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Liakos A, Ntakou-Zamplara KZ, Angelova N, Konstantopoulos D, Synacheri AC, Spyropoulou Z, Tsarmaklis IA, Korrou-Karava D, Nikolopoulos G, Lavigne MD, Fousteri M. Cockayne syndrome B protein is implicated in transcription and associated chromatin dynamics in homeostatic and genotoxic conditions. Aging Cell 2024:e14341. [PMID: 39370748 DOI: 10.1111/acel.14341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 07/05/2024] [Accepted: 08/29/2024] [Indexed: 10/08/2024] Open
Abstract
The integrity of the actively transcribed genome against helix-distorting DNA lesions relies on a multilayered cellular response that enhances Transcription-Coupled Nucleotide Excision Repair (TC-NER). When defective, TC-NER is causatively associated with Cockayne-Syndrome (CS), a rare severe human progeroid disorder. Although the presence of unresolved transcription-blocking lesions is considered a driver of the aging process, the molecular features of the transcription-driven response to genotoxic stress in CS-B cells remain largely unknown. Here, an in-depth view of the transcriptional and associated chromatin dynamics that occur in CS-B cells illuminates the role of CSB therein. By employing high-throughput genome-wide approaches, we observed that absence of a functional CSB protein results in a delay in transcription progression, more positioned +1 nucleosomes, and less dynamic chromatin structure, compared to normal cells. We found that early after exposure to UV, CS-B cells released RNA polymerase II (RNAPII) from promoter-proximal pause sites into elongation. However, the magnitude of this response and the progression of RNAPII were reduced compared to normal counterparts. Notably, we detected increased post-UV retainment of unprocessed nascent RNA transcripts and chromatin-associated elongating RNAPII molecules. Contrary to the prevailing models, we found that transcription initiation is operational in CS-B fibroblasts early after UV and that chromatin accessibility showed a marginal increase. Our study provides robust evidence for the role of CSB in shaping the transcription and chromatin landscape both in homeostasis and in response to genotoxic insults, which is independent of its known role in TC-NER, and which may underlie major aspects of the CS phenotype.
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Affiliation(s)
- Anastasios Liakos
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | | | - Nelina Angelova
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | | | - Anna-Chloe Synacheri
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Laboratory of Biology, School of Medicine, National and Kapodistrian University of Athens (NKUA), Athens, Greece
| | - Zoi Spyropoulou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Iason A Tsarmaklis
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | | | - Georgios Nikolopoulos
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Matthieu D Lavigne
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Maria Fousteri
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
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2
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Kerimov N, Tambets R, Hayhurst JD, Rahu I, Kolberg P, Raudvere U, Kuzmin I, Chowdhary A, Vija A, Teras HJ, Kanai M, Ulirsch J, Ryten M, Hardy J, Guelfi S, Trabzuni D, Kim-Hellmuth S, Rayner W, Finucane H, Peterson H, Mosaku A, Parkinson H, Alasoo K. eQTL Catalogue 2023: New datasets, X chromosome QTLs, and improved detection and visualisation of transcript-level QTLs. PLoS Genet 2023; 19:e1010932. [PMID: 37721944 PMCID: PMC10538656 DOI: 10.1371/journal.pgen.1010932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/28/2023] [Accepted: 08/22/2023] [Indexed: 09/20/2023] Open
Abstract
The eQTL Catalogue is an open database of uniformly processed human molecular quantitative trait loci (QTLs). We are continuously updating the resource to further increase its utility for interpreting genetic associations with complex traits. Over the past two years, we have increased the number of uniformly processed studies from 21 to 31 and added X chromosome QTLs for 19 compatible studies. We have also implemented Leafcutter to directly identify splice-junction usage QTLs in all RNA sequencing datasets. Finally, to improve the interpretability of transcript-level QTLs, we have developed static QTL coverage plots that visualise the association between the genotype and average RNA sequencing read coverage in the region for all 1.7 million fine mapped associations. To illustrate the utility of these updates to the eQTL Catalogue, we performed colocalisation analysis between vitamin D levels in the UK Biobank and all molecular QTLs in the eQTL Catalogue. Although most GWAS loci colocalised both with eQTLs and transcript-level QTLs, we found that visual inspection could sometimes be used to distinguish primary splicing QTLs from those that appear to be secondary consequences of large-effect gene expression QTLs. While these visually confirmed primary splicing QTLs explain just 6/53 of the colocalising signals, they are significantly less pleiotropic than eQTLs and identify a prioritised causal gene in 4/6 cases.
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Affiliation(s)
- Nurlan Kerimov
- Institute of Computer Science, University of Tartu, Tartu, Estonia
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Ralf Tambets
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - James D. Hayhurst
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Ida Rahu
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Peep Kolberg
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Uku Raudvere
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Ivan Kuzmin
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Anshika Chowdhary
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
| | - Andreas Vija
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Hans J. Teras
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Masahiro Kanai
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jacob Ulirsch
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Mina Ryten
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - John Hardy
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Sebastian Guelfi
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Daniah Trabzuni
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Sarah Kim-Hellmuth
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital LMU Munich, Munich, Germany
| | - William Rayner
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
| | - Hilary Finucane
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Hedi Peterson
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Abayomi Mosaku
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Helen Parkinson
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Kaur Alasoo
- Institute of Computer Science, University of Tartu, Tartu, Estonia
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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3
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Kerimov N, Tambets R, Hayhurst JD, Rahu I, Kolberg P, Raudvere U, Kuzmin I, Chowdhary A, Vija A, Teras HJ, Kanai M, Ulirsch J, Ryten M, Hardy J, Guelfi S, Trabzuni D, Kim-Hellmuth S, Rayner W, Finucane H, Peterson H, Mosaku A, Parkinson H, Alasoo K. Systematic visualisation of molecular QTLs reveals variant mechanisms at GWAS loci. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.06.535816. [PMID: 37066341 PMCID: PMC10104061 DOI: 10.1101/2023.04.06.535816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Splicing quantitative trait loci (QTLs) have been implicated as a common mechanism underlying complex trait associations. However, utilising splicing QTLs in target discovery and prioritisation has been challenging due to extensive data normalisation which often renders the direction of the genetic effect as well as its magnitude difficult to interpret. This is further complicated by the fact that strong expression QTLs often manifest as weak splicing QTLs and vice versa, making it difficult to uniquely identify the underlying molecular mechanism at each locus. We find that these ambiguities can be mitigated by visualising the association between the genotype and average RNA sequencing read coverage in the region. Here, we generate these QTL coverage plots for 1.7 million molecular QTL associations in the eQTL Catalogue identified with five quantification methods. We illustrate the utility of these QTL coverage plots by performing colocalisation between vitamin D levels in the UK Biobank and all molecular QTLs in the eQTL Catalogue. We find that while visually confirmed splicing QTLs explain just 6/53 of the colocalising signals, they are significantly less pleiotropic than eQTLs and identify a prioritised causal gene in 4/6 cases. All our association summary statistics and QTL coverage plots are freely available at https://www.ebi.ac.uk/eqtl/.
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Affiliation(s)
- Nurlan Kerimov
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ralf Tambets
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - James D Hayhurst
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ida Rahu
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Peep Kolberg
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Uku Raudvere
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Ivan Kuzmin
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Anshika Chowdhary
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
| | - Andreas Vija
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Hans J Teras
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Masahiro Kanai
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jacob Ulirsch
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mina Ryten
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London
| | - John Hardy
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London
| | - Sebastian Guelfi
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London
| | - Daniah Trabzuni
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London
| | - Sarah Kim-Hellmuth
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital LMU Munich, Munich, Germany
| | - Will Rayner
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
| | - Hilary Finucane
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hedi Peterson
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Abayomi Mosaku
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Helen Parkinson
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kaur Alasoo
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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4
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Offley SR, Pfleiderer MM, Zucco A, Fraudeau A, Welsh SA, Razew M, Galej WP, Gardini A. A combinatorial approach to uncover an additional Integrator subunit. Cell Rep 2023; 42:112244. [PMID: 36920904 DOI: 10.1016/j.celrep.2023.112244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/15/2022] [Accepted: 02/23/2023] [Indexed: 03/16/2023] Open
Abstract
RNA polymerase II (RNAPII) controls expression of all protein-coding genes and most noncoding loci in higher eukaryotes. Calibrating RNAPII activity requires an assortment of polymerase-associated factors that are recruited at sites of active transcription. The Integrator complex is one of the most elusive transcriptional regulators in metazoans, deemed to be recruited after initiation to help establish and modulate paused RNAPII. Integrator is known to be composed of 14 subunits that assemble and operate in a modular fashion. We employed proteomics and machine-learning structure prediction (AlphaFold2) to identify an additional Integrator subunit, INTS15. We report that INTS15 assembles primarily with the INTS13/14/10 module and interfaces with the Int-PP2A module. Functional genomics analysis further reveals a role for INTS15 in modulating RNAPII pausing at a subset of genes. Our study shows that omics approaches combined with AlphaFold2-based predictions provide additional insights into the molecular architecture of large and dynamic multiprotein complexes.
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Affiliation(s)
- Sarah R Offley
- The Wistar Institute, Philadelphia, PA 19103, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Moritz M Pfleiderer
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Avery Zucco
- The Wistar Institute, Philadelphia, PA 19103, USA
| | - Angelique Fraudeau
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | | | - Michal Razew
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Wojciech P Galej
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France.
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5
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Simmons JR, An R, Amankwaa B, Zayac S, Kemp J, Labrador M. Phosphorylated histone variant γH2Av is associated with chromatin insulators in Drosophila. PLoS Genet 2022; 18:e1010396. [PMID: 36197938 PMCID: PMC9576066 DOI: 10.1371/journal.pgen.1010396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 10/17/2022] [Accepted: 08/24/2022] [Indexed: 11/27/2022] Open
Abstract
Chromatin insulators are responsible for orchestrating long-range interactions between enhancers and promoters throughout the genome and align with the boundaries of Topologically Associating Domains (TADs). Here, we demonstrate an association between gypsy insulator proteins and the phosphorylated histone variant H2Av (γH2Av), normally a marker of DNA double strand breaks. Gypsy insulator components colocalize with γH2Av throughout the genome, in polytene chromosomes and in diploid cells in which Chromatin IP data shows it is enriched at TAD boundaries. Mutation of insulator components su(Hw) and Cp190 results in a significant reduction in γH2Av levels in chromatin and phosphatase inhibition strengthens the association between insulator components and γH2Av and rescues γH2Av localization in insulator mutants. We also show that γH2Av, but not H2Av, is a component of insulator bodies, which are protein condensates that form during osmotic stress. Phosphatase activity is required for insulator body dissolution after stress recovery. Together, our results implicate the H2A variant with a novel mechanism of insulator function and boundary formation.
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Affiliation(s)
- James R. Simmons
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Ran An
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Bright Amankwaa
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Shannon Zayac
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Justin Kemp
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Mariano Labrador
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail:
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6
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Kerimov N, Hayhurst JD, Peikova K, Manning JR, Walter P, Kolberg L, Samoviča M, Sakthivel MP, Kuzmin I, Trevanion SJ, Burdett T, Jupp S, Parkinson H, Papatheodorou I, Yates AD, Zerbino DR, Alasoo K. A compendium of uniformly processed human gene expression and splicing quantitative trait loci. Nat Genet 2021; 53:1290-1299. [PMID: 34493866 PMCID: PMC8423625 DOI: 10.1038/s41588-021-00924-w] [Citation(s) in RCA: 160] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022]
Abstract
Many gene expression quantitative trait locus (eQTL) studies have published their summary statistics, which can be used to gain insight into complex human traits by downstream analyses, such as fine mapping and co-localization. However, technical differences between these datasets are a barrier to their widespread use. Consequently, target genes for most genome-wide association study (GWAS) signals have still not been identified. In the present study, we present the eQTL Catalogue ( https://www.ebi.ac.uk/eqtl ), a resource of quality-controlled, uniformly re-computed gene expression and splicing QTLs from 21 studies. We find that, for matching cell types and tissues, the eQTL effect sizes are highly reproducible between studies. Although most QTLs were shared between most bulk tissues, we identified a greater diversity of cell-type-specific QTLs from purified cell types, a subset of which also manifested as new disease co-localizations. Our summary statistics are freely available to enable the systematic interpretation of human GWAS associations across many cell types and tissues.
