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Walsh S, Chaitanya L, Breslin K, Muralidharan C, Bronikowska A, Pospiech E, Koller J, Kovatsi L, Wollstein A, Branicki W, Liu F, Kayser M. Global skin colour prediction from DNA. Hum Genet 2017; 136:847-863. [PMID: 28500464 PMCID: PMC5487854 DOI: 10.1007/s00439-017-1808-5] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 05/03/2017] [Indexed: 12/14/2022]
Abstract
Human skin colour is highly heritable and externally visible with relevance in medical, forensic, and anthropological genetics. Although eye and hair colour can already be predicted with high accuracies from small sets of carefully selected DNA markers, knowledge about the genetic predictability of skin colour is limited. Here, we investigate the skin colour predictive value of 77 single-nucleotide polymorphisms (SNPs) from 37 genetic loci previously associated with human pigmentation using 2025 individuals from 31 global populations. We identified a minimal set of 36 highly informative skin colour predictive SNPs and developed a statistical prediction model capable of skin colour prediction on a global scale. Average cross-validated prediction accuracies expressed as area under the receiver-operating characteristic curve (AUC) ± standard deviation were 0.97 ± 0.02 for Light, 0.83 ± 0.11 for Dark, and 0.96 ± 0.03 for Dark-Black. When using a 5-category, this resulted in 0.74 ± 0.05 for Very Pale, 0.72 ± 0.03 for Pale, 0.73 ± 0.03 for Intermediate, 0.87±0.1 for Dark, and 0.97 ± 0.03 for Dark-Black. A comparative analysis in 194 independent samples from 17 populations demonstrated that our model outperformed a previously proposed 10-SNP-classifier approach with AUCs rising from 0.79 to 0.82 for White, comparable at the intermediate level of 0.63 and 0.62, respectively, and a large increase from 0.64 to 0.92 for Black. Overall, this study demonstrates that the chosen DNA markers and prediction model, particularly the 5-category level; allow skin colour predictions within and between continental regions for the first time, which will serve as a valuable resource for future applications in forensic and anthropologic genetics.
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Affiliation(s)
- Susan Walsh
- Department of Biology, Indiana University Purdue University Indianapolis (IUPUI), Indianapolis, IN, USA.
| | - Lakshmi Chaitanya
- Department of Genetic Identification, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Krystal Breslin
- Department of Biology, Indiana University Purdue University Indianapolis (IUPUI), Indianapolis, IN, USA
| | - Charanya Muralidharan
- Department of Biology, Indiana University Purdue University Indianapolis (IUPUI), Indianapolis, IN, USA
| | - Agnieszka Bronikowska
- Department of Dermatology, Collegium Medicum of the Jagiellonian University, Kraków, Poland
| | - Ewelina Pospiech
- Faculty of Biology and Earth Sciences, Institute of Zoology, Jagiellonian University, Kraków, Poland
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Julia Koller
- Department of Genetic Identification, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Leda Kovatsi
- Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Andreas Wollstein
- Section of Evolutionary Biology, Department of Biology II, University of Munich LMU, Planegg-Martinsried, Germany
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - Fan Liu
- Department of Genetic Identification, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands.
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102
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Denker A, de Laat W. The second decade of 3C technologies: detailed insights into nuclear organization. Genes Dev 2017; 30:1357-82. [PMID: 27340173 PMCID: PMC4926860 DOI: 10.1101/gad.281964.116] [Citation(s) in RCA: 225] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The relevance of three-dimensional (3D) genome organization for transcriptional regulation and thereby for cellular fate at large is now widely accepted. Our understanding of the fascinating architecture underlying this function is based on microscopy studies as well as the chromosome conformation capture (3C) methods, which entered the stage at the beginning of the millennium. The first decade of 3C methods rendered unprecedented insights into genome topology. Here, we provide an update of developments and discoveries made over the more recent years. As we discuss, established and newly developed experimental and computational methods enabled identification of novel, functionally important chromosome structures. Regulatory and architectural chromatin loops throughout the genome are being cataloged and compared between cell types, revealing tissue invariant and developmentally dynamic loops. Architectural proteins shaping the genome were disclosed, and their mode of action is being uncovered. We explain how more detailed insights into the 3D genome increase our understanding of transcriptional regulation in development and misregulation in disease. Finally, to help researchers in choosing the approach best tailored for their specific research question, we explain the differences and commonalities between the various 3C-derived methods.
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Affiliation(s)
- Annette Denker
- Hubrecht Institute-Koninklijke Nederlandse Akademie van Wetenschappen (KNAW) and University Medical Center Utrecht, 3584CT Utrecht, the Netherlands
| | - Wouter de Laat
- Hubrecht Institute-Koninklijke Nederlandse Akademie van Wetenschappen (KNAW) and University Medical Center Utrecht, 3584CT Utrecht, the Netherlands
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103
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Purfield DC, McParland S, Wall E, Berry DP. The distribution of runs of homozygosity and selection signatures in six commercial meat sheep breeds. PLoS One 2017; 12:e0176780. [PMID: 28463982 PMCID: PMC5413029 DOI: 10.1371/journal.pone.0176780] [Citation(s) in RCA: 155] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 04/17/2017] [Indexed: 11/18/2022] Open
Abstract
Domestication and the subsequent selection of animals for either economic or morphological features can leave a variety of imprints on the genome of a population. Genomic regions subjected to high selective pressures often show reduced genetic diversity and frequent runs of homozygosity (ROH). Therefore, the objective of the present study was to use 42,182 autosomal SNPs to identify genomic regions in 3,191 sheep from six commercial breeds subjected to selection pressure and to quantify the genetic diversity within each breed using ROH. In addition, the historical effective population size of each breed was also estimated and, in conjunction with ROH, was used to elucidate the demographic history of the six breeds. ROH were common in the autosomes of animals in the present study, but the observed breed differences in patterns of ROH length and burden suggested differences in breed effective population size and recent management. ROH provided a sufficient predictor of the pedigree inbreeding coefficient, with an estimated correlation between both measures of 0.62. Genomic regions under putative selection were identified using two complementary algorithms; the fixation index and hapFLK. The identified regions under putative selection included candidate genes associated with skin pigmentation, body size and muscle formation; such characteristics are often sought after in modern-day breeding programs. These regions of selection frequently overlapped with high ROH regions both within and across breeds. Multiple yet uncharacterised genes also resided within putative regions of selection. This further substantiates the need for a more comprehensive annotation of the sheep genome as these uncharacterised genes may contribute to traits of interest in the animal sciences. Despite this, the regions identified as under putative selection in the current study provide an insight into the mechanisms leading to breed differentiation and genetic variation in meat production.
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Affiliation(s)
- Deirdre C. Purfield
- Animal & Grassland Research and Innovation Center, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland
- * E-mail:
| | - Sinead McParland
- Animal & Grassland Research and Innovation Center, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland
| | - Eamon Wall
- Sheep Ireland, Bandon, Co. Cork, Ireland
| | - Donagh P. Berry
- Animal & Grassland Research and Innovation Center, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland
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104
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Campagna L, Repenning M, Silveira LF, Fontana CS, Tubaro PL, Lovette IJ. Repeated divergent selection on pigmentation genes in a rapid finch radiation. SCIENCE ADVANCES 2017; 3:e1602404. [PMID: 28560331 PMCID: PMC5443641 DOI: 10.1126/sciadv.1602404] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 03/31/2017] [Indexed: 05/09/2023]
Abstract
Instances of recent and rapid speciation are suitable for associating phenotypes with their causal genotypes, especially if gene flow homogenizes areas of the genome that are not under divergent selection. We study a rapid radiation of nine sympatric bird species known as capuchino seedeaters, which are differentiated in sexually selected characters of male plumage and song. We sequenced the genomes of a phenotypically diverse set of species to search for differentiated genomic regions. Capuchinos show differences in a small proportion of their genomes, yet selection has acted independently on the same targets in different members of this radiation. Many divergent regions contain genes involved in the melanogenesis pathway, with the strongest signal originating from putative regulatory regions. Selection has acted on these same genomic regions in different lineages, likely shaping the evolution of cis-regulatory elements, which control how more conserved genes are expressed and thereby generate diversity in classically sexually selected traits.
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Affiliation(s)
- Leonardo Campagna
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, 159 Sapsucker Woods Road, Ithaca, NY 14850, USA
- Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Road, Ithaca, NY 14853, USA
- Corresponding author.
| | - Márcio Repenning
- PUCRS- Curso de Pós-graduação em Zoologia, Laboratório de Ornitologia, Museu de Ciências e Tecnologia, Avenida Ipiranga 6681, 90619-900 Porto Alegre, Rio Grande do Sul, Brazil
| | - Luís Fábio Silveira
- Seção de Aves, Museu de Zoologia, Universidade de São Paulo, Caixa Postal 42.494, CEP 04218-970 São Paulo, São Paulo, Brasil
| | - Carla Suertegaray Fontana
- PUCRS- Curso de Pós-graduação em Zoologia, Laboratório de Ornitologia, Museu de Ciências e Tecnologia, Avenida Ipiranga 6681, 90619-900 Porto Alegre, Rio Grande do Sul, Brazil
| | - Pablo L. Tubaro
- División de Ornitología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN - CONICET), Avenida Ángel Gallardo 470, Ciudad de Buenos Aires, C1405DJR Buenos Aires, Argentina
| | - Irby J. Lovette
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, 159 Sapsucker Woods Road, Ithaca, NY 14850, USA
- Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Road, Ithaca, NY 14853, USA
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105
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Caliebe A, Walsh S, Liu F, Kayser M, Krawczak M. Likelihood ratio and posterior odds in forensic genetics: Two sides of the same coin. Forensic Sci Int Genet 2017; 28:203-210. [DOI: 10.1016/j.fsigen.2017.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 12/02/2016] [Accepted: 03/04/2017] [Indexed: 01/07/2023]
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106
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Brouwer RWW, van den Hout MCGN, van IJcken WFJ, Soler E, Stadhouders R. Unbiased Interrogation of 3D Genome Topology Using Chromosome Conformation Capture Coupled to High-Throughput Sequencing (4C-Seq). Methods Mol Biol 2017; 1507:199-220. [PMID: 27832542 DOI: 10.1007/978-1-4939-6518-2_15] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The development and widespread implementation of chromosome conformation capture (3C) technology has allowed unprecedented new insight into how chromosomes are folded in three-dimensional (3D) space. 3C and its derivatives have contributed tremendously to the now widely accepted view that genome topology plays an important role in many major cellular processes, at a chromosome-wide scale, but certainly also at the level of individual genetic loci. A particularly popular application of 3C technology is to study transcriptional regulation, allowing researchers to draw maps of gene regulatory connections beyond the linear genome through addition of the third dimension. In this chapter, we provide a highly detailed protocol describing 3C coupled to high-throughput sequencing (referred to as 3C-Seq or more commonly 4C-Seq), allowing the unbiased interrogation of genome-wide chromatin interactions with specific genomic regions of interest. Interactions between spatially clustered DNA fragments are revealed by crosslinking the cells with formaldehyde, digesting the genome with a restriction endonuclease and performing a proximity ligation step to link interacting genomic fragments. Next, interactions with a selected DNA fragment are extracted from the 3C library through a second round of digestion and ligation followed by an inverse PCR. The generated products are immediately compatible with high-throughput sequencing, and amplicons from different PCR reactions can easily be multiplexed to dramatically increase throughput. Finally, we provide suggestions for data analysis and visualization.
