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Gagnon D, Barry H, Barhdadi A, Oussaid E, Mongrain I, Lemieux Perreault LP, Dubé MP. A dataset of proteomic changes during human heat stress and heat acclimation. Sci Data 2023; 10:877. [PMID: 38062080 PMCID: PMC10703874 DOI: 10.1038/s41597-023-02809-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
Hotter climates have important impacts on human health and performance. Yet, the cellular and molecular responses involved in human heat stress and acclimation remain understudied. This dataset includes physiological measurements and the plasma concentration of 2,938 proteins collected from 10 healthy adults, before and during passive heat stress that was performed both prior to and after a 7-day heat acclimation protocol. Physiological measurements included body temperatures, sweat rate, cutaneous vascular conductance, blood pressure, and skin sympathetic nerve activity. The proteomic dataset was generated using the Olink Explore 3072 assay, enabling a high-multiplex antibody-based assessment of protein changes based on proximity extension assay technology. The data need to be interpreted in the context of the moderate level of body hyperthermia attained and the specific demographic of young, healthy adults. We have made this dataset publicly available to facilitate research into the cellular and molecular mechanisms involved in human heat stress and acclimation, crucial for addressing the health and performance challenges posed by rising temperatures.
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Affiliation(s)
- Daniel Gagnon
- Montreal Heart Institute, Montreal, QC, Canada.
- School of Kinesiology and Exercise Science, Université de Montréal, Montreal, QC, Canada.
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada.
| | - Hadiatou Barry
- Montreal Heart Institute, Montreal, QC, Canada
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada
| | - Amina Barhdadi
- Montreal Heart Institute, Montreal, QC, Canada
- Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, QC, Canada
| | - Essaid Oussaid
- Montreal Heart Institute, Montreal, QC, Canada
- Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, QC, Canada
| | - Ian Mongrain
- Montreal Heart Institute, Montreal, QC, Canada
- Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, QC, Canada
| | - Louis-Philippe Lemieux Perreault
- Montreal Heart Institute, Montreal, QC, Canada
- Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, QC, Canada
| | - Marie-Pierre Dubé
- Montreal Heart Institute, Montreal, QC, Canada.
- Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, QC, Canada.
- Department of Medicine and Department of Social and Preventive Medicine, Université de Montréal, Montreal, QC, Canada.
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2
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Laverdière J, Meloche M, Provost S, Leclair G, Oussaïd E, Jutras M, Perreault LPL, Valois D, Mongrain I, Busseuil D, Rouleau JL, Tardif JC, Dubé MP, Denus SD. Pharmacogenomic markers of metoprolol and α-OH-metoprolol concentrations: a genome-wide association study. Pharmacogenomics 2023; 24:441-448. [PMID: 37307170 DOI: 10.2217/pgs-2023-0067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023] Open
Abstract
Aim: Few genome-wide association studies (GWASs) have been conducted to identify predictors of drug concentrations. The authors therefore sought to discover the pharmacogenomic markers involved in metoprolol pharmacokinetics. Patients & methods: The authors performed a GWAS of a cross-sectional study of 993 patients from the Montreal Heart Institute Biobank taking metoprolol. Results: A total of 391 and 444 SNPs reached the significance threshold of 5 × 10-8 for metoprolol and α-OH-metoprolol concentrations, respectively. All were located on chromosome 22 at or near the CYP2D6 gene, encoding CYP450 2D6, metoprolol's main metabolizing enzyme. Conclusion: The results reinforce previous findings of the importance of the CYP2D6 locus for metoprolol concentrations and confirm that large biobanks can be used to identify genetic determinants of drug pharmacokinetics at a GWAS significance level.
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Affiliation(s)
- Jean Laverdière
- Faculty of Pharmacy, Université de Montréal, H3T 1J4, Montreal, Quebec, Canada
- Montreal Heart Institute, H1T 1C8, Montreal, Quebec, Canada
- Université de Montreal Beaulieu-Saucier Pharmacogenomics Centre, H1T 1C8, Montreal, Quebec, Canada
| | - Maxime Meloche
- Faculty of Pharmacy, Université de Montréal, H3T 1J4, Montreal, Quebec, Canada
- Montreal Heart Institute, H1T 1C8, Montreal, Quebec, Canada
- Université de Montreal Beaulieu-Saucier Pharmacogenomics Centre, H1T 1C8, Montreal, Quebec, Canada
| | - Sylvie Provost
- Montreal Heart Institute, H1T 1C8, Montreal, Quebec, Canada
- Université de Montreal Beaulieu-Saucier Pharmacogenomics Centre, H1T 1C8, Montreal, Quebec, Canada
| | - Grégoire Leclair
- Faculty of Pharmacy, Université de Montréal, H3T 1J4, Montreal, Quebec, Canada
| | - Essaïd Oussaïd
- Montreal Heart Institute, H1T 1C8, Montreal, Quebec, Canada
- Université de Montreal Beaulieu-Saucier Pharmacogenomics Centre, H1T 1C8, Montreal, Quebec, Canada
| | - Martin Jutras
- Faculty of Pharmacy, Université de Montréal, H3T 1J4, Montreal, Quebec, Canada
| | - Louis-Philippe Lemieux Perreault
- Montreal Heart Institute, H1T 1C8, Montreal, Quebec, Canada
- Université de Montreal Beaulieu-Saucier Pharmacogenomics Centre, H1T 1C8, Montreal, Quebec, Canada
| | - Diane Valois
- Montreal Heart Institute, H1T 1C8, Montreal, Quebec, Canada
- Université de Montreal Beaulieu-Saucier Pharmacogenomics Centre, H1T 1C8, Montreal, Quebec, Canada
| | - Ian Mongrain
- Montreal Heart Institute, H1T 1C8, Montreal, Quebec, Canada
- Université de Montreal Beaulieu-Saucier Pharmacogenomics Centre, H1T 1C8, Montreal, Quebec, Canada
| | - David Busseuil
- Montreal Heart Institute, H1T 1C8, Montreal, Quebec, Canada
- Université de Montreal Beaulieu-Saucier Pharmacogenomics Centre, H1T 1C8, Montreal, Quebec, Canada
| | - Jean Lucien Rouleau
- Montreal Heart Institute, H1T 1C8, Montreal, Quebec, Canada
- Faculty of Medicine, Université de Montréal, H3T 1J4, Montreal, Quebec, Canada
| | - Jean-Claude Tardif
- Montreal Heart Institute, H1T 1C8, Montreal, Quebec, Canada
- Université de Montreal Beaulieu-Saucier Pharmacogenomics Centre, H1T 1C8, Montreal, Quebec, Canada
- Faculty of Medicine, Université de Montréal, H3T 1J4, Montreal, Quebec, Canada
| | - Marie-Pierre Dubé
- Montreal Heart Institute, H1T 1C8, Montreal, Quebec, Canada
- Université de Montreal Beaulieu-Saucier Pharmacogenomics Centre, H1T 1C8, Montreal, Quebec, Canada
- Faculty of Medicine, Université de Montréal, H3T 1J4, Montreal, Quebec, Canada
| | - Simon de Denus
- Faculty of Pharmacy, Université de Montréal, H3T 1J4, Montreal, Quebec, Canada
- Montreal Heart Institute, H1T 1C8, Montreal, Quebec, Canada
- Université de Montreal Beaulieu-Saucier Pharmacogenomics Centre, H1T 1C8, Montreal, Quebec, Canada
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3
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Sun M, Cyr MC, Sandoval J, Lemieux Perreault LP, Busque L, Tardif JC, Dubé MP. Somatic mosaic chromosomal alterations and death of cardiovascular disease causes among cancer survivors. Cancer Epidemiol Biomarkers Prev 2023:719076. [PMID: 36976640 DOI: 10.1158/1055-9965.epi-22-1290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/16/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND Cancer survivors are at an increased risk of cardiovascular disease (CVD) compared to the general population. We sought to evaluate the impact of mosaic chromosomal alterations (mCAs) on death of CVD causes, coronary artery disease (CAD) causes, and of any cause in patients with a cancer diagnosis. METHODS The study was a prospective cohort analysis of 48,919 UK Biobank participants with a cancer diagnosis. mCAs were characterized using DNA genotyping array intensity data and long-range chromosomal phase inference. Multivariable Cox regression models were used to ascertain the associations of mCAs. Exploratory endpoints included various incident cardiovascular phenotypes. RESULTS Overall, 10,070 individuals (20.6%) carried ≥1 mCA clone. In adjusted analyses, mCA was associated with an increased risk of death of CAD causes (HR: 1.37, 95% CI: 1.09-1.71, P=0.006). In sub-analyses, we found that carriers of mCAs diagnosed with kidney cancer had an increased risk of death of CVD causes (HR: 2.03, 95% CI: 1.11-3.72, P=0.022) and CAD causes (HR: 3.57, 95% CI: 1.44-8.84, P=0.006). Women diagnosed with breast cancer who carried a mCA also had a higher risk of death of CAD causes (HR: 2.46, 95% CI: 1.23-4.92, P=0.011). CONCLUSIONS Among cancer survivors, carriers of any mCA are at an increased risk of CAD death compared to non-carriers. Mechanistic studies should be considered to better ascertain the biological mechanisms underneath the observed associations between mCAs and cardiovascular events for specific cancer types. IMPACT There may be clinical relevance in considering mCAs in patients diagnosed with cancer and undergoing treatment.