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Affiliation(s)
- Nurlan Kerimov
- Institute of Computer Science, University of Tartu, Tartu, Estonia
- Open Targets, Wellcome Genome Campus, Cambridge, UK
| | - James D Hayhurst
- Open Targets, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Kateryna Peikova
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Jonathan R Manning
- Open Targets, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Peter Walter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Liis Kolberg
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Marija Samoviča
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Manoj Pandian Sakthivel
- Open Targets, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Ivan Kuzmin
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Stephen J Trevanion
- Open Targets, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Tony Burdett
- Open Targets, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Simon Jupp
- Open Targets, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Helen Parkinson
- Open Targets, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Irene Papatheodorou
- Open Targets, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Andrew D Yates
- Open Targets, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Daniel R Zerbino
- Open Targets, Wellcome Genome Campus, Cambridge, UK.
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.
| | - Kaur Alasoo
- Institute of Computer Science, University of Tartu, Tartu, Estonia.
- Open Targets, Wellcome Genome Campus, Cambridge, UK.
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7
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Kulik M, Bothe M, Kibar G, Fuchs A, Schöne S, Prekovic S, Mayayo-Peralta I, Chung HR, Zwart W, Helsen C, Claessens F, Meijsing SH. Androgen and glucocorticoid receptor direct distinct transcriptional programs by receptor-specific and shared DNA binding sites. Nucleic Acids Res 2021; 49:3856-3875. [PMID: 33751115 PMCID: PMC8053126 DOI: 10.1093/nar/gkab185] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/16/2021] [Accepted: 03/12/2021] [Indexed: 12/22/2022] Open
Abstract
The glucocorticoid (GR) and androgen (AR) receptors execute unique functions in vivo, yet have nearly identical DNA binding specificities. To identify mechanisms that facilitate functional diversification among these transcription factor paralogs, we studied them in an equivalent cellular context. Analysis of chromatin and sequence suggest that divergent binding, and corresponding gene regulation, are driven by different abilities of AR and GR to interact with relatively inaccessible chromatin. Divergent genomic binding patterns can also be the result of subtle differences in DNA binding preference between AR and GR. Furthermore, the sequence composition of large regions (>10 kb) surrounding selectively occupied binding sites differs significantly, indicating a role for the sequence environment in guiding AR and GR to distinct binding sites. The comparison of binding sites that are shared shows that the specificity paradox can also be resolved by differences in the events that occur downstream of receptor binding. Specifically, shared binding sites display receptor-specific enhancer activity, cofactor recruitment and changes in histone modifications. Genomic deletion of shared binding sites demonstrates their contribution to directing receptor-specific gene regulation. Together, these data suggest that differences in genomic occupancy as well as divergence in the events that occur downstream of receptor binding direct functional diversification among transcription factor paralogs.
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Affiliation(s)
- Marina Kulik
- Max Planck Institute for Molecular Genetics, Ihnestraße 63–73, 14195 Berlin, Germany
| | - Melissa Bothe
- Max Planck Institute for Molecular Genetics, Ihnestraße 63–73, 14195 Berlin, Germany
| | - Gözde Kibar
- Max Planck Institute for Molecular Genetics, Ihnestraße 63–73, 14195 Berlin, Germany
| | - Alisa Fuchs
- Max Planck Institute for Molecular Genetics, Ihnestraße 63–73, 14195 Berlin, Germany
| | - Stefanie Schöne
- Max Planck Institute for Molecular Genetics, Ihnestraße 63–73, 14195 Berlin, Germany
| | - Stefan Prekovic
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Isabel Mayayo-Peralta
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ho-Ryun Chung
- Max Planck Institute for Molecular Genetics, Ihnestraße 63–73, 14195 Berlin, Germany
- Institute for Medical Bioinformatics and Biostatistics, Philipps University of Marburg, 35037, Marburg, Germany
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Christine Helsen
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Frank Claessens
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Sebastiaan H Meijsing
- Max Planck Institute for Molecular Genetics, Ihnestraße 63–73, 14195 Berlin, Germany
- Max Planck Unit for the Science of Pathogens, D-10117 Berlin, Germany
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8
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Trizzino M, Zucco A, Deliard S, Wang F, Barbieri E, Veglia F, Gabrilovich D, Gardini A. EGR1 is a gatekeeper of inflammatory enhancers in human macrophages. SCIENCE ADVANCES 2021; 7:7/3/eaaz8836. [PMID: 33523892 PMCID: PMC7806227 DOI: 10.1126/sciadv.aaz8836] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 11/20/2020] [Indexed: 05/20/2023]
Abstract
Monocytes and monocyte-derived macrophages originate through a multistep differentiation process. First, hematopoietic stem cells generate lineage-restricted progenitors that eventually develop into peripheral, postmitotic monocytes. Second, blood-circulating monocytes undergo differentiation into macrophages, which are specialized phagocytic cells capable of tissue infiltration. While monocytes mediate some level of inflammation and cell toxicity, macrophages boast the widest set of defense mechanisms against pathogens and elicit robust inflammatory responses. Here, we analyze the molecular determinants of monocytic and macrophagic commitment by profiling the EGR1 transcription factor. EGR1 is essential for monopoiesis and binds enhancers that regulate monocytic developmental genes such as CSF1R However, differentiating macrophages present a very different EGR1 binding pattern. We identify novel binding sites of EGR1 at a large set of inflammatory enhancers, even in the absence of its binding motif. We show that EGR1 repressive activity results in suppression of inflammatory genes and is mediated by the NuRD corepressor complex.
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Affiliation(s)
- Marco Trizzino
- The Wistar Institute, 3601 Spruce street, Philadelphia, PA 19104, USA
| | - Avery Zucco
- The Wistar Institute, 3601 Spruce street, Philadelphia, PA 19104, USA
| | - Sandra Deliard
- The Wistar Institute, 3601 Spruce street, Philadelphia, PA 19104, USA
| | - Fang Wang
- The Wistar Institute, 3601 Spruce street, Philadelphia, PA 19104, USA
| | - Elisa Barbieri
- The Wistar Institute, 3601 Spruce street, Philadelphia, PA 19104, USA
| | - Filippo Veglia
- The Wistar Institute, 3601 Spruce street, Philadelphia, PA 19104, USA
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9
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Barbieri E, Hill C, Quesnel-Vallières M, Zucco AJ, Barash Y, Gardini A. Rapid and Scalable Profiling of Nascent RNA with fastGRO. Cell Rep 2020; 33:108373. [PMID: 33176136 PMCID: PMC7702699 DOI: 10.1016/j.celrep.2020.108373] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 09/15/2020] [Accepted: 10/19/2020] [Indexed: 12/20/2022] Open
Abstract
Genome-wide profiling of nascent RNA has become a fundamental tool to study transcription regulation. Unlike steady-state RNA-sequencing (RNA-seq), nascent RNA profiling mirrors real-time activity of RNA polymerases and provides an accurate readout of transcriptome-wide variations. Some species of nuclear RNAs (i.e., large intergenic noncoding RNAs [lincRNAs] and eRNAs) have a short half-life and can only be accurately gauged by nascent RNA techniques. Furthermore, nascent RNA-seq detects post-cleavage RNA at termination sites and promoter-associated antisense RNAs, providing insights into RNA polymerase II (RNAPII) dynamics and processivity. Here, we present a run-on assay with 4-thio ribonucleotide (4-S-UTP) labeling, followed by reversible biotinylation and affinity purification via streptavidin. Our protocol allows streamlined sample preparation within less than 3 days. We named the technique fastGRO (fast Global Run-On). We show that fastGRO is highly reproducible and yields a more complete and extensive coverage of nascent RNA than comparable techniques can. Importantly, we demonstrate that fastGRO is scalable and can be performed with as few as 0.5 × 106 cells. Barbieri et al. developed fastGRO, a nascent RNA-sequencing technique based on nuclear run-on. Using a streamlined, under-3-days protocol, fastGRO tracks the activity of RNA polymerase for differential gene expression analysis, polymerase kinetic studies, and profiling of lowly expressed and unstable RNA species. A low-input fastGRO protocol profiles nascent RNA in as little as 0.5 × 106 cells.
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Affiliation(s)
- Elisa Barbieri
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Connor Hill
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Mathieu Quesnel-Vallières
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Avery J Zucco
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Alessandro Gardini
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA.
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10
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Erzurumluoglu AM, Liu M, Jackson VE, Barnes DR, Datta G, Melbourne CA, Young R, Batini C, Surendran P, Jiang T, Adnan SD, Afaq S, Agrawal A, Altmaier E, Antoniou AC, Asselbergs FW, Baumbach C, Bierut L, Bertelsen S, Boehnke M, Bots ML, Brazel DM, Chambers JC, Chang-Claude J, Chen C, Corley J, Chou YL, David SP, de Boer RA, de Leeuw CA, Dennis JG, Dominiczak AF, Dunning AM, Easton DF, Eaton C, Elliott P, Evangelou E, Faul JD, Foroud T, Goate A, Gong J, Grabe HJ, Haessler J, Haiman C, Hallmans G, Hammerschlag AR, Harris SE, Hattersley A, Heath A, Hsu C, Iacono WG, Kanoni S, Kapoor M, Kaprio J, Kardia SL, Karpe F, Kontto J, Kooner JS, Kooperberg C, Kuulasmaa K, Laakso M, Lai D, Langenberg C, Le N, Lettre G, Loukola A, Luan J, Madden PAF, Mangino M, Marioni RE, Marouli E, Marten J, Martin NG, McGue M, Michailidou K, Mihailov E, Moayyeri A, Moitry M, Müller-Nurasyid M, Naheed A, Nauck M, Neville MJ, Nielsen SF, North K, Perola M, Pharoah PDP, Pistis G, Polderman TJ, Posthuma D, Poulter N, Qaiser B, Rasheed A, Reiner A, Renström F, Rice J, Rohde R, Rolandsson O, Samani NJ, Samuel M, Schlessinger D, Scholte SH, Scott RA, Sever P, Shao Y, Shrine N, Smith JA, Starr JM, Stirrups K, Stram D, Stringham HM, Tachmazidou I, Tardif JC, Thompson DJ, Tindle HA, Tragante V, Trompet S, Turcot V, Tyrrell J, Vaartjes I, van der Leij AR, van der Meer P, Varga TV, Verweij N, Völzke H, Wareham NJ, Warren HR, Weir DR, Weiss S, Wetherill L, Yaghootkar H, Yavas E, Jiang Y, Chen F, Zhan X, Zhang W, Zhao W, Zhao W, Zhou K, Amouyel P, Blankenberg S, Caulfield MJ, Chowdhury R, Cucca F, Deary IJ, Deloukas P, Di Angelantonio E, Ferrario M, Ferrières J, Franks PW, Frayling TM, Frossard P, Hall IP, Hayward C, Jansson JH, Jukema JW, Kee F, Männistö S, Metspalu A, Munroe PB, Nordestgaard BG, Palmer CNA, Salomaa V, Sattar N, Spector T, Strachan DP, van der Harst P, Zeggini E, Saleheen D, Butterworth AS, Wain LV, Abecasis GR, Danesh J, Tobin MD, Vrieze S, Liu DJ, Howson JMM. Meta-analysis of up to 622,409 individuals identifies 40 novel smoking behaviour associated genetic loci. Mol Psychiatry 2020; 25:2392-2409. [PMID: 30617275 PMCID: PMC7515840 DOI: 10.1038/s41380-018-0313-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 09/30/2018] [Accepted: 11/14/2018] [Indexed: 02/02/2023]
Abstract
Smoking is a major heritable and modifiable risk factor for many diseases, including cancer, common respiratory disorders and cardiovascular diseases. Fourteen genetic loci have previously been associated with smoking behaviour-related traits. We tested up to 235,116 single nucleotide variants (SNVs) on the exome-array for association with smoking initiation, cigarettes per day, pack-years, and smoking cessation in a fixed effects meta-analysis of up to 61 studies (up to 346,813 participants). In a subset of 112,811 participants, a further one million SNVs were also genotyped and tested for association with the four smoking behaviour traits. SNV-trait associations with P < 5 × 10-8 in either analysis were taken forward for replication in up to 275,596 independent participants from UK Biobank. Lastly, a meta-analysis of the discovery and replication studies was performed. Sixteen SNVs were associated with at least one of the smoking behaviour traits (P < 5 × 10-8) in the discovery samples. Ten novel SNVs, including rs12616219 near TMEM182, were followed-up and five of them (rs462779 in REV3L, rs12780116 in CNNM2, rs1190736 in GPR101, rs11539157 in PJA1, and rs12616219 near TMEM182) replicated at a Bonferroni significance threshold (P < 4.5 × 10-3) with consistent direction of effect. A further 35 SNVs were associated with smoking behaviour traits in the discovery plus replication meta-analysis (up to 622,409 participants) including a rare SNV, rs150493199, in CCDC141 and two low-frequency SNVs in CEP350 and HDGFRP2. Functional follow-up implied that decreased expression of REV3L may lower the probability of smoking initiation. The novel loci will facilitate understanding the genetic aetiology of smoking behaviour and may lead to the identification of potential drug targets for smoking prevention and/or cessation.