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Affiliation(s)
| | | | | | - Eric Soler
- INSERM UMR967, CEA/DRF/iRCM, Université Paris-Diderot, Université Paris-Saclay, Fontenay-aux-Roses, France.
- Laboratory of Excellence GR-Ex, 75015, Paris, France.
- Institute of Molecular Genetics (IGMM), Laboratory of Molecular Hematopoiesis, Montpellier, 34293, France.
| | - Ralph Stadhouders
- Gene Regulation, Stem Cells andCancer Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain.
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107
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Preger-Ben Noon E, Davis FP, Stern DL. Evolved Repression Overcomes Enhancer Robustness. Dev Cell 2016; 39:572-584. [PMID: 27840106 DOI: 10.1016/j.devcel.2016.10.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/26/2016] [Accepted: 10/14/2016] [Indexed: 12/18/2022]
Abstract
Biological systems display extraordinary robustness. Robustness of transcriptional enhancers results mainly from clusters of binding sites for the same transcription factor, and it is not clear how robust enhancers can evolve loss of expression through point mutations. Here, we report the high-resolution functional dissection of a robust enhancer of the shavenbaby gene that has contributed to morphological evolution. We found that robustness is encoded by many binding sites for the transcriptional activator Arrowhead and that, during evolution, some of these activator sites were lost, weakening enhancer activity. Complete silencing of enhancer function, however, required evolution of a binding site for the spatially restricted potent repressor Abrupt. These findings illustrate that recruitment of repressor binding sites can overcome enhancer robustness and may minimize pleiotropic consequences of enhancer evolution. Recruitment of repression may be a general mode of evolution to break robust regulatory linkages.
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Affiliation(s)
- Ella Preger-Ben Noon
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA.
| | - Fred P Davis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - David L Stern
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA.
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108
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Abstract
Genetic variation associated with disease often appears in non-coding parts of the genome. Understanding the mechanisms by which this phenomenon leads to disease is necessary to translate results from genetic association studies to the clinic. Assigning function to this type of variation is notoriously difficult because the human genome harbours a complex regulatory landscape with a dizzying array of transcriptional regulatory sequences, such as enhancers that have unpredictable, promiscuous and context-dependent behaviour. In this Review, we discuss how technological advances have provided increasingly detailed information on genome folding; for example, genome folding forms loops that bring enhancers and target genes into close proximity. We also now know that enhancers function within topologically associated domains, which are structural and functional units of chromosomes. Studying disease-associated mutations and chromosomal rearrangements in the context of the 3D genome will enable the identification of dysregulated target genes and aid the progression from descriptive genetic association results to discovering molecular mechanisms underlying disease.
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109
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Kita R, Fraser HB. Local Adaptation of Sun-Exposure-Dependent Gene Expression Regulation in Human Skin. PLoS Genet 2016; 12:e1006382. [PMID: 27760139 PMCID: PMC5070784 DOI: 10.1371/journal.pgen.1006382] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 09/23/2016] [Indexed: 12/29/2022] Open
Abstract
Sun-exposure is a key environmental variable in the study of human evolution. Several skin-pigmentation genes serve as classical examples of positive selection, suggesting that sun-exposure has significantly shaped worldwide genomic variation. Here we investigate the interaction between genetic variation and sun-exposure, and how this impacts gene expression regulation. Using RNA-Seq data from 607 human skin samples, we identified thousands of transcripts that are differentially expressed between sun-exposed skin and non-sun-exposed skin. We then tested whether genetic variants may influence each individual’s gene expression response to sun-exposure. Our analysis revealed 10 sun-exposure-dependent gene expression quantitative trait loci (se-eQTLs), including genes involved in skin pigmentation (SLC45A2) and epidermal differentiation (RASSF9). The allele frequencies of the RASSF9 se-eQTL across diverse populations correlate with the magnitude of solar radiation experienced by these populations, suggesting local adaptation to varying levels of sunlight. These results provide the first examples of sun-exposure-dependent regulatory variation and suggest that this variation has contributed to recent human adaptation. Varying levels of sun-exposure across the world have significantly shaped human evolution. Previous analyses have found several skin pigmentation genes with evidence of strong evolutionary pressures throughout human history, manifesting as large differences in the frequency of genomic variants across populations. But even within populations, individuals respond differently to sun-exposure, suggesting variation in addition to the major differences in skin pigmentation across populations. Here we investigated whether genetic variants associate with response to sun-exposure within Europeans. To measure the response we analyzed gene expression in sun-exposed and non-sun-exposed skin, and identified ten genetic variants that associated with the sun-exposure response of nearby genes. One of these genetic variants, which associated with the sun-exposure response of the gene RASSF9, showed evidence of adaptation in humans in response to solar radiation. Together this evidence suggests that the regulation of gene expression is influenced by sun-exposure and that the sun-exposure dependent effect on RASSF9 expression may have had an effect on human fitness. To our knowledge, this is the first example of an environment-dependent regulatory variant with evidence of adaptation in humans.
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Affiliation(s)
- Ryosuke Kita
- Department of Biology, Stanford University, Stanford California
| | - Hunter B. Fraser
- Department of Biology, Stanford University, Stanford California
- * E-mail:
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110
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Zhou S, Treloar AE, Lupien M. Emergence of the Noncoding Cancer Genome: A Target of Genetic and Epigenetic Alterations. Cancer Discov 2016; 6:1215-1229. [PMID: 27807102 DOI: 10.1158/2159-8290.cd-16-0745] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 08/17/2016] [Indexed: 12/14/2022]
Abstract
The emergence of whole-genome annotation approaches is paving the way for the comprehensive annotation of the human genome across diverse cell and tissue types exposed to various environmental conditions. This has already unmasked the positions of thousands of functional cis-regulatory elements integral to transcriptional regulation, such as enhancers, promoters, and anchors of chromatin interactions that populate the noncoding genome. Recent studies have shown that cis-regulatory elements are commonly the targets of genetic and epigenetic alterations associated with aberrant gene expression in cancer. Here, we review these findings to showcase the contribution of the noncoding genome and its alteration in the development and progression of cancer. We also highlight the opportunities to translate the biological characterization of genetic and epigenetic alterations in the noncoding cancer genome into novel approaches to treat or monitor disease. SIGNIFICANCE The majority of genetic and epigenetic alterations accumulate in the noncoding genome throughout oncogenesis. Discriminating driver from passenger events is a challenge that holds great promise to improve our understanding of the etiology of different cancer types. Advancing our understanding of the noncoding cancer genome may thus identify new therapeutic opportunities and accelerate our capacity to find improved biomarkers to monitor various stages of cancer development. Cancer Discov; 6(11); 1215-29. ©2016 AACR.
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Affiliation(s)
- Stanley Zhou
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Aislinn E Treloar
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada
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111
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Butler MG. Benefits and limitations of prenatal screening for Prader-Willi syndrome. Prenat Diagn 2016; 37:81-94. [PMID: 27537837 DOI: 10.1002/pd.4914] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/11/2016] [Accepted: 08/12/2016] [Indexed: 12/15/2022]
Abstract
This review summarizes the status of genetic laboratory testing in Prader-Willi syndrome (PWS) with different genetic subtypes, most often a paternally derived 15q11-q13 deletion and discusses benefits and limitations related to prenatal screening. Medical literature was searched for prenatal screening and genetic laboratory testing methods in use or under development and discussed in relationship to PWS. Genetic testing includes six established laboratory diagnostic approaches for PWS with direct application to prenatal screening. Ultrasonographic, obstetric and cytogenetic reports were summarized in relationship to the cause of PWS and identification of specific genetic subtypes including maternal disomy 15. Advances in genetic technology were described for diagnosing PWS specifically DNA methylation and high-resolution chromosomal SNP microarrays as current tools for genetic screening and incorporating next generation DNA sequencing for noninvasive prenatal testing (NIPT) using cell-free fetal DNA. Positive experiences are reported with NIPT for detection of numerical chromosomal problems (aneuploidies) but not for structural problems (microdeletions). These reports will be discussed along with future directions for genetic screening of PWS. In summary, this review describes and discusses the status of established and ongoing genetic testing options for PWS applicable in prenatal screening including NIPT and future directions for early diagnosis in PWS. © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Merlin G Butler
- Departments of Psychiatry and Behavioral Sciences and Pediatrics, University of Kansas Medical Center, Kansas City, KS, USA
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112
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Roulin AC, Bourgeois Y, Stiefel U, Walser JC, Ebert D. A Photoreceptor Contributes to the Natural Variation of Diapause Induction inDaphnia magna. Mol Biol Evol 2016; 33:3194-3204. [DOI: 10.1093/molbev/msw200] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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113
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Martins H, Caye K, Luu K, Blum MGB, François O. Identifying outlier loci in admixed and in continuous populations using ancestral population differentiation statistics. Mol Ecol 2016; 25:5029-5042. [DOI: 10.1111/mec.13822] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 08/18/2016] [Indexed: 01/05/2023]
Affiliation(s)
- Helena Martins
- Centre National de la Recherche Scientifique; TIMC-IMAG UMR 5525; Université Grenoble-Alpes; Grenoble 38042 France
| | - Kevin Caye
- Centre National de la Recherche Scientifique; TIMC-IMAG UMR 5525; Université Grenoble-Alpes; Grenoble 38042 France
| | - Keurcien Luu
- Centre National de la Recherche Scientifique; TIMC-IMAG UMR 5525; Université Grenoble-Alpes; Grenoble 38042 France
| | - Michael G. B. Blum
- Centre National de la Recherche Scientifique; TIMC-IMAG UMR 5525; Université Grenoble-Alpes; Grenoble 38042 France
| | - Olivier François
- Centre National de la Recherche Scientifique; TIMC-IMAG UMR 5525; Université Grenoble-Alpes; Grenoble 38042 France
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114
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Genetic markers of pigmentation are novel risk loci for uveal melanoma. Sci Rep 2016; 6:31191. [PMID: 27499155 PMCID: PMC4976361 DOI: 10.1038/srep31191] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 07/13/2016] [Indexed: 11/22/2022] Open
Abstract
While the role of genetic risk factors in the etiology of uveal melanoma (UM) has been strongly suggested, the genetic susceptibility to UM is currently vastly unexplored. Due to shared epidemiological risk factors between cutaneous melanoma (CM) and UM, in this study we have selected 28 SNPs identified as risk variants in previous genome-wide association studies on CM or CM-related host phenotypes (such as pigmentation and eye color) and tested them for association with UM risk. By logistic regression analysis of 272 UM cases and 1782 controls using an additive model, we identified five variants significantly associated with UM risk, all passing adjustment for multiple testing. The three most significantly associated variants rs12913832 (OR = 0.529, 95% CI 0.415–0.673; p = 8.47E-08), rs1129038 (OR = 0.533, 95% CI 0.419–0.678; p = 1.19E-07) and rs916977 (OR = 0.465, 95% CI 0.339–0.637; p = 3.04E-07) are correlated (r2 > 0.5) and map at 15q12 in the region of HERC2/OCA2, which determines eye-color in the human population. Our data provides first evidence that the genetic factors associated with pigmentation traits are risk loci of UM susceptibility.
