1
|
Sridhar GR, Gumpeny L. Emerging significance of butyrylcholinesterase. World J Exp Med 2024; 14:87202. [PMID: 38590305 PMCID: PMC10999061 DOI: 10.5493/wjem.v14.i1.87202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/04/2023] [Accepted: 01/05/2024] [Indexed: 03/19/2024] Open
Abstract
Butyrylcholinesterase (BChE; EC 3.1.1.8), an enzyme structurally related to acetylcholinesterase, is widely distributed in the human body. It plays a role in the detoxification of chemicals such as succinylcholine, a muscle relaxant used in anesthetic practice. BChE is well-known due to variant forms of the enzyme with little or no hydrolytic activity which exist in some endogamous communities and result in prolonged apnea following the administration of succinylcholine. Its other functions include the ability to hydrolyze acetylcholine, the cholinergic neurotransmitter in the brain, when its primary hydrolytic enzyme, acetylcholinesterase, is absent. To assess its potential roles, BChE was studied in relation to insulin resistance, type 2 diabetes mellitus, cognition, hepatic disorders, cardiovascular and cerebrovascular diseases, and inflammatory conditions. Individuals who lack the enzyme activity of BChE are otherwise healthy, until they are given drugs hydrolyzed by this enzyme. Therefore, BChE is a candidate for the study of loss-of-function mutations in humans. Studying individuals with variant forms of BChE can provide insights into whether they are protected against metabolic diseases. The potential utility of the enzyme as a biomarker for Alzheimer's disease and the response to its drug treatment can also be assessed.
Collapse
Affiliation(s)
- Gumpeny R Sridhar
- Department of Endocrinology and Diabetes, Endocrine and Diabetes Centre, Visakhapatnam 530002, Andhra Pradesh, India
| | - Lakshmi Gumpeny
- Department of Internal Medicine, Gayatri Vidya Parishad Institute of Healthcare and Medical Technology, Visakhapatnam 530048, Andhra Pradesh, India
| |
Collapse
|
2
|
Font-Porterias N, Caro-Consuegra R, Lucas-Sánchez M, Lopez M, Giménez A, Carballo-Mesa A, Bosch E, Calafell F, Quintana-Murci L, Comas D. The Counteracting Effects of Demography on Functional Genomic Variation: The Roma Paradigm. Mol Biol Evol 2021; 38:2804-2817. [PMID: 33713133 PMCID: PMC8233508 DOI: 10.1093/molbev/msab070] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Demographic history plays a major role in shaping the distribution of genomic variation. Yet the interaction between different demographic forces and their effects in the genomes is not fully resolved in human populations. Here, we focus on the Roma population, the largest transnational ethnic minority in Europe. They have a South Asian origin and their demographic history is characterized by recent dispersals, multiple founder events, and extensive gene flow from non-Roma groups. Through the analyses of new high-coverage whole exome sequences and genome-wide array data for 89 Iberian Roma individuals together with forward simulations, we show that founder effects have reduced their genetic diversity and proportion of rare variants, gene flow has counteracted the increase in mutational load, runs of homozygosity show ancestry-specific patterns of accumulation of deleterious homozygotes, and selection signals primarily derive from preadmixture adaptation in the Roma population sources. The present study shows how two demographic forces, bottlenecks and admixture, act in opposite directions and have long-term balancing effects on the Roma genomes. Understanding how demography and gene flow shape the genome of an admixed population provides an opportunity to elucidate how genomic variation is modeled in human populations.
Collapse
Affiliation(s)
- Neus Font-Porterias
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Rocio Caro-Consuegra
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Marcel Lucas-Sánchez
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Marie Lopez
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Aaron Giménez
- Facultat de Sociologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Elena Bosch
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Reus, Spain
| | - Francesc Calafell
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Lluís Quintana-Murci
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR2000, CNRS, Paris, France.,Human Genomics and Evolution, Collège de France, Paris, France
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| |
Collapse
|
3
|
Xu YC, Guo YL. Less Is More, Natural Loss-of-Function Mutation Is a Strategy for Adaptation. PLANT COMMUNICATIONS 2020; 1:100103. [PMID: 33367264 PMCID: PMC7743898 DOI: 10.1016/j.xplc.2020.100103] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/08/2020] [Accepted: 08/12/2020] [Indexed: 05/12/2023]
Abstract
Gene gain and loss are crucial factors that shape the evolutionary success of diverse organisms. In the past two decades, more attention has been paid to the significance of gene gain through gene duplication or de novo genes. However, gene loss through natural loss-of-function (LoF) mutations, which is prevalent in the genomes of diverse organisms, has been largely ignored. With the development of sequencing techniques, many genomes have been sequenced across diverse species and can be used to study the evolutionary patterns of gene loss. In this review, we summarize recent advances in research on various aspects of LoF mutations, including their identification, evolutionary dynamics in natural populations, and functional effects. In particular, we discuss how LoF mutations can provide insights into the minimum gene set (or the essential gene set) of an organism. Furthermore, we emphasize their potential impact on adaptation. At the genome level, although most LoF mutations are neutral or deleterious, at least some of them are under positive selection and may contribute to biodiversity and adaptation. Overall, we highlight the importance of natural LoF mutations as a robust framework for understanding biological questions in general.