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Affiliation(s)
- Maxine Sun
- Montreal Heart Institute, Montreal, Canada
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4
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Legault MA, Barhdadi A, Gamache I, Lemaçon A, Lemieux Perreault LP, Grenier JC, Sylvestre MP, Hussin JG, Rhainds D, Tardif JC, Dubé MP. Study of effect modifiers of genetically predicted CETP reduction. Genet Epidemiol 2023; 47:198-212. [PMID: 36701426 DOI: 10.1002/gepi.22514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/11/2022] [Accepted: 01/11/2023] [Indexed: 01/27/2023]
Abstract
Genetic variants in drug targets can be used to predict the long-term, on-target effect of drugs. Here, we extend this principle to assess how sex and body mass index may modify the effect of genetically predicted lower CETP levels on biomarkers and cardiovascular outcomes. We found sex and body mass index (BMI) to be modifiers of the association between genetically predicted lower CETP and lipid biomarkers in UK Biobank participants. Female sex and lower BMI were associated with higher high-density lipoprotein cholesterol and lower low-density lipoprotein cholesterol for the same genetically predicted reduction in CETP concentration. We found that sex also modulated the effect of genetically lower CETP on cholesterol efflux capacity in samples from the Montreal Heart Institute Biobank. However, these modifying effects did not extend to sex differences in cardiovascular outcomes in our data. Our results provide insight into the clinical effects of CETP inhibitors in the presence of effect modification based on genetic data. The approach can support precision medicine applications and help assess the external validity of clinical trials.
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Affiliation(s)
- Marc-André Legault
- Montreal Heart Institute, Montreal, Quebec, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Quebec, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Amina Barhdadi
- Montreal Heart Institute, Montreal, Quebec, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Quebec, Canada
| | - Isabel Gamache
- Montreal Heart Institute, Montreal, Quebec, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Audrey Lemaçon
- Montreal Heart Institute, Montreal, Quebec, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Quebec, Canada
| | - Louis-Philippe Lemieux Perreault
- Montreal Heart Institute, Montreal, Quebec, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Quebec, Canada
| | | | - Marie-Pierre Sylvestre
- Research Centre of the University of Montreal Hospital Centre, Montreal, Quebec, Canada.,Department of Social and Preventive Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - Julie G Hussin
- Montreal Heart Institute, Montreal, Quebec, Canada.,Department of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | | | - Jean-Claude Tardif
- Montreal Heart Institute, Montreal, Quebec, Canada.,Department of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Marie-Pierre Dubé
- Montreal Heart Institute, Montreal, Quebec, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Quebec, Canada.,Department of Medicine, Université de Montréal, Montreal, Quebec, Canada
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5
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Peretz I, Ross J, Bourassa CV, Perreault LPL, Dion PA, Weiss MW, Felezeu M, Rouleau GA, Dubé MP. Do variants in the coding regions of FOXP2, a gene implicated in speech disorder, confer a risk for congenital amusia? Ann N Y Acad Sci 2022; 1517:279-285. [PMID: 35980667 DOI: 10.1111/nyas.14883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Congenital amusia is a lifelong disorder that compromises the normal development of musical abilities in 1.5-4% of the general population. There is a substantial genetic contribution to congenital amusia, and it bears similarities to neurodevelopmental disorders of language. Here, we examine the extent to which variants in the forkhead box P2 gene (FOXP2)-the first gene to be identified as causal in developmental speech deficits-are associated with the amusic trait. Using a cohort of 49 individuals with amusia, of which 27 were unrelated, the role of FOXP2 variants in amusia was evaluated. Fourteen variants were examined in the cohort. None segregated with the amusic trait among participants for whom family information was available; nor were they predicted to be deleterious to protein function. Thus, variants in FOXP2 are not likely to cause amusia. Implications for ongoing debates about the distinction between musicality and language are discussed.
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Affiliation(s)
- Isabelle Peretz
- Department of Psychology, University of Montreal, Montréal, Québec, Canada.,International Laboratory for Brain, Music, and Sound Research (BRAMS), Montréal, Québec, Canada
| | - Jay Ross
- Department of Human Genetics, McGill University, Montréal, Québec, Canada.,Montreal Neurological Institute and Hospital, McGill University, Montréal, Québec, Canada
| | - Cynthia V Bourassa
- Montreal Neurological Institute and Hospital, McGill University, Montréal, Québec, Canada.,Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital, McGill University, Montréal, Québec, Canada
| | | | - Patrick A Dion
- Montreal Neurological Institute and Hospital, McGill University, Montréal, Québec, Canada.,Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital, McGill University, Montréal, Québec, Canada
| | - Michael W Weiss
- Department of Psychology, University of Montreal, Montréal, Québec, Canada.,International Laboratory for Brain, Music, and Sound Research (BRAMS), Montréal, Québec, Canada
| | - Mihaela Felezeu
- Department of Psychology, University of Montreal, Montréal, Québec, Canada.,International Laboratory for Brain, Music, and Sound Research (BRAMS), Montréal, Québec, Canada
| | - Guy A Rouleau
- Department of Human Genetics, McGill University, Montréal, Québec, Canada.,Montreal Neurological Institute and Hospital, McGill University, Montréal, Québec, Canada.,Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital, McGill University, Montréal, Québec, Canada
| | - Marie-Pierre Dubé
- Montreal Neurological Institute and Hospital, McGill University, Montréal, Québec, Canada
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6
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Legault MA, Perreault LPL, Tardif JC, Dubé MP. ExPheWas: a platform for cis-Mendelian randomization and gene-based association scans. Nucleic Acids Res 2022; 50:W305-W311. [PMID: 35474380 PMCID: PMC9252780 DOI: 10.1093/nar/gkac289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/31/2022] [Accepted: 04/13/2022] [Indexed: 11/17/2022] Open
Abstract
Establishing the relationship between protein-coding genes and phenotypes has the potential to inform on the molecular etiology of diseases. Here, we describe ExPheWas (exphewas.ca), a gene-based phenome-wide association study browser and platform that enables the conduct of gene-based Mendelian randomization. The ExPheWas data repository includes sex-stratified and sex-combined gene-based association results from 26 616 genes with 1746 phenotypes measured in up to 413 133 individuals from the UK Biobank. Interactive visualizations are provided through a browser to facilitate data exploration supported by false discovery rate control, and it includes tools for enrichment analysis. The interactive Mendelian randomization module in ExPheWas allows the estimation of causal effects of a genetically predicted exposure on an outcome by using genetic variation in a single gene as the instrumental variable.
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Affiliation(s)
- Marc-André Legault
- Montreal Heart Institute, Montreal, QC H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, QC H1T 1C8, Canada.,Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Louis-Philippe Lemieux Perreault
- Montreal Heart Institute, Montreal, QC H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, QC H1T 1C8, Canada
| | - Jean-Claude Tardif
- Montreal Heart Institute, Montreal, QC H1T 1C8, Canada.,Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Marie-Pierre Dubé
- Montreal Heart Institute, Montreal, QC H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, QC H1T 1C8, Canada.,Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC H3T 1J4, Canada
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7
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Levinsson A, de Denus S, Sandoval J, Lemieux Perreault LP, Rouleau J, Tardif JC, Hussin J, Dubé MP. Construction of a femininity score in the UK Biobank and its association with angina diagnosis prior to myocardial infarction. Sci Rep 2022; 12:1780. [PMID: 35110607 PMCID: PMC8810762 DOI: 10.1038/s41598-022-05713-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 01/12/2022] [Indexed: 11/09/2022] Open
Abstract
Gender captures social components beyond biological sex and can add valuable insight to health studies in populations. However, assessment of gender typically relies on questionnaires which may not be available. The aim of this study is to construct a gender metric using available variables in the UK Biobank and to apply it to the study of angina diagnosis. Proxy variables for femininity characteristics were identified in the UK Biobank and regressed on sex to construct a composite femininity score (FS) validated using tenfold cross-validation. The FS was assessed as a predictor of angina diagnosis before incident myocardial infarction (MI) events. The FS was derived for 315,937 UK Biobank participants. In 3059 individuals with no history of MI at study entry who had an incident MI event, the FS was a significant predictor of angina diagnosis prior to MI (OR 1.24, 95% CI 1.10-1.39, P < 0.001) with a significant sex-by-FS interaction effect (P = 0.003). The FS was positively associated with angina diagnosis prior to MI in men (OR 1.37, 95% CI 1.19-1.57, P < 0.001), but not in women. We have provided a new tool to conduct gender-sensitive analyses in observational studies, and applied it to study of angina diagnosis prior to MI.
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Affiliation(s)
- Anna Levinsson
- Beaulieu-Saucier Université de Montréal Pharmacogenomics Centre, Montreal, QC, Canada.
- Montreal Heart Institute, Montreal, QC, Canada.
- Faculty of Medicine, Université de Montréal, Montreal, QC, Canada.
