Lo
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Chong Hyun Won
- Department of Dermatology, Asan Medical Center, Ulsan University College of Medicine, 05505 Seoul, Korea
| | - Conor L Evans
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Qing Yu Weng
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Hequn Wang
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Sam Osseiran
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Alyssa Lovas
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - István Németh
- Department of Dermatology and Allergology, University of Szeged, 6720 Szeged, Hungary
| | - Antonio Cozzio
- Department of Dermatology, Venerology, and Allergology, Kantonsspital St. Gallen, 9007 St. Gallen, Switzerland
| | - Alexander A Navarini
- Department of Dermatology, University Hospital of Basel, 4031 Basel, Switzerland
| | - Jennifer J Hsiao
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Nhu Nguyen
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Lajos V Kemény
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA; Department of Dermatology, Venereology, and Dermatooncology, Semmelweis University, 1085 Budapest, Hungary
| | - Othon Iliopoulos
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Carola Berking
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich Alexander University Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Thomas Ruzicka
- Department of Dermatology and Allergy, University Hospital Munich, Ludwig Maximilian University, 80337 Munich, Germany
| | - Rolando Gonzalez-José
- Instituto Patagónico de Ciencias Sociales y Humanas-Centro Nacional Patagónico, CONICET, Puerto Madryn U912OACD, Argentina
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México e Instituto Nacional de Medicina Genómica, Mexico City 04510, Mexico
| | | | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | - Gabriel Bedoya
- Genética Molecular (GENMOL), Universidad de Antioquia, Medellín 5001000, Colombia
| | - Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1000009, Chile; Programa de Genetica Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago 1027, Chile
| | - Shosuke Ito
- Institute for Melanin Chemistry, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Maria Vittoria Schiaffino
- Internal Medicine, Diabetes and Endocrinology Unit, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Luke H Chao
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah Tishkoff
- Departments of Genetics and Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Leonard I Zon
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and the Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Tamar Nijsten
- Department of Dermatology, Erasmus Medical Center, 3015 Rotterdam, the Netherlands
| | - Andrés Ruiz-Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200433, China; UMR 7268, CNRS-EFS-ADES, Aix-Marseille University, Marseille 13005, France
| | - David E Fisher
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA.
| | - Elisabeth Roider
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA; Department of Dermatology, University Hospital of Basel, 4031 Basel, Switzerland; Department of Dermatology and Allergology, University of Szeged, 6720 Szeged, Hungary.
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21
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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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22
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Feng Y, McQuillan MA, Tishkoff SA. Evolutionary genetics of skin pigmentation in African populations. Hum Mol Genet 2021; 30:R88-R97. [PMID: 33438000 PMCID: PMC8117430 DOI: 10.1093/hmg/ddab007] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/07/2021] [Accepted: 01/07/2021] [Indexed: 12/14/2022] Open
Abstract
Skin color is a highly heritable human trait, and global variation in skin pigmentation has been shaped by natural selection, migration and admixture. Ethnically diverse African populations harbor extremely high levels of genetic and phenotypic diversity, and skin pigmentation varies widely across Africa. Recent genome-wide genetic studies of skin pigmentation in African populations have advanced our understanding of pigmentation biology and human evolutionary history. For example, novel roles in skin pigmentation for loci near MFSD12 and DDB1 have recently been identified in African populations. However, due to an underrepresentation of Africans in human genetic studies, there is still much to learn about the evolutionary genetics of skin pigmentation. Here, we summarize recent progress in skin pigmentation genetics in Africans and discuss the importance of including more ethnically diverse African populations in future genetic studies. In addition, we discuss methods for functional validation of adaptive variants related to skin pigmentation.
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Affiliation(s)
- Yuanqing Feng
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael A McQuillan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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23
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Palmal S, Adhikari K, Mendoza-Revilla J, Fuentes-Guajardo M, Silva de Cerqueira CC, Bonfante B, Chacón-Duque JC, Sohail A, Hurtado M, Villegas V, Granja V, Jaramillo C, Arias W, Lozano RB, Everardo-Martínez P, Gómez-Valdés J, Villamil-Ramírez H, Hünemeier T, Ramallo V, Parolin ML, Gonzalez-José R, Schüler-Faccini L, Bortolini MC, Acuña-Alonzo V, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Balding D, Faux P, Ruiz-Linares A. Prediction of eye, hair and skin colour in Latin Americans. Forensic Sci Int Genet 2021; 53:102517. [PMID: 33865096 DOI: 10.1016/j.fsigen.2021.102517] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/19/2021] [Accepted: 03/30/2021] [Indexed: 10/21/2022]
Abstract
Here we evaluate the accuracy of prediction for eye, hair and skin pigmentation in a dataset of > 6500 individuals from Mexico, Colombia, Peru, Chile and Brazil (including genome-wide SNP data and quantitative/categorical pigmentation phenotypes - the CANDELA dataset CAN). We evaluated accuracy in relation to different analytical methods and various phenotypic predictors. As expected from statistical principles, we observe that quantitative traits are more sensitive to changes in the prediction models than categorical traits. We find that Random Forest or Linear Regression are generally the best performing methods. We also compare the prediction accuracy of SNP sets defined in the CAN dataset (including 56, 101 and 120 SNPs for eye, hair and skin colour prediction, respectively) to the well-established HIrisPlex-S SNP set (including 6, 22 and 36 SNPs for eye, hair and skin colour prediction respectively). When training prediction models on the CAN data, we observe remarkably similar performances for HIrisPlex-S and the larger CAN SNP sets for the prediction of hair (categorical) and eye (both categorical and quantitative), while the CAN sets outperform HIrisPlex-S for quantitative, but not for categorical skin pigmentation prediction. The performance of HIrisPlex-S, when models are trained in a world-wide sample (although consisting of 80% Europeans, https://hirisplex.erasmusmc.nl), is lower relative to training in the CAN data (particularly for hair and skin colour). Altogether, our observations are consistent with common variation of eye and hair colour having a relatively simple genetic architecture, which is well captured by HIrisPlex-S, even in admixed Latin Americans (with partial European ancestry). By contrast, since skin pigmentation is a more polygenic trait, accuracy is more sensitive to prediction SNP set size, although here this effect was only apparent for a quantitative measure of skin pigmentation. Our results support the use of HIrisPlex-S in the prediction of categorical pigmentation traits for forensic purposes in Latin America, while illustrating the impact of training datasets on its accuracy.
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Affiliation(s)
- Sagnik Palmal
- UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille 13005, France
| | - Kaustubh Adhikari
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Javier Mendoza-Revilla
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú; Unit of Human Evolutionary Genetics, Institut Pasteur, Paris 75015, France
| | - Macarena Fuentes-Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica 1000000, Chile
| | | | - Betty Bonfante
- UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille 13005, France
| | - Juan Camilo Chacón-Duque
- Division of Vertebrates and Anthropology, Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Anood Sohail
- Department of Biotechnology, Kinnaird College for Women, 93 - Jail Road, Lahore 54000, Pakistan
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Claudia Jaramillo
- Department of Biotechnology, Kinnaird College for Women, 93 - Jail Road, Lahore 54000, Pakistan; GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - William Arias
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - Rodrigo Barquera Lozano
- National Institute of Anthropology and History, Mexico City 6600, Mexico; Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena 07745, Germany
| | | | - Jorge Gómez-Valdés
- National Institute of Anthropology and History, Mexico City 6600, Mexico
| | - Hugo Villamil-Ramírez
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City 4510, Mexico
| | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP 05508-090, Brazil
| | - Virginia Ramallo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brazil; Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn U9129ACD, Argentina
| | - Maria-Laura Parolin
- Instituto de Diversidad y Evolución Austral (IDEAus), Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | - Rolando Gonzalez-José
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn U9129ACD, Argentina
| | - Lavinia Schüler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brazil
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brazil
| | | | - Samuel Canizales-Quinteros
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City 4510, Mexico
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 31, Perú
| | - Gabriel Bedoya
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1000000, Chile; Programa de Genetica Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Arica 1000000, Chile
| | - David Balding
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK; Melbourne Integrative Genomics, Schools of BioSciences and Mathematics & Statistics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Pierre Faux
- UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille 13005, France.
| | - Andrés Ruiz-Linares
- UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille 13005, France; Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK; Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, China.
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24
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Evaluation of supervised machine-learning methods for predicting appearance traits from DNA. Forensic Sci Int Genet 2021; 53:102507. [PMID: 33831816 DOI: 10.1016/j.fsigen.2021.102507] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 02/26/2021] [Accepted: 03/17/2021] [Indexed: 11/20/2022]
Abstract
The prediction of human externally visible characteristics (EVCs) based solely on DNA information has become an established approach in forensic and anthropological genetics in recent years. While for a large set of EVCs, predictive models have already been established using multinomial logistic regression (MLR), the prediction performances of other possible classification methods have not been thoroughly investigated thus far. Motivated by the question to identify a potential classifier that outperforms these specific trait models, we conducted a systematic comparison between the widely used MLR and three popular machine learning (ML) classifiers, namely support vector machines (SVM), random forest (RF) and artificial neural networks (ANN), that have shown good performance outside EVC prediction. As examples, we used eye, hair and skin color categories as phenotypes and genotypes based on the previously established IrisPlex, HIrisPlex, and HIrisPlex-S DNA markers. We compared and assessed the performances of each of the four methods, complemented by detailed hyperparameter tuning that was applied to some of the methods in order to maximize their performance. Overall, we observed that all four classification methods showed rather similar performance, with no method being substantially superior to the others for any of the traits, although performances varied slightly across the different traits and more so across the trait categories. Hence, based on our findings, none of the ML methods applied here provide any advantage on appearance prediction, at least when it comes to the categorical pigmentation traits and the selected DNA markers used here.