Collapse
Affiliation(s)
- Yong-Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
4
|
Srikanth K, Kim NY, Park W, Kim JM, Kim KD, Lee KT, Son JH, Chai HH, Choi JW, Jang GW, Kim H, Ryu YC, Nam JW, Park JE, Kim JM, Lim D. Comprehensive genome and transcriptome analyses reveal genetic relationship, selection signature, and transcriptome landscape of small-sized Korean native Jeju horse. Sci Rep 2019; 9:16672. [PMID: 31723199 PMCID: PMC6853925 DOI: 10.1038/s41598-019-53102-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 10/18/2019] [Indexed: 12/16/2022] Open
Abstract
The Jeju horse, indigenous to the Jeju Island in Korea may have originated from Mongolian horses. Adaptations to the local harsh environment have conferred Jeju horse with unique traits such as small-sized body, stocky head, and shorter limbs. These characteristics have not been studied previously at the genomic level. Therefore, we sequenced and compared the genome of 41 horses belonging to 6 breeds. We identified numerous breed-specific non-synonymous SNPs and loss-of-function mutants. Demographic and admixture analyses showed that, though Jeju horse is genetically the closest to the Mongolian breeds, its genetic ancestry is independent of that of the Mongolian breeds. Genome wide selection signature analysis revealed that genes such as LCORL, MSTN, HMGA2, ZFAT, LASP1, PDK4, and ACTN2, were positively selected in the Jeju horse. RNAseq analysis showed that several of these genes were also differentially expressed in Jeju horse compared to Thoroughbred horse. Comparative muscle fiber analysis showed that, the type I muscle fibre content was substantially higher in Jeju horse compared to Thoroughbred horse. Our results provide insights about the selection of complex phenotypic traits in the small-sized Jeju horse and the novel SNPs identified will aid in designing high-density SNP chip for studying other native horse breeds.
Collapse
Affiliation(s)
- Krishnamoorthy Srikanth
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Nam-Young Kim
- Subtropical Livestock Research Institute, National Institute of Animal Science, Rural Development Administration, Jeju-do, 63242, Republic of Korea
| | - WonCheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Jae-Min Kim
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Kyung-Tai Lee
- Animal Breeding and Genetics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Ju-Hwan Son
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Han-Ha Chai
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Jung-Woo Choi
- College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Gul-Won Jang
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | | | - Youn-Chul Ryu
- Division of Biotechnology, Jeju National University, Jeju, 63243, Republic of Korea
| | - Jin-Wu Nam
- Department of Life Science, Hanyang University, Seoul, 133-791, Republic of Korea
| | - Jong-Eun Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Jun-Mo Kim
- Department of Animal Science and Technology, College of Biotechnology and Natural Resources, Chung-Ang University, Ansung-si, 17546, Republic of Korea.
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea.