- Division of Social and Cultural Psychiatry, McGill University, Montreal, QC, Canada.
| | - Simon de Denus
- Beaulieu-Saucier Université de Montréal Pharmacogenomics Centre, Montreal, QC, Canada
- Montreal Heart Institute, Montreal, QC, Canada
- Faculty of Pharmacy, Université de Montréal, Montreal, QC, Canada
| | - Johanna Sandoval
- Beaulieu-Saucier Université de Montréal Pharmacogenomics Centre, Montreal, QC, Canada
- Montreal Heart Institute, Montreal, QC, Canada
| | - Louis-Philippe Lemieux Perreault
- Beaulieu-Saucier Université de Montréal Pharmacogenomics Centre, Montreal, QC, Canada
- Montreal Heart Institute, Montreal, QC, Canada
| | - Joëlle Rouleau
- Faculty of Arts and Sciences, Université de Montréal, Montreal, QC, Canada
| | - Jean-Claude Tardif
- Beaulieu-Saucier Université de Montréal Pharmacogenomics Centre, Montreal, QC, Canada
- Montreal Heart Institute, Montreal, QC, Canada
- Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Julie Hussin
- Montreal Heart Institute, Montreal, QC, Canada
- Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Marie-Pierre Dubé
- Beaulieu-Saucier Université de Montréal Pharmacogenomics Centre, Montreal, QC, Canada.
- Montreal Heart Institute, Montreal, QC, Canada.
- Faculty of Medicine, Université de Montréal, Montreal, QC, Canada.
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8
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Lumbers RT, Shah S, Lin H, Czuba T, Henry A, Swerdlow DI, Mälarstig A, Andersson C, Verweij N, Holmes MV, Ärnlöv J, Svensson P, Hemingway H, Sallah N, Almgren P, Aragam KG, Asselin G, Backman JD, Biggs ML, Bloom HL, Boersma E, Brandimarto J, Brown MR, Brunner-La Rocca HP, Carey DJ, Chaffin MD, Chasman DI, Chazara O, Chen X, Chen X, Chung JH, Chutkow W, Cleland JGF, Cook JP, de Denus S, Dehghan A, Delgado GE, Denaxas S, Doney AS, Dörr M, Dudley SC, Engström G, Esko T, Fatemifar G, Felix SB, Finan C, Ford I, Fougerousse F, Fouodjio R, Ghanbari M, Ghasemi S, Giedraitis V, Giulianini F, Gottdiener JS, Gross S, Guðbjartsson DF, Gui H, Gutmann R, Haggerty CM, van der Harst P, Hedman ÅK, Helgadottir A, Hillege H, Hyde CL, Jacob J, Jukema JW, Kamanu F, Kardys I, Kavousi M, Khaw KT, Kleber ME, Køber L, Koekemoer A, Kraus B, Kuchenbaecker K, Langenberg C, Lind L, Lindgren CM, London B, Lotta LA, Lovering RC, Luan J, Magnusson P, Mahajan A, Mann D, Margulies KB, Marston NA, März W, McMurray JJV, Melander O, Melloni G, Mordi IR, Morley MP, Morris AD, Morris AP, Morrison AC, Nagle MW, Nelson CP, Newton-Cheh C, Niessner A, Niiranen T, Nowak C, O'Donoghue ML, Owens AT, Palmer CNA, Paré G, Perola M, Perreault LPL, Portilla-Fernandez E, Psaty BM, Rice KM, Ridker PM, Romaine SPR, Roselli C, Rotter JI, Ruff CT, Sabatine MS, Salo P, Salomaa V, van Setten J, Shalaby AA, Smelser DT, Smith NL, Stefansson K, Stender S, Stott DJ, Sveinbjörnsson G, Tammesoo ML, Tardif JC, Taylor KD, Teder-Laving M, Teumer A, Thorgeirsson G, Thorsteinsdottir U, Torp-Pedersen C, Trompet S, Tuckwell D, Tyl B, Uitterlinden AG, Vaura F, Veluchamy A, Visscher PM, Völker U, Voors AA, Wang X, Wareham NJ, Weeke PE, Weiss R, White HD, Wiggins KL, Xing H, Yang J, Yang Y, Yerges-Armstrong LM, Yu B, Zannad F, Zhao F, Wilk JB, Holm H, Sattar N, Lubitz SA, Lanfear DE, Shah S, Dunn ME, Wells QS, Asselbergs FW, Hingorani AD, Dubé MP, Samani NJ, Lang CC, Cappola TP, Ellinor PT, Vasan RS, Smith JG. The genomics of heart failure: design and rationale of the HERMES consortium. ESC Heart Fail 2021; 8:5531-5541. [PMID: 34480422 PMCID: PMC8712846 DOI: 10.1002/ehf2.13517] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/09/2021] [Accepted: 07/05/2021] [Indexed: 12/28/2022] Open
Abstract
Aims The HERMES (HEart failure Molecular Epidemiology for Therapeutic targetS) consortium aims to identify the genomic and molecular basis of heart failure. Methods and results The consortium currently includes 51 studies from 11 countries, including 68 157 heart failure cases and 949 888 controls, with data on heart failure events and prognosis. All studies collected biological samples and performed genome‐wide genotyping of common genetic variants. The enrolment of subjects into participating studies ranged from 1948 to the present day, and the median follow‐up following heart failure diagnosis ranged from 2 to 116 months. Forty‐nine of 51 individual studies enrolled participants of both sexes; in these studies, participants with heart failure were predominantly male (34–90%). The mean age at diagnosis or ascertainment across all studies ranged from 54 to 84 years. Based on the aggregate sample, we estimated 80% power to genetic variant associations with risk of heart failure with an odds ratio of ≥1.10 for common variants (allele frequency ≥ 0.05) and ≥1.20 for low‐frequency variants (allele frequency 0.01–0.05) at P < 5 × 10−8 under an additive genetic model. Conclusions HERMES is a global collaboration aiming to (i) identify the genetic determinants of heart failure; (ii) generate insights into the causal pathways leading to heart failure and enable genetic approaches to target prioritization; and (iii) develop genomic tools for disease stratification and risk prediction.
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Affiliation(s)
- R Thomas Lumbers
- Institute of Health Informatics, University College London, Gower St, London, WC1E 7HB, UK.,Health Data Research UK London, University College London, London, UK.,BHF Research Accelerator, University College London, London, UK
| | - Sonia Shah
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.,Institute of Cardiovascular Science, University College London, London, UK
| | - Honghuang Lin
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA.,National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA, USA
| | - Tomasz Czuba
- Department of Cardiology, Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden
| | - Albert Henry
- Institute of Health Informatics, University College London, Gower St, London, WC1E 7HB, UK.,Institute of Cardiovascular Science, University College London, London, UK
| | - Daniel I Swerdlow
- Institute of Cardiovascular Science, University College London, London, UK.,Department of Medicine, Imperial College London, London, UK
| | - Anders Mälarstig
- Pfizer Worldwide Research & Development, Cambridge, MA, USA.,Cardiovascular Medicine Unit, Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
| | - Charlotte Andersson
- National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA, USA.,Department of Cardiology, Herlev Gentofte Hospital, Herlev, Denmark
| | - Niek Verweij
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Michael V Holmes
- Medical Research Council Population Health Research Unit at the University of Oxford, Oxford, UK.,Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, Big Data Institute, University of Oxford, Oxford, UK.,National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospital, Oxford, UK
| | - Johan Ärnlöv
- Department of Neurobiology, Care Sciences and Society/Section of Family Medicine and Primary Care, Karolinska Institutet, Stockholm, Sweden.,School of Health and Social Sciences, Dalarna University, Falun, Sweden
| | - Per Svensson
- Department of Clinical Science and Education, Karolinska Institutet, Södersjukhuset, Stockholm, Sweden.,Department of Cardiology, Södersjukhuset, Stockholm, Sweden
| | - Harry Hemingway
- Institute of Health Informatics, University College London, Gower St, London, WC1E 7HB, UK.,Health Data Research UK London, University College London, London, UK.,The National Institute for Health Research, University College London Hospitals Biomedical Research Centre, University College London, London, UK
| | - Neneh Sallah
- Institute of Health Informatics, University College London, Gower St, London, WC1E 7HB, UK.,Health Data Research UK London, University College London, London, UK.,UCL Genetics Institute, University College London, London, UK
| | - Peter Almgren
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Krishna G Aragam
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Mary L Biggs
- Department of Biostatistics, University of Washington, Seattle, WA, USA.,Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology and Health Services, University of Washington, Seattle, WA, USA
| | - Heather L Bloom
- Division of Cardiology, Department of Medicine, Emory University Medical Center, Atlanta, GA, USA
| | - Eric Boersma
- Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jeffrey Brandimarto
- Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael R Brown
- 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, TX, USA
| | | | - David J Carey
- Department of Molecular and Functional Genomics, Geisinger, Danville, PA, USA
| | - Mark D Chaffin
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Olympe Chazara
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Xing Chen
- Pfizer Worldwide Research & Development, Cambridge, MA, USA
| | - Xu Chen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | | | - William Chutkow
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - John G F Cleland
- Robertson Centre for Biostatistics & Glasgow Clinical Trials Unit, Institute of Health and Wellbeing, University of Glasgow, Glasgow Royal Infirmary, Glasgow, UK.,National Heart and Lung Institute, Imperial College, London, UK
| | - James P Cook
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Simon de Denus
- Montreal Heart Institute, Montreal, Quebec, Canada.,Faculty of Pharmacy, Université de Montréal, Montreal, Quebec, Canada
| | - Abbas Dehghan
- Department of Epidemiology and Biostatistics, Imperial College London, St Mary's Campus, London, UK.,MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, Imperial College London, St Mary's Campus, London, UK
| | - Graciela E Delgado
- Vth Department of Medicine (Nephrology, Hypertensiology, Endocrinology, Diabetology, Rheumatology), Medical Faculty of Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Spiros Denaxas
- Institute of Health Informatics, University College London, Gower St, London, WC1E 7HB, UK.,Health Data Research UK London, University College London, London, UK.,The National Institute for Health Research, University College London Hospitals Biomedical Research Centre, University College London, London, UK.,The Alan Turing Institute, British Library, London, UK
| | - Alexander S Doney
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Marcus Dörr
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany.,DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
| | - Samuel C Dudley
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Gunnar Engström
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Tõnu Esko
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Ghazaleh Fatemifar