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25
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Yousaf A, Lee J, Fang W, Kolodney MS. Association Between Alopecia Areata and Natural Hair Color Among White Individuals. JAMA Dermatol 2021:2777019. [PMID: 33688924 PMCID: PMC7948107 DOI: 10.1001/jamadermatol.2021.0144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 01/22/2021] [Indexed: 01/16/2023]
Abstract
IMPORTANCE Alopecia areata (AA) is a complex immune-mediated disorder that causes nonscarring hair loss. Previous reports have documented preferential targeting of pigmented hair follicles with sparing of gray, nonpigmented hair follicles in alopecia lesions. Thus, immune targeting of melanogenesis-associated proteins in melanocytes and keratinocytes represents a potential mechanism for the inflammation that targets anagen hairs in alopecia areata. OBJECTIVE To investigate the association of alopecia areata with hair color among White residents of the UK. DESIGN, SETTING, AND PARTICIPANTS This matched, case-control study conducted in October 2020 used a large prospectively acquired cohort and included data that were collected from the UK Biobank, a large-scale prospective resource designed to study phenotypic and genotypic determinants in adults. A total of 502 510 UK Biobank participants were reviewed for inclusion. Among these individuals, 1673 cases of alopecia areata with reported hair color were captured and matched by age and sex to 6692 controls without alopecia areata using 1:4 matching. MAIN OUTCOMES AND MEASURES Conditional logistic regression analysis was performed, in which the outcome variable was alopecia areata and the main predictor was natural hair color before graying. The variables considered included diabetes, hypothyroidism, hyperthyroidism, and vitiligo. RESULTS Of 464 353 participants, 254 505 (54.8%) were women, and the mean (SD) age for those with alopecia areata was 46.9 (16.5) years. Alopecia areata was significantly more common in individuals with black (adjusted odds ratio [aOR], 2.97; 95% CI, 2.38-3.71) and dark brown hair (aOR, 1.26; 95% CI, 1.11-1.42) compared with light brown hair. In contrast, blond individuals exhibited significantly decreased alopecia areata compared with those with light brown hair (aOR, 0.69; 95% CI, 0.56-0.85). Red hair color was not significantly different from light brown hair. CONCLUSIONS AND RELEVANCE The findings of this matched case-control study seem to indicate that alopecia areata is modulated by natural hair color, preferentially targeting darker hair. Our results support a previously proposed model of alopecia areata in which immunity is directed against melanogenesis-associated proteins in the anagen hair follicles. However, further study is needed to more precisely understand the immunopathogenic association between alopecia areata and hair color.
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Affiliation(s)
- Ahmed Yousaf
- Department of Dermatology, West Virginia University, Morgantown
| | - Justin Lee
- Department of Dermatology, West Virginia University, Morgantown
| | - Wei Fang
- West Virginia Clinical and Translational Science Institute, Morgantown
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26
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Lasisi T. The constraints of racialization: How classification and valuation hinder scientific research on human variation. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 175:376-386. [PMID: 33675042 DOI: 10.1002/ajpa.24264] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 12/18/2022]
Abstract
Human biological variation has historically been studied through the lens of racialization. Despite a general shift away from the use of overt racial terminologies, the underlying racialized frameworks used to describe and understand human variation still remain. Even in relatively recent anthropological and biomedical work, we can observe clear manifestations of such racial thinking. This paper shows how classification and valuation are two specific processes which facilitate racialization and hinder attempts to move beyond such frameworks. The bias induced by classification distorts descriptions of phenotypic variation in a way that erroneously portrays European populations as more variable than others. Implicit valuation occurs in tandem with classification and produces narratives of superiority/inferiority for certain phenotypic variants without an objective biological basis. The bias of racialization is a persistent impediment stemming from the inheritance of scientific knowledge developed under explicitly racial paradigms. It is also an internalized cognitive distortion cultivated through socialization in a world where racialization is inescapable. Though undeniably challenging, this does not present an insurmountable barrier, and this bias can be mitigated through the critical evaluation of past work, the active inclusion of marginalized perspectives, and the direct confrontation of institutional structures enforcing racialized paradigms.
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Affiliation(s)
- Tina Lasisi
- Department of Anthropology, Pennsylvania State University, State College, Pennsylvania, USA
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27
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Simcoe M, Valdes A, Liu F, Furlotte NA, Evans DM, Hemani G, Ring SM, Smith GD, Duffy DL, Zhu G, Gordon SD, Medland SE, Vuckovic D, Girotto G, Sala C, Catamo E, Concas MP, Brumat M, Gasparini P, Toniolo D, Cocca M, Robino A, Yazar S, Hewitt A, Wu W, Kraft P, Hammond CJ, Shi Y, Chen Y, Zeng C, Klaver CCW, Uitterlinden AG, Ikram MA, Hamer MA, van Duijn CM, Nijsten T, Han J, Mackey DA, Martin NG, Cheng CY, Hinds DA, Spector TD, Kayser M, Hysi PG. Genome-wide association study in almost 195,000 individuals identifies 50 previously unidentified genetic loci for eye color. SCIENCE ADVANCES 2021; 7:7/11/eabd1239. [PMID: 33692100 PMCID: PMC7946369 DOI: 10.1126/sciadv.abd1239] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 01/25/2021] [Indexed: 05/03/2023]
Abstract
Human eye color is highly heritable, but its genetic architecture is not yet fully understood. We report the results of the largest genome-wide association study for eye color to date, involving up to 192,986 European participants from 10 populations. We identify 124 independent associations arising from 61 discrete genomic regions, including 50 previously unidentified. We find evidence for genes involved in melanin pigmentation, but we also find associations with genes involved in iris morphology and structure. Further analyses in 1636 Asian participants from two populations suggest that iris pigmentation variation in Asians is genetically similar to Europeans, albeit with smaller effect sizes. Our findings collectively explain 53.2% (95% confidence interval, 45.4 to 61.0%) of eye color variation using common single-nucleotide polymorphisms. Overall, our study outcomes demonstrate that the genetic complexity of human eye color considerably exceeds previous knowledge and expectations, highlighting eye color as a genetically highly complex human trait.
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Affiliation(s)
- Mark Simcoe
- Department of Twins Research and Genetic Epidemiology, King's College London, London, UK
- Department of Ophthalmology, King's College London, London, UK
| | - Ana Valdes
- Department of Twins Research and Genetic Epidemiology, King's College London, London, UK
- Division of Rheumatology, Orthopaedics and Dermatology, School of Medicine, University of Nottingham, Nottingham, UK
| | - Fan Liu
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, 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
| | | | - David M Evans
- University of Queensland Diamantina Institute, University of Queensland, Brisbane, Queensland, Australia
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences Bristol Medical School University of Bristol, Bristol, UK
| | - Susan M Ring
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences Bristol Medical School University of Bristol, Bristol, UK
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences Bristol Medical School University of Bristol, Bristol, UK
| | - David L Duffy
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Gu Zhu
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Scott D Gordon
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Sarah E Medland
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Dragana Vuckovic
- Department of Medical Sciences, University of Trieste, Trieste, Italy
- Institute for Maternal and Child Health IRCCS "Burlo Garofolo", Trieste, Italy
- Epidemiology and Biostatistics Department, Faculty of Medicine, School of Public Health, Imperial College London, London, UK
| | - Giorgia Girotto
- Department of Medical Sciences, University of Trieste, Trieste, Italy
- Institute for Maternal and Child Health IRCCS "Burlo Garofolo", Trieste, Italy
| | - Cinzia Sala
- Division of Genetics of Common Disorders, S. Raffaele Scientific Institute, Milan, Italy
| | - Eulalia Catamo
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Maria Pina Concas
- Institute for Maternal and Child Health IRCCS "Burlo Garofolo", Trieste, Italy
| | - Marco Brumat
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Paolo Gasparini
- Department of Medical Sciences, University of Trieste, Trieste, Italy
- Institute for Maternal and Child Health IRCCS "Burlo Garofolo", Trieste, Italy
| | - Daniela Toniolo
- Division of Genetics of Common Disorders, S. Raffaele Scientific Institute, Milan, Italy
| | - Massimiliano Cocca
- Institute for Maternal and Child Health IRCCS "Burlo Garofolo", Trieste, Italy
| | - Antonietta Robino
- Institute for Maternal and Child Health IRCCS "Burlo Garofolo", Trieste, Italy
| | - Seyhan Yazar
- Centre for Ophthalmology and Visual Science, University of Western Australia, Lions Eye Institute, Perth, Australia
| | - Alex Hewitt
- Centre for Ophthalmology and Visual Science, University of Western Australia, Lions Eye Institute, Perth, Australia
- Centre for Eye Research Australia, University of Melbourne, Department of Ophthalmology, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
- School of Medicine, Menzies Research Institute Tasmania, University of Tasmania, Hobart, Australia
| | - Wenting Wu
- Department of Epidemiology, Fairbanks School of Public Health, Indiana University, and Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN, USA
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Christopher J Hammond
- Department of Twins Research and Genetic Epidemiology, King's College London, London, UK
- Department of Ophthalmology, King's College London, London, UK
| | - Yuan Shi
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore
| | - Yan Chen
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, 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
| | - Changqing Zeng
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Caroline C W Klaver
- Department of Ophthalmology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Andre G Uitterlinden
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
- Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Merel A Hamer
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Tamar Nijsten
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Jiali Han
- Department of Epidemiology, Fairbanks School of Public Health, Indiana University, and Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN, USA
| | - David A Mackey
- Centre for Ophthalmology and Visual Science, University of Western Australia, Lions Eye Institute, Perth, Australia
| | - Nicholas G Martin
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore
- Duke-NUS Medical School, Singapore
| | | | - Timothy D Spector
- Department of Twins Research and Genetic Epidemiology, King's College London, London, UK
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands.
| | - Pirro G Hysi
- Department of Twins Research and Genetic Epidemiology, King's College London, London, UK.