| |
Collapse
|
5
|
Halachev M, Meynert A, Taylor MS, Vitart V, Kerr SM, Klaric L, Aitman TJ, Haley CS, Prendergast JG, Pugh C, Hume DA, Harris SE, Liewald DC, Deary IJ, Semple CA, Wilson JF. Increased ultra-rare variant load in an isolated Scottish population impacts exonic and regulatory regions. PLoS Genet 2019; 15:e1008480. [PMID: 31765389 PMCID: PMC6901239 DOI: 10.1371/journal.pgen.1008480] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 12/09/2019] [Accepted: 10/15/2019] [Indexed: 01/03/2023] Open
Abstract
Human population isolates provide a snapshot of the impact of historical demographic processes on population genetics. Such data facilitate studies of the functional impact of rare sequence variants on biomedical phenotypes, as strong genetic drift can result in higher frequencies of variants that are otherwise rare. We present the first whole genome sequencing (WGS) study of the VIKING cohort, a representative collection of samples from the isolated Shetland population in northern Scotland, and explore how its genetic characteristics compare to a mainland Scottish population. Our analyses reveal the strong contributions played by the founder effect and genetic drift in shaping genomic variation in the VIKING cohort. About one tenth of all high-quality variants discovered are unique to the VIKING cohort or are seen at frequencies at least ten fold higher than in more cosmopolitan control populations. Multiple lines of evidence also suggest relaxation of purifying selection during the evolutionary history of the Shetland isolate. We demonstrate enrichment of ultra-rare VIKING variants in exonic regions and for the first time we also show that ultra-rare variants are enriched within regulatory regions, particularly promoters, suggesting that gene expression patterns may diverge relatively rapidly in human isolates.
Collapse
Affiliation(s)
- Mihail Halachev
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Alison Meynert
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Martin S. Taylor
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Veronique Vitart
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Shona M. Kerr
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Lucija Klaric
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | | | - Timothy J. Aitman
- Centre for Genomic and Experimental Medicine, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Chris S. Haley
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - James G. Prendergast
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Carys Pugh
- Centre for Clinical Brain Sciences, Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, United Kingdom
| | - David A. Hume
- Mater Research Institute, University of Queensland, Woolloongabba, Australia
| | - Sarah E. Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, School of Philosophy, Psychology and Language Sciences, University of Edinburgh, George Square, Edinburgh, United Kingdom
| | - David C. Liewald
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, School of Philosophy, Psychology and Language Sciences, University of Edinburgh, George Square, Edinburgh, United Kingdom
| | - Ian J. Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, School of Philosophy, Psychology and Language Sciences, University of Edinburgh, George Square, Edinburgh, United Kingdom
| | - Colin A. Semple
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - James F. Wilson
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, United Kingdom
| |
Collapse
|
6
|
An actionable KCNH2 Long QT Syndrome variant detected by sequence and haplotype analysis in a population research cohort. Sci Rep 2019; 9:10964. [PMID: 31358886 PMCID: PMC6662790 DOI: 10.1038/s41598-019-47436-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/17/2019] [Indexed: 12/12/2022] Open
Abstract
The Viking Health Study Shetland is a population-based research cohort of 2,122 volunteer participants with ancestry from the Shetland Isles in northern Scotland. The high kinship and detailed phenotype data support a range of approaches for associating rare genetic variants, enriched in this isolate population, with quantitative traits and diseases. As an exemplar, the c.1750G > A; p.Gly584Ser variant within the coding sequence of the KCNH2 gene implicated in Long QT Syndrome (LQTS), which occurred once in 500 whole genome sequences from this population, was investigated. Targeted sequencing of the KCNH2 gene in family members of the initial participant confirmed the presence of the sequence variant and identified two further members of the same family pedigree who shared the variant. Investigation of these three related participants for whom single nucleotide polymorphism (SNP) array genotypes were available allowed a unique shared haplotype of 1.22 Mb to be defined around this locus. Searching across the full cohort for this haplotype uncovered two additional apparently unrelated individuals with no known genealogical connection to the original kindred. All five participants with the defined haplotype were shown to share the rare variant by targeted Sanger sequencing. If this result were verified in a healthcare setting, it would be considered clinically actionable, and has been actioned in relatives ascertained independently through clinical presentation. The General Practitioners of four study participants with the rare variant were alerted to the research findings by letters outlining the phenotype (prolonged electrocardiographic QTc interval). A lack of detectable haplotype sharing between c.1750G > A; p.Gly584Ser chromosomes from previously reported individuals from Finland and those in this study from Shetland suggests that this mutation has arisen more than once in human history. This study showcases the potential value of isolate population-based research resources for genomic medicine. It also illustrates some challenges around communication of actionable findings in research participants in this context.