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Affiliation(s)
| | - Mengzhen Liu
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Victoria E Jackson
- Department of Health Sciences, University of Leicester, Leicester, UK
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde, 3052, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, 3010, Parkville, Australia
| | - Daniel R Barnes
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Gargi Datta
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
| | - Carl A Melbourne
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Robin Young
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Chiara Batini
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Praveen Surendran
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Tao Jiang
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Sheikh Daud Adnan
- National Institute of Cardiovascular Diseases, Sher-e-Bangla Nagar, Dhaka, Bangladesh
| | - Saima Afaq
- Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, UK
| | - Arpana Agrawal
- Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Elisabeth Altmaier
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Folkert W Asselbergs
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
- Durrer Center for Cardiovascular Research, Netherlands Heart Institute, Utrecht, The Netherlands
- Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London, UK
- Farr Institute of Health Informatics Research and Institute of Health Informatics, University College London, London, UK
| | - Clemens Baumbach
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Laura Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Sarah Bertelsen
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Michiel L Bots
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3508GA, Utrecht, The Netherlands
- Center for Circulatory Health, University Medical Center Utrecht, 3508GA, Utrecht, The Netherlands
| | - David M Brazel
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - John C Chambers
- Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
- Department of Cardiology, Ealing Hospital, Middlesex, UB1 3HW, UK
- Imperial College Healthcare NHS Trust, London, W12 0HS, UK
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg (UCCH), Hamburg, Germany
| | - Chu Chen
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Janie Corley
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Yi-Ling Chou
- Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Sean P David
- Department of Medicine, Stanford University, Stanford, CA, USA
| | - Rudolf A de Boer
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Christiaan A de Leeuw
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, Netherlands
| | - Joe G Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Anna F Dominiczak
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, Cambridge Centre, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, Cambridge Centre, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Charles Eaton
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, W2 1PG, UK
- National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare NHS Trust and Imperial College London, London, UK
- UK Dementia Research Institute (UK DRI) at Imperial College London, London, UK
| | - Evangelos Evangelou
- Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, UK
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
| | - Jessica D Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Alison Goate
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jian Gong
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Hans J Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17475, Greifswald, Germany
| | - Jeff Haessler
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Christopher Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Göran Hallmans
- Department of Public Health and Clinical Medicine, Nutritional research, Umeå University, Umeå, Sweden
| | - Anke R Hammerschlag
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, Netherlands
| | - Sarah E Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Andrew Hattersley
- Genetics of Complex Traits, University of Exeter Medical School, Exeter, UK
| | - Andrew Heath
- Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Chris Hsu
- University of Southern California, California, CA, USA
| | - William G Iacono
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Stavroula Kanoni
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- Centre for Genomic Health, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Manav Kapoor
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Sharon L Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Fredrik Karpe
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- Oxford National Institute for Health Research, Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Jukka Kontto
- Department of Public Health Solutions, National Institute for Health and Welfare, FI-00271, Helsinki, Finland
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, Middlesex, UB1 3HW, UK
- Imperial College Healthcare NHS Trust, London, W12 0HS, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, W2 1PG, UK
- National Heart and Lung Institute, Imperial College London, London, W12 0NN, UK
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Biostatistics, University of Washington School of Medicine, Seattle, WA, USA
| | - Kari Kuulasmaa
- Department of Public Health Solutions, National Institute for Health and Welfare, FI-00271, Helsinki, Finland
| | | | - Dongbing Lai
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | - Nhung Le
- Department of Medical Microbiology, Immunology and Cell Biology, Southern Illinois University School of Medicine, Springfield, IL, USA
| | - Guillaume Lettre
- Montreal Heart Institute, Montreal, Quebec, H1T 1C8, Canada
- Department of Medicine, Faculty of Medicine, Universite de Montreal, Montreal, Quebec, H3T 1J4, Canada
| | - Anu Loukola
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Jian'an Luan
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | | | - Massimo Mangino
- NIHR Biomedical Research Centre at Guy's and St Thomas' Foundation Trust, London, SE1 9RT, UK
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, SE1 7EH, UK
| | - Riccardo E Marioni
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Eirini Marouli
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- Centre for Genomic Health, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Jonathan Marten
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | | | - Matt McGue
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, 1683, Nicosia, Cyprus
| | | | - Alireza Moayyeri
- Institute of Health Informatics, University College London, London, UK
| | - Marie Moitry
- Department of Epidemiology and Public health, University Hospital of Strasbourg, Strasbourg, France
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Department of Medicine I, Ludwig-Maximilians-University Munich, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Aliya Naheed
- Initiative for Noncommunicable Diseases, Health Systems and Population Studies Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b) International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Matthias Nauck
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, 17475, Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, University Medicine, Greifswald, Germany
| | - Matthew J Neville
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- Oxford National Institute for Health Research, Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Sune Fallgaard Nielsen
- Department of Clinical Biochemistry Herlev Hospital, Copenhagen University Hospital, Herlev Ringvej 74, DK-2730, Herlev, Denmark
| | - Kari North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Markus Perola
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Public Health Solutions, National Institute for Health and Welfare, FI-00271, Helsinki, Finland
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, Cambridge Centre, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Giorgio Pistis
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Tinca J Polderman
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, Netherlands
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, Netherlands
- Department of Clinical Genetics, VU University Medical Centre Amsterdam, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Neil Poulter
- International Centre for Circulatory Health, Imperial College London, London, UK
| | - Beenish Qaiser
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Asif Rasheed
- Centre for Non-Communicable Diseases, Karachi, Pakistan
| | - Alex Reiner
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Frida Renström
- Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Department of Clinical Sciences, Skåne University Hospital, Lund University, SE-214 28, Malmö, Sweden
- Department of Biobank Research, Umeå University, SE-901 87, Umeå, Sweden
| | - John Rice
- Departments of Psychiatry and Mathematics, Washington University St. Louis, St. Louis, MO, USA
| | | | - Olov Rolandsson
- Department of Public Health & Clinical Medicine, Section for Family Medicine, Umeå universitet, SE, 90185, Umeå, Sweden
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Cardiovascular Research Centre, Glenfield Hospital, Leicester, LE3 9QP, UK
| | - Maria Samuel
- Centre for Non-Communicable Diseases, Karachi, Pakistan
| | - David Schlessinger
- National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Steven H Scholte
- Department of Psychology, University of Amsterdam & Amsterdam Brain and Cognition, University of Amsterdam, Amsterdam, Netherlands
| | - Robert A Scott
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | - Peter Sever
- National Heart and Lung Institute, Imperial College London, London, W12 0NN, UK
- International Centre for Circulatory Health, Imperial College London, London, UK
| | - Yaming Shao
- University of North Carolina, Chapel Hill, NC, USA
| | - Nick Shrine
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - John M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Alzheimer Scotland Research Centre, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Kathleen Stirrups
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- Department of Haematology, University of Cambridge, Cambridge, CB2 0PT, UK
| | - Danielle Stram
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Heather M Stringham
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | | | - Jean-Claude Tardif
- Montreal Heart Institute, Montreal, Quebec, H1T 1C8, Canada
- Department of Medicine, Faculty of Medicine, Universite de Montreal, Montreal, Quebec, H3T 1J4, Canada
| | - Deborah J Thompson
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Hilary A Tindle
- Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Vinicius Tragante
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht University, 3508GA, Utrecht, The Netherlands
| | - Stella Trompet
- Department of gerontology and geriatrics, Leiden University Medical Center, Leiden, The Netherlands
- Department of cardiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Valerie Turcot
- Montreal Heart Institute, Montreal, Quebec, H1T 1C8, Canada
| | - Jessica Tyrrell
- Genetics of Complex Traits, University of Exeter Medical School, Exeter, UK
| | - Ilonca Vaartjes
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3508GA, Utrecht, The Netherlands
- Center for Circulatory Health, University Medical Center Utrecht, 3508GA, Utrecht, The Netherlands
| | - Andries R van der Leij
- Department of Psychology, University of Amsterdam & Amsterdam Brain and Cognition, University of Amsterdam, Amsterdam, Netherlands
| | - Peter van der Meer
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Tibor V Varga
- Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Department of Clinical Sciences, Skåne University Hospital, Lund University, SE-214 28, Malmö, Sweden
| | - Niek Verweij
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 301 Binney Street, Cambridge, MA, 02142, USA
| | - Henry Völzke
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, University Medicine, Greifswald, Germany
- Institute for Community Medicine, University Medicine Greifswald, 17475, Greifswald, Germany
| | - Nicholas J Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | - Helen R Warren
- Clinical Pharmacology, William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - David R Weir
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Stefan Weiss
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, University Medicine, Greifswald, Germany
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine and Ernst-Moritz-Arndt-University Greifswald, 17475, Greifswald, Germany
| | - Leah Wetherill
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Hanieh Yaghootkar
- Genetics of Complex Traits, University of Exeter Medical School, Exeter, UK
| | - Ersin Yavas
- Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, UK
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, Pennsylvania, PA, 16802, USA
| | - Yu Jiang
- Institute of Personalized Medicine, Penn State College of Medicine, Hershey, PA, USA
| | - Fang Chen
- Institute of Personalized Medicine, Penn State College of Medicine, Hershey, PA, USA
| | - Xiaowei Zhan
- Department of Clinical Science, Center for Genetics of Host Defense, University of Texas Southwestern, Dallas, TX, USA
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, UK
- Department of Cardiology, Ealing Hospital, London North West Healthcare NHS Trust, Middlesex, UB1 3HW, UK
| | - Wei Zhao
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Pennsylvania, PA, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Kaixin Zhou
- School of Medicine, University of Dundee, Dundee, UK
| | - Philippe Amouyel
- Department of Epidemiology and Public Health, Institut Pasteur de Lille, Lille, France
| | - Stefan Blankenberg
- Department of General and Interventional Cardiology, University Heart Center Hamburg, Hamburg, Germany
- University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Mark J Caulfield
- Clinical Pharmacology, William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Rajiv Chowdhury
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Emanuele Di Angelantonio
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Marco Ferrario
- EPIMED Research Centre, Department of Medicine and Surgery, University of Insubria at Varese, Varese, Italy
| | - Jean Ferrières
- Department of Epidemiology, UMR 1027- INSERM, Toulouse University-CHU Toulouse, Toulouse, France
| | - Paul W Franks
- Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Department of Clinical Sciences, Skåne University Hospital, Lund University, SE-214 28, Malmö, Sweden
- Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Tim M Frayling
- Genetics of Complex Traits, University of Exeter Medical School, Exeter, UK
| | | | - Ian P Hall
- Division of Respiratory Medicine and NIHR Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Caroline Hayward
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Jan-Håkan Jansson
- Department of Public Health and Clinical Medicine, Skellefteå Research Unit, Umeå University, Umeå, Sweden
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
- The Interuniversity Cardiology Institute of the Netherlands, Utrecht, The Netherlands
| | - Frank Kee
- UKCRC Centre of Excellence for Public Health, Queens, University, Belfast, Belfast, UK
| | - Satu Männistö
- Department of Public Health Solutions, National Institute for Health and Welfare, FI-00271, Helsinki, Finland
| | | | - Patricia B Munroe
- Clinical Pharmacology, William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Børge Grønne Nordestgaard
- Department of Clinical Biochemistry Herlev Hospital, Copenhagen University Hospital, Herlev Ringvej 74, DK-2730, Herlev, Denmark
| | - Colin N A Palmer
- Medical Research Institute, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Veikko Salomaa
- Department of Public Health Solutions, National Institute for Health and Welfare, FI-00271, Helsinki, Finland
| | - Naveed Sattar
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Timothy Spector
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, SE1 7EH, UK
| | - David Peter Strachan
- Population Health Research Institute, St George!s, University of London, London, SW17 0RE, UK
| | - Pim van der Harst
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Danish Saleheen
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, PA, USA
- Center for Non-Communicable Diseases, Karachi, Pakistan
| | - Adam S Butterworth
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK
- National Institute for Health Research Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Goncalo R Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - John Danesh
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK
- National Institute for Health Research Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Scott Vrieze
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Dajiang J Liu
- Institute of Personalized Medicine, Penn State College of Medicine, Hershey, PA, USA.
| | - Joanna M M Howson
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK.