- Department of Ophthalmology, King's College London, London, UK
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Kling D, Phillips C, Kennett D, Tillmar A. Investigative genetic genealogy: Current methods, knowledge and practice. Forensic Sci Int Genet 2021; 52:102474. [PMID: 33592389 DOI: 10.1016/j.fsigen.2021.102474] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/12/2021] [Accepted: 01/27/2021] [Indexed: 12/15/2022]
Abstract
Investigative genetic genealogy (IGG) has emerged as a new, rapidly growing field of forensic science. We describe the process whereby dense SNP data, commonly comprising more than half a million markers, are employed to infer distant relationships. By distant we refer to degrees of relatedness exceeding that of first cousins. We review how methods of relationship matching and SNP analysis on an enlarged scale are used in a forensic setting to identify a suspect in a criminal investigation or a missing person. There is currently a strong need in forensic genetics not only to understand the underlying models to infer relatedness but also to fully explore the DNA technologies and data used in IGG. This review brings together many of the topics and examines their effectiveness and operational limits, while suggesting future directions for their forensic validation. We further investigated the methods used by the major direct-to-consumer (DTC) genetic ancestry testing companies as well as submitting a questionnaire where providers of forensic genetic genealogy summarized their operation/services. Although most of the DTC market, and genetic genealogy in general, has undisclosed, proprietary algorithms we review the current knowledge where information has been discussed and published more openly.
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Affiliation(s)
- Daniel Kling
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden; Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway.
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain.
| | - Debbie Kennett
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Andreas Tillmar
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden; Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
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Herrera-Rivero M, Hochfeld LM, Sivalingam S, Nöthen MM, Heilmann-Heimbach S. Mapping of cis-acting expression quantitative trait loci in human scalp hair follicles. BMC DERMATOLOGY 2020; 20:16. [PMID: 33167971 PMCID: PMC7653834 DOI: 10.1186/s12895-020-00113-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 10/30/2020] [Indexed: 01/27/2023]
Abstract
BACKGROUND The association of molecular phenotypes, such as gene transcript levels, with human common genetic variation can help to improve our understanding of interindividual variability of tissue-specific gene regulation and its implications for disease. METHODS With the aim to capture the spectrum of biological processes affected by regulatory common genetic variants (minor allele frequency ≥ 1%) in healthy hair follicles (HFs) from scalp tissue, we performed a genome-wide mapping of cis-acting expression quantitative trait loci (eQTLs) in plucked HFs, and applied these eQTLs to help further explain genomic findings for hair-related traits. RESULTS We report 374 high-confidence eQTLs found in occipital scalp tissue, whose associated genes (eGenes) showed enrichments for metabolic, mitotic and immune processes, as well as responses to steroid hormones. We were able to replicate 68 of these associations in a smaller, independent dataset, in either frontal and/or occipital scalp tissue. Furthermore, we found three genomic regions overlapping reported genetic loci for hair shape and hair color. We found evidence to confirm the contributions of PADI3 to human variation in hair traits and suggest a novel potential candidate gene within known loci for androgenetic alopecia. CONCLUSIONS Our study shows that an array of basic cellular functions relevant for hair growth are genetically regulated within the HF, and can be applied to aid the interpretation of interindividual variability on hair traits, as well as genetic findings for common hair disorders.
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Affiliation(s)
- Marisol Herrera-Rivero
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, 53127, Bonn, Germany.,Present address: Department of Genetic Epidemiology, Institute of Human Genetics, University of Münster, 48149, Münster, Germany
| | - Lara M Hochfeld
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, 53127, Bonn, Germany
| | - Sugirthan Sivalingam
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, 53127, Bonn, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, 53127, Bonn, Germany
| | - Stefanie Heilmann-Heimbach
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, 53127, Bonn, Germany.
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Katsara MA, Branicki W, Pośpiech E, Hysi P, Walsh S, Kayser M, Nothnagel M. Testing the impact of trait prevalence priors in Bayesian-based genetic prediction modeling of human appearance traits. Forensic Sci Int Genet 2020; 50:102412. [PMID: 33260052 DOI: 10.1016/j.fsigen.2020.102412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 09/09/2020] [Accepted: 10/25/2020] [Indexed: 11/26/2022]
Abstract
The prediction of appearance traits by use of solely genetic information has become an established approach and a number of statistical prediction models have already been developed for this purpose. However, given limited knowledge on appearance genetics, currently available models are incomplete and do not include all causal genetic variants as predictors. Therefore such prediction models may benefit from the inclusion of additional information that acts as a proxy for this unknown genetic background. Use of priors, possibly informed by trait category prevalence values in biogeographic ancestry groups, in a Bayesian framework may thus improve the prediction accuracy of previously predicted externally visible characteristics, but has not been investigated as of yet. In this study, we assessed the impact of using trait prevalence-informed priors on the prediction performance in Bayesian models for eye, hair and skin color as well as hair structure and freckles in comparison to the respective prior-free models. Those prior-free models were either similarly defined either very close to the already established ones by using a reduced predictive marker set. However, these differences in the number of the predictive markers should not affect significantly our main outcomes. We observed that such priors often had a strong effect on the prediction performance, but to varying degrees between different traits and also different trait categories, with some categories barely showing an effect. While we found potential for improving the prediction accuracy of many of the appearance trait categories tested by using priors, our analyses also showed that misspecification of those prior values often severely diminished the accuracy compared to the respective prior-free approach. This emphasizes the importance of accurate specification of prevalence-informed priors in Bayesian prediction modeling of appearance traits. However, the existing literature knowledge on spatial prevalence is sparse for most appearance traits, including those investigated here. Due to the limitations in appearance trait prevalence knowledge, our results render the use of trait prevalence-informed priors in DNA-based appearance trait prediction currently infeasible.
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Affiliation(s)
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland; Central Forensic Laboratory of the Police, Warsaw, Poland
| | - Ewelina Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Pirro Hysi
- Department of Twin Research & Genetic Epidemiology, St Thomas Hospital, Campus, Kings College London (KCL), London, UK
| | - Susan Walsh
- Department of Biology, Indiana University Purdue University Indianapolis (IUPUI), Indianapolis, IN, USA
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Michael Nothnagel
- Cologne Center for Genomics, University of Cologne, Cologne, Germany; University Hospital Cologne, Cologne, Germany.
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Mekić S, Wigmann C, Gunn DA, Jacobs LC, Kayser M, Schikowski T, Nijsten T, Pardo LM. Genetics of facial telangiectasia in the Rotterdam Study: a genome-wide association study and candidate gene approach. J Eur Acad Dermatol Venereol 2020; 35:749-754. [PMID: 33095951 DOI: 10.1111/jdv.17014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 10/05/2020] [Indexed: 12/27/2022]
Abstract
BACKGROUND The severity of facial telangiectasia or red veins is associated with many lifestyle factors. However, the genetic predisposition remains unclear. OBJECTIVES We performed a genome-wide association study (GWAS) on facial telangiectasia in the Rotterdam Study (RS) and tested for replication in two independent cohorts. Additionally, a candidate gene approach with known pigmentation genes was performed. METHODS Facial telangiectasia were extracted from standardized facial photographs (collected from 2010-2013) of 2842 northwestern European participants (median age 66.9, 56.8% female) from the RS. Our GWAS top hits (P-value <10-6 ) were tested for replication in 460 elderly women of the SALIA cohort and in 576 additional men and women of the RS. Associations of top single nucleotide polymorphisms (SNPs) with expression quantitative trait loci (eQTL) in various tissues were reviewed (GTEx database) alongside phenotype associations in the UK biobank database. SNP-based associations between known pigmentation genes and facial telangiectasia were tested. Conditional analysis on skin colour was additionally performed. RESULTS Our most significant GWAS signal was rs4417318 (P-value 5.38*10-7 ), an intergenic SNP on chromosome 12 mapping to the SLC16A7 gene. Other suggestive SNPs tagged genes ZNF211, ZSCAN4, ICOS and KCNN3; SNP eQTLs and phenotype associations tagged links to the vascular system. However, the top signals did not pass significance in the two replication cohorts. The pigmentation genes KIAA0930, SLCA45A2 and MC1R, were significantly associated with telangiectasia in a candidate gene approach but not independently of skin colour. CONCLUSION In this GWAS on telangiectasia in a northwestern European population, no genome-wide significant SNPs were found, although suggestive signals indicate genes involved in the vascular system might be involved in telangiectasia. Significantly associated pigmentation genes underline the link between skin colour and telangiectasia.