Collapse
|
7
|
Tian D, Wenlock S, Kabir M, Tzotzos G, Doig AJ, Hentges KE. Identifying mouse developmental essential genes using machine learning. Dis Model Mech 2018; 11:11/12/dmm034546. [PMID: 30563825 PMCID: PMC6307915 DOI: 10.1242/dmm.034546] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 10/19/2018] [Indexed: 12/20/2022] Open
Abstract
The genes that are required for organismal survival are annotated as ‘essential genes’. Identifying all the essential genes of an animal species can reveal critical functions that are needed during the development of the organism. To inform studies on mouse development, we developed a supervised machine learning classifier based on phenotype data from mouse knockout experiments. We used this classifier to predict the essentiality of mouse genes lacking experimental data. Validation of our predictions against a blind test set of recent mouse knockout experimental data indicated a high level of accuracy (>80%). We also validated our predictions for other mouse mutagenesis methodologies, demonstrating that the predictions are accurate for lethal phenotypes isolated in random chemical mutagenesis screens and embryonic stem cell screens. The biological functions that are enriched in essential and non-essential genes have been identified, showing that essential genes tend to encode intracellular proteins that interact with nucleic acids. The genome distribution of predicted essential and non-essential genes was analysed, demonstrating that the density of essential genes varies throughout the genome. A comparison with human essential and non-essential genes was performed, revealing conservation between human and mouse gene essentiality status. Our genome-wide predictions of mouse essential genes will be of value for the planning of mouse knockout experiments and phenotyping assays, for understanding the functional processes required during mouse development, and for the prioritisation of disease candidate genes identified in human genome and exome sequence datasets. Summary: Here, we used computer-based machine learning methodology to predict which genes in the mouse genome are essential for development, and present a database of mouse essential and non-essential genes.
Collapse
Affiliation(s)
- David Tian
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Stephanie Wenlock
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Mitra Kabir
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - George Tzotzos
- Department of Agriculture, Food and Environmental Sciences, Marche Polytechnic University, Ancona 60121, Italy
| | - Andrew J Doig
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK .,Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
| | - Kathryn E Hentges
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| |
Collapse
|
8
|
Rehberg J, Stipčić A, Ćorić T, Kolčić I, Polašek O. Mortality patterns in Southern Adriatic islands of Croatia: a registry-based study. Croat Med J 2018; 59:118-123. [PMID: 29972734 PMCID: PMC6045898 DOI: 10.3325/cmj.2018.59.118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Aim To investigate the mortality patterns on the Southern Adriatic islands of Croatia and compare them with those in two, mainly coastal, mainland counties. Methods In this registry-based study we used the official mortality register data to analyze the mortality patterns on seven Croatian islands (Brač, Hvar, Korčula, Lastovo, Mljet, Šolta, and Vis) and Pelješac peninsula in the 1998-2013 period and calculated the average lifespan, life expectancy, and standardized mortality ratios (SMR). We compared the leading causes of death with those in the mainland population of two southernmost Croatian counties. Results The average lifespan of the island population was 3-10 years longer for men and 2-7 years longer for women than that on the mainland. All-cause SMRs were significantly lower for both men and women on Korčula, Brač, Mljet, and Pelješac but significantly higher for women on Šolta (1.22; 95% confidence intervals 1.07-1.38). The leading causes of death on the islands were cardiovascular diseases, with higher percentages in men and lower in women in comparison with those on the mainland. There were no substantial differences in the life expectancy at birth. Conclusions Despite longer lifespan, lack of differences in life expectancy at birth suggests that the recent generations of islanders no longer show beneficial mortality patterns, possibly due to diminishing adherence to the Mediterranean diet and lifestyle. Restoring the traditional lifestyles is a public health priority, with the ultimate aim of reducing inequalities and improving the health of island inhabitants.
Collapse
Affiliation(s)
| | | | | | | | - Ozren Polašek
- Ozren Polašek, University of Split School of Medicine, Šoltanska 2, 21220 Split, Croatia,
| |
Collapse
|
9
|
Ceballos FC, Joshi PK, Clark DW, Ramsay M, Wilson JF. Runs of homozygosity: windows into population history and trait architecture. Nat Rev Genet 2018; 19:220-234. [PMID: 29335644 DOI: 10.1038/nrg.2017.109] [Citation(s) in RCA: 356] [Impact Index Per Article: 59.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Long runs of homozygosity (ROH) arise when identical haplotypes are inherited from each parent and thus a long tract of genotypes is homozygous. Cousin marriage or inbreeding gives rise to such autozygosity; however, genome-wide data reveal that ROH are universally common in human genomes even among outbred individuals. The number and length of ROH reflect individual demographic history, while the homozygosity burden can be used to investigate the genetic architecture of complex disease. We discuss how to identify ROH in genome-wide microarray and sequence data, their distribution in human populations and their application to the understanding of inbreeding depression and disease risk.