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11
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Yang T, Kim J, Wu C, Ma Y, Wei P, Pan W. An adaptive test for meta-analysis of rare variant association studies. Genet Epidemiol 2020; 44:104-116. [PMID: 31830326 PMCID: PMC6980317 DOI: 10.1002/gepi.22273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 11/12/2019] [Accepted: 11/25/2019] [Indexed: 01/02/2023]
Abstract
Single genome-wide studies may be underpowered to detect trait-associated rare variants with moderate or weak effect sizes. As a viable alternative, meta-analysis is widely used to increase power by combining different studies. The power of meta-analysis critically depends on the underlying association patterns and heterogeneity levels, which are unknown and vary from locus to locus. However, existing methods mainly focus on one or only a few combinations of the association pattern and heterogeneity level, thus may lose power in many situations. To address this issue, we propose a general and unified framework by combining a class of tests including and beyond some existing ones, leading to high power across a wide range of scenarios. We demonstrate that the proposed test is more powerful than some existing methods in simulation studies, then show their performance with the NHLBI Exome-Sequencing Project (ESP) data. One gene (B4GALNT2) was found by our proposed test, but not by others, to be statistically significantly associated with plasma triglyceride. The signal was driven by African-ancestry subjects but it was previously reported to be associated with coronary artery disease among European-ancestry subjects. We implemented our method in an R package aSPUmeta, publicly available at https://github.com/ytzhong/metaRV and will be on CRAN soon.
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Affiliation(s)
- Tianzhong Yang
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Junghi Kim
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Chong Wu
- Department of Statistics, Florida State University, Tallahassee, FL, USA
| | - Yiding Ma
- Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Peng Wei
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wei Pan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
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12
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Trizzino M, Barbieri E, Petracovici A, Wu S, Welsh SA, Owens TA, Licciulli S, Zhang R, Gardini A. The Tumor Suppressor ARID1A Controls Global Transcription via Pausing of RNA Polymerase II. Cell Rep 2019; 23:3933-3945. [PMID: 29949775 DOI: 10.1016/j.celrep.2018.05.097] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/20/2018] [Accepted: 05/30/2018] [Indexed: 12/17/2022] Open
Abstract
AT-rich interactive domain-containing proteins 1A and 1B (ARID1A and ARID1B) are mutually exclusive subunits of the chromatin remodeler SWI/SNF. ARID1A is the most frequently mutated chromatin regulator across all cancers, and ovarian clear cell carcinoma (OCCC) carries the highest prevalence of ARID1A mutations (∼57%). Despite evidence implicating ARID1A in tumorigenesis, the mechanism remains elusive. Here, we demonstrate that ARID1A binds active regulatory elements in OCCC. Depletion of ARID1A represses RNA polymerase II (RNAPII) transcription but results in modest changes to accessibility. Specifically, pausing of RNAPII is severely impaired after loss of ARID1A. Compromised pausing results in transcriptional dysregulation of active genes, which is compensated by upregulation of ARID1B. However, a subset of ARID1A-dependent genes is not rescued by ARID1B, including many p53 and estrogen receptor (ESR1) targets. Our results provide insight into ARID1A-mediated tumorigenesis and unveil functions of SWI/SNF in modulating RNAPII dynamics.
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Affiliation(s)
- Marco Trizzino
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Elisa Barbieri
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Ana Petracovici
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Shuai Wu
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Sarah A Welsh
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Tori A Owens
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Silvia Licciulli
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Rugang Zhang
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Alessandro Gardini
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA.
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13
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Early chromatin shaping predetermines multipotent vagal neural crest into neural, neuronal and mesenchymal lineages. Nat Cell Biol 2019; 21:1504-1517. [PMID: 31792380 PMCID: PMC7188519 DOI: 10.1038/s41556-019-0428-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 10/28/2019] [Indexed: 01/28/2023]
Abstract
The enteric nervous system (ENS) predominantly originates from vagal neural crest cells (VNC) that emerge from the caudal hindbrain, invade the foregut and populate the gastrointestinal tract. However, the gene regulatory network (GRN) orchestrating the early specification of VNC remains unknown. Using an EdnrB enhancer, we generated a comprehensive temporal map of the chromatin and transcriptional landscape of VNC in the avian model, revealing three VNC cell clusters (neural, neurogenic and mesenchymal), each predetermined epigenetically prior to neural tube delamination. We identify and functionally validate regulatory cores (Sox10/Tfap2B/SoxB/Hbox) mediating each programme and elucidate their combinatorial activities with other spatiotemporally-specific transcription factors (bHLH/NR). Our global deconstruction of the VNC-GRN in vivo sheds light on critical early regulatory mechanisms that may influence the divergent neural phenotypes in enteric neuropathies.
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14
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Williams RM, Candido-Ferreira I, Repapi E, Gavriouchkina D, Senanayake U, Ling ITC, Telenius J, Taylor S, Hughes J, Sauka-Spengler T. Reconstruction of the Global Neural Crest Gene Regulatory Network In Vivo. Dev Cell 2019; 51:255-276.e7. [PMID: 31639368 PMCID: PMC6838682 DOI: 10.1016/j.devcel.2019.10.003] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 05/31/2019] [Accepted: 10/01/2019] [Indexed: 02/07/2023]
Abstract
Precise control of developmental processes is encoded in the genome in the form of gene regulatory networks (GRNs). Such multi-factorial systems are difficult to decode in vertebrates owing to their complex gene hierarchies and dynamic molecular interactions. Here we present a genome-wide in vivo reconstruction of the GRN underlying development of the multipotent neural crest (NC) embryonic cell population. By coupling NC-specific epigenomic and transcriptional profiling at population and single-cell levels with genome/epigenome engineering in vivo, we identify multiple regulatory layers governing NC ontogeny, including NC-specific enhancers and super-enhancers, novel trans-factors, and cis-signatures allowing reverse engineering of the NC-GRN at unprecedented resolution. Furthermore, identification and dissection of divergent upstream combinatorial regulatory codes has afforded new insights into opposing gene circuits that define canonical and neural NC fates early during NC ontogeny. Our integrated approach, allowing dissection of cell-type-specific regulatory circuits in vivo, has broad implications for GRN discovery and investigation.
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Affiliation(s)
- Ruth M Williams
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Ivan Candido-Ferreira
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Emmanouela Repapi
- University of Oxford, MRC Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK
| | - Daria Gavriouchkina
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Upeka Senanayake
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Irving T C Ling
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK; University of Oxford, Department of Paediatric Surgery, Children's Hospital Oxford, Oxford, UK
| | - Jelena Telenius
- University of Oxford, MRC Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK; University of Oxford, MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Stephen Taylor
- University of Oxford, MRC Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK
| | - Jim Hughes
- University of Oxford, MRC Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, UK; University of Oxford, MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Tatjana Sauka-Spengler
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK.
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15
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Ritari J, Hyvärinen K, Koskela S, Niittyvuopio R, Nihtinen A, Salmenniemi U, Putkonen M, Volin L, Kwan T, Pastinen T, Itälä-Remes M, Partanen J. Computational Analysis of HLA-presentation of Non-synonymous Recipient Mismatches Indicates Effect on the Risk of Chronic Graft-vs.-Host Disease After Allogeneic HSCT. Front Immunol 2019; 10:1625. [PMID: 31379830 PMCID: PMC6646417 DOI: 10.3389/fimmu.2019.01625] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 07/01/2019] [Indexed: 12/20/2022] Open
Abstract
Genetic mismatches in protein coding genes between allogeneic hematopoietic stem cell transplantation (allo-HSCT) recipient and donor can elicit an alloimmunity response via peptides presented by the recipient HLA receptors as minor histocompatibility antigens (mHAs). While the impact of individual mHAs on allo-HSCT outcome such as graft-vs.-host and graft-vs.-leukemia effects has been demonstrated, it is likely that established mHAs constitute only a small fraction of all immunogenic non-synonymous variants. In the present study, we have analyzed the genetic mismatching in 157 exome-sequenced sibling allo-HSCT pairs to evaluate the significance of polymorphic HLA class I associated peptides on clinical outcome. We applied computational mismatch estimation approaches based on experimentally verified HLA ligands available in public repositories, published mHAs, and predicted HLA-peptide affinites, and analyzed their associations with chronic graft-vs.-host disease (cGvHD) grades. We found that higher estimated recipient mismatching consistently increased the risk of severe cGvHD, suggesting that HLA-presented mismatching influences the likelihood of long-term complications in the patient. Furthermore, computational approaches focusing on estimation of HLA-presentation instead of all non-synonymous mismatches indiscriminately may be beneficial for analysis sensitivity and could help identify novel mHAs.
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Affiliation(s)
- Jarmo Ritari
- Finnish Red Cross Blood Service, Helsinki, Finland
| | | | - Satu Koskela
- Finnish Red Cross Blood Service, Helsinki, Finland
| | - Riitta Niittyvuopio
- Stem Cell Transplantation Unit, Department of Hematology, Comprehensive Cancer Center, Helsinki University Hospital, Helsinki, Finland
| | - Anne Nihtinen
- Stem Cell Transplantation Unit, Department of Hematology, Comprehensive Cancer Center, Helsinki University Hospital, Helsinki, Finland
| | - Urpu Salmenniemi
- Stem Cell Transplantation Unit, Division of Medicine, Department of Hematology, Turku University Hospital, Turku, Finland
| | - Mervi Putkonen
- Stem Cell Transplantation Unit, Division of Medicine, Department of Hematology, Turku University Hospital, Turku, Finland
| | - Liisa Volin
- Stem Cell Transplantation Unit, Department of Hematology, Comprehensive Cancer Center, Helsinki University Hospital, Helsinki, Finland
| | - Tony Kwan
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, McGill University, Montreal, QC, Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, McGill University, Montreal, QC, Canada.,Center for Pediatric Genomic Medicine, Children's Mercy, Kansas City, MO, United States
| | - Maija Itälä-Remes
- Stem Cell Transplantation Unit, Division of Medicine, Department of Hematology, Turku University Hospital, Turku, Finland
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16
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Brazel DM, Jiang Y, Hughey JM, Turcot V, Zhan X, Gong J, Batini C, Weissenkampen JD, Liu M, Barnes DR, Bertelsen S, Chou YL, Erzurumluoglu AM, Faul JD, Haessler J, Hammerschlag AR, Hsu C, Kapoor M, Lai D, Le N, de Leeuw CA, Loukola A, Mangino M, Melbourne CA, Pistis G, Qaiser B, Rohde R, Shao Y, Stringham H, Wetherill L, Zhao W, Agrawal A, Bierut L, Chen C, Eaton CB, Goate A, Haiman C, Heath A, Iacono WG, Martin NG, Polderman TJ, Reiner A, Rice J, Schlessinger D, Scholte HS, Smith JA, Tardif JC, Tindle HA, van der Leij AR, Boehnke M, Chang-Claude J, Cucca F, David SP, Foroud T, Howson JMM, Kardia SLR, Kooperberg C, Laakso M, Lettre G, Madden P, McGue M, North K, Posthuma D, Spector T, Stram D, Tobin MD, Weir DR, Kaprio J, Abecasis GR, Liu DJ, Vrieze S. Exome Chip Meta-analysis Fine Maps Causal Variants and Elucidates the Genetic Architecture of Rare Coding Variants in Smoking and Alcohol Use. Biol Psychiatry 2019; 85:946-955. [PMID: 30679032 PMCID: PMC6534468 DOI: 10.1016/j.biopsych.2018.11.024] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/05/2018] [Accepted: 11/29/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND Smoking and alcohol use have been associated with common genetic variants in multiple loci. Rare variants within these loci hold promise in the identification of biological mechanisms in substance use. Exome arrays and genotype imputation can now efficiently genotype rare nonsynonymous and loss of function variants. Such variants are expected to have deleterious functional consequences and to contribute to disease risk. METHODS We analyzed ∼250,000 rare variants from 16 independent studies genotyped with exome arrays and augmented this dataset with imputed data from the UK Biobank. Associations were tested for five phenotypes: cigarettes per day, pack-years, smoking initiation, age of smoking initiation, and alcoholic drinks per week. We conducted stratified heritability analyses, single-variant tests, and gene-based burden tests of nonsynonymous/loss-of-function coding variants. We performed a novel fine-mapping analysis to winnow the number of putative causal variants within associated loci. RESULTS Meta-analytic sample sizes ranged from 152,348 to 433,216, depending on the phenotype. Rare coding variation explained 1.1% to 2.2% of phenotypic variance, reflecting 11% to 18% of the total single nucleotide polymorphism heritability of these phenotypes. We identified 171 genome-wide associated loci across all phenotypes. Fine mapping identified putative causal variants with double base-pair resolution at 24 of these loci, and between three and 10 variants for 65 loci. Twenty loci contained rare coding variants in the 95% credible intervals. CONCLUSIONS Rare coding variation significantly contributes to the heritability of smoking and alcohol use. Fine-mapping genome-wide association study loci identifies specific variants contributing to the biological etiology of substance use behavior.