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Affiliation(s)
- S Mekić
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - C Wigmann
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - D A Gunn
- Colworth Science Park, Unilever Research and Development, Sharnbrook, UK
| | - L C Jacobs
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - M Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - T Schikowski
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - T Nijsten
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - L M Pardo
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
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Chen Y, Branicki W, Walsh S, Nothnagel M, Kayser M, Liu F. The impact of correlations between pigmentation phenotypes and underlying genotypes on genetic prediction of pigmentation traits. Forensic Sci Int Genet 2020; 50:102395. [PMID: 33070049 DOI: 10.1016/j.fsigen.2020.102395] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/25/2020] [Accepted: 09/15/2020] [Indexed: 12/31/2022]
Abstract
Predicting appearance phenotypes from genotypes is relevant for various areas of human genetic research and applications such as genetic epidemiology, human history, anthropology, and particularly in forensics. Many appearance phenotypes, and thus their underlying genotypes, are highly correlated, with pigmentation traits serving as primary examples. However, all available genetic prediction models, including those for pigmentation traits currently used in forensic DNA phenotyping, ignore phenotype correlations. Here, we investigated the impact of appearance phenotype correlations on genetic appearance prediction in the exemplary case of three pigmentation traits. We used data for categorical eye, hair and skin colour as well as 41 DNA markers utilized in the recently established HIrisPlex-S system from 762 individuals with complete phenotype and genotype information. Based on these data, we performed genetic prediction modelling of eye, hair and skin colour via three different strategies, namely the established approach of predicting phenotypes solely based on genotypes while not considering phenotype correlations, and two novel approaches that considered phenotype correlations, either incorporating truly observed correlated phenotypes or DNA-predicted correlated phenotypes in addition to the DNA predictors. We found that using truly observed correlated pigmentation phenotypes as additional predictors increased the DNA-based prediction accuracies for almost all eye, hair and skin colour categories, with the largest increase for intermediate eye colour, brown hair colour, dark to black skin colour, and particularly for dark skin colour. Outcomes of dedicated computer simulations suggest that this prediction accuracy increase is due to the additional genetic information that is implicitly provided by the truly observed correlated pigmentation phenotypes used, yet not covered by the DNA predictors applied. In contrast, considering DNA-predicted correlated pigmentation phenotypes as additional predictors did not improve the performance of the genetic prediction of eye, hair and skin colour, which was in line with the results from our computer simulations. Hence, in practical applications of DNA-based appearance prediction where no phenotype knowledge is available, such as in forensic DNA phenotyping, it is not advised to use DNA-predicted correlated phenotypes as predictors in addition to the DNA predictors. In the very least, this is not recommended for the pigmentation traits and the established pigmentation DNA predictors tested here.
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Affiliation(s)
- Yan Chen
- 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; University of Chinese Academy of Sciences, Beijing, China
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Susan Walsh
- Department of Biology, Indiana University Purdue University Indianapolis (IUPUI), Indianapolis, IN, USA
| | - Michael Nothnagel
- Cologne Center for Genomics, University of Cologne, Cologne, Germany; University Hospital Cologne, Cologne, Germany
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - 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; University of Chinese Academy of Sciences, Beijing, China.
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Vicuña L, Klimenkova O, Norambuena T, Martinez FI, Fernandez MI, Shchur V, Eyheramendy S. Postadmixture Selection on Chileans Targets Haplotype Involved in Pigmentation, Thermogenesis and Immune Defense against Pathogens. Genome Biol Evol 2020; 12:1459-1470. [PMID: 32614437 PMCID: PMC7487163 DOI: 10.1093/gbe/evaa136] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2020] [Indexed: 12/13/2022] Open
Abstract
Detection of positive selection signatures in populations around the world is helping to uncover recent human evolutionary history as well as the genetic basis of diseases. Most human evolutionary genomic studies have been performed in European, African, and Asian populations. However, populations with Native American ancestry have been largely underrepresented. Here, we used a genome-wide local ancestry enrichment approach complemented with neutral simulations to identify postadmixture adaptations underwent by admixed Chileans through gene flow from Europeans into local Native Americans. The top significant hits (P = 2.4×10-7) are variants in a region on chromosome 12 comprising multiple regulatory elements. This region includes rs12821256, which regulates the expression of KITLG, a well-known gene involved in lighter hair and skin pigmentation in Europeans as well as in thermogenesis. Another variant from that region is associated with the long noncoding RNA RP11-13A1.1, which has been specifically involved in the innate immune response against infectious pathogens. Our results suggest that these genes were relevant for adaptation in Chileans following the Columbian exchange.
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Affiliation(s)
- Lucas Vicuña
- Faculty of Engineering and Sciences, Universidad Adolfo Ibañez, Peñalolén, Santiago, Chile
| | - Olga Klimenkova
- National Research University Higher School of Economics, Russian Federation, Moscow, Russia
| | - Tomás Norambuena
- Faculty of Engineering and Sciences, Universidad Adolfo Ibañez, Peñalolén, Santiago, Chile
| | - Felipe I Martinez
- Center for Intercultural and Indigenous Research, School of Anthropology, Faculty of Social Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Mario I Fernandez
- Department of Urology, Clínica Alemana, Santiago, Chile
- Center for Genetics and Genomics, Faculty of Medicine, Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Vladimir Shchur
- National Research University Higher School of Economics, Russian Federation, Moscow, Russia
| | - Susana Eyheramendy
- Faculty of Engineering and Sciences, Universidad Adolfo Ibañez, Peñalolén, Santiago, Chile
- Instituto Milenio de Investigación sobre los Fundamentos de los Datos (IMFD)
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Evaluation of the VISAGE Basic Tool for Appearance and Ancestry Prediction Using PowerSeq Chemistry on the MiSeq FGx System. Genes (Basel) 2020; 11:genes11060708. [PMID: 32604780 PMCID: PMC7349024 DOI: 10.3390/genes11060708] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 01/23/2023] Open
Abstract
The study of DNA to predict externally visible characteristics (EVCs) and the biogeographical ancestry (BGA) from unknown samples is gaining relevance in forensic genetics. Technical developments in Massively Parallel Sequencing (MPS) enable the simultaneous analysis of hundreds of DNA markers, which improves successful Forensic DNA Phenotyping (FDP). The EU-funded VISAGE (VISible Attributes through GEnomics) Consortium has developed various targeted MPS-based lab tools to apply FDP in routine forensic analyses. Here, we present an evaluation of the VISAGE Basic tool for appearance and ancestry prediction based on PowerSeq chemistry (Promega) on a MiSeq FGx System (Illumina). The panel consists of 153 single nucleotide polymorphisms (SNPs) that provide information about EVCs (41 SNPs for eye, hair and skin color from HIrisPlex-S) and continental BGA (115 SNPs; three overlap with the EVCs SNP set). The assay was evaluated for sensitivity, repeatability and genotyping concordance, as well as its performance with casework-type samples. This targeted MPS assay provided complete genotypes at all 153 SNPs down to 125 pg of input DNA and 99.67% correct genotypes at 50 pg. It was robust in terms of repeatability and concordance and provided useful results with casework-type samples. The results suggest that this MPS assay is a useful tool for basic appearance and ancestry prediction in forensic genetics for users interested in applying PowerSeq chemistry and MiSeq for this purpose.
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Corbin LJ, Pope J, Sanson J, Antczak DF, Miller D, Sadeghi R, Brooks SA. An Independent Locus Upstream of ASIP Controls Variation in the Shade of the Bay Coat Colour in Horses. Genes (Basel) 2020; 11:E606. [PMID: 32486210 PMCID: PMC7349280 DOI: 10.3390/genes11060606] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/20/2020] [Accepted: 05/27/2020] [Indexed: 01/09/2023] Open
Abstract
Novel coat colour phenotypes often emerge during domestication, and there is strong evidence of genetic selection for the two main genes that control base coat colour in horses-ASIP and MC1R. These genes direct the type of pigment produced, red pheomelanin (MC1R) or black eumelanin (ASIP), as well as the relative concentration and the temporal-spatial distribution of melanin pigment deposits in the skin and hair coat. Here, we describe a genome-wide association study (GWAS) to identify novel genic regions involved in the determination of the shade of bay. In total, 126 horses from five different breeds were ranked according to the extent of the distribution of eumelanin: spanning variation in phenotype from black colour restricted only to the extremities to the presence of some black pigment across nearly all the body surface. We identified a single region associated with the shade of bay ranking spanning approximately 0.5 MB on ECA22, just upstream of the ASIP gene (p = 9.76 × 10-15). This candidate region encompasses the distal 5' end of the ASIP transcript (as predicted from other species) as well as the RALY gene. Both loci are viable candidates based on the presence of similar alleles in other species. These results contribute to the growing understanding of coat colour genetics in the horse and to the mapping of genetic determinants of pigmentation on a molecular level. Given pleiotropic phenotypes in behaviour and obesity for ASIP alleles, especially those in the 5' regulatory region, improved understanding of this new Shade allele may have implications for health management in the horse.
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Affiliation(s)
- Laura J. Corbin
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK;
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol BS8 2BN, UK
| | - Jessica Pope
- Bristol Veterinary School, University of Bristol, Bristol BS8 1QU, UK;
| | - Jacqueline Sanson
- Department of Animal Sciences, University of Florida, Gainesville, FL 32610, USA;
| | - Douglas F. Antczak
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA; (D.F.A.); (D.M.); (R.S.)
| | - Donald Miller
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA; (D.F.A.); (D.M.); (R.S.)
| | - Raheleh Sadeghi
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA; (D.F.A.); (D.M.); (R.S.)
| | - Samantha A. Brooks
- Department of Animal Sciences, University of Florida, Gainesville, FL 32610, USA;
- UF Genetics Institute, University of Florida, Gainesville, FL 32611, USA
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36
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Pan H, Edwards SW, Ives C, Covert H, Harville EW, Lichtveld MY, Wickliffe JK, Hamilton CM. An Assessment of Environmental Health Measures in the Deepwater Horizon Research Consortia. CURRENT OPINION IN TOXICOLOGY 2020; 16:75-82. [PMID: 32457927 DOI: 10.1016/j.cotox.2019.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Research consortia play a key role in our understanding of how environmental exposures influence health and wellbeing, especially in the case of catastrophic events such as the Deepwater Horizon oil spill. A common challenge that prevents the optimal use of these data is the difficulty of harmonizing data regarding the environmental exposures and health effects across the studies within and among consortia. A review of the measures used by members of the Deepwater Horizon Research Consortia highlights the challenges associated with balancing timely implementation of a study to support disaster relief with optimizing the long-term value of the data. The inclusion of common, standard measures at the study design phase and a priori discussions regarding harmonization of study-specific measures among consortia members are key to overcoming this challenge. As more resources become available to support the use of standard measures, researchers now have the tools needed to rapidly coordinate their studies without compromising research focus or timely completion of the original study goals.