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115
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Baghel R, Grover S, Kaur H, Jajodia A, Parween S, Sinha J, Srivastava A, Srivastava AK, Bala K, Chandna P, Kushwaha S, Agarwal R, Kukreti R. Synergistic association of STX1A and VAMP2 with cryptogenic epilepsy in North Indian population. Brain Behav 2016; 6:e00490. [PMID: 27458546 PMCID: PMC4951625 DOI: 10.1002/brb3.490] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 03/05/2016] [Accepted: 03/29/2016] [Indexed: 12/18/2022] Open
Abstract
INTRODUCTION "Common epilepsies", merely explored for genetics are the most frequent, nonfamilial, sporadic cases in hospitals. Because of their much debated molecular pathology, there is a need to focus on other neuronal pathways including the existing ion channels. METHODS For this study, a total of 214 epilepsy cases of North Indian ethnicity comprising 59.81% generalized, 40.19% focal seizures, and based on epilepsy types, 17.29% idiopathic, 37.38% cryptogenic, and 45.33% symptomatic were enrolled. Additionally, 170 unrelated healthy individuals were also enrolled. Here, we hypothesize the involvement of epilepsy pathophysiology genes, that is, synaptic vesicle cycle, SVC genes (presynapse), ion channels and their functionally related genes (postsynapse). An interactive analysis was initially performed in SVC genes using multifactor dimensionality reduction (MDR). Further, in order to understand the influence of ion channels and their functionally related genes, their interaction analysis with SVC genes was also performed. RESULTS A significant interactive two-locus model of STX1A_rs4363087|VAMP2_rs2278637 (presynaptic genes) was observed among SVC variants in all epilepsy cases (P 1000-value = 0.054; CVC = 9/10; OR = 2.86, 95%CI = 1.88-4.35). Further, subgroup analysis revealed stronger interaction for the same model in cryptogenic epilepsy patients only (P 1000-value = 0.012; CVC = 10/10; OR = 4.59, 95%CI = 2.57-8.22). However, interactive analysis of presynaptic and postsynaptic genes did not show any significant association. CONCLUSIONS Significant synergistic interaction of SVC genes revealed the possible functional relatedness of presynapse with pathophysiology of cryptogenic epilepsy. Further, to establish the clinical utility of the results, replication in a large and similar phenotypic group of patients is warranted.
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Affiliation(s)
- Ruchi Baghel
- Council of Scientific and Industrial Research (CSIR) Institute of Genomics and Integrative Biology (IGIB) Mall Road Delhi 110 007 India
| | - Sandeep Grover
- Council of Scientific and Industrial Research (CSIR) Institute of Genomics and Integrative Biology (IGIB) Mall Road Delhi 110 007 India; Division of Pneumonology-Immunology Department of Paediatrics Charité University Medical Centre Berlin Germany
| | - Harpreet Kaur
- Council of Scientific and Industrial Research (CSIR) Institute of Genomics and Integrative Biology (IGIB) Mall Road Delhi 110 007 India
| | - Ajay Jajodia
- Council of Scientific and Industrial Research (CSIR) Institute of Genomics and Integrative Biology (IGIB) Mall Road Delhi 110 007 India
| | - Shama Parween
- Council of Scientific and Industrial Research (CSIR) Institute of Genomics and Integrative Biology (IGIB) Mall Road Delhi 110 007 India
| | - Juhi Sinha
- Council of Scientific and Industrial Research (CSIR) Institute of Genomics and Integrative Biology (IGIB) Mall Road Delhi 110 007 India
| | - Ankit Srivastava
- Council of Scientific and Industrial Research (CSIR) Institute of Genomics and Integrative Biology (IGIB) Mall Road Delhi 110 007 India
| | - Achal Kumar Srivastava
- Neurology Department Neuroscience Centre All India Institute of Medical Sciences (AIIMS) New Delhi India
| | - Kiran Bala
- Institute of Human Behavior & Allied Sciences (IHBAS) Dilshad Garden Delhi 110 095 India
| | | | - Suman Kushwaha
- Institute of Human Behavior & Allied Sciences (IHBAS) Dilshad Garden Delhi 110 095 India
| | - Rachna Agarwal
- Institute of Human Behavior & Allied Sciences (IHBAS) Dilshad Garden Delhi 110 095 India
| | - Ritushree Kukreti
- Council of Scientific and Industrial Research (CSIR) Institute of Genomics and Integrative Biology (IGIB) Mall Road Delhi 110 007 India
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Pośpiech E, Karłowska-Pik J, Ziemkiewicz B, Kukla M, Skowron M, Wojas-Pelc A, Branicki W. Further evidence for population specific differences in the effect of DNA markers and gender on eye colour prediction in forensics. Int J Legal Med 2016; 130:923-934. [PMID: 27221533 PMCID: PMC4912978 DOI: 10.1007/s00414-016-1388-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/09/2016] [Indexed: 11/30/2022]
Abstract
The genetics of eye colour has been extensively studied over the past few years, and the identified polymorphisms have been applied with marked success in the field of Forensic DNA Phenotyping. A picture that arises from evaluation of the currently available eye colour prediction markers shows that only the analysis of HERC2-OCA2 complex has similar effectiveness in different populations, while the predictive potential of other loci may vary significantly. Moreover, the role of gender in the explanation of human eye colour variation should not be neglected in some populations. In the present study, we re-investigated the data for 1020 Polish individuals and using neural networks and logistic regression methods explored predictive capacity of IrisPlex SNPs and gender in this population sample. In general, neural networks provided higher prediction accuracy comparing to logistic regression (AUC increase by 0.02–0.06). Four out of six IrisPlex SNPs were associated with eye colour in the studied population. HERC2 rs12913832, OCA2 rs1800407 and SLC24A4 rs12896399 were found to be the most important eye colour predictors (p < 0.007) while the effect of rs16891982 in SLC45A2 was less significant. Gender was found to be significantly associated with eye colour with males having ~1.5 higher odds for blue eye colour comparing to females (p = 0.002) and was ranked as the third most important factor in blue/non-blue eye colour determination. However, the implementation of gender into the developed prediction models had marginal and ambiguous impact on the overall accuracy of prediction confirming that the effect of gender on eye colour in this population is small. Our study indicated the advantage of neural networks in prediction modeling in forensics and provided additional evidence for population specific differences in the predictive importance of the IrisPlex SNPs and gender.
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Affiliation(s)
- Ewelina Pośpiech
- Institute of Zoology, Faculty of Biology and Earth Sciences, Jagiellonian University, Kraków, Poland. .,Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland.
| | - Joanna Karłowska-Pik
- Faculty of Mathematics and Computer Science, Nicolaus Copernicus University, Toruń, Poland
| | - Bartosz Ziemkiewicz
- Faculty of Mathematics and Computer Science, Nicolaus Copernicus University, Toruń, Poland
| | - Magdalena Kukla
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Małgorzata Skowron
- Department of Dermatology, Collegium Medicum of the Jagiellonian University, Kraków, Poland
| | - Anna Wojas-Pelc
- Department of Dermatology, Collegium Medicum of the Jagiellonian University, Kraków, Poland
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
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117
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Chen GB, Lee SH, Zhu ZX, Benyamin B, Robinson MR. EigenGWAS: finding loci under selection through genome-wide association studies of eigenvectors in structured populations. Heredity (Edinb) 2016; 117:51-61. [PMID: 27142779 DOI: 10.1038/hdy.2016.25] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 03/02/2016] [Accepted: 03/07/2016] [Indexed: 12/13/2022] Open
Abstract
We develop a novel approach to identify regions of the genome underlying population genetic differentiation in any genetic data where the underlying population structure is unknown, or where the interest is assessing divergence along a gradient. By combining the statistical framework for genome-wide association studies (GWASs) with eigenvector decomposition (EigenGWAS), which is commonly used in population genetics to characterize the structure of genetic data, loci under selection can be identified without a requirement for discrete populations. We show through theory and simulation that our approach can identify regions under selection along gradients of ancestry, and in real data we confirm this by demonstrating LCT to be under selection between HapMap CEU-TSI cohorts, and we then validate this selection signal across European countries in the POPRES samples. HERC2 was also found to be differentiated between both the CEU-TSI cohort and within the POPRES sample, reflecting the likely anthropological differences in skin and hair colour between northern and southern European populations. Controlling for population stratification is of great importance in any quantitative genetic study and our approach also provides a simple, fast and accurate way of predicting principal components in independent samples. With ever increasing sample sizes across many fields, this approach is likely to be greatly utilized to gain individual-level eigenvectors avoiding the computational challenges associated with conducting singular value decomposition in large data sets. We have developed freely available software, Genetic Analysis Repository (GEAR), to facilitate the application of the methods.
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Affiliation(s)
- G-B Chen
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - S H Lee
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia.,School of Environmental and Rural Science, The University of New England, Armidale, New South Wales, Australia
| | - Z-X Zhu
- SPLUS Game, Guangzhou, Guangdong, China
| | - B Benyamin
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - M R Robinson
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
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118
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Naz M, Kodamullil AT, Hofmann-Apitius M. Reasoning over genetic variance information in cause-and-effect models of neurodegenerative diseases. Brief Bioinform 2016; 17:505-16. [PMID: 26249223 PMCID: PMC4870396 DOI: 10.1093/bib/bbv063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 07/09/2015] [Indexed: 12/18/2022] Open
Abstract
The work we present here is based on the recent extension of the syntax of the Biological Expression Language (BEL), which now allows for the representation of genetic variation information in cause-and-effect models. In our article, we describe, how genetic variation information can be used to identify candidate disease mechanisms in diseases with complex aetiology such as Alzheimer's disease and Parkinson's disease. In those diseases, we have to assume that many genetic variants contribute moderately to the overall dysregulation that in the case of neurodegenerative diseases has such a long incubation time until the first clinical symptoms are detectable. Owing to the multilevel nature of dysregulation events, systems biomedicine modelling approaches need to combine mechanistic information from various levels, including gene expression, microRNA (miRNA) expression, protein-protein interaction, genetic variation and pathway. OpenBEL, the open source version of BEL, has recently been extended to match this requirement, and we demonstrate in our article, how candidate mechanisms for early dysregulation events in Alzheimer's disease can be identified based on an integrative mining approach that identifies 'chains of causation' that include single nucleotide polymorphism information in BEL models.