Collapse
Affiliation(s)
- Francisco C Ceballos
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, Johannesburg, South Africa.,Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
| | - David W Clark
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, Johannesburg, South Africa.,Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Braamfontein 2000, Johannesburg, South Africa
| | - James F Wilson
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK.,Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
| |
Collapse
|
10
|
Popadin K, Peischl S, Garieri M, Sailani MR, Letourneau A, Santoni F, Lukowski SW, Bazykin GA, Nikolaev S, Meyer D, Excoffier L, Reymond A, Antonarakis SE. Slightly deleterious genomic variants and transcriptome perturbations in Down syndrome embryonic selection. Genome Res 2017; 28:1-10. [PMID: 29237728 PMCID: PMC5749173 DOI: 10.1101/gr.228411.117] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 11/20/2017] [Indexed: 12/13/2022]
Abstract
The majority of aneuploid fetuses are spontaneously miscarried. Nevertheless, some aneuploid individuals survive despite the strong genetic insult. Here, we investigate if the survival probability of aneuploid fetuses is affected by the genome-wide burden of slightly deleterious variants. We analyzed two cohorts of live-born Down syndrome individuals (388 genotyped samples and 16 fibroblast transcriptomes) and observed a deficit of slightly deleterious variants on Chromosome 21 and decreased transcriptome-wide variation in the expression level of highly constrained genes. We interpret these results as signatures of embryonic selection, and propose a genetic handicap model whereby an individual bearing an extremely severe deleterious variant (such as aneuploidy) could escape embryonic lethality if the genome-wide burden of slightly deleterious variants is sufficiently low. This approach can be used to study the composition and effect of the numerous slightly deleterious variants in humans and model organisms.
Collapse
Affiliation(s)
- Konstantin Popadin
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland.,Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland.,Immanuel Kant Baltic Federal University, Kaliningrad, 236041, Russia.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Stephan Peischl
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Interfaculty Bioinformatics Unit, University of Bern, 3012 Bern, Switzerland
| | - Marco Garieri
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - M Reza Sailani
- Stanford School of Medicine, Stanford University, Stanford, California 94305, USA
| | - Audrey Letourneau
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Federico Santoni
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Samuel W Lukowski
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Georgii A Bazykin
- Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, 127051, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Skolkovo, 143026, Russia
| | - Sergey Nikolaev
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, University of Sao Paulo, 05508-090, Sao Paulo, Brazil
| | - Laurent Excoffier
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Institute for Ecology and Evolution, University of Bern, CH-3012 Bern, Switzerland
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| |
Collapse
|
11
|
Borger P. Natural Knockouts: Natural Selection Knocked Out. BIOLOGY 2017; 6:biology6040043. [PMID: 29231847 PMCID: PMC5745448 DOI: 10.3390/biology6040043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/17/2017] [Accepted: 10/25/2017] [Indexed: 12/21/2022]
Abstract
In functional genomics studies, research is dedicated to unveiling the function of genes using gene-knockouts, model organisms in which a gene is artificially inactivated. The idea is that, by knocking out the gene, the provoked phenotype would inform us about the function of the gene. Still, the function of many genes cannot be elucidated, because disruption of conserved sequences, including protein-coding genes, often does not directly affect the phenotype. Since the phenomenon was first observed in the early nineties of the last century, these so-called 'no-phenotype knockouts' have met with great skepticism and resistance by died-in-the-wool selectionists. Still, functional genomics of the late 20th and early 21st centuries has taught us two important lessons. First, two or more unrelated genes can often substitute for each other; and second, some genes are only present in the genome in a silent state. In the laboratory, the disruption of such genes does not negatively influence reproductive success, and does not show measurable fitness effects of the species. The genes are redundant. Genetic redundancy, one of the big surprises of modern biology, can thus be defined as the condition in which the inactivation of a gene is selectively neutral. The no-phenotype knockout is not just a freak of the laboratory. Genetic variants known as homozygous loss-of-function (HLOF) variants are of considerable scientific and clinical interest, as they represent experiments of nature qualifying as "natural knockouts". Such natural knockouts challenge the conventional NeoDarwinian appraisal that genetic information is the result of natural selection acting on random genetic variation.