- Institute of Health Informatics, University College London, Gower St, London, WC1E 7HB, UK.,Health Data Research UK London, University College London, London, UK
| | - Stephan B Felix
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany.,DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
| | - Chris Finan
- Institute of Cardiovascular Science, University College London, London, UK
| | - Ian Ford
- Robertson Centre for Biostatistics & Glasgow Clinical Trials Unit, Institute of Health and Wellbeing, University of Glasgow, Glasgow Royal Infirmary, Glasgow, UK
| | - Francoise Fougerousse
- Translational and Clinical Research, Servier Cardiovascular Center for Therapeutic Innovation, Suresnes, France
| | | | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Sahar Ghasemi
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany.,Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Vilmantas Giedraitis
- Department of Public Health and Caring Sciences, Geriatrics, Uppsala University, Uppsala, Sweden
| | - Franco Giulianini
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - John S Gottdiener
- Department of Medicine, Division of Cardiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Stefan Gross
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany.,DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
| | - Daníel F Guðbjartsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Hongsheng Gui
- Center for Individualized and Genomic Medicine Research, Department of Internal Medicine, Henry Ford Hospital, Detroit, MI, USA
| | - Rebecca Gutmann
- Division of Cardiovascular Medicine, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | | | - Pim van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Durrer Center for Cardiogenetic Research, ICIN-Netherlands Heart Institute, Utrecht, The Netherlands
| | - Åsa K Hedman
- Cardiovascular Medicine Unit, Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
| | | | - Hans Hillege
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Craig L Hyde
- Pfizer Worldwide Research & Development, Cambridge, MA, USA
| | - Jaison Jacob
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands.,Netherlands Heart Institute, Utrecht, The Netherlands
| | - Frederick Kamanu
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,TIMI Study Group, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Isabella Kardys
- Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Kay-Tee Khaw
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Marcus E Kleber
- Vth Department of Medicine (Nephrology, Hypertensiology, Endocrinology, Diabetology, Rheumatology), Medical Faculty of Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Lars Køber
- Department of Cardiology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Andrea Koekemoer
- Department of Cardiovascular Sciences, University of Leicester and NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Bill Kraus
- Duke Molecular Physiology Institute, Durham, NC, USA
| | - Karoline Kuchenbaecker
- UCL Genetics Institute, University College London, London, UK.,Division of Psychiatry, University College of London, London, UK
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Cecilia M Lindgren
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Big Data Institute at the Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Barry London
- Division of Cardiovascular Medicine and Abboud Cardiovascular Research Center, University of Iowa, Iowa City, IA, USA
| | - Luca A Lotta
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Ruth C Lovering
- Institute of Cardiovascular Science, University College London, London, UK
| | - Jian'an Luan
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Patrik Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | | | - Douglas Mann
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kenneth B Margulies
- Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicholas A Marston
- TIMI Study Group, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Winfried März
- Vth Department of Medicine (Nephrology, Hypertensiology, Endocrinology, Diabetology, Rheumatology), Medical Faculty of Mannheim, University of Heidelberg, Heidelberg, Germany.,Synlab Academy, Synlab Holding Deutschland GmbH, Mannheim, Germany.,Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
| | - John J V McMurray
- BHF Cardiovascular Research Centre, University of Glasgow, Glasgow, UK
| | - Olle Melander
- Department of Internal Medicine, Clinical Sciences, Lund University and Skåne University Hospital, Malmö, Sweden
| | - Giorgio Melloni
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,TIMI Study Group, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ify R Mordi
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Michael P Morley
- Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew D Morris
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Andrew P Morris
- Department of Biostatistics, University of Liverpool, Liverpool, UK.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, 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, TX, USA
| | | | - Christopher P Nelson
- Department of Cardiovascular Sciences, University of Leicester and NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Christopher Newton-Cheh
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.,Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
| | - Alexander Niessner
- Department of Internal Medicine II, Division of Cardiology, Medical University of Vienna, Vienna, Austria
| | - Teemu Niiranen
- Finnish Institute for Health and Welfare, Helsinki, Finland.,Department of Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Christoph Nowak
- Department of Neurobiology, Care Sciences and Society/Section of Family Medicine and Primary Care, Karolinska Institutet, Stockholm, Sweden
| | - Michelle L O'Donoghue
- TIMI Study Group, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Anjali T Owens
- Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Colin N A Palmer
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Guillaume Paré
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Markus Perola
- National Institute for Health and Welfare, Helsinki, Finland
| | | | - Eliana Portilla-Fernandez
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Division of Vascular Medicine and Pharmacology, Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology and Health Services, University of Washington, Seattle, WA, USA.,Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA, USA
| | - Kenneth M Rice
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Simon P R Romaine
- Department of Cardiovascular Sciences, University of Leicester and NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Carolina Roselli
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Christian T Ruff
- TIMI Study Group, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Marc S Sabatine
- TIMI Study Group, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Perttu Salo
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Veikko Salomaa
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Jessica van Setten
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Alaa A Shalaby
- Division of Cardiology, Department of Medicine, University of Pittsburgh Medical Center and VA Pittsburgh HCS, Pittsburgh, PA, USA
| | - Diane T Smelser
- Department of Molecular and Functional Genomics, Geisinger, Danville, PA, USA
| | - Nicholas L Smith
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA, USA.,Department of Epidemiology, University of Washington, Seattle, WA, USA.,Department of Veterans Affairs Office of Research and Development, Seattle Epidemiologic Research and Information Center, Seattle, WA, USA
| | - Kari Stefansson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,Faculty of Medicine, Department of Medicine, University of Iceland, Reykjavik, Iceland
| | - Steen Stender
- Department of Clinical Biochemistry, Copenhagen University Hospital, Herlev and Gentofte, Denmark
| | - David J Stott
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | | | - Mari-Liis Tammesoo
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Jean-Claude Tardif
- Montreal Heart Institute, Montreal, Quebec, Canada.,Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Maris Teder-Laving
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Alexander Teumer
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany.,Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Guðmundur Thorgeirsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,Faculty of Medicine, Department of Medicine, University of Iceland, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,Faculty of Medicine, Department of Medicine, University of Iceland, Reykjavik, Iceland
| | - Christian Torp-Pedersen
- Department of Epidemiology and Biostatistics, Aalborg University Hospital, Aalborg, Denmark.,Department of Health, Science and Technology, Aalborg University Hospital, Aalborg, Denmark.,Department of Cardiology, Aalborg University Hospital, Aalborg, Denmark
| | - Stella Trompet
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands.,Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Danny Tuckwell
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Benoit Tyl
- Translational and Clinical Research, Servier Cardiovascular Center for Therapeutic Innovation, Suresnes, France
| | - Andre G Uitterlinden
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Felix Vaura
- Finnish Institute for Health and Welfare, Helsinki, Finland.,Department of Clinical Medicine, University of Turku, Turku, Finland
| | - Abirami Veluchamy
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Uwe Völker
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany.,Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Adriaan A Voors
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Xiaosong Wang
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Nicholas J Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Peter E Weeke
- Department of Cardiology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Raul Weiss
- Division of Cardiovascular Medicine, Department of Internal Medicine, The Ohio State University Medical Center, Columbus, OH, USA
| | - Harvey D White
- Green Lane Cardiovascular Service, Auckland City Hospital, Auckland, New Zealand
| | - Kerri L Wiggins
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Heming Xing
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Jian Yang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Yifan Yang
- Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Bing Yu
- 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, TX, USA
| | - Faiez Zannad
- CHU de Nancy, Inserm and INI-CRCT (F-CRIN), Institut Lorrain du Coeur et des Vaisseaux, Université de Lorraine, Nancy, France