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119
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Nakaoka H, Gurumurthy A, Hayano T, Ahmadloo S, Omer WH, Yoshihara K, Yamamoto A, Kurose K, Enomoto T, Akira S, Hosomichi K, Inoue I. Allelic Imbalance in Regulation of ANRIL through Chromatin Interaction at 9p21 Endometriosis Risk Locus. PLoS Genet 2016; 12:e1005893. [PMID: 27055116 PMCID: PMC4824487 DOI: 10.1371/journal.pgen.1005893] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 02/02/2016] [Indexed: 12/19/2022] Open
Abstract
Genome-wide association studies (GWASs) have discovered numerous single nucleotide polymorphisms (SNPs) associated with human complex disorders. However, functional characterization of the disease-associated SNPs remains a formidable challenge. Here we explored regulatory mechanism of a SNP on chromosome 9p21 associated with endometriosis by leveraging “allele-specific” functional genomic approaches. By re-sequencing 1.29 Mb of 9p21 region and scrutinizing DNase-seq data from the ENCODE project, we prioritized rs17761446 as a candidate functional variant that was in perfect linkage disequilibrium with the original GWAS SNP (rs10965235) and located on DNase I hypersensitive site. Chromosome conformation capture followed by high-throughput sequencing revealed that the protective G allele of rs17761446 exerted stronger chromatin interaction with ANRIL promoter. We demonstrated that the protective allele exhibited preferential binding affinities to TCF7L2 and EP300 by bioinformatics and chromatin immunoprecipitation (ChIP) analyses. ChIP assays for histone H3 lysine 27 acetylation and RNA polymerase II reinforced the enhancer activity of the SNP site. The allele specific expression analysis for eutopic endometrial tissues and endometrial carcinoma cell lines showed that rs17761446 was a cis-regulatory variant where G allele was associated with increased ANRIL expression. Our work illuminates the allelic imbalances in a series of transcriptional regulation from factor binding to gene expression mediated by chromatin interaction underlie the molecular mechanism of 9p21 endometriosis risk locus. Functional genomics on common disease will unlock functional aspect of genotype-phenotype correlations in the post-GWAS stage. A large number of variants associated with human complex diseases have been discovered by genome-wide association studies (GWASs). These discoveries have been anticipated to be translated into the definitive understanding of disease pathogeneses; however, functional characterization of the disease-associated SNPs remains a formidable challenge. Here we explored regulatory mechanism of a variant on chromosome 9p21 associated with endometriosis, a common gynecological disorder. By scrutinizing linkage disequilibrium structure and DNase I hypersensitive sites across the risk locus, we prioritized rs17761446 as a candidate causal variant. The results of our “allele-specific” functional genomic approaches sheds light on regulatory mechanisms underlying 9p21 endometriosis risk locus, in which preferential bindings of TCF7L2 and its coactivator EP300 to the protective G allele of rs17761446 lead to stronger chromatin interaction with the promoter of ANRIL, which in turn activate transcription of the non-coding RNA. Motivated by the fact that TCF7L2 was a key transcription factor of Wnt signaling pathway, we postulated that the induction of Wnt signaling activated expression levels of ANRIL and cell cycle inhibitors, CDKN2A/2B. Functional genomics on common disease will unlock functional aspect of genotype-phenotype correlations in the post-GWAS stage.
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Affiliation(s)
- Hirofumi Nakaoka
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Aishwarya Gurumurthy
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Takahide Hayano
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Somayeh Ahmadloo
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Waleed H Omer
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Kosuke Yoshihara
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata, Japan
| | - Akihito Yamamoto
- Department of Obstetrics and Gynecology, Nippon Medical School, Bunkyo-ku, Tokyo, Japan
| | - Keisuke Kurose
- Department of Obstetrics and Gynecology, Nippon Medical School, Bunkyo-ku, Tokyo, Japan
| | - Takayuki Enomoto
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata, Japan
| | - Shigeo Akira
- Department of Obstetrics and Gynecology, Nippon Medical School, Bunkyo-ku, Tokyo, Japan
| | - Kazuyoshi Hosomichi
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Ituro Inoue
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
- * E-mail:
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120
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Andersen JD, Pietroni C, Johansen P, Andersen MM, Pereira V, Børsting C, Morling N. Importance of nonsynonymous OCA2 variants in human eye color prediction. Mol Genet Genomic Med 2016; 4:420-30. [PMID: 27468418 PMCID: PMC4947861 DOI: 10.1002/mgg3.213] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 02/09/2016] [Accepted: 02/12/2016] [Indexed: 11/24/2022] Open
Abstract
Background The color of the eyes is one of the most prominent phenotypes in humans and it is often used to describe the appearance of an individual. The intensity of pigmentation in the iris is strongly associated with one single‐nucleotide polymorphism (SNP), rs12913832:A>G that is located in the promotor region of OCA2 (OMIM #611409). Nevertheless, many eye colors cannot be explained by only considering rs12913832:A>G. Methods In this study, we searched for additional variants in OCA2 to explain human eye color by sequencing a 500 kbp region, encompassing OCA2 and its promotor region. Results We identified three nonsynonymous OCA2 variants as important for eye color, including rs1800407:G>A (p.Arg419Gln) and two variants, rs74653330:A>T (p.Ala481Thr) and rs121918166:G>A (p.Val443Ile), not previously described as important for eye color variation. It was shown that estimated haplotypes consisting of four variants (rs12913832:A>G, rs1800407:G>A (p.Arg419Gln), rs74653330:A>T (p.Ala481Thr), and rs121918166:G>A (p.Val443Ile)) explained 75.6% (adjusted R2 = 0.76) of normal eye color variation, whereas rs12913832:A>G alone explained 68.8% (adjusted R2 = 0.69). Moreover, rs74653330:A>T (p.Ala481Thr) and rs121918166:G>A (p.Val443Ile) had a measurable effect on quantitative skin color (P = 0.008). Conclusion Our data showed that rs74653330:A>T (p.Ala481Thr) and rs121918166:G>A (p.Val443Ile) have a measurable effect on normal pigmentation variation.
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Affiliation(s)
- Jeppe D Andersen
- Section of Forensic Genetics Department of Forensic Medicine Faculty of Health and Medical Sciences University of Copenhagen DK-2100 Copenhagen Denmark
| | - Carlotta Pietroni
- Section of Forensic Genetics Department of Forensic Medicine Faculty of Health and Medical Sciences University of Copenhagen DK-2100 Copenhagen Denmark
| | - Peter Johansen
- Section of Forensic Genetics Department of Forensic Medicine Faculty of Health and Medical Sciences University of Copenhagen DK-2100 Copenhagen Denmark
| | - Mikkel M Andersen
- Department of Mathematical Sciences Aalborg University DK-9000 Aalborg Denmark
| | - Vania Pereira
- Section of Forensic Genetics Department of Forensic Medicine Faculty of Health and Medical Sciences University of Copenhagen DK-2100 Copenhagen Denmark
| | - Claus Børsting
- Section of Forensic Genetics Department of Forensic Medicine Faculty of Health and Medical Sciences University of Copenhagen DK-2100 Copenhagen Denmark
| | - Niels Morling
- Section of Forensic Genetics Department of Forensic Medicine Faculty of Health and Medical Sciences University of Copenhagen DK-2100 Copenhagen Denmark
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121
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Asgari MM, Wang W, Ioannidis NM, Itnyre J, Hoffmann T, Jorgenson E, Whittemore AS. Identification of Susceptibility Loci for Cutaneous Squamous Cell Carcinoma. J Invest Dermatol 2016; 136:930-937. [PMID: 26829030 DOI: 10.1016/j.jid.2016.01.013] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/04/2016] [Accepted: 01/06/2016] [Indexed: 12/20/2022]
Abstract
We report a genome-wide association study of cutaneous squamous cell carcinoma conducted among non-Hispanic white members of the Kaiser Permanente Northern California health care system. The study includes a genome-wide screen of 61,457 members (6,891 cases and 54,566 controls) genotyped on the Affymetrix Axiom European array and a replication phase involving an independent set of 6,410 additional members (810 cases and 5,600 controls). Combined analysis of screening and replication phases identified 10 loci containing single-nucleotide polymorphisms (SNPs) with P-values < 5 × 10(-8). Six loci contain genes in the pigmentation pathway; SNPs at these loci appear to modulate squamous cell carcinoma risk independently of the pigmentation phenotypes. Another locus contains HLA class II genes studied in relation to elevated squamous cell carcinoma risk following immunosuppression. SNPs at the remaining three loci include an intronic SNP in FOXP1 at locus 3p13, an intergenic SNP at 3q28 near TP63, and an intergenic SNP at 9p22 near BNC2. These findings provide insights into the genetic factors accounting for inherited squamous cell carcinoma susceptibility.
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Affiliation(s)
- Maryam M Asgari
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts, USA; Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
| | - Wei Wang
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, California, USA
| | - Nilah M Ioannidis
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, California, USA; Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Jacqueline Itnyre
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, California, USA
| | - Thomas Hoffmann
- Department of Epidemiology and Biostatistics and Institute for Human Genetics, University of California, San Francisco, California, USA
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
| | - Alice S Whittemore
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, California, USA.
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122
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Dhont L, Mascaux C, Belayew A. The helicase-like transcription factor (HLTF) in cancer: loss of function or oncomorphic conversion of a tumor suppressor? Cell Mol Life Sci 2016; 73:129-47. [PMID: 26472339 PMCID: PMC11108516 DOI: 10.1007/s00018-015-2060-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Revised: 09/21/2015] [Accepted: 10/01/2015] [Indexed: 12/21/2022]
Abstract
The Helicase-like Transcription Factor (HLTF) belongs to the SWI/SNF family of proteins involved in chromatin remodeling. In addition to its role in gene transcription, HLTF has been implicated in DNA repair, which suggests that this protein acts as a tumor suppressor. Accumulating evidence indicates that HLTF expression is altered in various cancers via two mechanisms: gene silencing through promoter hypermethylation or alternative mRNA splicing, which leads to the expression of truncated proteins that lack DNA repair domains. In either case, the alteration of HLTF expression in cancer has a poor prognosis. In this review, we gathered published clinical and molecular data on HLTF. Our purposes are (a) to address whether HLTF alterations could be considered as cancer drivers or passengers and (b) to determine whether its different functions (transcription or DNA repair) could be diverted in clonal selection during cancer progression.
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Affiliation(s)
- Ludovic Dhont
- Laboratory of Molecular Biology, University of Mons, Avenue du Champ de Mars 6, Pentagone 3A, B-7000 Mons, Belgium
- Laboratory of Medicine and Pathobiology, University of Toronto, Toronto Medical Discovery Tower, 101 College Street, 14th floor, Toronto, ON M5G 1L7 Canada
| | - Céline Mascaux
- Laboratory of Medicine and Pathobiology, University of Toronto, Toronto Medical Discovery Tower, 101 College Street, 14th floor, Toronto, ON M5G 1L7 Canada
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Toronto, ON M5G 2L9 Canada
| | - Alexandra Belayew
- Laboratory of Molecular Biology, University of Mons, Avenue du Champ de Mars 6, Pentagone 3A, B-7000 Mons, Belgium
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123
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Barr CL, Misener VL. Decoding the non-coding genome: elucidating genetic risk outside the coding genome. GENES, BRAIN, AND BEHAVIOR 2016; 15:187-204. [PMID: 26515765 PMCID: PMC4833497 DOI: 10.1111/gbb.12269] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 10/19/2015] [Accepted: 10/28/2015] [Indexed: 12/11/2022]
Abstract
Current evidence emerging from genome-wide association studies indicates that the genetic underpinnings of complex traits are likely attributable to genetic variation that changes gene expression, rather than (or in combination with) variation that changes protein-coding sequences. This is particularly compelling with respect to psychiatric disorders, as genetic changes in regulatory regions may result in differential transcriptional responses to developmental cues and environmental/psychosocial stressors. Until recently, however, the link between transcriptional regulation and psychiatric genetic risk has been understudied. Multiple obstacles have contributed to the paucity of research in this area, including challenges in identifying the positions of remote (distal from the promoter) regulatory elements (e.g. enhancers) and their target genes and the underrepresentation of neural cell types and brain tissues in epigenome projects - the availability of high-quality brain tissues for epigenetic and transcriptome profiling, particularly for the adolescent and developing brain, has been limited. Further challenges have arisen in the prediction and testing of the functional impact of DNA variation with respect to multiple aspects of transcriptional control, including regulatory-element interaction (e.g. between enhancers and promoters), transcription factor binding and DNA methylation. Further, the brain has uncommon DNA-methylation marks with unique genomic distributions not found in other tissues - current evidence suggests the involvement of non-CG methylation and 5-hydroxymethylation in neurodevelopmental processes but much remains unknown. We review here knowledge gaps as well as both technological and resource obstacles that will need to be overcome in order to elucidate the involvement of brain-relevant gene-regulatory variants in genetic risk for psychiatric disorders.