Collapse
Affiliation(s)
- Peter Borger
- The Independent Research Initiative on Information & Origins, 79540 Loerrach, Germany.
| |
Collapse
|
12
|
New insights into the pharmacogenomics of antidepressant response from the GENDEP and STAR*D studies: rare variant analysis and high-density imputation. THE PHARMACOGENOMICS JOURNAL 2017; 18:413-421. [DOI: 10.1038/tpj.2017.44] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 06/02/2017] [Accepted: 06/07/2017] [Indexed: 12/27/2022]
|
13
|
Eilbeck K, Quinlan A, Yandell M. Settling the score: variant prioritization and Mendelian disease. Nat Rev Genet 2017; 18:599-612. [PMID: 28804138 PMCID: PMC5935497 DOI: 10.1038/nrg.2017.52] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
When investigating Mendelian disease using exome or genome sequencing, distinguishing disease-causing genetic variants from the multitude of candidate variants is a complex, multidimensional task. Many prioritization tools and online interpretation resources exist, and professional organizations have offered clinical guidelines for review and return of prioritization results. In this Review, we describe the strengths and weaknesses of widely used computational approaches, explain their roles in the diagnostic and discovery process and discuss how they can inform (and misinform) expert reviewers. We place variant prioritization in the wider context of gene prioritization, burden testing and genotype-phenotype association, and we discuss opportunities and challenges introduced by whole-genome sequencing.
Collapse
Affiliation(s)
- Karen Eilbeck
- Department of Biomedical Informatics, School of Medicine, University of Utah, 421 Wakara Way, Suite 120, Salt Lake City, Utah 84108, USA
| | - Aaron Quinlan
- Department of Biomedical Informatics, School of Medicine, University of Utah, 421 Wakara Way, Suite 120, Salt Lake City, Utah 84108, USA
- Department of Human Genetics, Eccles Institute of Human Genetics, School of Medicine, University of Utah, 15 S 2030 E, Salt Lake City, Utah 84112, USA
| | - Mark Yandell
- Department of Human Genetics, Eccles Institute of Human Genetics, School of Medicine, University of Utah, 15 S 2030 E, Salt Lake City, Utah 84112, USA
| |
Collapse
|
14
|
Ehler E, Vanek D. Forensic genetic analyses in isolated populations with examples of central European Valachs and Roma. J Forensic Leg Med 2017; 48:46-52. [PMID: 28454050 DOI: 10.1016/j.jflm.2017.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 03/22/2017] [Accepted: 04/09/2017] [Indexed: 01/27/2023]
Abstract
Isolated populations present a constant threat to the correctness of forensic genetic casework. In this review article we present several examples of how analyzing samples from isolated populations can bias the results of the forensic statistics and analyses. We select our examples from isolated populations from central and southeastern Europe, namely the Valachs and the European Roma. We also provide the reader with general strategies and principles to improve the laboratory practice (best practice) and reporting of samples from supposedly isolated populations. These include reporting the precise population data used for computing the forensic statistics, using the appropriate θ correction factor for calculating allele frequencies, typing ancestry informative markers in samples of unknown or uncertain ethnicity and establishing ethnic-specific forensic databases.
Collapse
Affiliation(s)
- Edvard Ehler
- Department of Biology and Environmental Studies, Charles University in Prague, Faculty of Education, Magdaleny Rettigove 4, Prague, 116 39, Czech Republic; Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614, Poznan, Poland.
| | - Daniel Vanek
- Forensic DNA Service, Janovskeho 18, Prague 7, 170 00, Czech Republic; Charles University in Prague, 2nd Faculty of Medicine, V Uvalu 84, Prague, 150 06, Czech Republic; Nemocnice Na Bulovce, Institute of Legal Medicine, Budinova 2, Prague, 180 81, Czech Republic.
| |
Collapse
|
15
|
Intellectual Disability & Rare Disorders: A Diagnostic Challenge. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1031:39-54. [PMID: 29214565 DOI: 10.1007/978-3-319-67144-4_3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Rare disorders constitute a large and heterogeneous group of diagnoses of which many cause chronic disabilities with significant impact on the lives of affected individuals and their families as well as on the health-care system. Each individual disorder is rare, but when considered as a group, rare disorders are common with a total prevalence of approximately 6-8%. The clinical presentation of these disorders includes a broad diversity of symptoms and signs, often involving the nervous system and resulting in symptoms such as intellectual disability, neuropsychiatric disorders, epilepsy and motor dysfunction. The methods for establishing an etiological diagnosis in patients with rare disorders have improved dramatically during recent years. With the introduction of genomic screening methods, it has been shown that the cause is genetic in the majority of the patients and many will receive an etiological diagnosis in a clinical setting. However, there are a lot of challenges in diagnosing these disorders and despite recent years' advances, a large number of patients with rare disorders still go without an etiological diagnosis. In this chapter we will review the etiology of rare disorders with focus on intellectual disability and what has been learned from massive parallel sequencing studies in deciphering the genetic basis. Furthermore, we will discuss challenges in the etiological diagnostics of these disorders including issues that regard interpretation of the numerous genetic variants detected by genomic screening methods and challenges in the translation of massive parallel sequencing technologies into clinical practice.