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Affiliation(s)
- David M Brazel
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, Colorado; Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado
| | - Yu Jiang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, Pennsylvania
| | - Jordan M Hughey
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, Pennsylvania
| | - Valérie Turcot
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada; Montreal Heart Institute, Montreal, Quebec, Canada
| | - Xiaowei Zhan
- Department of Clinical Science, Center for Genetics of Host Defense, University of Texas Southwestern, Dallas, Texas
| | - Jian Gong
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Chiara Batini
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - J Dylan Weissenkampen
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, Pennsylvania
| | - MengZhen Liu
- Department of Psychology, University of Minnesota, Minneapolis, Minnesota
| | - Daniel R Barnes
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Sarah Bertelsen
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Yi-Ling Chou
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri
| | | | - Jessica D Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan
| | - Jeff Haessler
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Anke R Hammerschlag
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, University of Amsterdam, Amsterdam, the Netherlands
| | - Chris Hsu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Manav Kapoor
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Dongbing Lai
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Nhung Le
- Department of Medical Microbiology, Immunology and Cell Biology, Southern Illinois University School of Medicine, Springfield, Illinois
| | - Christiaan A de Leeuw
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, University of Amsterdam, Amsterdam, the Netherlands
| | - Anu Loukola
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland; Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom; National Institute for Health Research Biomedical Research Centre at Guy's and St Thomas' Foundation Trust, London, United Kingdom
| | - Carl A Melbourne
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - Giorgio Pistis
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Italy
| | - Beenish Qaiser
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland; Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Rebecca Rohde
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Yaming Shao
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Heather Stringham
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan
| | - Leah Wetherill
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Wei Zhao
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan
| | - Arpana Agrawal
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri
| | - Laura Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri
| | - Chu Chen
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Epidemiology, Head and Neck Surgery Center, University of Washington, Seattle, Washington; Department of Otolaryngology, Head and Neck Surgery Center, University of Washington, Seattle, Washington
| | - Charles B Eaton
- Department of Family Medicine, Brown University, Providence, Rhode Island
| | - Alison Goate
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Christopher Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Andrew Heath
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri
| | - William G Iacono
- Department of Psychology, University of Minnesota, Minneapolis, Minnesota
| | | | - Tinca J Polderman
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, University of Amsterdam, Amsterdam, the Netherlands
| | - Alex Reiner
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Epidemiology, Head and Neck Surgery Center, University of Washington, Seattle, Washington
| | - John Rice
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri; Department of Mathematics, Washington University in St. Louis, St. Louis, Missouri
| | - David Schlessinger
- National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | - H Steven Scholte
- Department of Psychology, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Brain and Cognition, University of Amsterdam, Amsterdam, the Netherlands
| | - Jennifer A Smith
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan
| | - Jean-Claude Tardif
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada; Montreal Heart Institute, Montreal, Quebec, Canada
| | - Hilary A Tindle
- Department of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Andries R van der Leij
- Department of Psychology, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Brain and Cognition, University of Amsterdam, Amsterdam, the Netherlands
| | - Michael Boehnke
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Italy
| | - Sean P David
- Department of Medicine, Stanford University, Stanford, California
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Joanna M M Howson
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Sharon L R Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Markku Laakso
- Department of Internal Medicine, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Guillaume Lettre
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada; Montreal Heart Institute, Montreal, Quebec, Canada
| | - Pamela Madden
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri
| | - Matt McGue
- Department of Psychology, University of Minnesota, Minneapolis, Minnesota
| | - Kari North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, University of Amsterdam, Amsterdam, the Netherlands; Department of Clinical Genetics, VU University Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - Timothy Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Daniel Stram
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - David R Weir
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland; Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Gonçalo R Abecasis
- Regeneron Pharmaceuticals, Tarrytown, New York; Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan
| | - Dajiang J Liu
- Institute of Personalized Medicine, Penn State College of Medicine, Hershey, Pennsylvania.
| | - Scott Vrieze
- Department of Psychology, University of Minnesota, Minneapolis, Minnesota.
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17
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Cazaly E, Saad J, Wang W, Heckman C, Ollikainen M, Tang J. Making Sense of the Epigenome Using Data Integration Approaches. Front Pharmacol 2019; 10:126. [PMID: 30837884 PMCID: PMC6390500 DOI: 10.3389/fphar.2019.00126] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 01/31/2019] [Indexed: 12/19/2022] Open
Abstract
Epigenetic research involves examining the mitotically heritable processes that regulate gene expression, independent of changes in the DNA sequence. Recent technical advances such as whole-genome bisulfite sequencing and affordable epigenomic array-based technologies, allow researchers to measure epigenetic profiles of large cohorts at a genome-wide level, generating comprehensive high-dimensional datasets that may contain important information for disease development and treatment opportunities. The epigenomic profile for a certain disease is often a result of the complex interplay between multiple genetic and environmental factors, which poses an enormous challenge to visualize and interpret these data. Furthermore, due to the dynamic nature of the epigenome, it is critical to determine causal relationships from the many correlated associations. In this review we provide an overview of recent data analysis approaches to integrate various omics layers to understand epigenetic mechanisms of complex diseases, such as obesity and cancer. We discuss the following topics: (i) advantages and limitations of major epigenetic profiling techniques, (ii) resources for standardization, annotation and harmonization of epigenetic data, and (iii) statistical methods and machine learning methods for establishing data-driven hypotheses of key regulatory mechanisms. Finally, we discuss the future directions for data integration that shall facilitate the discovery of epigenetic-based biomarkers and therapies.
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Affiliation(s)
- Emma Cazaly
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Joseph Saad
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Wenyu Wang
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Caroline Heckman
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Jing Tang
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,Department of Mathematics and Statistics, University of Turku, Turku, Finland.,Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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18
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Liu M, Jiang Y, Wedow R, Li Y, Brazel DM, Chen F, Datta G, Davila-Velderrain J, McGuire D, Tian C, Zhan X, Choquet H, Docherty AR, Faul JD, Foerster JR, Fritsche LG, Gabrielsen ME, Gordon SD, Haessler J, Hottenga JJ, Huang H, Jang SK, Jansen PR, Ling Y, Mägi R, Matoba N, McMahon G, Mulas A, Orrù V, Palviainen T, Pandit A, Reginsson GW, Skogholt AH, Smith JA, Taylor AE, Turman C, Willemsen G, Young H, Young KA, Zajac GJM, Zhao W, Zhou W, Bjornsdottir G, Boardman JD, Boehnke M, Boomsma DI, Chen C, Cucca F, Davies GE, Eaton CB, Ehringer MA, Esko T, Fiorillo E, Gillespie NA, Gudbjartsson DF, Haller T, Harris KM, Heath AC, Hewitt JK, Hickie IB, Hokanson JE, Hopfer CJ, Hunter DJ, Iacono WG, Johnson EO, Kamatani Y, Kardia SLR, Keller MC, Kellis M, Kooperberg C, Kraft P, Krauter KS, Laakso M, Lind PA, Loukola A, Lutz SM, Madden PAF, Martin NG, McGue M, McQueen MB, Medland SE, Metspalu A, Mohlke KL, Nielsen JB, Okada Y, Peters U, Polderman TJC, Posthuma D, Reiner AP, Rice JP, Rimm E, Rose RJ, Runarsdottir V, Stallings MC, Stančáková A, Stefansson H, Thai KK, Tindle HA, Tyrfingsson T, Wall TL, Weir DR, Weisner C, Whitfield JB, Winsvold BS, Yin J, Zuccolo L, Bierut LJ, Hveem K, Lee JJ, Munafò MR, Saccone NL, Willer CJ, Cornelis MC, David SP, Hinds DA, Jorgenson E, Kaprio J, Stitzel JA, Stefansson K, Thorgeirsson TE, Abecasis G, Liu DJ, Vrieze S. Association studies of up to 1.2 million individuals yield new insights into the genetic etiology of tobacco and alcohol use. Nat Genet 2019; 51:237-244. [PMID: 30643251 PMCID: PMC6358542 DOI: 10.1038/s41588-018-0307-5] [Citation(s) in RCA: 1123] [Impact Index Per Article: 224.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 11/06/2018] [Indexed: 12/21/2022]
Abstract
Tobacco and alcohol use are leading causes of mortality that influence risk for many complex diseases and disorders1. They are heritable2,3 and etiologically related4,5 behaviors that have been resistant to gene discovery efforts6-11. In sample sizes up to 1.2 million individuals, we discovered 566 genetic variants in 406 loci associated with multiple stages of tobacco use (initiation, cessation, and heaviness) as well as alcohol use, with 150 loci evidencing pleiotropic association. Smoking phenotypes were positively genetically correlated with many health conditions, whereas alcohol use was negatively correlated with these conditions, such that increased genetic risk for alcohol use is associated with lower disease risk. We report evidence for the involvement of many systems in tobacco and alcohol use, including genes involved in nicotinic, dopaminergic, and glutamatergic neurotransmission. The results provide a solid starting point to evaluate the effects of these loci in model organisms and more precise substance use measures.