| | - Faye Zhao
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | -
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Jemma B Wilk
- Pfizer Worldwide Research & Development, Cambridge, MA, USA
| | - Hilma Holm
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
| | - Naveed Sattar
- BHF Cardiovascular Research Centre, University of Glasgow, Glasgow, UK
| | - Steven A Lubitz
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Cardiac Arrhythmia Service and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - David E Lanfear
- Center for Individualized and Genomic Medicine Research, Department of Internal Medicine, Henry Ford Hospital, Detroit, MI, USA.,Heart and Vascular Institute, Henry Ford Hospital, Detroit, MI, USA
| | - Svati Shah
- Duke Molecular Physiology Institute, Durham, NC, USA.,Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, NC, USA.,Duke Clinical Research Institute, Durham, NC, USA
| | - Michael E Dunn
- Regeneron Pharmaceuticals, Cardiovascular Research, Tarrytown, NY, USA
| | - Quinn S Wells
- Division of Cardiovascular Medicine and the Vanderbilt Translational and Clinical Cardiovascular Research Center, Vanderbilt University, Nashville, TN, USA
| | - Folkert W Asselbergs
- Health Data Research UK London, University College London, London, UK.,BHF Research Accelerator, University College London, London, UK.,Institute of Cardiovascular Science, University College London, London, UK.,Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Aroon D Hingorani
- BHF Research Accelerator, University College London, London, UK.,Institute of Cardiovascular Science, University College London, London, UK
| | - Marie-Pierre Dubé
- Montreal Heart Institute, Montreal, Quebec, Canada.,Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester and NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Chim C Lang
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Thomas P Cappola
- Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Patrick T Ellinor
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Cardiac Arrhythmia Service and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Ramachandran S Vasan
- National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA, USA.,Sections of Cardiology, Preventive Medicine and Epidemiology, Department of Medicine, Boston University Schools of Medicine and Public Health, Boston, MA, USA
| | - J Gustav Smith
- Department of Cardiology, Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden.,Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Wallenberg Center for Molecular Medicine and Lund University Diabetes Center, Lund University, Lund, Sweden.,The Wallenberg Laboratory/Department of Molecular and Clinical Medicine, Institute of Medicine, Gothenburg University and the Department of Cardiology, Sahlgrenska University Hospital, Gothenburg, Sweden
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9
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Dubé MP, Lemaçon A, Barhdadi A, Lemieux Perreault LP, Oussaïd E, Asselin G, Provost S, Sun M, Sandoval J, Legault MA, Mongrain I, Dubois A, Valois D, Dedelis E, Lousky J, Choi J, Goulet E, Savard C, Chicoine LM, Cossette M, Chabot-Blanchet M, Guertin MC, de Denus S, Bouabdallaoui N, Marchand R, Bassevitch Z, Nozza A, Gaudet D, L'Allier PL, Hussin J, Boivin G, Busseuil D, Tardif JC. Genetics of symptom remission in outpatients with COVID-19. Sci Rep 2021; 11:10847. [PMID: 34035401 PMCID: PMC8149390 DOI: 10.1038/s41598-021-90365-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/11/2021] [Indexed: 01/09/2023] Open
Abstract
We conducted a genome-wide association study of time to remission of COVID-19 symptoms in 1723 outpatients with at least one risk factor for disease severity from the COLCORONA clinical trial. We found a significant association at 5p13.3 (rs1173773; P = 4.94 × 10-8) near the natriuretic peptide receptor 3 gene (NPR3). By day 15 of the study, 44%, 54% and 59% of participants with 0, 1, or 2 copies of the effect allele respectively, had symptom remission. In 851 participants not treated with colchicine (placebo), there was a significant association at 9q33.1 (rs62575331; P = 2.95 × 10-8) in interaction with colchicine (P = 1.19 × 10-5) without impact on risk of hospitalisations, highlighting a possibly shared mechanistic pathway. By day 15 of the study, 46%, 62% and 64% of those with 0, 1, or 2 copies of the effect allele respectively, had symptom remission. The findings need to be replicated and could contribute to the biological understanding of COVID-19 symptom remission.
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Affiliation(s)
- Marie-Pierre Dubé
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada. .,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada. .,Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, Canada.
| | - Audrey Lemaçon
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada.,Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Amina Barhdadi
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada
| | - Louis-Philippe Lemieux Perreault
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada
| | - Essaïd Oussaïd
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada
| | - Géraldine Asselin
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada
| | - Sylvie Provost
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada
| | - Maxine Sun
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada.,Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Johanna Sandoval
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada
| | - Marc-André Legault
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada.,Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Ian Mongrain
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada
| | - Anick Dubois
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada
| | - Diane Valois
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada
| | - Emma Dedelis
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada
| | - Jennifer Lousky
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada
| | - Julie Choi
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada
| | - Elisabeth Goulet
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada
| | - Christiane Savard
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada
| | - Lea-Mei Chicoine
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada
| | - Mariève Cossette
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Montreal Health Innovations Coordinating Centre, Montreal, Canada
| | - Malorie Chabot-Blanchet
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Montreal Health Innovations Coordinating Centre, Montreal, Canada
| | - Marie-Claude Guertin
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Montreal Health Innovations Coordinating Centre, Montreal, Canada
| | - Simon de Denus
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada.,Faculty of Pharmacy, Université de Montréal, Montreal, Canada
| | | | - Richard Marchand
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada
| | - Zohar Bassevitch
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Montreal Health Innovations Coordinating Centre, Montreal, Canada
| | - Anna Nozza
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Montreal Health Innovations Coordinating Centre, Montreal, Canada
| | - Daniel Gaudet
- Ecogene-21 and Department of Medicine, Université de Montréal, Chicoutimi, Canada
| | | | - Julie Hussin
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada.,Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, Canada.,Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Guy Boivin
- Centre Hospitalier de l'Université Laval, Quebec City, Canada
| | - David Busseuil
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada
| | - Jean-Claude Tardif
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada. .,Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, Canada.
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10
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Dubé MP, Legault MA, Lemaçon A, Lemieux Perreault LP, Fouodjio R, Waters DD, Kouz S, Pinto FJ, Maggioni AP, Diaz R, Berry C, Koenig W, Lopez-Sendon J, Gamra H, Kiwan GS, Asselin G, Provost S, Barhdadi A, Sun M, Cossette M, Blondeau L, Mongrain I, Dubois A, Rhainds D, Bouabdallaoui N, Samuel M, de Denus S, L'Allier PL, Guertin MC, Roubille F, Tardif JC. Pharmacogenomics of the Efficacy and Safety of Colchicine in COLCOT. Circ Genom Precis Med 2021; 14:e003183. [PMID: 33560138 PMCID: PMC8284376 DOI: 10.1161/circgen.120.003183] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Supplemental Digital Content is available in the text. Background: The randomized, placebo-controlled COLCOT (Colchicine Cardiovascular Outcomes Trial) has shown the benefits of colchicine 0.5 mg daily to lower the rate of ischemic cardiovascular events in patients with a recent myocardial infarction. Here, we conducted a post hoc pharmacogenomic study of COLCOT with the aim to identify genetic predictors of the efficacy and safety of treatment with colchicine. Methods: There were 1522 participants of European ancestry from the COLCOT trial available for the pharmacogenomic study of COLCOT trial. The pharmacogenomic study’s primary cardiovascular end point was defined as for the main trial, as time to first occurrence of cardiovascular death, resuscitated cardiac arrest, myocardial infarction, stroke, or urgent hospitalization for angina requiring coronary revascularization. The safety end point was time to the first report of gastrointestinal events. Patients’ DNA was genotyped using the Illumina Global Screening array followed by imputation. We performed a genome-wide association study in colchicine-treated patients. Results: None of the genetic variants passed the genome-wide association study significance threshold for the primary cardiovascular end point conducted in 702 patients in the colchicine arm who were compliant to medication. The genome-wide association study for gastrointestinal events was conducted in all 767 patients in the colchicine arm and found 2 significant association signals, one with lead variant rs6916345 (hazard ratio, 1.89 [95% CI, 1.52–2.35], P=7.41×10−9) in a locus which colocalizes with Crohn disease, and one with lead variant rs74795203 (hazard ratio, 2.51 [95% CI, 1.82–3.47]; P=2.70×10−8), an intronic variant in gene SEPHS1. The interaction terms between the genetic variants and treatment with colchicine versus placebo were significant. Conclusions: We found 2 genomic regions associated with gastrointestinal events in patients treated with colchicine. Those findings will benefit from replication to confirm that some patients may have genetic predispositions to lower tolerability of treatment with colchicine.