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Affiliation(s)
- Huaqin Pan
- RTI International, 3040 East Cornwallis Road, Research Triangle Park, NC 27709
| | - Stephen W Edwards
- RTI International, 3040 East Cornwallis Road, Research Triangle Park, NC 27709
| | - Cataia Ives
- RTI International, 3040 East Cornwallis Road, Research Triangle Park, NC 27709
| | - Hannah Covert
- Tulane University School of Public Health and Tropical Medicine, 1440 Canal Street, New Orleans, LA 70112
| | - Emily W Harville
- Tulane University School of Public Health and Tropical Medicine, 1440 Canal Street, New Orleans, LA 70112
| | - Maureen Y Lichtveld
- Tulane University School of Public Health and Tropical Medicine, 1440 Canal Street, New Orleans, LA 70112
| | - Jeffrey K Wickliffe
- Tulane University School of Public Health and Tropical Medicine, 1440 Canal Street, New Orleans, LA 70112
| | - Carol M Hamilton
- RTI International, 3040 East Cornwallis Road, Research Triangle Park, NC 27709
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37
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Ancient genomes from present-day France unveil 7,000 years of its demographic history. Proc Natl Acad Sci U S A 2020; 117:12791-12798. [PMID: 32457149 DOI: 10.1073/pnas.1918034117] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Genomic studies conducted on ancient individuals across Europe have revealed how migrations have contributed to its present genetic landscape, but the territory of present-day France has yet to be connected to the broader European picture. We generated a large dataset comprising the complete mitochondrial genomes, Y-chromosome markers, and genotypes of a number of nuclear loci of interest of 243 individuals sampled across present-day France over a period spanning 7,000 y, complemented with a partially overlapping dataset of 58 low-coverage genomes. This panel provides a high-resolution transect of the dynamics of maternal and paternal lineages in France as well as of autosomal genotypes. Parental lineages and genomic data both revealed demographic patterns in France for the Neolithic and Bronze Age transitions consistent with neighboring regions, first with a migration wave of Anatolian farmers followed by varying degrees of admixture with autochthonous hunter-gatherers, and then substantial gene flow from individuals deriving part of their ancestry from the Pontic steppe at the onset of the Bronze Age. Our data have also highlighted the persistence of Magdalenian-associated ancestry in hunter-gatherer populations outside of Spain and thus provide arguments for an expansion of these populations at the end of the Paleolithic Period more northerly than what has been described so far. Finally, no major demographic changes were detected during the transition between the Bronze and Iron Ages.
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38
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Andersen JD, Meyer OS, Simão F, Jannuzzi J, Carvalho E, Andersen MM, Pereira V, Børsting C, Morling N, Gusmão L. Skin pigmentation and genetic variants in an admixed Brazilian population of primarily European ancestry. Int J Legal Med 2020; 134:1569-1579. [PMID: 32385594 DOI: 10.1007/s00414-020-02307-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 04/22/2020] [Indexed: 01/16/2023]
Abstract
Although many genes have been shown to be associated with human pigmentary traits and forensic prediction assays exist (e.g. HIrisPlex-S), the genetic knowledge about skin colour remains incomplete. The highly admixed Brazilian population is an interesting study population for investigation of the complex genotype-phenotype architecture of human skin colour because of its large variation. Here, we compared variants in 22 pigmentary genes with quantitative skin pigmentation levels on the buttock, arm, and forehead areas of 266 genetically admixed Brazilian individuals. The genetic ancestry of each individual was estimated by typing 46 AIM-InDels. The mean proportion of genetic ancestry was 68.8% European, 20.8% Sub-Saharan African, and 10.4% Native American. A high correlation (adjusted R2 = 0.65, p < 0.05) was observed between nine SNPs and quantitative skin pigmentation using multiple linear regression analysis. The correlations were notably smaller between skin pigmentation and biogeographic ancestry (adjusted R2 = 0.45, p < 0.05), or markers in the leading forensic skin colour prediction system, the HIrisPlex-S (adjusted R2 = 0.54, p < 0.05). Four of the nine SNPs, OCA2 rs1448484 (rank 2), APBA2 rs4424881 (rank 4), MFSD12 rs10424065 (rank 8), and TYRP1 1408799 (rank 9) were not investigated as part of the HIrisPlex-S selection process, and therefore not included in the HIrisPlex-S model. Our results indicate that these SNPs account for a substantial part of the skin colour variation in individuals of admixed ancestry. Hence, we suggest that these SNPs are considered when developing future skin colour prediction models.
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Affiliation(s)
- Jeppe D Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100, Copenhagen, Denmark.
| | - Olivia S Meyer
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | - Filipa Simão
- DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Juliana Jannuzzi
- DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Elizeu Carvalho
- DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Mikkel M Andersen
- Department of Mathematical Sciences, Aalborg University, DK-9000, Aalborg, Denmark
| | - Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
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Orteu A, Jiggins CD. The genomics of coloration provides insights into adaptive evolution. Nat Rev Genet 2020; 21:461-475. [PMID: 32382123 DOI: 10.1038/s41576-020-0234-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2020] [Indexed: 01/31/2023]
Abstract
Coloration is an easily quantifiable visual trait that has proven to be a highly tractable system for genetic analysis and for studying adaptive evolution. The application of genomic approaches to evolutionary studies of coloration is providing new insight into the genetic architectures underlying colour traits, including the importance of large-effect mutations and supergenes, the role of development in shaping genetic variation and the origins of adaptive variation, which often involves adaptive introgression. Improved knowledge of the genetic basis of traits can facilitate field studies of natural selection and sexual selection, making it possible for strong selection and its influence on the genome to be demonstrated in wild populations.
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Affiliation(s)
- Anna Orteu
- Department of Zoology, University of Cambridge, Cambridge, UK.
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, UK.
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40
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Ikram MA, Brusselle G, Ghanbari M, Goedegebure A, Ikram MK, Kavousi M, Kieboom BCT, Klaver CCW, de Knegt RJ, Luik AI, Nijsten TEC, Peeters RP, van Rooij FJA, Stricker BH, Uitterlinden AG, Vernooij MW, Voortman T. Objectives, design and main findings until 2020 from the Rotterdam Study. Eur J Epidemiol 2020; 35:483-517. [PMID: 32367290 PMCID: PMC7250962 DOI: 10.1007/s10654-020-00640-5] [Citation(s) in RCA: 298] [Impact Index Per Article: 74.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/23/2020] [Indexed: 12/19/2022]
Abstract
The Rotterdam Study is an ongoing prospective cohort study that started in 1990 in the city of Rotterdam, The Netherlands. The study aims to unravel etiology, preclinical course, natural history and potential targets for intervention for chronic diseases in mid-life and late-life. The study focuses on cardiovascular, endocrine, hepatic, neurological, ophthalmic, psychiatric, dermatological, otolaryngological, locomotor, and respiratory diseases. As of 2008, 14,926 subjects aged 45 years or over comprise the Rotterdam Study cohort. Since 2016, the cohort is being expanded by persons aged 40 years and over. The findings of the Rotterdam Study have been presented in over 1700 research articles and reports. This article provides an update on the rationale and design of the study. It also presents a summary of the major findings from the preceding 3 years and outlines developments for the coming period.