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Affiliation(s)
- Mengzhen Liu
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Yu Jiang
- Department of Public Health Sciences, College of Medicine, Pennsylvania State University, Hershey, PA, USA
- Institute of Personalized Medicine, College of Medicine, Pennsylvania State University, Hershey, PA, USA
| | - Robbee Wedow
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department of Sociology, University of Colorado Boulder, Boulder, CO, USA
- Institute of Behavioral Science, University of Colorado Boulder, Boulder, CO, USA
| | - Yue Li
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David M Brazel
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
- Interdisciplinary Quantitative Biology Graduate Group, University of Colorado Boulder, Boulder, CO, USA
| | - Fang Chen
- Department of Public Health Sciences, College of Medicine, Pennsylvania State University, Hershey, PA, USA
- Institute of Personalized Medicine, College of Medicine, Pennsylvania State University, Hershey, PA, USA
| | - Gargi Datta
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Jose Davila-Velderrain
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel McGuire
- Department of Public Health Sciences, College of Medicine, Pennsylvania State University, Hershey, PA, USA
- Institute of Personalized Medicine, College of Medicine, Pennsylvania State University, Hershey, PA, USA
| | - Chao Tian
- 23andMe, Inc., Mountain View, CA, USA
| | - Xiaowei Zhan
- Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for the Genetics of Host Defense, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hélène Choquet
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Anna R Docherty
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
- Department of Psychiatry and Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Jessica D Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Johanna R Foerster
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Lars G Fritsche
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Maiken Elvestad Gabrielsen
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
| | - Scott D Gordon
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Hongyan Huang
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Seon-Kyeong Jang
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Philip R Jansen
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Department of Child and Adolescent Psychiatry, Erasmus MC Rotterdam, Rotterdam, the Netherlands
| | - Yueh Ling
- Department of Public Health Sciences, College of Medicine, Pennsylvania State University, Hershey, PA, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Nana Matoba
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama City, Japan
| | - George McMahon
- Department of Population Health Science, Bristol Medical School, Oakfield Grove, Bristol, UK
| | - Antonella Mulas
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Italy
| | - Valeria Orrù
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Italy
| | - Teemu Palviainen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Anita Pandit
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | | | - Anne Heidi Skogholt
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jennifer A Smith
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Amy E Taylor
- Department of Population Health Science, Bristol Medical School, Oakfield Grove, Bristol, UK
| | - Constance Turman
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Gonneke Willemsen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Hannah Young
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Kendra A Young
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Gregory J M Zajac
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Wei Zhao
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Wei Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | | | - Jason D Boardman
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department of Sociology, University of Colorado Boulder, Boulder, CO, USA
- Institute of Behavioral Science, University of Colorado Boulder, Boulder, CO, USA
| | - Michael Boehnke
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Chu Chen
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Italy
| | | | - Charles B Eaton
- Department of Family Medicine and Community Health, Alpert Medical School, Brown University, Providence, RI, USA
| | - Marissa A Ehringer
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Tõnu Esko
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Edoardo Fiorillo
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Italy
| | - Nathan A Gillespie
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Toomas Haller
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Kathleen Mullan Harris
- Department of Sociology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Andrew C Heath
- Department of Psychiatry, Washington University in St. Louis, St. Louis, MO, USA
| | - John K Hewitt
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Ian B Hickie
- Brain and Mind Centre, University of Sydney, Sydney, New South Wales, Australia
| | - John E Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Christian J Hopfer
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department of Psychiatry, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - David J Hunter
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - William G Iacono
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Eric O Johnson
- Fellows Program, RTI International, Research Triangle Park, NC, USA
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama City, Japan
| | - Sharon L R Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Matthew C Keller
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Kenneth S Krauter
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Markku Laakso
- Department of Internal Medicine, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
- Department of Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Penelope A Lind
- Psychiatric Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Anu Loukola
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Sharon M Lutz
- Department of Biostatistics and Bioinformatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Pamela A F Madden
- Department of Psychiatry, Washington University in St. Louis, St. Louis, MO, USA
| | - Nicholas G Martin
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Matt McGue
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Matthew B McQueen
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Sarah E Medland
- Psychiatric Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | | | - Karen L Mohlke
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jonas B Nielsen
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Yukinori Okada
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama City, Japan
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Tinca J C Polderman
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Department of Clinical Genetics, VU Medical Centre Amsterdam, Amsterdam, the Netherlands
| | - Alexander P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - John P Rice
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Eric Rimm
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Richard J Rose
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, USA
| | | | - Michael C Stallings
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Alena Stančáková
- Department of Internal Medicine, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | | | - Khanh K Thai
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Hilary A Tindle
- Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | | | - Tamara L Wall
- Department of Psychiatry, University of California, San Diego, San Diego, CA, USA
| | - David R Weir
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Constance Weisner
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - John B Whitfield
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | | | - Jie Yin
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Luisa Zuccolo
- Department of Population Health Science, Bristol Medical School, Oakfield Grove, Bristol, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Laura J Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, Norwegian University of Science and Technology, Levanger, Norway
- Department of Medicine, Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
| | - James J Lee
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Marcus R Munafò
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- UK Centre for Tobacco and Alcohol Studies, School of Psychological Science, University of Bristol, Bristol, UK
| | - Nancy L Saccone
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Cristen J Willer
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Marilyn C Cornelis
- Department of Preventative Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sean P David
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Jerry A Stitzel
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Kari Stefansson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | | | - Gonçalo Abecasis
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Dajiang J Liu
- Department of Public Health Sciences, College of Medicine, Pennsylvania State University, Hershey, PA, USA.
- Institute of Personalized Medicine, College of Medicine, Pennsylvania State University, Hershey, PA, USA.
| | - Scott Vrieze
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, USA.
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19
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Baron RV, Stickel JR, Weeks DE. The Mega2R package: R tools for accessing and processing genetic data in common formats. F1000Res 2018; 7:1352. [PMID: 30271589 PMCID: PMC6137409 DOI: 10.12688/f1000research.15949.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/28/2019] [Indexed: 02/02/2023] Open
Abstract
The standalone C++ Mega2 program has been facilitating data-reformatting for linkage and association analysis programs since 2000. Support for more analysis programs has been added over time. Currently, Mega2 converts data from several different genetic data formats (including PLINK, VCF, BCF, and IMPUTE2) into the specific data requirements for over 40 commonly-used linkage and association analysis programs (including Mendel, Merlin, Morgan, SHAPEIT, ROADTRIPS, MaCH/minimac3). Recently, Mega2 has been enhanced to use a SQLite database as an intermediate data representation. Additionally, Mega2 now stores bialleleic genotype data in a highly compressed form, like that of the GenABEL R package and the PLINK binary format. Our new Mega2R package now makes it easy to load Mega2 SQLite databases directly into R as data frames. In addition, Mega2R is memory efficient, keeping its genotype data in a compressed format, portions of which are only expanded when needed. Mega2R has functions that ease the process of applying gene-based tests by looping over genes, efficiently pulling out genotypes for variants within the desired boundaries. We have also created several more functions that illustrate how to use the data frames: these permit one to run the pedgene package to carry out gene-based association tests on family data, to run the SKAT package to carry out gene-based association tests, to output the Mega2R data as a VCF file and related files (for phenotype and family data), and to convert the data frames into GenABEL format. The Mega2R package enhances GenABEL since it supports additional input data formats (such as PLINK, VCF, and IMPUTE2) not currently supported by GenABEL. The Mega2 program and the Mega2R R package are both open source and are freely available, along with extensive documentation, from
https://watson.hgen.pitt.edu/register for Mega2 and
https://CRAN.R-project.org/package=Mega2R for Mega2R.
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Affiliation(s)
- Robert V Baron
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, USA
| | - Justin R Stickel
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, USA
| | - Daniel E Weeks
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, USA.,Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, USA
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20
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Barbieri E, Trizzino M, Welsh SA, Owens TA, Calabretta B, Carroll M, Sarma K, Gardini A. Targeted Enhancer Activation by a Subunit of the Integrator Complex. Mol Cell 2018; 71:103-116.e7. [PMID: 30008316 DOI: 10.1016/j.molcel.2018.05.031] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 04/11/2018] [Accepted: 05/24/2018] [Indexed: 01/12/2023]
Abstract
The control of cell fate is an epigenetic process initiated by transcription factors (TFs) that recognize DNA motifs and recruit activator complexes and transcriptional machineries to chromatin. Lineage specificity is thought to be provided solely by TF-motif pairing, while the recruited activators are passive. Here, we show that INTS13, a subunit of the Integrator complex, operates as monocytic/macrophagic differentiation factor. Integrator is a general activator of transcription at coding genes and is required for eRNA maturation. Here, we show that INTS13 functions as an independent sub-module and targets enhancers through Early Growth Response (EGR1/2) TFs and their co-factor NAB2. INTS13 binds poised monocytic enhancers eliciting chromatin looping and activation. Independent depletion of INTS13, EGR1, or NAB2 impairs monocytic differentiation of cell lines and primary human progenitors. Our data demonstrate that Integrator is not functionally homogeneous and has TF-specific regulatory potential, revealing a new enhancer regulatory axis that controls myeloid differentiation.
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Affiliation(s)
- Elisa Barbieri
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Marco Trizzino
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Sarah Ann Welsh
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Tori Alexandra Owens
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Bruno Calabretta
- Sidney Kimmel Cancer Center, Thomas Jefferson Medical School, Philadelphia, PA, USA
| | - Martin Carroll
- Division of Hematology and Oncology, University of Pennsylvania, Philadelphia, PA, USA
| | - Kavitha Sarma
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Alessandro Gardini
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA.
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Hidden genomic MHC disparity between HLA-matched sibling pairs in hematopoietic stem cell transplantation. Sci Rep 2018; 8:5396. [PMID: 29599509 PMCID: PMC5876349 DOI: 10.1038/s41598-018-23682-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 03/16/2018] [Indexed: 12/30/2022] Open
Abstract
Matching classical HLA alleles between donor and recipient is an important factor in avoiding adverse immunological effects in HSCT. Siblings with no differences in HLA alleles, either due to identical-by-state or identical-by-descent status, are considered to be optimal donors. We carried out a retrospective genomic sequence and SNP analysis of 336 fully HLA-A, -B, -DRB1 matched and 14 partially HLA-matched sibling HSCT pairs to determine the level of undetected mismatching within the MHC segment as well as to map their recombination sites. The genomic sequence of 34 genes locating in the MHC region revealed allelic mismatching at 1 to 8 additional genes in partially HLA-matched pairs. Also, fully matched pairs were found to have mismatching either at HLA-DPB1 or at non-HLA region within the MHC segment. Altogether, 3.9% of fully HLA-matched HSCT pairs had large genomic mismatching in the MHC segment. Recombination sites mapped to certain restricted locations. The number of mismatched nucleotides correlated with the risk of GvHD supporting the central role of full HLA matching in HSCT. High-density genome analysis revealed that fully HLA-matched siblings may not have identical MHC segments and even single allelic mismatching at any classical HLA gene often implies larger genomic differences along MHC.
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22
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Liu DJ, Peloso GM, Yu H, Butterworth AS, Wang X, Mahajan A, Saleheen D, Emdin C, Alam D, Alves AC, Amouyel P, di Angelantonio E, Arveiler D, Assimes TL, Auer PL, Baber U, Ballantyne CM, Bang LE, Benn M, Bis JC, Boehnke M, Boerwinkle E, Bork-Jensen J, Bottinger EP, Brandslund I, Brown M, Busonero F, Caulfield MJ, Chambers JC, Chasman DI, Chen YE, Chen YDI, Chowdhury R, Christensen C, Chu AY, Connell JM, Cucca F, Cupples LA, Damrauer SM, Davies G, Deary IJ, Dedoussis G, Denny JC, Dominiczak A, Dubé MP, Ebeling T, Eiriksdottir G, Esko T, Farmaki AE, Feitosa MF, Ferrario M, Ferrieres J, Ford I, Fornage M, Franks PW, Frayling TM, Frikke-Schmidt R, Fritsche L, Frossard P, Fuster V, Ganesh SK, Gao W, Garcia ME, Gieger C, Giulianini F, Goodarzi MO, Grallert H, Grarup N, Groop L, Grove ML, Gudnason V, Hansen T, Harris TB, Hayward C, Hirschhorn JN, Holmen OL, Huffman J, Huo Y, Hveem K, Jabeen S, Jackson AU, Jakobsdottir J, Jarvelin MR, Jensen GB, Jørgensen ME, Jukema JW, Justesen JM, Kamstrup PR, Kanoni S, Karpe F, Kee F, Khera AV, Klarin D, Koistinen HA, Kooner JS, Kooperberg C, Kuulasmaa K, Kuusisto J, Laakso M, Lakka T, Langenberg C, Langsted A, Launer LJ, Lauritzen T, Liewald DCM, Lin LA, Linneberg A, Loos RJ, Lu Y, Lu X, Mägi R, Malarstig A, Manichaikul A, Manning AK, Mäntyselkä P, Marouli E, Masca NGD, Maschio A, Meigs JB, Melander O, Metspalu A, Morris AP, Morrison AC, Mulas A, Müller-Nurasyid M, Munroe PB, Neville MJ, Nielsen JB, Nielsen SF, Nordestgaard BG, Ordovas JM, Mehran R, O’Donnell CJ, Orho-Melander M, Molony CM, Muntendam P, Padmanabhan S, Palmer CNA, Pasko D, Patel AP, Pedersen O, Perola M, Peters A, Pisinger C, Pistis G, Polasek O, Poulter N, Psaty BM, Rader DJ, Rasheed A, Rauramaa R, Reilly D, Reiner AP, Renström F, Rich SS, Ridker PM, Rioux JD, Robertson NR, Roden DM, Rotter JI, Rudan I, Salomaa V, Samani NJ, Sanna S, Sattar N, Schmidt EM, Scott RA, Sever P, Sevilla RS, Shaffer CM, Sim X, Sivapalaratnam S, Small KS, Smith AV, Smith BH, Somayajula S, Southam L, Spector TD, Speliotes EK, Starr JM, Stirrups KE, Stitziel N, Strauch K, Stringham HM, Surendran P, Tada H, Tall AR, Tang H, Tardif JC, Taylor KD, Trompet S, Tsao PS, Tuomilehto J, Tybjaerg-Hansen A, van Zuydam NR, Varbo A, Varga TV, Virtamo J, Waldenberger M, Wang N, Wareham NJ, Warren HR, Weeke PE, Weinstock J, Wessel J, Wilson JG, Wilson PWF, Xu M, Yaghootkar H, Young R, Zeggini E, Zhang H, Zheng NS, Zhang W, Zhang Y, Zhou W, Zhou Y, Zoledziewska M, Howson JMM, Danesh J, McCarthy MI, Cowan C, Abecasis G, Deloukas P, Musunuru K, Willer CJ, Kathiresan S. Exome-wide association study of plasma lipids in >300,000 individuals. Nat Genet 2017; 49:1758-1766. [PMID: 29083408 PMCID: PMC5709146 DOI: 10.1038/ng.3977] [Citation(s) in RCA: 406] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 09/26/2017] [Indexed: 02/02/2023]
Abstract
We screened variants on an exome-focused genotyping array in >300,000 participants (replication in >280,000 participants) and identified 444 independent variants in 250 loci significantly associated with total cholesterol (TC), high-density-lipoprotein cholesterol (HDL-C), low-density-lipoprotein cholesterol (LDL-C), and/or triglycerides (TG). At two loci (JAK2 and A1CF), experimental analysis in mice showed lipid changes consistent with the human data. We also found that: (i) beta-thalassemia trait carriers displayed lower TC and were protected from coronary artery disease (CAD); (ii) excluding the CETP locus, there was not a predictable relationship between plasma HDL-C and risk for age-related macular degeneration; (iii) only some mechanisms of lowering LDL-C appeared to increase risk for type 2 diabetes (T2D); and (iv) TG-lowering alleles involved in hepatic production of TG-rich lipoproteins (TM6SF2 and PNPLA3) tracked with higher liver fat, higher risk for T2D, and lower risk for CAD, whereas TG-lowering alleles involved in peripheral lipolysis (LPL and ANGPTL4) had no effect on liver fat but decreased risks for both T2D and CAD.