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Affiliation(s)
- C. L. Barr
- Toronto Western Research Institute, University Health Network, Toronto, ON, Canada
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON, Canada
| | - V. L. Misener
- Toronto Western Research Institute, University Health Network, Toronto, ON, Canada
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124
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Edwards M, Cha D, Krithika S, Johnson M, Cook G, Parra EJ. Iris pigmentation as a quantitative trait: variation in populations of European, East Asian and South Asian ancestry and association with candidate gene polymorphisms. Pigment Cell Melanoma Res 2015; 29:141-62. [DOI: 10.1111/pcmr.12435] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 11/02/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Melissa Edwards
- Department of Anthropology University of Toronto Mississauga Mississauga ON Canada
| | - David Cha
- Department of Anthropology University of Toronto Mississauga Mississauga ON Canada
| | - S. Krithika
- Department of Anthropology University of Toronto Mississauga Mississauga ON Canada
| | - Monique Johnson
- Department of Anthropology University of Toronto Mississauga Mississauga ON Canada
| | - Gillian Cook
- Department of Anthropology University of Toronto Mississauga Mississauga ON Canada
| | - Esteban J. Parra
- Department of Anthropology University of Toronto Mississauga Mississauga ON Canada
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125
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Huang T, Shu Y, Cai YD. Genetic differences among ethnic groups. BMC Genomics 2015; 16:1093. [PMID: 26690364 PMCID: PMC4687076 DOI: 10.1186/s12864-015-2328-0] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 12/15/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Many differences between different ethnic groups have been observed, such as skin color, eye color, height, susceptibility to some diseases, and response to certain drugs. However, the genetic bases of such differences have been under-investigated. Since the HapMap project, large-scale genotype data from Caucasian, African and Asian population samples have been available. The project found that these populations were located in different areas of the PCA (Principal Component Analysis) plot. However, as an unsupervised method, PCA does not measure the differences in each single nucleotide polymorphism (SNP) among populations. RESULTS We applied an advanced mutual information-based feature selection method to detect associations between SNP status and ethnic groups using the latest HapMap Phase 3 release version 3, which included more sub-populations. A total of 299 SNPs were identified, and they can accurately predicted the ethnicity of all HapMap populations. The 10-fold cross validation accuracy of the SMO (sequential minimal optimization) model on training dataset was 0.901, and the accuracy on independent test dataset was 0.895. CONCLUSIONS In-depth functional analysis of these SNPs and their nearby genes revealed the genetic bases of skin and eye color differences among populations.
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Affiliation(s)
- Tao Huang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, P. R. China.
| | - Yang Shu
- Sate Key Laboratory of Biotherapy, Sichuan University, Sichuan, 610041, P. R. China.
| | - Yu-Dong Cai
- College of Life Science, Shanghai University, Shanghai, 200444, P. R. China.
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Abstract
The hypothalamic-pituitary-adrenal axis provides physiological adaptations to various environmental stimuli in mammals. These stimuli including maternal care, diet, immune challenge, stress, and others have the potential to stably modify or program the functioning of the HPA axis when experienced early in life or at later critical stages of development. Epigenetic mechanisms mediate the biological embedding of environmental stimuli or conditions. These changes are influenced by the genotype and both, environment and genotype contribute to the development of a specific phenotype with regard to the stress response that might be more susceptible or resilient to the development of mental conditions. The effects of stress might be a result of cumulative stress or a mismatch between the environments experienced early in life versus the conditions much later. These effects including the associated epigenetic modifications are potentially reversible.
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Affiliation(s)
- Jan P Buschdorf
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Michael J Meaney
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Canadian Neuroepigenetics Network, Douglas Mental Health University Institute, McGill University, Montreal, Quebec, Canada
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127
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Matharu N, Ahituv N. Minor Loops in Major Folds: Enhancer-Promoter Looping, Chromatin Restructuring, and Their Association with Transcriptional Regulation and Disease. PLoS Genet 2015; 11:e1005640. [PMID: 26632825 PMCID: PMC4669122 DOI: 10.1371/journal.pgen.1005640] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The organization and folding of chromatin within the nucleus can determine the outcome of gene expression. Recent technological advancements have enabled us to study chromatin interactions in a genome-wide manner at high resolution. These studies have increased our understanding of the hierarchy and dynamics of chromatin domains that facilitate cognate enhancer–promoter looping, defining the transcriptional program of different cell types. In this review, we focus on vertebrate chromatin long-range interactions as they relate to transcriptional regulation. In addition, we describe how the alteration of boundaries that mark discrete regions in the genome with high interaction frequencies within them, called topological associated domains (TADs), could lead to various phenotypes, including human diseases, which we term as “TADopathies.”
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Affiliation(s)
- Navneet Matharu
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California, United States of America
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail:
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128
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Liu F, Hamer MA, Heilmann S, Herold C, Moebus S, Hofman A, Uitterlinden AG, Nöthen MM, van Duijn CM, Nijsten TE, Kayser M. Prediction of male-pattern baldness from genotypes. Eur J Hum Genet 2015; 24:895-902. [PMID: 26508577 DOI: 10.1038/ejhg.2015.220] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 08/27/2015] [Accepted: 09/01/2015] [Indexed: 01/21/2023] Open
Abstract
The global demand for products that effectively prevent the development of male-pattern baldness (MPB) has drastically increased. However, there is currently no established genetic model for the estimation of MPB risk. We conducted a prediction analysis using single-nucleotide polymorphisms (SNPs) identified from previous GWASs of MPB in a total of 2725 German and Dutch males. A logistic regression model considering the genotypes of 25 SNPs from 12 genomic loci demonstrates that early-onset MPB risk is predictable at an accuracy level of 0.74 when 14 SNPs were included in the model, and measured using the area under the receiver-operating characteristic curves (AUC). Considering age as an additional predictor, the model can predict normal MPB status in middle-aged and elderly individuals at a slightly lower accuracy (AUC 0.69-0.71) when 6-11 SNPs were used. A variance partitioning analysis suggests that 55.8% of early-onset MPB genetic liability can be explained by common autosomal SNPs and 23.3% by X-chromosome SNPs. For normal MPB status in elderly individuals, the proportion of explainable variance is lower (42.4% for autosomal and 9.8% for X-chromosome SNPs). The gap between GWAS findings and the variance partitioning results could be explained by a large body of common DNA variants with small effects that will likely be identified in GWAS of increased sample sizes. Although the accuracy obtained here has not reached a clinically desired level, our model was highly informative for up to 19% of Europeans, thus may assist decision making on early MPB intervention actions and in forensic investigations.
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Affiliation(s)
- 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
| | - Merel A Hamer
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Stefanie Heilmann
- Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany.,Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Christine Herold
- German Center for Neurodegenerative Disease (DZNE), Bonn, Germany
| | - Susanne Moebus
- Institute of Medical Informatics, Biometry, and Epidemiology, University Hospital of Essen, University Duisburg-Essen, Essen, Germany
| | - Albert Hofman
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Markus M Nöthen
- Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany.,Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Tamar Ec Nijsten
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
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129
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Ochiai H. Single-Base Pair Genome Editing in Human Cells by Using Site-Specific Endonucleases. Int J Mol Sci 2015; 16:21128-37. [PMID: 26404258 PMCID: PMC4613245 DOI: 10.3390/ijms160921128] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 08/27/2015] [Accepted: 08/28/2015] [Indexed: 02/02/2023] Open
Abstract
Genome-wide association studies have identified numerous single-nucleotide polymorphisms (SNPs) associated with human diseases or phenotypes. However, causal relationships between most SNPs and the associated disease have not been established, owing to technical challenges such as unavailability of suitable cell lines. Recently, efficient editing of a single base pair in the genome was achieved using programmable site-specific nucleases. This technique enables experimental confirmation of the causality between SNPs and disease, and is potentially valuable in clinical applications. In this review, I introduce the molecular basis and describe examples of single-base pair editing in human cells. I also discuss the challenges associated with the technique, as well as possible solutions.
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Affiliation(s)
- Hiroshi Ochiai
- Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, Higashi-Hiroshima 739-8530, Japan.
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130
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Forensic DNA Phenotyping: Predicting human appearance from crime scene material for investigative purposes. Forensic Sci Int Genet 2015; 18:33-48. [DOI: 10.1016/j.fsigen.2015.02.003] [Citation(s) in RCA: 227] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 01/29/2015] [Accepted: 02/11/2015] [Indexed: 01/17/2023]
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131
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Meyer WK, Venkat A, Kermany AR, van de Geijn B, Zhang S, Przeworski M. Evolutionary history inferred from the de novo assembly of a nonmodel organism, the blue-eyed black lemur. Mol Ecol 2015. [PMID: 26198179 PMCID: PMC4557055 DOI: 10.1111/mec.13327] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Lemurs, the living primates most distantly related to humans, demonstrate incredible diversity in behaviour, life history patterns and adaptive traits. Although many lemur species are endangered within their native Madagascar, there is no high-quality genome assembly from this taxon, limiting population and conservation genetic studies. One critically endangered lemur is the blue-eyed black lemur Eulemur flavifrons. This species is fixed for blue irises, a convergent trait that evolved at least four times in primates and was subject to positive selection in humans, where 5′ regulatory variation of OCA2 explains most of the brown/blue eye colour differences. We built a de novo genome assembly for E. flavifrons, providing the most complete lemur genome to date, and a high confidence consensus sequence for close sister species E. macaco, the (brown-eyed) black lemur. From diversity and divergence patterns across the genomes, we estimated a recent split time of the two species (160 Kya) and temporal fluctuations in effective population sizes that accord with known environmental changes. By looking for regions of unusually low diversity, we identified potential signals of directional selection in E. flavifrons at MITF, a melanocyte development gene that regulates OCA2 and has previously been associated with variation in human iris colour, as well as at several other genes involved in melanin biosynthesis in mammals. Our study thus illustrates how whole-genome sequencing of a few individuals can illuminate the demographic and selection history of nonmodel species.