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Affiliation(s)
- M Arfan Ikram
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Guy Brusselle
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.,Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - André Goedegebure
- Department of Otorhinolaryngology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - M Kamran Ikram
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.,Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Brenda C T Kieboom
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Caroline C W Klaver
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.,Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Robert J de Knegt
- Department of Gastroenterology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Annemarie I Luik
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Tamar E C Nijsten
- Department of Dermatology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Robin P Peeters
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Frank J A van Rooij
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Bruno H Stricker
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Meike W Vernooij
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.,Department of Radiology and Nuclear Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Trudy Voortman
- Department of Epidemiology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
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41
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Kukla-Bartoszek M, Szargut M, Pośpiech E, Diepenbroek M, Zielińska G, Jarosz A, Piniewska-Róg D, Arciszewska J, Cytacka S, Spólnicka M, Branicki W, Ossowski A. The challenge of predicting human pigmentation traits in degraded bone samples with the MPS-based HIrisPlex-S system. Forensic Sci Int Genet 2020; 47:102301. [PMID: 32387914 DOI: 10.1016/j.fsigen.2020.102301] [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: 11/27/2019] [Revised: 03/02/2020] [Accepted: 04/10/2020] [Indexed: 10/24/2022]
Abstract
Identification of human remains is an important part of human DNA analysis studies. STR and mitochondrial DNA markers are well suited for the analysis of degraded biological samples including bone material. However, these DNA markers may be useless when reference material is not available. In these cases, predictive DNA analysis can support the process of human identification by providing investigative leads. Forensic DNA phenotyping has progressed significantly by offering new methods based on massively parallel sequencing technology, but the frequent degradation processes observed in skeletal remains can make analysis of such samples challenging. In this study, we demonstrate the usefulness of a recently established Ion AmpliSeqTM HIrisPlex-S panel using Ion Torrent technology for analyzing bone samples that show different levels of DNA degradation. In total, 63 bone samples at post-mortem intervals up to almost 80 years were genotyped and eye, hair and skin colour predictions were performed using the HIrisPlex-S models. Following the recommended coverage thresholds, it was possible to establish full DNA profiles comprising of 41 DNA variants for 35 samples (55.6%). For 5 samples (7.9%) no DNA profiles were generated. The remaining 23 samples (36.5%) produced partial profiles and showed a clear underperformance of 3 HIrisPlex-S SNPs - rs1545397 (OCA2), rs1470608 (OCA2) and rs10756819 (BNC2), all used for skin colour prediction only. None of the 23 samples gave complete genotypes needed for skin colour prediction was obtained, and in 7 of them (25.9%) the 3 underperformed SNPs were the cause. At the same time, the prediction of eye and hair colour using complete IrisPlex and HIrisPlex profiles could be made for these 23 samples in 20 (87.0%) and 12 cases (52.2%), respectively. Complete HIrisPlex-S profiles were generated from as little as 49 pg of template DNA. Five samples for which the HIrisPlex-S analysis failed, consistently failed in standard STR analysis. Importantly, the 3 underperforming SNPs produced significantly lower number of reads in good quality samples. Nonetheless, the AUC loss resulting from missing data for these 3 SNPs is not considered large (≤0.004) and the prediction of pigmentation from partial profiles is also available in the current HPS tool. The study shows that DNA degradation and the resulting loss of data are the most serious challenge to DNA phenotyping of skeletal remains. Although the newly developed HIrisPlex-S panel has been successfully validated in the current research, primer redesign for the 3 underperforming SNPs in the MPS design should be considered in the future.
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Affiliation(s)
- Magdalena Kukla-Bartoszek
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa St. 7, 30-387, Kraków, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa St. 7A, 30-387, Kraków, Poland
| | - Maria Szargut
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland; The Polish Genetic Database of Totalitarianism Victims, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland
| | - Ewelina Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa St. 7A, 30-387, Kraków, Poland
| | - Marta Diepenbroek
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland; The Polish Genetic Database of Totalitarianism Victims, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland; Institut für Rechtsmedizin der Universität München, Nußbaumstr. 26, 80336, München, Germany
| | - Grażyna Zielińska
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland; The Polish Genetic Database of Totalitarianism Victims, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland
| | - Agata Jarosz
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa St. 7A, 30-387, Kraków, Poland
| | - Danuta Piniewska-Róg
- Department of Forensic Medicine, Jagiellonian University Medical College, Grzegórzecka St. 16, 31-531, Kraków, Poland
| | - Joanna Arciszewska
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland; The Polish Genetic Database of Totalitarianism Victims, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland
| | - Sandra Cytacka
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland; The Polish Genetic Database of Totalitarianism Victims, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland
| | - Magdalena Spólnicka
- Biology Department, Central Forensic Laboratory of the Police, Aleje Ujazdowskie 7, 00-583, Warszawa, Poland
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa St. 7A, 30-387, Kraków, Poland; Department of Forensic Medicine, Jagiellonian University Medical College, Grzegórzecka St. 16, 31-531, Kraków, Poland
| | - Andrzej Ossowski
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland; The Polish Genetic Database of Totalitarianism Victims, Powstancow Wlkp. St. 72, 70-111, Szczecin, Poland
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42
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Mechanisms of a near-orthogonal ultra-fast evolution of human behaviour as a source of culture development. Behav Brain Res 2020; 384:112521. [DOI: 10.1016/j.bbr.2020.112521] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/24/2020] [Accepted: 01/29/2020] [Indexed: 12/15/2022]
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43
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Hysi PG, Choquet H, Khawaja AP, Wojciechowski R, Tedja MS, Yin J, Simcoe MJ, Patasova K, Mahroo OA, Thai KK, Cumberland PM, Melles RB, Verhoeven VJM, Vitart V, Segre A, Stone RA, Wareham N, Hewitt AW, Mackey DA, Klaver CCW, MacGregor S, Khaw PT, Foster PJ, Guggenheim JA, Rahi JS, Jorgenson E, Hammond CJ. Meta-analysis of 542,934 subjects of European ancestry identifies new genes and mechanisms predisposing to refractive error and myopia. Nat Genet 2020; 52:401-407. [PMID: 32231278 PMCID: PMC7145443 DOI: 10.1038/s41588-020-0599-0] [Citation(s) in RCA: 157] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 02/24/2020] [Indexed: 01/10/2023]
Abstract
Refractive errors, in particular myopia, are a leading cause of morbidity and disability worldwide. Genetic investigation can improve understanding of the molecular mechanisms that underlie abnormal eye development and impaired vision. We conducted a meta-analysis of genome-wide association studies (GWAS) that involved 542,934 European participants and identified 336 novel genetic loci associated with refractive error. Collectively, all associated genetic variants explain 18.4% of heritability and improve the accuracy of myopia prediction (area under the curve (AUC) = 0.75). Our results suggest that refractive error is genetically heterogeneous, driven by genes that participate in the development of every anatomical component of the eye. In addition, our analyses suggest that genetic factors controlling circadian rhythm and pigmentation are also involved in the development of myopia and refractive error. These results may enable the prediction of refractive error and the development of personalized myopia prevention strategies in the future.
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Affiliation(s)
- Pirro G Hysi
- Section of Ophthalmology, School of Life Course Sciences, King's College London, London, UK. .,Department of Twin Research and Genetic Epidemiology, King's College London, London, UK. .,UCL Great Ormond Street Institute of Child Health, University College London, London, UK.
| | - Hélène Choquet
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Anthony P Khawaja
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK.,Department of Public Health and Primary Care, Institute of Public Health, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Robert Wojciechowski
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA.,Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Milly S Tedja
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands.,Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Jie Yin
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Mark J Simcoe
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Karina Patasova
- Section of Ophthalmology, School of Life Course Sciences, King's College London, London, UK
| | - Omar A Mahroo
- Section of Ophthalmology, School of Life Course Sciences, King's College London, London, UK.,NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - Khanh K Thai
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Phillippa M Cumberland
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK.,Ulverscroft Vision Research Group, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Ronald B Melles
- Department of Ophthalmology Kaiser Permanente Northern California, Redwood City, CA, USA
| | - Virginie J M Verhoeven
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands.,Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands.,Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Veronique Vitart
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Ayellet Segre
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear, Boston, MA, USA
| | - Richard A Stone
- Department of Ophthalmology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Nick Wareham
- Department of Public Health and Primary Care, Institute of Public Health, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Alex W Hewitt
- Department of Ophthalmology, Royal Hobart Hospital, Hobart, Tasmania, Australia
| | - David A Mackey
- Department of Ophthalmology, Royal Hobart Hospital, Hobart, Tasmania, Australia.,Centre for Ophthalmology and Visual Science, University of Western Australia, Lions Eye Institute, Perth, Western Australia, Australia
| | - Caroline C W Klaver
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands.,Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands.,Department of Ophthalmology, Radboud University Medical Center, Rotterdam, the Netherlands.,Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - Stuart MacGregor
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | | | - Peng T Khaw
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - Paul J Foster
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK.,Division of Genetics and Epidemiology, UCL Institute of Ophthalmology, London, UK
| | | | | | | | - Jugnoo S Rahi
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK.,NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK.,Ulverscroft Vision Research Group, UCL Great Ormond Street Institute of Child Health, University College London, London, UK.,Department of Ophthalmology and NIHR, Biomedical Research Centre, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Christopher J Hammond
- Section of Ophthalmology, School of Life Course Sciences, King's College London, London, UK.,Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
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44
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Hollis B, Day FR, Busch AS, Thompson DJ, Soares ALG, Timmers PRHJ, Kwong A, Easton DF, Joshi PK, Timpson NJ, Ong KK, Perry JRB. Genomic analysis of male puberty timing highlights shared genetic basis with hair colour and lifespan. Nat Commun 2020; 11:1536. [PMID: 32210231 PMCID: PMC7093467 DOI: 10.1038/s41467-020-14451-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 12/16/2019] [Indexed: 12/19/2022] Open
Abstract
The timing of puberty is highly variable and is associated with long-term health outcomes. To date, understanding of the genetic control of puberty timing is based largely on studies in women. Here, we report a multi-trait genome-wide association study for male puberty timing with an effective sample size of 205,354 men. We find moderately strong genomic correlation in puberty timing between sexes (rg = 0.68) and identify 76 independent signals for male puberty timing. Implicated mechanisms include an unexpected link between puberty timing and natural hair colour, possibly reflecting common effects of pituitary hormones on puberty and pigmentation. Earlier male puberty timing is genetically correlated with several adverse health outcomes and Mendelian randomization analyses show a genetic association between male puberty timing and shorter lifespan. These findings highlight the relationships between puberty timing and health outcomes, and demonstrate the value of genetic studies of puberty timing in both sexes.