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Affiliation(s)
- Dajiang J. Liu
- Department of Public Health Sciences, Institute of Personalized Medicine, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Gina M. Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Haojie Yu
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, USA
| | - Adam S. Butterworth
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics at the University of Cambridge, Cambridge, UK
| | - Xiao Wang
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Danish Saleheen
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, USA
- Center for Non-Communicable Diseases, Karachi, Pakistan
| | - Connor Emdin
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | | | - Philippe Amouyel
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk factors and molecular determinants of aging-related diseases, Lille, France
| | - Emanuele di Angelantonio
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics at the University of Cambridge, Cambridge, UK
| | - Dominique Arveiler
- Department of Epidemiology and Public Health, EA 3430, University of Strasbourg, Strasbourg, France
| | - Themistocles L. Assimes
- VA Palo Alto Health Care System, Palo Alto, California, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Paul L. Auer
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Usman Baber
- Cardiovascular Institute, Mount Sinai Medical Center, Icahn School of Medicine, Mount Sinai, New York, New York, USA
| | | | - Lia E. Bang
- Department of Cardiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Marianne Benn
- Department of Clinical Biochemistry and The Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark
- Faculty of Health and Medical Sciences, University of Denmark, Denmark
| | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Michael Boehnke
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Jette Bork-Jensen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Erwin P. Bottinger
- The Charles Bronfman Institute for Personalized Medicine, Ichan School of Medicine at Mount Sinai, New York, New York, USA
| | - Ivan Brandslund
- Department of Clinical Biochemistry, Lillebaelt Hospital, Vejle, Denmark
- Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Morris Brown
- Clinical Pharmacology Unit, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
| | - Fabio Busonero
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Mark J Caulfield
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London, Queen Mary University of London, Charterhouse Square, London, UK
- The Barts Heart Centre, William Harvey Research Institute, Queen Mary University of London, Charterhouse Square, London, UK
| | - John C Chambers
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, Norfolk Place, London, UK
- Department of Cardiology, Ealing Hospital NHS Trust, Uxbridge Road, Southall, Middlesex, UK
- Imperial College Healthcare NHS Trust, London, UK
| | - Daniel I. Chasman
- Division of Preventive Medicine, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Y. Eugene Chen
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Departments of Pediatrics and Medicine, Los Angeles, California, USA
| | - Rajiv Chowdhury
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - Audrey Y. Chu
- Division of Preventive Medicine, Boston, Massachusetts, USA
- NHLBI Framingham Heart Study, Framingham, Massachusetts, USA
| | - John M Connell
- Medical Research Institute, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
- Dipartimento di Scienze Biomediche, Universita’ degli Studi di Sassari, Sassari, Italy
| | - L. Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
- NHLBI Framingham Heart Study, Framingham, Massachusetts, USA
| | - Scott M. Damrauer
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania, USA
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gail Davies
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece
| | - Joshua C. Denny
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Anna Dominiczak
- British Heart Foundation Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Marie-Pierre Dubé
- Montreal Heart Institute, Montreal, Quebec, Canada
- Université de Montréal Beaulieu-Saucier Pharmacogenomics Center, Montreal, Quebec, Canada
- Université de Montréal, Montreal, Quebec, Canada
| | - Tapani Ebeling
- Department of Medicine, Oulu University Hospital and University of Oulu, Oulu, Finland
| | | | - Tõnu Esko
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Aliki-Eleni Farmaki
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece
| | - Mary F Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Marco Ferrario
- Research Centre in Epidemiology and Preventive Medicine – EPIMED, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Jean Ferrieres
- Department of Epidemiology, UMR 1027- INSERM, Toulouse University-CHU Toulouse, Toulouse, France
| | - Ian Ford
- University of Glasgow, Glasgow, UK
| | - Myriam Fornage
- Institute of Molecular Medicine, the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Paul W. Franks
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University, Malmö, Sweden
- Department of Public Health & Clinical Medicine, Umeå University, Umeå, Sweden
- Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Timothy M. Frayling
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Ruth Frikke-Schmidt
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars Fritsche
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | | | - Valentin Fuster
- Cardiovascular Institute, Mount Sinai Medical Center, Icahn School of Medicine, Mount Sinai, New York, New York, USA
| | - Santhi K. Ganesh
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Wei Gao
- Department of Cardiology, Peking University Third Hospital, Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides, Ministry of Health, Beijing, China
| | | | - Christian Gieger
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | | | - Mark O. Goodarzi
- Department of Medicine and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Division of Endocrinology, Diabetes and Metabolism, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Harald Grallert
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Niels Grarup
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Leif Groop
- Department of Clinical Sciences, Diabetes and Endocrinology, Clinical Research Centre, Lund University, Malmö, Sweden
| | - Megan L. Grove
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Vilmundur Gudnason
- The Icelandic Heart Association, Kopavogur, Iceland
- The University of Iceland, Reykjavik, Iceland
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Tamara B. Harris
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Bethesda, Maryland, USA
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Joel N. Hirschhorn
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
- Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children’s Hospital, Boston, MA, USA
| | - Oddgeir L. Holmen
- Department of Public Health and General Practice, HUNT Research Centre, Norwegian University of Science and Technology, Levanger, Norway
- St Olav Hospital, Trondheim University Hospital, 7030 Trondheim, Norway
| | - Jennifer Huffman
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Yong Huo
- Department of Cardiology, Peking University First Hospital, Beijing, China
| | - Kristian Hveem
- K. G. Jebsen Center for Genetic Epidemiology, Dept of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | | | - Anne U Jackson
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Johanna Jakobsdottir
- The Icelandic Heart Association, Kopavogur, Iceland
- The University of Iceland, Reykjavik, Iceland
| | | | - Gorm B Jensen
- The Copenhagen City Heart Study, Frederiksberg Hospital, Denmark
| | - Marit E. Jørgensen
- Steno Diabetes Center, Gentofte, Denmark
- National Institute of Public Health, Southern Denmark University, Denmark
| | - J. Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
- The Interuniversity Cardiology Institute of the Netherlands, Utrecht, The Netherlands
| | - Johanne M. Justesen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pia R. Kamstrup
- Department of Clinical Biochemistry and The Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark
| | - Stavroula Kanoni
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Fredrik Karpe
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, UK
| | - Frank Kee
- Director, UKCRC Centre of Excellence for Public Health, Queens University, Belfast, Northern Ireland
| | - Amit V. Khera
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Derek Klarin
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA
| | - Heikki A. Koistinen
- Department of Health, National Institute for Health and Welfare, Helsinki, Finland
- University of Helsinki; and Department of Medicine, and Abdominal Center: Endocrinology, Helsinki University Central Hospital, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital NHS Trust, Uxbridge Road, Southall, Middlesex, UK
- Imperial College Healthcare NHS Trust, London, UK
- National Heart and Lung Institute, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Kari Kuulasmaa
- Department of Health, National Institute for Health and Welfare, Helsinki, Finland
| | - Johanna Kuusisto
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Timo Lakka
- Department of Physiology, Institute of Biomedicine, University of Eastern Finland, Kuopio Campus, Kuopio, Finland
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Anne Langsted
- Department of Clinical Biochemistry and The Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark
- Faculty of Health and Medical Sciences, University of Denmark, Denmark
| | - Lenore J. Launer
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Bethesda, Maryland, USA
| | - Torsten Lauritzen
- Department of Public Health, Section of General Practice, University of Aarhus, Aarhus, Denmark
| | - David CM Liewald
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Li An Lin
- Institute of Molecular Medicine, the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Allan Linneberg
- Department of Clinical Experimental Research, Rigshospitalet, Glostrup, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Research Center for Prevention and Health, Capital Region of Denmark, Copenhagen, Denmark
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Ichan School of Medicine at Mount Sinai, New York, New York, USA
- The Mindich Child Health and Development Institute, Ichan School of Medicine at Mount Sinai, New York, New York, USA
| | - Yingchang Lu
- The Charles Bronfman Institute for Personalized Medicine, Ichan School of Medicine at Mount Sinai, New York, New York, USA
| | - Xiangfeng Lu
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, Michigan, USA
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Anders Malarstig
- Cardiovascular Genetics and Genomics Group, Cardiovascular Medicine Unit, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
- Pharmatherapeutics Clinical Research, Pfizer Worldwide R&D, Sollentuna, Sweden
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Alisa K. Manning
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Pekka Mäntyselkä
- Unit of Primary Health Care, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Eirini Marouli
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Nicholas GD Masca
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester UK
| | - Andrea Maschio
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - James B. Meigs
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Olle Melander
- Department of Clinical Sciences, University Hospital Malmo Clinical Research Center, Lund University, Malmo, Sweden
| | | | - Andrew P Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Alanna C. Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Antonella Mulas
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Martina Müller-Nurasyid
- Department of Medicine I, Ludwig-Maximilians-University, Munich, Germany
- DZHK German Centre for Cardiovascular Research, partner site Munich Heart Alliance, Munich, Germany
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Germany
| | - Patricia B. Munroe
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London, Queen Mary University of London, Charterhouse Square, London, UK
- NIHR Barts Cardiovascular Biomedical Research Unit, Queen Mary University of London, London, UK
| | - Matt J Neville
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jonas B. Nielsen
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Sune F Nielsen
- Department of Clinical Biochemistry and The Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark
- Faculty of Health and Medical Sciences, University of Denmark, Denmark
| | - Børge G Nordestgaard
- Department of Clinical Biochemistry and The Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark
- Faculty of Health and Medical Sciences, University of Denmark, Denmark
| | - Jose M. Ordovas
- Department of Cardiovascular Epidemiology and Population Genetics, National Center for Cardiovascular Investigation, Madrid, Spain
- IMDEA-Alimentacion, Madrid, Spain
- Nutrition and Genomics Laboratory, Jean Mayer-USDA Human Nutrition Research Center on Aging at Tufts University, Boston, Massachusetts, USA
| | - Roxana Mehran
- Cardiovascular Institute, Mount Sinai Medical Center, Icahn School of Medicine, Mount Sinai, New York, New York, USA
| | - Christoper J. O’Donnell
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Marju Orho-Melander
- Department of Clinical Sciences, University Hospital Malmo Clinical Research Center, Lund University, Malmo, Sweden
| | - Cliona M. Molony
- Genetics, Merck Sharp & Dohme Corp., Kenilworth, New Jersey, USA
| | | | - Sandosh Padmanabhan
- British Heart Foundation Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Colin NA Palmer
- Medical Research Institute, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Dorota Pasko
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Aniruddh P. Patel
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Markus Perola
- Department of Health, National Institute for Health and Welfare, Helsinki, Finland
- Institute of Molecular Medicine FIMM, University of Helsinki, Finland
| | - Annette Peters
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- DZHK German Centre for Cardiovascular Research, partner site Munich Heart Alliance, Munich, Germany
| | - Charlotta Pisinger
- Research Center for Prevention and Health, Capital Region of Denmark, Copenhagen, Denmark
| | - Giorgio Pistis
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Ozren Polasek
- Faculty of Medicine, University of Split, Split, Croatia
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Neil Poulter
- International Centre for Circulatory Health, Imperial College London, UK