Collapse
|
16
|
Simons YB, Sella G. The impact of recent population history on the deleterious mutation load in humans and close evolutionary relatives. Curr Opin Genet Dev 2016; 41:150-158. [PMID: 27744216 DOI: 10.1016/j.gde.2016.09.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 09/13/2016] [Accepted: 09/18/2016] [Indexed: 01/22/2023]
Abstract
Over the past decade, there has been both great interest and confusion about whether recent demographic events-notably the Out-of-Africa-bottleneck and recent population growth-have led to differences in mutation load among human populations. The confusion can be traced to the use of different summary statistics to measure load, which lead to apparently conflicting results. We argue, however, that when statistics more directly related to load are used, the results of different studies and data sets consistently reveal little or no difference in the load of non-synonymous mutations among human populations. Theory helps to understand why no such differences are seen, as well as to predict in what settings they are to be expected. In particular, as predicted by modeling, there is evidence for changes in the load of recessive loss of function mutations in founder and inbred human populations. Also as predicted, eastern subspecies of gorilla, Neanderthals and Denisovans, who are thought to have undergone reductions in population sizes that exceed the human Out-of-Africa bottleneck in duration and severity, show evidence for increased load of non-synonymous mutations (relative to western subspecies of gorillas and modern humans, respectively). A coherent picture is thus starting to emerge about the effects of demographic history on the mutation load in populations of humans and close evolutionary relatives.
Collapse
Affiliation(s)
- Yuval B Simons
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Guy Sella
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
| |
Collapse
|
17
|
Jagannathan S, Bradley RK. Translational plasticity facilitates the accumulation of nonsense genetic variants in the human population. Genome Res 2016; 26:1639-1650. [PMID: 27646533 PMCID: PMC5131816 DOI: 10.1101/gr.205070.116] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 09/16/2016] [Indexed: 01/12/2023]
Abstract
Genetic variants that disrupt protein-coding DNA are ubiquitous in the human population, with about 100 such loss-of-function variants per individual. While most loss-of-function variants are rare, a subset have risen to high frequency and occur in a homozygous state in healthy individuals. It is unknown why these common variants are well tolerated, even though some affect essential genes implicated in Mendelian disease. Here, we combine genomic, proteomic, and biochemical data to demonstrate that many common nonsense variants do not ablate protein production from their host genes. We provide computational and experimental evidence for diverse mechanisms of gene rescue, including alternative splicing, stop codon readthrough, alternative translation initiation, and C-terminal truncation. Our results suggest a molecular explanation for the mild fitness costs of many common nonsense variants and indicate that translational plasticity plays a prominent role in shaping human genetic diversity.
Collapse
Affiliation(s)
- Sujatha Jagannathan
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| |
Collapse
|
18
|
Lessard S, Manning AK, Low-Kam C, Auer PL, Giri A, Graff M, Schurmann C, Yaghootkar H, Luan J, Esko T, Karaderi T, Bottinger EP, Lu Y, Carlson C, Caulfield M, Dubé MP, Jackson RD, Kooperberg C, McKnight B, Mongrain I, Peters U, Reiner AP, Rhainds D, Sotoodehnia N, Hirschhorn JN, Scott RA, Munroe PB, Frayling TM, Loos RJF, North KE, Edwards TL, Tardif JC, Lindgren CM, Lettre G. Testing the role of predicted gene knockouts in human anthropometric trait variation. Hum Mol Genet 2016; 25:2082-2092. [PMID: 26908616 PMCID: PMC5062577 DOI: 10.1093/hmg/ddw055] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 02/15/2016] [Indexed: 11/12/2022] Open
Abstract
Although the role of complete gene inactivation by two loss-of-function mutations inherited in trans is well-established in recessive Mendelian diseases, we have not yet explored how such gene knockouts (KOs) could influence complex human phenotypes. Here, we developed a statistical framework to test the association between gene KOs and quantitative human traits. Our method is flexible, publicly available, and compatible with common genotype format files (e.g. PLINK and vcf). We characterized gene KOs in 4498 participants from the NHLBI Exome Sequence Project (ESP) sequenced at high coverage (>100×), 1976 French Canadians from the Montreal Heart Institute Biobank sequenced at low coverage (5.7×), and >100 000 participants from the Genetic Investigation of ANthropometric Traits (GIANT) Consortium genotyped on an exome array. We tested associations between gene KOs and three anthropometric traits: body mass index (BMI), height and BMI-adjusted waist-to-hip ratio (WHR). Despite our large sample size and multiple datasets available, we could not detect robust associations between specific gene KOs and quantitative anthropometric traits. Our results highlight several limitations and challenges for future gene KO studies in humans, in particular when there is no prior knowledge on the phenotypes that might be affected by the tested gene KOs. They also suggest that gene KOs identified with current DNA sequencing methodologies probably do not strongly influence normal variation in BMI, height, and WHR in the general human population.