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Affiliation(s)
- Wynn K Meyer
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Aarti Venkat
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Amir R Kermany
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.,Howard Hughes Medical Institute, University of Chicago, Chicago, IL, 60637, USA
| | - Bryce van de Geijn
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Sidi Zhang
- Biological Sciences Collegiate Division, University of Chicago, Chicago, IL, 60637, USA
| | - Molly Przeworski
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.,Howard Hughes Medical Institute, University of Chicago, Chicago, IL, 60637, USA.,Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA
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132
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Caliebe A, Harder M, Schuett R, Krawczak M, Nebel A, von Wurmb-Schwark N. The more the merrier? How a few SNPs predict pigmentation phenotypes in the Northern German population. Eur J Hum Genet 2015; 24:739-47. [PMID: 26286644 DOI: 10.1038/ejhg.2015.167] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 04/01/2015] [Accepted: 06/07/2015] [Indexed: 01/24/2023] Open
Abstract
Human pigmentation traits are of great interest to many research areas, from ancient DNA analysis to forensic science. We developed a gene-based predictive model for pigmentation phenotypes in a realistic target population for forensic case work from Northern Germany and compared our model with those brought forth by previous studies of genetically more heterogeneous populations. In doing so, we aimed at answering the following research questions: (1) do existing models allow good prediction of high-quality phenotypes in a genetically similar albeit more homogeneous population? (2) Would a model specifically set up for the more homogeneous population perform notably better than existing models? (3) Can the number of markers included in existing models be reduced without compromising their predictive capability in the more homogenous population? We investigated the association between eye, hair and skin colour and 12 candidate single-nucleotide polymorphisms (SNPs) from six genes. Our study comprised two samples of 300 and 100 individuals from Northern Germany. SNP rs12913832 in HERC2 was found to be strongly associated with blue eye colour (odds ratio=40.0, P<1.2 × 10(-4)) and to yield moderate predictive power (AUC: 77%; sensitivity: 90%, specificity: 63%, both at a 0.5 threshold for blue eye colour probability). SNP associations with hair and skin colour were weaker and genotypes less predictive. A comparison with two recently published sets of markers to predict eye and hair colour revealed that the consideration of additional SNPs with weak-to-moderate effect increased the predictive power for eye colour, but not for hair colour.
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Affiliation(s)
- Amke Caliebe
- Institute of Medical Informatics and Statistics, Christian-Albrechts University Kiel, Kiel, Germany
| | - Melanie Harder
- Institute of Legal Medicine, Christian-Albrechts University Kiel, Kiel, Germany
| | - Rebecca Schuett
- Institute of Legal Medicine, Christian-Albrechts University Kiel, Kiel, Germany
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian-Albrechts University Kiel, Kiel, Germany
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Christian-Albrechts University Kiel, Kiel, Germany
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133
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Barón AE, Asdigian NL, Gonzalez V, Aalborg J, Terzian T, Stiegmann RA, Torchia EC, Berwick M, Dellavalle RP, Morelli JG, Mokrohisky ST, Crane LA, Box NF. Interactions between ultraviolet light and MC1R and OCA2 variants are determinants of childhood nevus and freckle phenotypes. Cancer Epidemiol Biomarkers Prev 2015; 23:2829-39. [PMID: 25410285 DOI: 10.1158/1055-9965.epi-14-0633] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Melanocytic nevi (moles) and freckles are well known biomarkers of melanoma risk, and they are influenced by similar UV light exposures and genetic susceptibilities to those that increase melanoma risk. Nevertheless, the selective interactions between UV exposures and nevus and freckling genes remain largely undescribed. METHODS We conducted a longitudinal study from ages 6 through 10 years in 477 Colorado children who had annual information collected for sun exposure, sun protection behaviors, and full body skin exams. MC1R and HERC2/OCA2 rs12913832 were genotyped and linear mixed models were used to identify main and interaction effects. RESULTS All measures of sun exposure (chronic, sunburns, and waterside vacations) contributed to total nevus counts, and cumulative chronic exposure acted as the major driver of nevus development. Waterside vacations strongly increased total nevus counts in children with rs12913832 blue eye color alleles and facial freckling scores in those with MC1R red hair color variants. Sunburns increased the numbers of larger nevi (≥2 mm) in subjects with certain MC1R and rs12913832 genotypes. CONCLUSIONS Complex interactions between different UV exposure profiles and genotype combinations determine nevus numbers and size, and the degree of facial freckling. IMPACT Our findings emphasize the importance of implementing sun-protective behavior in childhood regardless of genetic make-up, although children with particular genetic variants may benefit from specifically targeted preventive measures to counteract their inherent risk of melanoma. Moreover, we demonstrate, for the first time, that longitudinal studies are a highly powered tool to uncover new gene-environment interactions that increase cancer risk.
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Affiliation(s)
- Anna E Barón
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Nancy L Asdigian
- Department of Community and Behavioral Health, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Victoria Gonzalez
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, Colorado. Charles C. Gates Center for Regenerative Medicine and Stem Cell Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Jenny Aalborg
- Department of Community and Behavioral Health, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Tamara Terzian
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, Colorado. Charles C. Gates Center for Regenerative Medicine and Stem Cell Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Regan A Stiegmann
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, Colorado. Charles C. Gates Center for Regenerative Medicine and Stem Cell Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Enrique C Torchia
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, Colorado. Charles C. Gates Center for Regenerative Medicine and Stem Cell Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Marianne Berwick
- Division of Epidemiology, University of New Mexico, Albuquerque, New Mexico
| | - Robert P Dellavalle
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, Colorado. Dermatology Service, Department of Veterans Affairs, Eastern Colorado Health Care System, Denver, Colorado. Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Joseph G Morelli
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | | | - Lori A Crane
- Department of Community and Behavioral Health, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Neil F Box
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, Colorado. Charles C. Gates Center for Regenerative Medicine and Stem Cell Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado.
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134
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Lin BD, Mbarek H, Willemsen G, Dolan CV, Fedko IO, Abdellaoui A, de Geus EJ, Boomsma DI, Hottenga JJ. Heritability and Genome-Wide Association Studies for Hair Color in a Dutch Twin Family Based Sample. Genes (Basel) 2015; 6:559-76. [PMID: 26184321 PMCID: PMC4584317 DOI: 10.3390/genes6030559] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 06/25/2015] [Accepted: 06/29/2015] [Indexed: 01/19/2023] Open
Abstract
Hair color is one of the most visible and heritable traits in humans. Here, we estimated heritability by structural equation modeling (N = 20,142), and performed a genome wide association (GWA) analysis (N = 7091) and a GCTA study (N = 3340) on hair color within a large cohort of twins, their parents and siblings from the Netherlands Twin Register (NTR). Self-reported hair color was analyzed as five binary phenotypes, namely “blond versus non-blond”, “red versus non-red”, “brown versus non-brown”, “black versus non-black”, and “light versus dark”. The broad-sense heritability of hair color was estimated between 73% and 99% and the genetic component included non-additive genetic variance. Assortative mating for hair color was significant, except for red and black hair color. From GCTA analyses, at most 24.6% of the additive genetic variance in hair color was explained by 1000G well-imputed SNPs. Genome-wide association analysis for each hair color showed that SNPs in the MC1R region were significantly associated with red, brown and black hair, and also with light versus dark hair color. Five other known genes (HERC2, TPCN2, SLC24A4, IRF4, and KITLG) gave genome-wide significant hits for blond, brown and light versus dark hair color. We did not find and replicate any new loci for hair color.
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Affiliation(s)
- Bochao Danae Lin
- Department of Biological Psychology, VU University, Amsterdam 1081 BT, The Netherlands.
| | - Hamdi Mbarek
- Department of Biological Psychology, VU University, Amsterdam 1081 BT, The Netherlands.
| | - Gonneke Willemsen
- Department of Biological Psychology, VU University, Amsterdam 1081 BT, The Netherlands.
| | - Conor V Dolan
- Department of Biological Psychology, VU University, Amsterdam 1081 BT, The Netherlands.
| | - Iryna O Fedko
- Department of Biological Psychology, VU University, Amsterdam 1081 BT, The Netherlands.
| | - Abdel Abdellaoui
- Department of Biological Psychology, VU University, Amsterdam 1081 BT, The Netherlands.
| | - Eco J de Geus
- Department of Biological Psychology, VU University, Amsterdam 1081 BT, The Netherlands.
| | - Dorret I Boomsma
- Department of Biological Psychology, VU University, Amsterdam 1081 BT, The Netherlands.
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, VU University, Amsterdam 1081 BT, The Netherlands.
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135
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Söchtig J, Phillips C, Maroñas O, Gómez-Tato A, Cruz R, Alvarez-Dios J, de Cal MÁC, Ruiz Y, Reich K, Fondevila M, Carracedo Á, Lareu MV. Exploration of SNP variants affecting hair colour prediction in Europeans. Int J Legal Med 2015; 129:963-75. [PMID: 26162598 DOI: 10.1007/s00414-015-1226-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 06/23/2015] [Indexed: 10/23/2022]
Abstract
DNA profiling is a key tool for forensic analysis; however, current methods identify a suspect either by direct comparison or from DNA database searches. In cases with unidentified suspects, prediction of visible physical traits e.g. pigmentation or hair distribution of the DNA donors can provide important probative information. This study aimed to explore single nucleotide polymorphism (SNP) variants for their effect on hair colour prediction. A discovery panel of 63 SNPs consisting of already established hair colour markers from the HIrisPlex hair colour phenotyping assay as well as additional markers for which associations to human pigmentation traits were previously identified was used to develop multiplex assays based on SNaPshot single-base extension technology. A genotyping study was performed on a range of European populations (n = 605). Hair colour phenotyping was accomplished by matching donor's hair to a graded colour category system of reference shades and photography. Since multiple SNPs in combination contribute in varying degrees to hair colour predictability in Europeans, we aimed to compile a compact marker set that could provide a reliable hair colour inference from the fewest SNPs. The predictive approach developed uses a naïve Bayes classifier to provide hair colour assignment probabilities for the SNP profiles of the key SNPs and was embedded into the Snipper online SNP classifier ( http://mathgene.usc.es/snipper/ ). Results indicate that red, blond, brown and black hair colours are predictable with informative probabilities in a high proportion of cases. Our study resulted in the identification of 12 most strongly associated SNPs to hair pigmentation variation in six genes.
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Affiliation(s)
- Jens Söchtig
- Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, A Coruña, Spain
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136
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Liu F, Visser M, Duffy DL, Hysi PG, Jacobs LC, Lao O, Zhong K, Walsh S, Chaitanya L, Wollstein A, Zhu G, Montgomery GW, Henders AK, Mangino M, Glass D, Bataille V, Sturm RA, Rivadeneira F, Hofman A, van IJcken WFJ, Uitterlinden AG, Palstra RJTS, Spector TD, Martin NG, Nijsten TEC, Kayser M. Genetics of skin color variation in Europeans: genome-wide association studies with functional follow-up. Hum Genet 2015; 134:823-35. [PMID: 25963972 PMCID: PMC4495261 DOI: 10.1007/s00439-015-1559-0] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 04/20/2015] [Indexed: 02/05/2023]
Abstract
In the International Visible Trait Genetics (VisiGen) Consortium, we investigated the genetics of human skin color by combining a series of genome-wide association studies (GWAS) in a total of 17,262 Europeans with functional follow-up of discovered loci. Our GWAS provide the first genome-wide significant evidence for chromosome 20q11.22 harboring the ASIP gene being explicitly associated with skin color in Europeans. In addition, genomic loci at 5p13.2 (SLC45A2), 6p25.3 (IRF4), 15q13.1 (HERC2/OCA2), and 16q24.3 (MC1R) were confirmed to be involved in skin coloration in Europeans. In follow-up gene expression and regulation studies of 22 genes in 20q11.22, we highlighted two novel genes EIF2S2 and GSS, serving as competing functional candidates in this region and providing future research lines. A genetically inferred skin color score obtained from the 9 top-associated SNPs from 9 genes in 940 worldwide samples (HGDP-CEPH) showed a clear gradual pattern in Western Eurasians similar to the distribution of physical skin color, suggesting the used 9 SNPs as suitable markers for DNA prediction of skin color in Europeans and neighboring populations, relevant in future forensic and anthropological
investigations.