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, Washington, USA
- Departments of Epidemiology and Health Services, University of Washington, Seattle, Washington, USA
| | - Daniel J. Rader
- Departments of Genetics, Medicine, and Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Asif Rasheed
- Center for Non-Communicable Diseases, Karachi, Pakistan
| | - Rainer Rauramaa
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Dermot Reilly
- Genetics, Merck Sharp & Dohme Corp., Kenilworth, New Jersey, USA
| | - Alex P. Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Frida Renström
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University, Malmö, Sweden
- Department of Biobank Research, Umeå University, Umeå, Sweden
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Paul M Ridker
- Division of Preventive Medicine, Boston, Massachusetts, USA
| | | | - Neil R Robertson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Dan M. Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Departments of Pediatrics and Medicine, Los Angeles, California, USA
| | - Igor Rudan
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Veikko Salomaa
- Department of Health, National Institute for Health and Welfare, Helsinki, Finland
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester UK
| | - Serena Sanna
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Naveed Sattar
- British Heart Foundation Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Ellen M. Schmidt
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Robert A. Scott
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Peter Sever
- International Centre for Circulatory Health, Imperial College London, UK
| | | | - Christian M. Shaffer
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Xueling Sim
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, 117549, Singapore
| | - Suthesh Sivapalaratnam
- Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, NL
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Albert V. Smith
- The Icelandic Heart Association, Kopavogur, Iceland
- The University of Iceland, Reykjavik, Iceland
| | - Blair H Smith
- Division of Population Health Sciences, Ninewells Hospital and Medical School, University of Dundee, Dundee, Scotland
- Generation Scotland, Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, UK
| | | | - Lorraine Southam
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, UK
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Elizabeth K. Speliotes
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, Michigan, USA
| | - John M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, UK
| | - Kathleen E Stirrups
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Nathan Stitziel
- Cardiovascular Division, Departments of Medicine and Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Heather M Stringham
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Praveen Surendran
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Hayato Tada
- Division of Cardiovascular Medicine, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Alan R. Tall
- Division of Molecular Medicine, Department of Medicine, Columbia University, New York, New York, USA
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Jean-Claude Tardif
- Montreal Heart Institute, Montreal, Quebec, Canada
- Université de Montréal, Montreal, Quebec, Canada
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Departments of Pediatrics and Medicine, Los Angeles, California, USA
| | - Stella Trompet
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Philip S. Tsao
- VA Palo Alto Health Care System, Palo Alto, California, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Jaakko Tuomilehto
- Chronic Disease Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland
- Dasman Diabetes Institute, Dasman, Kuwait
- Centre for Vascular Prevention, Danube-University Krems, Krems, Austria
- Saudi Diabetes Research Group, King Abdulaziz University, Fahd Medical Research Center, Jeddah, Saudi Arabia
| | - Anne Tybjaerg-Hansen
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Natalie R van Zuydam
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Medical Research Institute, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Anette Varbo
- Department of Clinical Biochemistry and The Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark
- Faculty of Health and Medical Sciences, University of Denmark, Denmark
| | - Tibor V Varga
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University, Malmö, Sweden
| | - Jarmo Virtamo
- Department of Health, National Institute for Health and Welfare, Helsinki, Finland
| | - Melanie Waldenberger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Nan Wang
- Division of Molecular Medicine, Department of Medicine, Columbia University, New York, New York, USA
| | - Nick J. Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Helen R Warren
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London, Queen Mary University of London, Charterhouse Square, London, UK
- NIHR Barts Cardiovascular Biomedical Research Unit, Queen Mary University of London, London, UK
| | - Peter E. Weeke
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- The Heart Centre, Department of Cardiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Joshua Weinstock
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Jennifer Wessel
- Department of Epidemiology, Indiana University Fairbanks School of Public Health, Indianapolis, Indiana, USA
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - James G. Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Peter W. F. Wilson
- Atlanta VA Medical Center, Decatur, Georgia, USA
- Emory Clinical Cardiovascular Research Institute, Atlanta, Georgia, USA
| | - Ming Xu
- Department of Cardiology, Institute of Vascular Medicine, Peking University Third Hospital, Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, Beijing, China
| | - Hanieh Yaghootkar
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Robin Young
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - He Zhang
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Weihua Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, Norfolk Place, London, UK
| | - Yan Zhang
- Department of Cardiology, Peking University First Hospital, Beijing, China
| | - Wei Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Yanhua Zhou
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Magdalena Zoledziewska
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | | | - Joanna MM Howson
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - John Danesh
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics at the University of Cambridge, Cambridge, UK
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, UK
| | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, UK
| | - Chad Cowan
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Goncalo Abecasis
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Panos Deloukas
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Kiran Musunuru
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Cristen J. Willer
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Sekar Kathiresan
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA
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23
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Grinde KE, Arbet J, Green A, O'Connell M, Valcarcel A, Westra J, Tintle N. Illustrating, Quantifying, and Correcting for Bias in Post-hoc Analysis of Gene-Based Rare Variant Tests of Association. Front Genet 2017; 8:117. [PMID: 28959274 PMCID: PMC5603735 DOI: 10.3389/fgene.2017.00117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 08/25/2017] [Indexed: 11/13/2022] Open
Abstract
To date, gene-based rare variant testing approaches have focused on aggregating information across sets of variants to maximize statistical power in identifying genes showing significant association with diseases. Beyond identifying genes that are associated with diseases, the identification of causal variant(s) in those genes and estimation of their effect is crucial for planning replication studies and characterizing the genetic architecture of the locus. However, we illustrate that straightforward single-marker association statistics can suffer from substantial bias introduced by conditioning on gene-based test significance, due to the phenomenon often referred to as "winner's curse." We illustrate the ramifications of this bias on variant effect size estimation and variant prioritization/ranking approaches, outline parameters of genetic architecture that affect this bias, and propose a bootstrap resampling method to correct for this bias. We find that our correction method significantly reduces the bias due to winner's curse (average two-fold decrease in bias, p < 2.2 × 10-6) and, consequently, substantially improves mean squared error and variant prioritization/ranking. The method is particularly helpful in adjustment for winner's curse effects when the initial gene-based test has low power and for relatively more common, non-causal variants. Adjustment for winner's curse is recommended for all post-hoc estimation and ranking of variants after a gene-based test. Further work is necessary to continue seeking ways to reduce bias and improve inference in post-hoc analysis of gene-based tests under a wide variety of genetic architectures.
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Affiliation(s)
- Kelsey E Grinde
- Department of Biostatistics, University of WashingtonSeattle, WA, United States
| | - Jaron Arbet
- Department of Biostatistics, University of MinnesotaMinneapolis, MN, United States
| | - Alden Green
- Department of Statistics, Carnegie Mellon UniversityPittsburgh, PA, United States
| | - Michael O'Connell
- Department of Biostatistics, University of MinnesotaMinneapolis, MN, United States
| | - Alessandra Valcarcel
- Department of Biostatistics and Epidemiology, University of PennsylvaniaPhiladelphia, PA, United States
| | - Jason Westra
- Department of Statistics, Iowa State UniversityAmes, IA, United States.,Department of Mathematics, Statistics, and Computer Science, Dordt CollegeSioux Center, IA, United States
| | - Nathan Tintle
- Department of Mathematics, Statistics, and Computer Science, Dordt CollegeSioux Center, IA, United States
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24
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Zhan X, Hu Y, Li B, Abecasis GR, Liu DJ. RVTESTS: an efficient and comprehensive tool for rare variant association analysis using sequence data. Bioinformatics 2016; 32:1423-6. [PMID: 27153000 PMCID: PMC4848408 DOI: 10.1093/bioinformatics/btw079] [Citation(s) in RCA: 274] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 12/16/2015] [Accepted: 02/05/2016] [Indexed: 12/18/2022] Open
Abstract
MOTIVATION Next-generation sequencing technologies have enabled the large-scale assessment of the impact of rare and low-frequency genetic variants for complex human diseases. Gene-level association tests are often performed to analyze rare variants, where multiple rare variants in a gene region are analyzed jointly. Applying gene-level association tests to analyze sequence data often requires integrating multiple heterogeneous sources of information (e.g. annotations, functional prediction scores, allele frequencies, genotypes and phenotypes) to determine the optimal analysis unit and prioritize causal variants. Given the complexity and scale of current sequence datasets and bioinformatics databases, there is a compelling need for more efficient software tools to facilitate these analyses. To answer this challenge, we developed RVTESTS, which implements a broad set of rare variant association statistics and supports the analysis of autosomal and X-linked variants for both unrelated and related individuals. RVTESTS also provides useful companion features for annotating sequence variants, integrating bioinformatics databases, performing data quality control and sample selection. We illustrate the advantages of RVTESTS in functionality and efficiency using the 1000 Genomes Project data. AVAILABILITY AND IMPLEMENTATION RVTESTS is available on Linux, MacOS and Windows. Source code and executable files can be obtained at https://github.com/zhanxw/rvtests CONTACT zhanxw@gmail.com; goncalo@umich.edu; dajiang.liu@outlook.com SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xiaowei Zhan
- Department of Clinical Science, Quantitative Biomedical Research Center, Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Youna Hu
- A9.Com Inc, Palo Alto, CA 94301, USA
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37240, USA
| | - Goncalo R Abecasis
- Center of Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dajiang J Liu
- Division of Biostatistics and Bioinformatics, Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA 17033, USA and Institute for Personalized Medicine, Penn State College of Medicine, Hershey, PA 17033, USA
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25
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Belonogova NM, Svishcheva GR, Axenovich TI. FREGAT: an R package for region-based association analysis. ACTA ACUST UNITED AC 2016; 32:2392-3. [PMID: 27153598 DOI: 10.1093/bioinformatics/btw160] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 03/20/2016] [Indexed: 11/14/2022]
Abstract
UNLABELLED Several approaches to the region-based association analysis of quantitative traits have recently been developed and successively applied. However, no software package has been developed that implements all of these approaches for either independent or structured samples. Here we introduce FREGAT (Family REGional Association Tests), an R package that can handle family and population samples and implements a wide range of region-based association methods including burden tests, functional linear models, and kernel machine-based regression. FREGAT can be used in genome/exome-wide region-based association studies of quantitative traits and candidate gene analysis. FREGAT offers many useful options to empower its users and increase the effectiveness and applicability of region-based association analysis. AVAILABILITY AND IMPLEMENTATION https://cran.r-project.org/web/packages/FREGAT/index.html SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics Online. CONTACT belon@bionet.nsc.ru.
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Affiliation(s)
- Nadezhda M Belonogova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk
| | - Gulnara R Svishcheva
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk Vavilov Institute of General Genetics, the Russian Academy of Sciences, Moscow, Russia
| | - Tatiana I Axenovich
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk Novosibirsk State University, Novosibirsk, Russia
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