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Affiliation(s)
- Ben Hollis
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus Box 285, Cambridge, CB2 0QQ, UK
| | - Felix R Day
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus Box 285, Cambridge, CB2 0QQ, UK
| | - Alexander S Busch
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus Box 285, Cambridge, CB2 0QQ, UK
- Department of Growth and Reproduction, Rigshospitalet, University of Copenhagen, 2100, Copenhagen O, Denmark
- International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health, Rigshospitalet, University of Copenhagen, 2100, Copenhagen O, Denmark
| | - Deborah J Thompson
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Ana Luiza G Soares
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Paul R H J Timmers
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, UK
| | - Alex Kwong
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- IUMSP, Biopôle, Secteur Vennes-Bâtiment SV-A, Route de la Corniche 10, 1010, Lausanne, Switzerland
- School of Geographical Sciences, University of Bristol, Bristol, UK
- Centre for Multilevel Modelling, University of Bristol, Bristol, UK
| | - Doug F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Peter K Joshi
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, UK
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
| | - Ken K Ong
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus Box 285, Cambridge, CB2 0QQ, UK.
- Department of Paediatrics, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus Box 181, Cambridge, CB2 0QQ, UK.
| | - John R B Perry
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus Box 285, Cambridge, CB2 0QQ, UK.
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Zorina-Lichtenwalter K, Lichtenwalter RN, Zaykin DV, Parisien M, Gravel S, Bortsov A, Diatchenko L. A study in scarlet: MC1R as the main predictor of red hair and exemplar of the flip-flop effect. Hum Mol Genet 2020; 28:2093-2106. [PMID: 30657907 DOI: 10.1093/hmg/ddz018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 01/04/2019] [Accepted: 01/08/2019] [Indexed: 12/11/2022] Open
Abstract
Genetic variation in melanocortin-1 receptor (MC1R) is a known contributor to disease-free red hair in humans. Three loss-of-function single-nucleotide variants (rs1805007, rs1805008 and rs1805009) have been established as strongly correlated with red hair. The contribution of other loss-of-function MC1R variants (in particular rs1805005, rs2228479 and rs885479) and the extent to which other genetic loci are involved in red hair colour is less well understood. Here, we used the UK Biobank cohort to capture a comprehensive list of MC1R variants contributing to red hair colour. We report a correlation with red hair for both strong-effect variants (rs1805007, rs1805008 and rs1805009) and weak-effect variants (rs1805005, rs2228479 and rs885479) and show that their coefficients differ by two orders of magnitude. On the haplotype level, both strong- and weak-effect variants contribute to the red hair phenotype, but when considered individually, weak-effect variants show a reverse, negative association with red hair. The reversal of association direction in the single-variant analysis is facilitated by a distinguishing structure of MC1R, in which loss-of-function variants are never found to co-occur on the same haplotype. The other previously reported hair colour genes' variants do not substantially improve the MC1R red hair colour predictive model. Our best model for predicting red versus other hair colours yields an unparalleled area under the receiver operating characteristic of 0.96 using only MC1R variants. In summary, we present a comprehensive statistically derived characterization of the role of MC1R variants in red hair colour and offer a powerful, economical and parsimonious model that achieves unsurpassed performance.
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Affiliation(s)
| | - Ryan N Lichtenwalter
- Anesthesia and the Alan Edwards Centre for Research on Pain, McGill University, Montreal, Canada
| | - Dima V Zaykin
- Biostatistics, National Institutes of Health, Research Triangle Park, NC, USA
| | - Marc Parisien
- Anesthesia and the Alan Edwards Centre for Research on Pain, McGill University, Montreal, Canada
| | - Simon Gravel
- Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, Canada
| | - Andrey Bortsov
- Department of Anesthesiology, Center for Translational Pain Medicine, Durham, NC, USA
| | - Luda Diatchenko
- Anesthesia and the Alan Edwards Centre for Research on Pain, McGill University, Montreal, Canada
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46
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Yuan H, Yu T, Wang L, Yang L, Zhang Y, Liu H, Li M, Tang X, Liu Z, Li Z, Lu C, Chen X, Pang D, Ouyang H. Efficient base editing by RNA-guided cytidine base editors (CBEs) in pigs. Cell Mol Life Sci 2020; 77:719-733. [PMID: 31302752 PMCID: PMC11105001 DOI: 10.1007/s00018-019-03205-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 06/11/2019] [Accepted: 06/20/2019] [Indexed: 10/26/2022]
Abstract
Cytidine base editors (CBEs) have been demonstrated to be useful for precisely inducing C:G-to-T:A base mutations in various organisms. In this study, we showed that the BE4-Gam system induced the targeted C-to-T base conversion in porcine blastocysts at an efficiency of 66.7-71.4% via the injection of a single sgRNA targeting a xeno-antigen-related gene and BE4-Gam mRNA. Furthermore, the efficiency of simultaneous three gene base conversion via the injection of three targeting sgRNAs and BE4-Gam mRNA into porcine parthenogenetic embryos was 18.1%. We also obtained beta-1,4-N-acetyl-galactosaminyl transferase 2, alpha-1,3-galactosyltransferase, and cytidine monophosphate-N-acetylneuraminic acid hydroxylase deficient pig by somatic cell nuclear transfer, which exhibited significantly decreased activity. In addition, a new CBE version (termed AncBE4max) was used to edit genes in blastocysts and porcine fibroblasts (PFFs) for the first time. While this new version demonstrated a three genes base-editing rate of 71.4% at the porcine GGTA1, B4galNT2, and CMAH loci, it increased the frequency of bystander edits, which ranged from 17.8 to 71.4%. In this study, we efficiently and precisely mutated bases in porcine blastocysts and PFFs using CBEs and successfully generated C-to-T and C-to-G mutations in pigs. These results suggest that CBEs provide a more simple and efficient method for improving economic traits, reducing the breeding cycle, and increasing disease tolerance in pigs, thus aiding in the development of human disease models.
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Affiliation(s)
- Hongming Yuan
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Tingting Yu
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Lingyu Wang
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Lin Yang
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Yuanzhu Zhang
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Huan Liu
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Mengjing Li
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Xiaochun Tang
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Zhiquan Liu
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Zhanjun Li
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Chao Lu
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Xue Chen
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China
| | - Daxin Pang
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China.
| | - Hongsheng Ouyang
- Key Lab for Zoonoses Research, Ministry of Education, Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, 130062, Jilin, People's Republic of China.
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47
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Orozco LD, Chen HH, Cox C, Katschke KJ, Arceo R, Espiritu C, Caplazi P, Nghiem SS, Chen YJ, Modrusan Z, Dressen A, Goldstein LD, Clarke C, Bhangale T, Yaspan B, Jeanne M, Townsend MJ, van Lookeren Campagne M, Hackney JA. Integration of eQTL and a Single-Cell Atlas in the Human Eye Identifies Causal Genes for Age-Related Macular Degeneration. Cell Rep 2020; 30:1246-1259.e6. [PMID: 31995762 DOI: 10.1016/j.celrep.2019.12.082] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/04/2019] [Accepted: 12/19/2019] [Indexed: 12/11/2022] Open
Abstract
Age-related macular degeneration (AMD) is a leading cause of vision loss. To better understand disease pathogenesis and identify causal genes in GWAS loci for AMD risk, we present a comprehensive database of human retina and retinal pigment epithelium (RPE). Our database comprises macular and non-macular RNA sequencing (RNA-seq) profiles from 129 donors, a genome-wide expression quantitative trait loci (eQTL) dataset that includes macula-specific retina and RPE/choroid, and single-nucleus RNA-seq (NucSeq) from human retina and RPE with subtype resolution from more than 100,000 cells. Using NucSeq, we find enriched expression of AMD candidate genes in RPE cells. We identify 15 putative causal genes for AMD on the basis of co-localization of genetic association signals for AMD risk and eye eQTL, including the genes TSPAN10 and TRPM1. These results demonstrate the value of our human eye database for elucidating genetic pathways and potential therapeutic targets for ocular diseases.
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Affiliation(s)
- Luz D Orozco
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA
| | - Hsu-Hsin Chen
- Department of Biomarker Discovery OMNI, Genentech, South San Francisco, CA 94080, USA
| | - Christian Cox
- Department of Immunology Discovery, Genentech, South San Francisco, CA 94080, USA
| | - Kenneth J Katschke
- Department of Immunology Discovery, Genentech, South San Francisco, CA 94080, USA
| | - Rommel Arceo
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Carmina Espiritu
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Patrick Caplazi
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | | | - Ying-Jiun Chen
- Department of Molecular Biology, Genentech, South San Francisco, CA 94080, USA
| | - Zora Modrusan
- Department of Molecular Biology, Genentech, South San Francisco, CA 94080, USA
| | - Amy Dressen
- Department of Human Genetics, Genentech, South San Francisco, CA 94080, USA
| | - Leonard D Goldstein
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA; Department of Molecular Biology, Genentech, South San Francisco, CA 94080, USA
| | - Christine Clarke
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA
| | - Tushar Bhangale
- Department of Human Genetics, Genentech, South San Francisco, CA 94080, USA
| | - Brian Yaspan
- Department of Human Genetics, Genentech, South San Francisco, CA 94080, USA
| | - Marion Jeanne
- Department of Immunology Discovery, Genentech, South San Francisco, CA 94080, USA
| | - Michael J Townsend
- Department of Biomarker Discovery OMNI, Genentech, South San Francisco, CA 94080, USA.
| | | | - Jason A Hackney
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA.