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Affiliation(s)
- Fan Liu
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands,
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137
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Yucesoy B, Kaufman KM, Lummus ZL, Weirauch MT, Zhang G, Cartier A, Boulet LP, Sastre J, Quirce S, Tarlo SM, Cruz MJ, Munoz X, Harley JB, Bernstein DI. Genome-Wide Association Study Identifies Novel Loci Associated With Diisocyanate-Induced Occupational Asthma. Toxicol Sci 2015; 146:192-201. [PMID: 25918132 DOI: 10.1093/toxsci/kfv084] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Diisocyanates, reactive chemicals used to produce polyurethane products, are the most common causes of occupational asthma. The aim of this study is to identify susceptibility gene variants that could contribute to the pathogenesis of diisocyanate asthma (DA) using a Genome-Wide Association Study (GWAS) approach. Genome-wide single nucleotide polymorphism (SNP) genotyping was performed in 74 diisocyanate-exposed workers with DA and 824 healthy controls using Omni-2.5 and Omni-5 SNP microarrays. We identified 11 SNPs that exceeded genome-wide significance; the strongest association was for the rs12913832 SNP located on chromosome 15, which has been mapped to the HERC2 gene (p = 6.94 × 10(-14)). Strong associations were also found for SNPs near the ODZ3 and CDH17 genes on chromosomes 4 and 8 (rs908084, p = 8.59 × 10(-9) and rs2514805, p = 1.22 × 10(-8), respectively). We also prioritized 38 SNPs with suggestive genome-wide significance (p < 1 × 10(-6)). Among them, 17 SNPs map to the PITPNC1, ACMSD, ZBTB16, ODZ3, and CDH17 gene loci. Functional genomics data indicate that 2 of the suggestive SNPs (rs2446823 and rs2446824) are located within putative binding sites for the CCAAT/Enhancer Binding Protein (CEBP) and Hepatocyte Nuclear Factor 4, Alpha transcription factors (TFs), respectively. This study identified SNPs mapping to the HERC2, CDH17, and ODZ3 genes as potential susceptibility loci for DA. Pathway analysis indicated that these genes are associated with antigen processing and presentation, and other immune pathways. Overlap of 2 suggestive SNPs with likely TF binding sites suggests possible roles in disruption of gene regulation. These results provide new insights into the genetic architecture of DA and serve as a basis for future functional and mechanistic studies.
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Affiliation(s)
- Berran Yucesoy
- *Division of Immunology, Allergy and Rheumatology, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Kenneth M Kaufman
- Cincinnati Children's Hospital Medical Center, Center for Autoimmune Genomics and Etiology, and Cincinnati VA Medical Center
| | - Zana L Lummus
- *Division of Immunology, Allergy and Rheumatology, University of Cincinnati College of Medicine, Cincinnati, Ohio,Cincinnati Children's Hospital Medical Center, Center for Autoimmune Genomics and Etiology, and Cincinnati VA Medical Center,Cincinnati Children's Hospital Medical Center, Divisions of Biomedical Informatics and Developmental Biology,Cincinnati Children's Hospital Medical Center, Division of Human Genetics,Université de Montréal, Hôpital du Sacré-Coeur de Montréal, Montreal, Quebec, Canada,Université Laval, Hôpital Laval, Sainte-Foy, Québec, Canada,Department of Allergy, Fundación Jiménez Díaz and CIBER de Enfermedades Respiratorias CIBERES, Madrid, Spain,Department of Allergy, Hospital La Paz-IdiPAZ and CIBER de Enfermedades Respiratorias CIBERES, Madrid, Spain,University of Toronto, Toronto, Ontario, Canada and**Hospitals Vall D'Hebron, Barcelona and CIBER de Enfermedades Respiratorias CIBERES, Madrid, Spain
| | - Matthew T Weirauch
- Cincinnati Children's Hospital Medical Center, Center for Autoimmune Genomics and Etiology, and Cincinnati VA Medical Center, Cincinnati Children's Hospital Medical Center, Divisions of Biomedical Informatics and Developmental Biology
| | - Ge Zhang
- Cincinnati Children's Hospital Medical Center, Division of Human Genetics
| | - André Cartier
- Université de Montréal, Hôpital du Sacré-Coeur de Montréal, Montreal, Quebec, Canada
| | | | - Joaquin Sastre
- Department of Allergy, Fundación Jiménez Díaz and CIBER de Enfermedades Respiratorias CIBERES, Madrid, Spain
| | - Santiago Quirce
- Department of Allergy, Hospital La Paz-IdiPAZ and CIBER de Enfermedades Respiratorias CIBERES, Madrid, Spain
| | | | - Maria-Jesus Cruz
- **Hospitals Vall D'Hebron, Barcelona and CIBER de Enfermedades Respiratorias CIBERES, Madrid, Spain
| | - Xavier Munoz
- **Hospitals Vall D'Hebron, Barcelona and CIBER de Enfermedades Respiratorias CIBERES, Madrid, Spain
| | - John B Harley
- Cincinnati Children's Hospital Medical Center, Center for Autoimmune Genomics and Etiology, and Cincinnati VA Medical Center
| | - David I Bernstein
- *Division of Immunology, Allergy and Rheumatology, University of Cincinnati College of Medicine, Cincinnati, Ohio,
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138
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Gorkin DU, Leung D, Ren B. The 3D genome in transcriptional regulation and pluripotency. Cell Stem Cell 2015; 14:762-75. [PMID: 24905166 DOI: 10.1016/j.stem.2014.05.017] [Citation(s) in RCA: 267] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
It can be convenient to think of the genome as simply a string of nucleotides, the linear order of which encodes an organism's genetic blueprint. However, the genome does not exist as a linear entity within cells where this blueprint is actually utilized. Inside the nucleus, the genome is organized in three-dimensional (3D) space, and lineage-specific transcriptional programs that direct stem cell fate are implemented in this native 3D context. Here, we review principles of 3D genome organization in mammalian cells. We focus on the emerging relationship between genome organization and lineage-specific transcriptional regulation, which we argue are inextricably linked.
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Affiliation(s)
- David U Gorkin
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - Danny Leung
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Cellular and Molecular Medicine, Institute of Genome Medicine, Moores Cancer Center, University of California, San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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139
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Fung JN, Rogers PA, Montgomery GW. Identifying the Biological Basis of GWAS Hits for Endometriosis1. Biol Reprod 2015; 92:87. [DOI: 10.1095/biolreprod.114.126458] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 02/05/2015] [Indexed: 12/18/2022] Open
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140
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Abstract
Abstract
An intimate relationship exists between nuclear architecture and gene activity. Unraveling the fine-scale three-dimensional structure of the genome and its impact on gene regulation is a major goal of current epigenetic research, one with direct implications for understanding the molecular mechanisms underlying human phenotypic variation and disease susceptibility. In this context, the novel revolutionary genome editing technologies and emerging new ways to manipulate genome folding offer new promises for the treatment of human disorders.
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141
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Huang Q. Genetic study of complex diseases in the post-GWAS era. J Genet Genomics 2015; 42:87-98. [PMID: 25819085 DOI: 10.1016/j.jgg.2015.02.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 02/01/2015] [Accepted: 02/03/2015] [Indexed: 12/20/2022]
Abstract
Genome-wide association studies (GWASs) have identified thousands of genes and genetic variants (mainly SNPs) that contribute to complex diseases in humans. Functional characterization and mechanistic elucidation of these SNPs and genes action are the next major challenge. It has been well established that SNPs altering the amino acids of protein-coding genes can drastically impact protein function, and play an important role in molecular pathogenesis. Functions of regulatory SNPs can be complex and elusive, and involve gene expression regulation through the effect on RNA splicing, transcription factor binding, DNA methylation and miRNA recruitment. In the present review, we summarize the recent progress in our understanding of functional consequences of GWAS-associated non-coding regulatory SNPs, and discuss the application of systems genetics and network biology in the interpretation of GWAS findings.
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Affiliation(s)
- Qingyang Huang
- College of Life Sciences, Central China Normal University, Wuhan 430079, China.
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142
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Ishikawa A, Sugiyama M, Hondo E, Kinoshita K, Yamagishi Y. Development of a novel pink-eyed dilution mouse model showing progressive darkening of the eyes and coat hair with aging. Exp Anim 2015; 64:207-20. [PMID: 25739360 PMCID: PMC4427736 DOI: 10.1538/expanim.14-0101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Oca2p-cas (oculocutaneous albinism II; pink-eyed dilution
castaneus) is a coat color mutant gene on mouse chromosome 7 that arose spontaneously in
wild Mus musculus castaneus mice. Mice homozygous for
Oca2p-cas usually exhibit pink eyes and gray coat hair on
the non-agouti genetic background, and this ordinary phenotype remains unchanged
throughout life. During breeding of a mixed strain carrying this gene on the C57BL/6J
background, we discovered a novel spontaneous mutation that causes darkening of the eyes
and coat hair with aging. In this study, we developed a novel mouse model showing this
unique phenotype. Gross observations revealed that the pink eyes and gray coat hair of the
novel mutant young mice became progressively darker in color by approximately 3 months
after birth. Light and transmission-electron microscopic observations revealed a marked
increase in melanin pigmentation of coat hair shafts and choroid of the eye in the novel
mice compared to that in the ordinary mice. Sequence analysis of
Oca2p-cas revealed a 4.1-kb deletion involving exons 15
and 16 of its wild-type gene. However, there was no sequence difference between the two
types of mutant mice. Mating experiments suggested that the novel mutant phenotype was not
inherited in a simple fashion, due to incomplete penetrance. The novel spontaneous mutant
mouse is the first example of progressive hair darkening animals and is an essential
animal model for understanding of the regulation mechanisms of melanin biosynthesis with
aging.
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Affiliation(s)
- Akira Ishikawa
- Laboratory of Animal Genetics, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
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143
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Bailey SD, Zhang X, Desai K, Aid M, Corradin O, Cowper-Sal Lari R, Akhtar-Zaidi B, Scacheri PC, Haibe-Kains B, Lupien M. ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters. Nat Commun 2015; 2:6186. [PMID: 25645053 PMCID: PMC4431651 DOI: 10.1038/ncomms7186] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 12/30/2014] [Indexed: 12/21/2022] Open
Abstract
Chromatin interactions connect distal regulatory elements to target gene promoters
guiding stimulus- and lineage-specific transcription. Few factors securing chromatin
interactions have so far been identified. Here, by integrating chromatin interaction
maps with the large collection of transcription factor-binding profiles provided by
the ENCODE project, we demonstrate that the zinc-finger protein ZNF143 preferentially occupies anchors of
chromatin interactions connecting promoters with distal regulatory elements. It
binds directly to promoters and associates with lineage-specific chromatin
interactions and gene expression. Silencing ZNF143 or modulating its DNA-binding affinity using
single-nucleotide polymorphisms (SNPs) as a surrogate of site-directed mutagenesis
reveals the sequence dependency of chromatin interactions at gene promoters. We also
find that chromatin interactions alone do not regulate gene expression. Together,
our results identify ZNF143 as a
novel chromatin-looping factor that contributes to the architectural foundation of
the genome by providing sequence specificity at promoters connected with distal
regulatory elements. Chromatin interactions can connect distal regulatory elements to
promoters via protein factors, but few such factors have been identified. Here, the
authors show that zinc-finger protein ZNF143 is a sequence-specific chromatin-looping
factor that connects promoters with distal regulatory elements.