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Affiliation(s)
- Marie-Pierre Dubé
- Montreal Heart Institute (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., M.C., L.B., I.M., A.D., D.R., N.B., M.S., S.d.D., P.L.L., M.-C.G., J.-C.T.), Université de Montréal, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., I.M., A.D., S.d.D.), Université de Montréal, Canada.,Department of Medicine (M.-P.D., A.L., M.S., N.B., M.S., J.-C.T.), Université de Montréal, Canada
| | - Marc-André Legault
- Montreal Heart Institute (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., M.C., L.B., I.M., A.D., D.R., N.B., M.S., S.d.D., P.L.L., M.-C.G., J.-C.T.), Université de Montréal, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., I.M., A.D., S.d.D.), Université de Montréal, Canada.,Departments of Biochemistry and Molecular Medicine, Faculty of Medicine (M.-A.L.), Université de Montréal, Canada
| | - Audrey Lemaçon
- Montreal Heart Institute (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., M.C., L.B., I.M., A.D., D.R., N.B., M.S., S.d.D., P.L.L., M.-C.G., J.-C.T.), Université de Montréal, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., I.M., A.D., S.d.D.), Université de Montréal, Canada.,Department of Medicine (M.-P.D., A.L., M.S., N.B., M.S., J.-C.T.), Université de Montréal, Canada
| | - Louis-Philippe Lemieux Perreault
- Montreal Heart Institute (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., M.C., L.B., I.M., A.D., D.R., N.B., M.S., S.d.D., P.L.L., M.-C.G., J.-C.T.), Université de Montréal, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., I.M., A.D., S.d.D.), Université de Montréal, Canada
| | - René Fouodjio
- Montreal Heart Institute (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., M.C., L.B., I.M., A.D., D.R., N.B., M.S., S.d.D., P.L.L., M.-C.G., J.-C.T.), Université de Montréal, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., I.M., A.D., S.d.D.), Université de Montréal, Canada
| | | | - Simon Kouz
- Centre Hospitalier Régional de Lanaudière, Joliette, Canada (S.K.)
| | - Fausto J Pinto
- Santa Maria University Hospital (CHULN), CAML, CCUL, Faculdade de Medicina da Universidade de Lisboa, Portugal (F.J.P.)
| | - Aldo P Maggioni
- Maria Cecilia Hospital, GVM Care and Research, Italy (A.P.M.)
| | - Rafael Diaz
- Estudios Clinicos Latinoamerica, Rosario, Argentina (R.D.)
| | - Colin Berry
- University of Glasgow, NHS Glasgow Clinical Research Facility, United Kingsom (C.B.)
| | - Wolfgang Koenig
- Deutsches Herzzentrum München, Technische Universität München, Munich, Germany (W.K.).,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany (W.K.).,Institute of Epidemiology and Medical Biometry, University of Ulm, Germany (W.K.)
| | | | - Habib Gamra
- Fattouma Bourguiba University Hospital, Monastir, Tunisia (H.G.)
| | | | - Géraldine Asselin
- Montreal Heart Institute (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., M.C., L.B., I.M., A.D., D.R., N.B., M.S., S.d.D., P.L.L., M.-C.G., J.-C.T.), Université de Montréal, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., I.M., A.D., S.d.D.), Université de Montréal, Canada
| | - Sylvie Provost
- Montreal Heart Institute (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., M.C., L.B., I.M., A.D., D.R., N.B., M.S., S.d.D., P.L.L., M.-C.G., J.-C.T.), Université de Montréal, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., I.M., A.D., S.d.D.), Université de Montréal, Canada
| | - Amina Barhdadi
- Montreal Heart Institute (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., M.C., L.B., I.M., A.D., D.R., N.B., M.S., S.d.D., P.L.L., M.-C.G., J.-C.T.), Université de Montréal, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., I.M., A.D., S.d.D.), Université de Montréal, Canada
| | - Maxine Sun
- Montreal Heart Institute (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., M.C., L.B., I.M., A.D., D.R., N.B., M.S., S.d.D., P.L.L., M.-C.G., J.-C.T.), Université de Montréal, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., I.M., A.D., S.d.D.), Université de Montréal, Canada.,Department of Medicine (M.-P.D., A.L., M.S., N.B., M.S., J.-C.T.), Université de Montréal, Canada
| | - Mariève Cossette
- Montreal Heart Institute (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., M.C., L.B., I.M., A.D., D.R., N.B., M.S., S.d.D., P.L.L., M.-C.G., J.-C.T.), Université de Montréal, Canada.,Montreal Health Innovation Coordinating Centre, Canada (M.C., L.B., M.-C.G.)
| | - Lucie Blondeau
- Montreal Heart Institute (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., M.C., L.B., I.M., A.D., D.R., N.B., M.S., S.d.D., P.L.L., M.-C.G., J.-C.T.), Université de Montréal, Canada.,Montreal Health Innovation Coordinating Centre, Canada (M.C., L.B., M.-C.G.)
| | - Ian Mongrain
- Montreal Heart Institute (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., M.C., L.B., I.M., A.D., D.R., N.B., M.S., S.d.D., P.L.L., M.-C.G., J.-C.T.), Université de Montréal, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., I.M., A.D., S.d.D.), Université de Montréal, Canada
| | - Anick Dubois
- Montreal Heart Institute (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., M.C., L.B., I.M., A.D., D.R., N.B., M.S., S.d.D., P.L.L., M.-C.G., J.-C.T.), Université de Montréal, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., I.M., A.D., S.d.D.), Université de Montréal, Canada
| | - David Rhainds
- Montreal Heart Institute (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., M.C., L.B., I.M., A.D., D.R., N.B., M.S., S.d.D., P.L.L., M.-C.G., J.-C.T.), Université de Montréal, Canada
| | - Nadia Bouabdallaoui
- Montreal Heart Institute (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., M.C., L.B., I.M., A.D., D.R., N.B., M.S., S.d.D., P.L.L., M.-C.G., J.-C.T.), Université de Montréal, Canada.,Department of Medicine (M.-P.D., A.L., M.S., N.B., M.S., J.-C.T.), Université de Montréal, Canada
| | - Michelle Samuel
- Montreal Heart Institute (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., M.C., L.B., I.M., A.D., D.R., N.B., M.S., S.d.D., P.L.L., M.-C.G., J.-C.T.), Université de Montréal, Canada.,Department of Medicine (M.-P.D., A.L., M.S., N.B., M.S., J.-C.T.), Université de Montréal, Canada
| | - Simon de Denus
- Montreal Heart Institute (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., M.C., L.B., I.M., A.D., D.R., N.B., M.S., S.d.D., P.L.L., M.-C.G., J.-C.T.), Université de Montréal, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., I.M., A.D., S.d.D.), Université de Montréal, Canada.,Université de Montréal, Faculty of Pharmacy, Canada (S.d.D.)
| | - Philippe L L'Allier
- Montreal Heart Institute (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., M.C., L.B., I.M., A.D., D.R., N.B., M.S., S.d.D., P.L.L., M.-C.G., J.-C.T.), Université de Montréal, Canada
| | - Marie-Claude Guertin
- Montreal Heart Institute (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., M.C., L.B., I.M., A.D., D.R., N.B., M.S., S.d.D., P.L.L., M.-C.G., J.-C.T.), Université de Montréal, Canada.,Montreal Health Innovation Coordinating Centre, Canada (M.C., L.B., M.-C.G.)
| | - François Roubille
- PhyMedExp (Physiologie et Médecine Expérimentale du Coeur et des Muscles), Université de Montpellier, INSERM, Centre National de la Recherche Scientifique, Cardiology Department, CHU de Montpellier, France (F.R.)
| | - Jean-Claude Tardif
- Montreal Heart Institute (M.-P.D., M.-A.L., A.L., L.-P.L.P., R.F., G.A., S.P., A.B., M.S., M.C., L.B., I.M., A.D., D.R., N.B., M.S., S.d.D., P.L.L., M.-C.G., J.-C.T.), Université de Montréal, Canada.,Department of Medicine (M.-P.D., A.L., M.S., N.B., M.S., J.-C.T.), Université de Montréal, Canada
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11
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Legault MA, Sandoval J, Provost S, Barhdadi A, Lemieux Perreault LP, Shah S, Lumbers RT, de Denus S, Tyl B, Tardif JC, Dubé MP. A genetic model of ivabradine recapitulates results from randomized clinical trials. PLoS One 2020; 15:e0236193. [PMID: 32692755 PMCID: PMC7373274 DOI: 10.1371/journal.pone.0236193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 06/30/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Naturally occurring human genetic variants provide a valuable tool to identify drug targets and guide drug prioritization and clinical trial design. Ivabradine is a heart rate lowering drug with protective effects on heart failure despite increasing the risk of atrial fibrillation. In patients with coronary artery disease without heart failure, the drug does not protect against major cardiovascular adverse events prompting questions about the ability of genetics to have predicted those effects. This study evaluates the effect of a variant in HCN4, ivabradine's drug target, on safety and efficacy endpoints. METHODS We used genetic association testing and Mendelian randomization to predict the effect of ivabradine and heart rate lowering on cardiovascular outcomes. RESULTS Using data from the UK Biobank and large GWAS consortia, we evaluated the effect of a heart rate-reducing genetic variant at the HCN4 locus encoding ivabradine's drug target. These genetic association analyses showed increases in risk for atrial fibrillation (OR 1.09, 95% CI: 1.06-1.13, P = 9.3 ×10-9) in the UK Biobank. In a cause-specific competing risk model to account for the increased risk of atrial fibrillation, the HCN4 variant reduced incident heart failure in participants that did not develop atrial fibrillation (HR 0.90, 95% CI: 0.83-0.98, P = 0.013). In contrast, the same heart rate reducing HCN4 variant did not prevent a composite endpoint of myocardial infarction or cardiovascular death (OR 0.99, 95% CI: 0.93-1.04, P = 0.61). CONCLUSION Genetic modelling of ivabradine recapitulates its benefits in heart failure, promotion of atrial fibrillation, and neutral effect on myocardial infarction.