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48
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Xiong Z, Dankova G, Howe LJ, Lee MK, Hysi PG, de Jong MA, Zhu G, Adhikari K, Li D, Li Y, Pan B, Feingold E, Marazita ML, Shaffer JR, McAloney K, Xu SH, Jin L, Wang S, de Vrij FMS, Lendemeijer B, Richmond S, Zhurov A, Lewis S, Sharp GC, Paternoster L, Thompson H, Gonzalez-Jose R, Bortolini MC, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Uitterlinden AG, Ikram MA, Wolvius E, Kushner SA, Nijsten TEC, Palstra RJTS, Boehringer S, Medland SE, Tang K, Ruiz-Linares A, Martin NG, Spector TD, Stergiakouli E, Weinberg SM, Liu F, Kayser M. Novel genetic loci affecting facial shape variation in humans. eLife 2019; 8:e49898. [PMID: 31763980 PMCID: PMC6905649 DOI: 10.7554/elife.49898] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 11/22/2019] [Indexed: 12/14/2022] Open
Abstract
The human face represents a combined set of highly heritable phenotypes, but knowledge on its genetic architecture remains limited, despite the relevance for various fields. A series of genome-wide association studies on 78 facial shape phenotypes quantified from 3-dimensional facial images of 10,115 Europeans identified 24 genetic loci reaching study-wide suggestive association (p < 5 × 10-8), among which 17 were previously unreported. A follow-up multi-ethnic study in additional 7917 individuals confirmed 10 loci including six unreported ones (padjusted < 2.1 × 10-3). A global map of derived polygenic face scores assembled facial features in major continental groups consistent with anthropological knowledge. Analyses of epigenomic datasets from cranial neural crest cells revealed abundant cis-regulatory activities at the face-associated genetic loci. Luciferase reporter assays in neural crest progenitor cells highlighted enhancer activities of several face-associated DNA variants. These results substantially advance our understanding of the genetic basis underlying human facial variation and provide candidates for future in-vivo functional studies.
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Affiliation(s)
- Ziyi Xiong
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
- Department of EpidemiologyErasmus MC University Medical Center RotterdamRotterdamNetherlands
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of GenomicsUniversity of Chinese Academy of Sciences (CAS)BeijingChina
| | - Gabriela Dankova
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Laurence J Howe
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
| | - Myoung Keun Lee
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
| | - Pirro G Hysi
- Department of Twin Research and Genetic EpidemiologyKing’s College LondonLondonUnited Kingdom
| | - Markus A de Jong
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
- Department of Oral & Maxillofacial Surgery, Special Dental Care, and OrthodonticsErasmus MC University Medical Center RotterdamRotterdamNetherlands
- Department of Biomedical Data SciencesLeiden University Medical CenterLeidenNetherlands
| | - Gu Zhu
- QIMR Berghofer Medical Research InstituteBrisbaneAustralia
| | - Kaustubh Adhikari
- Department of Genetics, Evolution, and EnvironmentUniversity College LondonLondonUnited Kingdom
| | - Dan Li
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
| | - Yi Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of GenomicsUniversity of Chinese Academy of Sciences (CAS)BeijingChina
| | - Bo Pan
- Department of Auricular ReconstructionPlastic Surgery HospitalBeijingChina
| | - Eleanor Feingold
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
- Department of Human GeneticsUniversity of PittsburghPittsburghUnited States
| | - John R Shaffer
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
- Department of Human GeneticsUniversity of PittsburghPittsburghUnited States
| | | | - Shu-Hua Xu
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
| | - Li Jin
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life SciencesFudan UniversityShanghaiChina
| | - Sijia Wang
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
| | - Femke MS de Vrij
- Department of PsychiatryErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Bas Lendemeijer
- Department of PsychiatryErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Stephen Richmond
- Applied Clinical Research and Public Health, University Dental SchoolCardiff UniversityCardiffUnited Kingdom
| | - Alexei Zhurov
- Applied Clinical Research and Public Health, University Dental SchoolCardiff UniversityCardiffUnited Kingdom
| | - Sarah Lewis
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
| | - Gemma C Sharp
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
- School of Oral and Dental SciencesUniversity of BristolBristolUnited Kingdom
| | - Lavinia Paternoster
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
| | - Holly Thompson
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
| | - Rolando Gonzalez-Jose
- Instituto Patagonico de Ciencias Sociales y Humanas, CENPAT-CONICETPuerto MadrynArgentina
| | | | - Samuel Canizales-Quinteros
- UNAM-Instituto Nacional de Medicina Genomica, Facultad de QuımicaUnidad de Genomica de Poblaciones Aplicada a la SaludMexico CityMexico
| | - Carla Gallo
- Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y FilosofıaUniversidad Peruana Cayetano HerediaLimaPeru
| | - Giovanni Poletti
- Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y FilosofıaUniversidad Peruana Cayetano HerediaLimaPeru
| | - Gabriel Bedoya
- GENMOL (Genetica Molecular)Universidad de AntioquiaMedellınColombia
| | | | - André G Uitterlinden
- Department of EpidemiologyErasmus MC University Medical Center RotterdamRotterdamNetherlands
- Department of Internal MedicineErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - M Arfan Ikram
- Department of EpidemiologyErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Eppo Wolvius
- Department of Oral & Maxillofacial Surgery, Special Dental Care, and OrthodonticsErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Steven A Kushner
- Department of PsychiatryErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Tamar EC Nijsten
- Department of DermatologyErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Robert-Jan TS Palstra
- Department of BiochemistryErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Stefan Boehringer
- Department of Biomedical Data SciencesLeiden University Medical CenterLeidenNetherlands
| | | | - Kun Tang
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
| | - Andres Ruiz-Linares
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life SciencesFudan UniversityShanghaiChina
- Aix-Marseille Université, CNRS, EFS, ADESMarseilleFrance
| | | | - Timothy D Spector
- Department of Twin Research and Genetic EpidemiologyKing’s College LondonLondonUnited Kingdom
| | - Evie Stergiakouli
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
- School of Oral and Dental SciencesUniversity of BristolBristolUnited Kingdom
| | - Seth M Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
- Department of Human GeneticsUniversity of PittsburghPittsburghUnited States
- Department of AnthropologyUniversity of PittsburghPittsburghUnited States
| | - Fan Liu
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of GenomicsUniversity of Chinese Academy of Sciences (CAS)BeijingChina
| | - Manfred Kayser
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
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49
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Koch SL, Tridico SR, Bernard BA, Shriver MD, Jablonski NG. The biology of human hair: A multidisciplinary review. Am J Hum Biol 2019; 32:e23316. [DOI: 10.1002/ajhb.23316] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 07/21/2019] [Accepted: 08/17/2019] [Indexed: 12/22/2022] Open
Affiliation(s)
- Sandra L. Koch
- Department of AnthropologyPennsylvania State University State College Pennsylvania
| | | | | | - Mark D. Shriver
- Department of AnthropologyPennsylvania State University State College Pennsylvania
| | - Nina G. Jablonski
- Department of AnthropologyPennsylvania State University State College Pennsylvania
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50
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Fufa TD, Baxter LL, Wedel JC, Gildea DE, Loftus SK, Pavan WJ. MEK inhibition remodels the active chromatin landscape and induces SOX10 genomic recruitment in BRAF(V600E) mutant melanoma cells. Epigenetics Chromatin 2019; 12:50. [PMID: 31399133 PMCID: PMC6688322 DOI: 10.1186/s13072-019-0297-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/28/2019] [Indexed: 01/03/2023] Open
Abstract
Background The MAPK/ERK signaling pathway is an essential regulator of numerous cell processes that are crucial for normal development as well as cancer progression. While much is known regarding MAPK/ERK signal conveyance from the cell membrane to the nucleus, the transcriptional and epigenetic mechanisms that govern gene expression downstream of MAPK signaling are not fully elucidated. Results This study employed an integrated epigenome analysis approach to interrogate the effects of MAPK/ERK pathway inhibition on the global transcriptome, the active chromatin landscape, and protein–DNA interactions in 501mel melanoma cells. Treatment of these cells with the small-molecule MEK inhibitor AZD6244 induces hyperpigmentation, widespread gene expression changes including alteration of genes linked to pigmentation, and extensive epigenomic reprogramming of transcriptionally distinct regulatory regions associated with the active chromatin mark H3K27ac. Regulatory regions with differentially acetylated H3K27ac regions following AZD6244 treatment are enriched in transcription factor binding motifs of ETV/ETS and ATF family members as well as the lineage-determining factors MITF and SOX10. H3K27ac-dense enhancer clusters known as super-enhancers show similar transcription factor motif enrichment, and furthermore, these super-enhancers are associated with genes encoding MITF, SOX10, and ETV/ETS proteins. Along with genome-wide resetting of the active enhancer landscape, MEK inhibition also results in widespread SOX10 recruitment throughout the genome, including increased SOX10 binding density at H3K27ac-marked enhancers. Importantly, these MEK inhibitor-responsive enhancers marked by H3K27ac and occupied by SOX10 are located near melanocyte lineage-specific and pigmentation genes and overlap numerous human SNPs associated with pigmentation and melanoma phenotypes, highlighting the variants located within these regions for prioritization in future studies. Conclusions These results reveal the epigenetic reprogramming underlying the re-activation of melanocyte pigmentation and developmental transcriptional programs in 501mel cells in response to MEK inhibition and suggest extensive involvement of a MEK-SOX10 axis in the regulation of these processes. The dynamic chromatin changes identified here provide a rich genomic resource for further analyses of the molecular mechanisms governing the MAPK pathway in pigmentation- and melanocyte-associated diseases. Electronic supplementary material The online version of this article (10.1186/s13072-019-0297-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Temesgen D Fufa
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.,Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Laura L Baxter
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Julia C Wedel
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Derek E Gildea
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Stacie K Loftus
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - William J Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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