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Affiliation(s)
- Swneke D Bailey
- The Princess Margaret Cancer Centre-University Health Network, Toronto, M5G 1L7, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Ontario, Canada
| | - Xiaoyang Zhang
- Department of Genetics, Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, 03755, New Hampshire, USA.,Present address: Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Kinjal Desai
- Department of Genetics, Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, 03755, New Hampshire, USA
| | - Malika Aid
- Bioinformatics and Computational Genomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, H2W 1R7, Quebec, Canada
| | - Olivia Corradin
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, 44106, Ohio, USA
| | - Richard Cowper-Sal Lari
- The Princess Margaret Cancer Centre-University Health Network, Toronto, M5G 1L7, Ontario, Canada.,Present address: The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
| | - Batool Akhtar-Zaidi
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, 44106, Ohio, USA.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, 44106, Ohio, USA.,Present address: Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02142, USA
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, 44106, Ohio, USA.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, 44106, Ohio, USA
| | - Benjamin Haibe-Kains
- The Princess Margaret Cancer Centre-University Health Network, Toronto, M5G 1L7, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Ontario, Canada.,Bioinformatics and Computational Genomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, H2W 1R7, Quebec, Canada
| | - Mathieu Lupien
- The Princess Margaret Cancer Centre-University Health Network, Toronto, M5G 1L7, Ontario, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Ontario, Canada. .,Ontario Institute for Cancer Research, Toronto, M5G 1L7, Ontario, Canada.
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144
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Visser M, Palstra RJ, Kayser M. Allele-specific transcriptional regulation of IRF4 in melanocytes is mediated by chromatin looping of the intronic rs12203592 enhancer to the IRF4 promoter. Hum Mol Genet 2015; 24:2649-61. [PMID: 25631878 DOI: 10.1093/hmg/ddv029] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 01/24/2015] [Indexed: 01/07/2023] Open
Abstract
The majority of significant single-nucleotide polymorphisms (SNPs) identified with genome-wide association studies are located in non-coding regions of the genome; it is therefore possible that they are involved in transcriptional regulation of a nearby gene rather than affecting an encoded protein's function. Previously, it was demonstrated that the SNP rs12203592, located in intron 4 of the IRF4 gene, is strongly associated with human skin pigmentation and modulates an enhancer element that controls expression of IRF4. In our study, we investigated the allele-specific effect of rs12203592 on IRF4 expression in epidermal skin samples and in melanocytic cells from donors of different skin color. We focused on the characteristics and activity of the enhancer, and on long-range chromatin interactions in melanocytic cells homozygous and heterozygous for rs12203592. We found that, irrespective of the trans-activating environment, IRF4 transcription is strongly correlated with the allelic status of rs12203592, the activity of the rs12203592 enhancer and that the chromatin features depend on the rs12203592 genotype. Furthermore, we demonstrate that the rs12203592 enhancer physically interacts with the IRF4 promoter through an allele-dependent chromatin loop, and suggest that subsequent allele-specific activation of IRF4 transcription is stabilized by another allele-specific loop from the rs12203592 enhancer to an additional regulatory element in IRF4. We conclude that the non-coding SNP rs12203592 is located in a regulatory region and affects a wide range of enhancer characteristics, resulting into modulation of the enhancer's activity, its interaction with the IRF4 promoter and subsequent allele-specific transcription of IRF4. Our findings provide another example of a non-coding SNP affecting skin color by modulating enhancer-mediated transcriptional regulation.
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Affiliation(s)
- Mijke Visser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Robert-Jan Palstra
- Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Manfred Kayser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
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145
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Haltaufderhyde KD, Oancea E. Genome-wide transcriptome analysis of human epidermal melanocytes. Genomics 2014; 104:482-9. [PMID: 25451175 DOI: 10.1016/j.ygeno.2014.09.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 09/19/2014] [Accepted: 09/22/2014] [Indexed: 01/09/2023]
Abstract
Because human epidermal melanocytes (HEMs) provide critical protection against skin cancer, sunburn, and photoaging, a genome-wide perspective of gene expression in these cells is vital to understanding human skin physiology. In this study we performed high throughput sequencing of HEMs to obtain a complete data set of transcript sizes, abundances, and splicing. As expected, we found that melanocyte specific genes that function in pigmentation were among the highest expressed genes. We analyzed receptor, ion channel and transcription factor gene families to get a better understanding of the cell signaling pathways used by melanocytes. We also performed a comparative transcriptomic analysis of lightly versus darkly pigmented HEMs and found 16 genes differentially expressed in the two pigmentation phenotypes; of those, only one putative melanosomal transporter (SLC45A2) has known function in pigmentation. In addition, we found 166 transcript isoforms expressed exclusively in one pigmentation phenotype, 17 of which are genes involved in signal transduction. Our melanocyte transcriptome study provides a comprehensive view and may help identify novel pigmentation genes and potential pharmacological targets.
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Affiliation(s)
- Kirk D Haltaufderhyde
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02192, USA
| | - Elena Oancea
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02192, USA.
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146
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Visser M, Kayser M, Grosveld F, Palstra RJ. Genetic variation in regulatory DNA elements: the case of OCA2 transcriptional regulation. Pigment Cell Melanoma Res 2014; 27:169-77. [PMID: 24387780 DOI: 10.1111/pcmr.12210] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 12/20/2013] [Indexed: 12/16/2022]
Abstract
Mutations within the OCA2 gene or the complete absence of the OCA2 protein leads to oculocutaneous albinism type 2. The OCA2 protein plays a central role in melanosome biogenesis, and it is a strong determinant of the eumelanin content in melanocytes. Transcript levels of the OCA2 gene are strongly correlated with pigmentation intensities. Recent studies demonstrated that the transcriptional level of OCA2 is to a large extent determined by the noncoding SNP rs12913832 located 21.5 kb upstream of the OCA2 gene promoter. In this review, we discuss current hypotheses and the available data on the mechanism of OCA2 transcriptional regulation and how this is influenced by genetic variation. Finally, we will explore how future epigenetic studies can be used to advance our insight into the functional biology that connects genetic variation to human pigmentation.
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Affiliation(s)
- Mijke Visser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
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147
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Du M, Yuan T, Schilter KF, Dittmar RL, Mackinnon A, Huang X, Tschannen M, Worthey E, Jacob H, Xia S, Gao J, Tillmans L, Lu Y, Liu P, Thibodeau SN, Wang L. Prostate cancer risk locus at 8q24 as a regulatory hub by physical interactions with multiple genomic loci across the genome. Hum Mol Genet 2014; 24:154-66. [PMID: 25149474 DOI: 10.1093/hmg/ddu426] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Chromosome 8q24 locus contains regulatory variants that modulate genetic risk to various cancers including prostate cancer (PC). However, the biological mechanism underlying this regulation is not well understood. Here, we developed a chromosome conformation capture (3C)-based multi-target sequencing technology and systematically examined three PC risk regions at the 8q24 locus and their potential regulatory targets across human genome in six cell lines. We observed frequent physical contacts of this risk locus with multiple genomic regions, in particular, inter-chromosomal interaction with CD96 at 3q13 and intra-chromosomal interaction with MYC at 8q24. We identified at least five interaction hot spots within the predicted functional regulatory elements at the 8q24 risk locus. We also found intra-chromosomal interaction genes PVT1, FAM84B and GSDMC and inter-chromosomal interaction gene CXorf36 in most of the six cell lines. Other gene regions appeared to be cell line-specific, such as RRP12 in LNCaP, USP14 in DU-145 and SMIN3 in lymphoblastoid cell line. We further found that the 8q24 functional domains more likely interacted with genomic regions containing genes enriched in critical pathways such as Wnt signaling and promoter motifs such as E2F1 and TCF3. This result suggests that the risk locus may function as a regulatory hub by physical interactions with multiple genes important for prostate carcinogenesis. Further understanding genetic effect and biological mechanism of these chromatin interactions will shed light on the newly discovered regulatory role of the risk locus in PC etiology and progression.
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Affiliation(s)
- Meijun Du
- Department of Pathology and Cancer Center
| | | | | | | | | | | | | | | | | | - Shu Xia
- Department of Pathology and Cancer Center Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jianzhong Gao
- Beijing 3H Medical Technology Co. Ltd., Beijing 100176, China and
| | - Lori Tillmans
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Yan Lu
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Pengyuan Liu
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stephen N Thibodeau
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Liang Wang
- Department of Pathology and Cancer Center
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148
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Cuba: exploring the history of admixture and the genetic basis of pigmentation using autosomal and uniparental markers. PLoS Genet 2014; 10:e1004488. [PMID: 25058410 PMCID: PMC4109857 DOI: 10.1371/journal.pgen.1004488] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 05/20/2014] [Indexed: 11/19/2022] Open
Abstract
We carried out an admixture analysis of a sample comprising 1,019 individuals from all the provinces of Cuba. We used a panel of 128 autosomal Ancestry Informative Markers (AIMs) to estimate the admixture proportions. We also characterized a number of haplogroup diagnostic markers in the mtDNA and Y-chromosome in order to evaluate admixture using uniparental markers. Finally, we analyzed the association of 16 single nucleotide polymorphisms (SNPs) with quantitative estimates of skin pigmentation. In the total sample, the average European, African and Native American contributions as estimated from autosomal AIMs were 72%, 20% and 8%, respectively. The Eastern provinces of Cuba showed relatively higher African and Native American contributions than the Western provinces. In particular, the highest proportion of African ancestry was observed in the provinces of Guantánamo (40%) and Santiago de Cuba (39%), and the highest proportion of Native American ancestry in Granma (15%), Holguín (12%) and Las Tunas (12%). We found evidence of substantial population stratification in the current Cuban population, emphasizing the need to control for the effects of population stratification in association studies including individuals from Cuba. The results of the analyses of uniparental markers were concordant with those observed in the autosomes. These geographic patterns in admixture proportions are fully consistent with historical and archaeological information. Additionally, we identified a sex-biased pattern in the process of gene flow, with a substantially higher European contribution from the paternal side, and higher Native American and African contributions from the maternal side. This sex-biased contribution was particularly evident for Native American ancestry. Finally, we observed that SNPs located in the genes SLC24A5 and SLC45A2 are strongly associated with melanin levels in the sample.
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149
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Pośpiech E, Wojas-Pelc A, Walsh S, Liu F, Maeda H, Ishikawa T, Skowron M, Kayser M, Branicki W. The common occurrence of epistasis in the determination of human pigmentation and its impact on DNA-based pigmentation phenotype prediction. Forensic Sci Int Genet 2014; 11:64-72. [DOI: 10.1016/j.fsigen.2014.01.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 01/30/2014] [Accepted: 01/31/2014] [Indexed: 01/19/2023]
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150
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Pietroni C, Andersen JD, Johansen P, Andersen MM, Harder S, Paulsen R, Børsting C, Morling N. The effect of gender on eye colour variation in European populations and an evaluation of the IrisPlex prediction model. Forensic Sci Int Genet 2014; 11:1-6. [DOI: 10.1016/j.fsigen.2014.02.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 01/29/2014] [Accepted: 02/02/2014] [Indexed: 11/25/2022]
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