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Affiliation(s)
- Marc-André Legault
- Montreal Heart Institute, Montreal, Canada
- Department of biochemistry and molecular medicine, Université de Montréal, Montreal, Canada
- Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada
| | - Johanna Sandoval
- Montreal Heart Institute, Montreal, Canada
- Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada
| | - Sylvie Provost
- Montreal Heart Institute, Montreal, Canada
- Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada
| | - Amina Barhdadi
- Montreal Heart Institute, Montreal, Canada
- Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada
| | | | - Sonia Shah
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - R Thomas Lumbers
- Institute of Health Informatics, University College London, London, United Kingdom
- Health Data Research UK London, University College London, London, United Kingdom
- Bart's Heart Centre, St. Bartholomew's Hospital, London, United Kingdom
| | - Simon de Denus
- Montreal Heart Institute, Montreal, Canada
- Faculty of Pharmacy, Université de Montréal, Montreal, Canada
| | - Benoit Tyl
- Cardiovascular Center for Therapeutic Innovation, Institut de Recherches Internationales Servier, Suresnes, France
| | - Jean-Claude Tardif
- Montreal Heart Institute, Montreal, Canada
- Department of medicine, Université de Montréal, Montreal, Canada
| | - Marie-Pierre Dubé
- Montreal Heart Institute, Montreal, Canada
- Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal, Canada
- Department of medicine, Université de Montréal, Montreal, Canada
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12
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Lemieux Perreault LP, Zaïd N, Cameron M, Mongrain I, Dubé MP. Pharmacogenetic content of commercial genome-wide genotyping arrays. Pharmacogenomics 2018; 19:1159-1167. [DOI: 10.2217/pgs-2017-0129] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Aim: We have evaluated the pharmacogenetic content of commercial human genome-wide genotyping arrays, as it is a critical determinant to enabling pharmacogenomic discoveries. Methods: Using bioinformatics approaches, we assessed 27,811 genetic variants in 3146 genes for their presence in 18 Illumina and 15 Affymetrix genome-wide arrays. Results: The pharmacogenetic content of the arrays varied greatly. The combination of the Affymetrix precision medicine array and PharmacoScan arrays (Affymetrix) had the highest coverage for a set of clinically actionable absorption, distribution, metabolism and excretion (ADME) variants, single nucleotide ADME variants and ADME insertions/deletions, with a physical coverage of 125/130 (96.2%), 9924/24,138 (41.1%) and 2252/3994 (56.4%), respectively. Conclusion: The combination of the Affymetrix precision medicine array and PharmacoScan arrays provided both genome-wide and pharmacogene coverage, which is crucial in the discovering of new variants responsible for drug adverse effects. These results will help in the design of pharmacogenomic studies and will enable a critical review of results from past studies.
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Affiliation(s)
- Louis-Philippe Lemieux Perreault
- Beaulieu-Saucier Université de Montréal Pharmacogenomics Centre, 5000 Belanger Street, Montreal, H1T 1C8, Canada
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada
| | - Nabil Zaïd
- Beaulieu-Saucier Université de Montréal Pharmacogenomics Centre, 5000 Belanger Street, Montreal, H1T 1C8, Canada
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada
- Université Mohammed V – Faculté des Sciences, Avenue des Nations Unies, Agdal, Rabat Morocco
| | - Michel Cameron
- Beaulieu-Saucier Université de Montréal Pharmacogenomics Centre, 5000 Belanger Street, Montreal, H1T 1C8, Canada
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada
- BiogeniQ, 4105-G Boulevard Matte, Brossard, J4Y 2P4, Canada
| | - Ian Mongrain
- Beaulieu-Saucier Université de Montréal Pharmacogenomics Centre, 5000 Belanger Street, Montreal, H1T 1C8, Canada
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada
| | - Marie-Pierre Dubé
- Beaulieu-Saucier Université de Montréal Pharmacogenomics Centre, 5000 Belanger Street, Montreal, H1T 1C8, Canada
- Montreal Heart Institute, 5000 Belanger Street, Montreal, H1T 1C8, Canada
- Université de Montréal, Faculty of Medicine, 2900 Boulevard Edouard-Montpetit, Montreal, H3T 1J4, Canada
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13
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Rivollier F, Chaumette B, Bendjemaa N, Chayet M, Millet B, Jaafari N, Barhdadi A, Lemieux Perreault LP, Provost S, Dubé MP, Gaillard R, Krebs MO, Kebir O. Methylomic changes in individuals with psychosis, prenatally exposed to endocrine disrupting compounds: Lessons from diethylstilbestrol. PLoS One 2017; 12:e0174783. [PMID: 28406917 PMCID: PMC5390994 DOI: 10.1371/journal.pone.0174783] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/15/2017] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND In the Western world, between 1940 and 1970, more than 2 million people were exposed in utero to diethylstilbestrol (DES). In exposed individuals, and in their descendants, adverse outcomes have been linked to such exposure, including cancers, genital malformations, and less consistently, psychiatric disorders. We aimed to explore whether prenatal DES exposure would be associated with DNA methylation changes, and whether these epigenetic modifications would be associated with increased risk of psychosis. METHODS From 247 individuals born from mothers exposed to DES, we selected 69 siblings from 30 families. In each family, at least one sibling was exposed in utero to DES. We performed a methylome-wide association study using HumanMethylation450 DNA Analysis BeadChip® in peripheral blood. We analyzed methylation changes at individual CpGs or regions in exposed (n = 37) versus unexposed individuals (n = 32). We also compared exposed individuals with (n = 7) and without psychosis (n = 30). RESULTS There were more individuals with schizophrenia in the DES-exposed group. We found no significant differences between exposed and unexposed individuals with respect to differentially methylated CpGs or regions. The largest difference was in a region near the promoter of an ADAMTS proteoglycanase gene (ADAMTS9). Compared to exposed individuals without psychosis, exposed individuals with psychosis had differential methylation in the region encompassing the gene encoding the zinc finger protein 57 (ZFP57). CONCLUSIONS In utero exposure to DES was not associated with methylation changes at specific CpG or regions. In exposed individuals, however, psychosis was associated with specific methylomic modifications that could impact neurodevelopment and neuroplasticity.
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Affiliation(s)
- Fabrice Rivollier
- Université Paris Descartes, Université Paris Sorbonne Paris Cité, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France
- INSERM, Laboratoire de Physiopathologie des Maladies Psychiatriques, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France
- CNRS, GDR3557-Institut de Psychiatrie, Paris, France
- Faculté de Médecine Paris Descartes, Centre Hospitalier Sainte-Anne, Service Hospitalo-Universitaire, Paris, France
| | - Boris Chaumette
- Université Paris Descartes, Université Paris Sorbonne Paris Cité, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France
- INSERM, Laboratoire de Physiopathologie des Maladies Psychiatriques, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France
- CNRS, GDR3557-Institut de Psychiatrie, Paris, France
- Faculté de Médecine Paris Descartes, Centre Hospitalier Sainte-Anne, Service Hospitalo-Universitaire, Paris, France
| | - Narjes Bendjemaa
- Université Paris Descartes, Université Paris Sorbonne Paris Cité, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France
- INSERM, Laboratoire de Physiopathologie des Maladies Psychiatriques, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France
- CNRS, GDR3557-Institut de Psychiatrie, Paris, France
- Faculté de Médecine Paris Descartes, Centre Hospitalier Sainte-Anne, Service Hospitalo-Universitaire, Paris, France
| | - Mélanie Chayet
- Faculté de Médecine Paris Descartes, Centre Hospitalier Sainte-Anne, Service Hospitalo-Universitaire, Paris, France
| | - Bruno Millet
- Department of Adults Psychiatry, ICM-A-IHU, UPMC UMR S 975, Inserm U 1127, CNRS UMR 7225, GH Pitié-Salpêtrière, Paris, France
| | - Nematollah Jaafari
- Unité de Recherche Clinique en Psychiatrie Pierre Deniker, Centre Hospitalier Henri Laborit, INSERM CIC-P 1402, INSERM U 1084 Laboratoire Expérimental et Clinique en Neurosciences, Univ Poitiers, CHU Poitiers, Groupement De Recherche CNRS 3557, Poitiers, France
| | - Amina Barhdadi
- Université de Montréal, Beaulieu-Saucier Pharmacogenomics Center, Montréal Heart Institute, Montréal, QC, Canada
| | | | - Sylvie Provost
- Université de Montréal, Beaulieu-Saucier Pharmacogenomics Center, Montréal Heart Institute, Montréal, QC, Canada
| | - Marie-Pierre Dubé
- Université de Montréal, Beaulieu-Saucier Pharmacogenomics Center, Montréal Heart Institute, Montréal, QC, Canada
| | - Raphaël Gaillard
- Université Paris Descartes, Université Paris Sorbonne Paris Cité, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France