Collapse
Affiliation(s)
- Samuel Lessard
- Montreal Heart Institute, Montréal, Québec H1T 1C8, Canada Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Alisa K Manning
- Medical and Population Genetics Program, Broad Institute, Cambridge, MA 02142, USA Center for Human Genetics Research, Massachusetts General Hospital, Boston, MA 02114, USA Department of Medicine and
| | - Cécile Low-Kam
- Montreal Heart Institute, Montréal, Québec H1T 1C8, Canada Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Paul L Auer
- School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI 53201-0413, USA
| | - Ayush Giri
- Division of Epidemiology, Institute for Medicine and Public Health and
| | - Mariaelisa Graff
- University of North Carolina Gillings School of Global Public Health, Chapel Hill, NC 27599, USA
| | - Claudia Schurmann
- The Charles Bronfman Institute for Personalized Medicine and The Mindich Child Health and Development Institute, the Genetics of Obesity and Related Metabolic Traits Program, The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hanieh Yaghootkar
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Jian'an Luan
- Medical Research Council Epidemiology Unit, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Tonu Esko
- Medical and Population Genetics Program, Broad Institute, Cambridge, MA 02142, USA Estonian Genome Center, University of Tartu, Tartu, Estonia Division of Endocrinology, Genetics and Basic and Translational Obesity Research, Children's Hospital Boston, Boston, MA 02115, USA
| | - Tugce Karaderi
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | | | | | | | | | | | - Yingchang Lu
- The Charles Bronfman Institute for Personalized Medicine and
| | - Chris Carlson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Mark Caulfield
- Clinical Pharmacology, William Harvey Research Institute and NIHR Barts Cardiovascular Biomedical Research Unit, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Marie-Pierre Dubé
- Montreal Heart Institute, Montréal, Québec H1T 1C8, Canada Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Rebecca D Jackson
- Division of Endocrinology, Diabetes and Metabolism, Ohio State University, Columbus, OH 43210, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Barbara McKnight
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Ian Mongrain
- Montreal Heart Institute, Montréal, Québec H1T 1C8, Canada
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Alex P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - David Rhainds
- Montreal Heart Institute, Montréal, Québec H1T 1C8, Canada
| | - Nona Sotoodehnia
- Division of Cardiology, Cardiovascular Health Research Unit, University of Washington, Seattle, WA 98195-6422, USA
| | - Joel N Hirschhorn
- Medical and Population Genetics Program, Broad Institute, Cambridge, MA 02142, USA Department of Genetics, Harvard Medical School, Boston, MA 02115, USA Division of Endocrinology, Genetics and Basic and Translational Obesity Research, Children's Hospital Boston, Boston, MA 02115, USA
| | - Robert A Scott
- Medical Research Council Epidemiology Unit, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Patricia B Munroe
- Clinical Pharmacology, William Harvey Research Institute and NIHR Barts Cardiovascular Biomedical Research Unit, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Timothy M Frayling
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine and The Mindich Child Health and Development Institute, the Genetics of Obesity and Related Metabolic Traits Program, The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kari E North
- University of North Carolina Gillings School of Global Public Health, Chapel Hill, NC 27599, USA
| | - Todd L Edwards
- Division of Epidemiology, Institute for Medicine and Public Health and Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Jean-Claude Tardif
- Montreal Heart Institute, Montréal, Québec H1T 1C8, Canada Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Cecilia M Lindgren
- Medical and Population Genetics Program, Broad Institute, Cambridge, MA 02142, USA Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK The Big Data Institute, University of Oxford, Oxford, UK
| | - Guillaume Lettre
- Montreal Heart Institute, Montréal, Québec H1T 1C8, Canada Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| |
Collapse
|