- INSERM, Laboratoire de Physiopathologie des Maladies Psychiatriques, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France
- CNRS, GDR3557-Institut de Psychiatrie, Paris, France
- Faculté de Médecine Paris Descartes, Centre Hospitalier Sainte-Anne, Service Hospitalo-Universitaire, Paris, France
| | - Marie-Odile Krebs
- Université Paris Descartes, Université Paris Sorbonne Paris Cité, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France
- INSERM, Laboratoire de Physiopathologie des Maladies Psychiatriques, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France
- CNRS, GDR3557-Institut de Psychiatrie, Paris, France
- Faculté de Médecine Paris Descartes, Centre Hospitalier Sainte-Anne, Service Hospitalo-Universitaire, Paris, France
| | - Oussama Kebir
- Université Paris Descartes, Université Paris Sorbonne Paris Cité, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France
- INSERM, Laboratoire de Physiopathologie des Maladies Psychiatriques, Centre de Psychiatrie et Neurosciences, UMR S 894, Paris, France
- CNRS, GDR3557-Institut de Psychiatrie, Paris, France
- Faculté de Médecine Paris Descartes, Centre Hospitalier Sainte-Anne, Service Hospitalo-Universitaire, Paris, France
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Lemieux Perreault LP, Legault MA, Asselin G, Dubé MP. genipe: an automated genome-wide imputation pipeline with automatic reporting and statistical tools. Bioinformatics 2016; 32:3661-3663. [PMID: 27497439 PMCID: PMC5181529 DOI: 10.1093/bioinformatics/btw487] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 06/30/2016] [Accepted: 07/18/2016] [Indexed: 11/24/2022] Open
Abstract
Summary: Genotype imputation is now commonly performed following genome-wide genotyping experiments. Imputation increases the density of analyzed genotypes in the dataset, enabling fine-mapping across the genome. However, the process of imputation using the most recent publicly available reference datasets can require considerable computation power and the management of hundreds of large intermediate files. We have developed genipe, a complete genome-wide imputation pipeline which includes automatic reporting, imputed data indexing and management, and a suite of statistical tests for imputed data commonly used in genetic epidemiology (Sequence Kernel Association Test, Cox proportional hazards for survival analysis, and linear mixed models for repeated measurements in longitudinal studies). Availability and Implementation: The genipe package is an open source Python software and is freely available for non-commercial use (CC BY-NC 4.0) at https://github.com/pgxcentre/genipe. Documentation and tutorials are available at http://pgxcentre.github.io/genipe. Contact:louis-philippe.lemieux.perreault@statgen.org or marie-pierre.dube@statgen.org Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Louis-Philippe Lemieux Perreault
- Beaulieu-Saucier Université de Montréal Pharmacogenomics Centre, Montreal Heart Institute Research Center, Montréal, Canada H1T 1C8
| | - Marc-André Legault
- Beaulieu-Saucier Université de Montréal Pharmacogenomics Centre, Montreal Heart Institute Research Center, Montréal, Canada H1T 1C8.,Department of Biochemistry and molecular medicine, Université de Montréal, Montreal, Canada H3T 1J4
| | - Géraldine Asselin
- Beaulieu-Saucier Université de Montréal Pharmacogenomics Centre, Montreal Heart Institute Research Center, Montréal, Canada H1T 1C8
| | - Marie-Pierre Dubé
- Beaulieu-Saucier Université de Montréal Pharmacogenomics Centre, Montreal Heart Institute Research Center, Montréal, Canada H1T 1C8.,Department of Medicine, Université de Montréal, Montreal, Canada H3T 1J4
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15
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Stitziel NO, Stirrups KE, Masca NGD, Erdmann J, Ferrario PG, König IR, Weeke PE, Webb TR, Auer PL, Schick UM, Lu Y, Zhang H, Dube MP, Goel A, Farrall M, Peloso GM, Won HH, Do R, van Iperen E, Kanoni S, Kruppa J, Mahajan A, Scott RA, Willenberg C, Braund PS, van Capelleveen JC, Doney ASF, Donnelly LA, Asselta R, Merlini PA, Duga S, Marziliano N, Denny JC, Shaffer CM, El-Mokhtari NE, Franke A, Gottesman O, Heilmann S, Hengstenberg C, Hoffman P, Holmen OL, Hveem K, Jansson JH, Jöckel KH, Kessler T, Kriebel J, Laugwitz KL, Marouli E, Martinelli N, McCarthy MI, Van Zuydam NR, Meisinger C, Esko T, Mihailov E, Escher SA, Alver M, Moebus S, Morris AD, Müller-Nurasyid M, Nikpay M, Olivieri O, Lemieux Perreault LP, AlQarawi A, Robertson NR, Akinsanya KO, Reilly DF, Vogt TF, Yin W, Asselbergs FW, Kooperberg C, Jackson RD, Stahl E, Strauch K, Varga TV, Waldenberger M, Zeng L, Kraja AT, Liu C, Ehret GB, Newton-Cheh C, Chasman DI, Chowdhury R, Ferrario M, Ford I, Jukema JW, Kee F, Kuulasmaa K, Nordestgaard BG, Perola M, Saleheen D, Sattar N, Surendran P, Tregouet D, Young R, Howson JMM, Butterworth AS, Danesh J, Ardissino D, Bottinger EP, Erbel R, Franks PW, Girelli D, Hall AS, Hovingh GK, Kastrati A, Lieb W, Meitinger T, Kraus WE, Shah SH, McPherson R, Orho-Melander M, Melander O, Metspalu A, Palmer CNA, Peters A, Rader D, Reilly MP, Loos RJF, Reiner AP, Roden DM, Tardif JC, Thompson JR, Wareham NJ, Watkins H, Willer CJ, Kathiresan S, Deloukas P, Samani NJ, Schunkert H. Coding Variation in ANGPTL4, LPL, and SVEP1 and the Risk of Coronary Disease. N Engl J Med 2016; 374:1134-44. [PMID: 26934567 PMCID: PMC4850838 DOI: 10.1056/nejmoa1507652] [Citation(s) in RCA: 359] [Impact Index Per Article: 44.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND The discovery of low-frequency coding variants affecting the risk of coronary artery disease has facilitated the identification of therapeutic targets. METHODS Through DNA genotyping, we tested 54,003 coding-sequence variants covering 13,715 human genes in up to 72,868 patients with coronary artery disease and 120,770 controls who did not have coronary artery disease. Through DNA sequencing, we studied the effects of loss-of-function mutations in selected genes. RESULTS We confirmed previously observed significant associations between coronary artery disease and low-frequency missense variants in the genes LPA and PCSK9. We also found significant associations between coronary artery disease and low-frequency missense variants in the genes SVEP1 (p.D2702G; minor-allele frequency, 3.60%; odds ratio for disease, 1.14; P=4.2×10(-10)) and ANGPTL4 (p.E40K; minor-allele frequency, 2.01%; odds ratio, 0.86; P=4.0×10(-8)), which encodes angiopoietin-like 4. Through sequencing of ANGPTL4, we identified 9 carriers of loss-of-function mutations among 6924 patients with myocardial infarction, as compared with 19 carriers among 6834 controls (odds ratio, 0.47; P=0.04); carriers of ANGPTL4 loss-of-function alleles had triglyceride levels that were 35% lower than the levels among persons who did not carry a loss-of-function allele (P=0.003). ANGPTL4 inhibits lipoprotein lipase; we therefore searched for mutations in LPL and identified a loss-of-function variant that was associated with an increased risk of coronary artery disease (p.D36N; minor-allele frequency, 1.9%; odds ratio, 1.13; P=2.0×10(-4)) and a gain-of-function variant that was associated with protection from coronary artery disease (p.S447*; minor-allele frequency, 9.9%; odds ratio, 0.94; P=2.5×10(-7)). CONCLUSIONS We found that carriers of loss-of-function mutations in ANGPTL4 had triglyceride levels that were lower than those among noncarriers; these mutations were also associated with protection from coronary artery disease. (Funded by the National Institutes of Health and others.).
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16
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Tardif JC, Rhéaume E, Lemieux Perreault LP, Grégoire JC, Feroz Zada Y, Asselin G, Provost S, Barhdadi A, Rhainds D, L'Allier PL, Ibrahim R, Upmanyu R, Niesor EJ, Benghozi R, Suchankova G, Laghrissi-Thode F, Guertin MC, Olsson AG, Mongrain I, Schwartz GG, Dubé MP. Pharmacogenomic determinants of the cardiovascular effects of dalcetrapib. ACTA ACUST UNITED AC 2015; 8:372-82. [PMID: 25583994 DOI: 10.1161/circgenetics.114.000663] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 12/16/2014] [Indexed: 11/16/2022]
Abstract
BACKGROUND Dalcetrapib did not improve clinical outcomes, despite increasing high-density lipoprotein cholesterol by 30%. These results differ from other evidence supporting high-density lipoprotein as a therapeutic target. Responses to dalcetrapib may vary according to patients' genetic profile. METHODS AND RESULTS We conducted a pharmacogenomic evaluation using a genome-wide approach in the dal-OUTCOMES study (discovery cohort, n=5749) and a targeted genotyping panel in the dal-PLAQUE-2 imaging trial (support cohort, n=386). The primary endpoint for the discovery cohort was a composite of cardiovascular events. The change from baseline in carotid intima-media thickness on ultrasonography at 6 and 12 months was evaluated as supporting evidence. A single-nucleotide polymorphism was found to be associated with cardiovascular events in the dalcetrapib arm, identifying the ADCY9 gene on chromosome 16 (rs1967309; P=2.41×10(-8)), with 8 polymorphisms providing P<10(-6) in this gene. Considering patients with genotype AA at rs1967309, there was a 39% reduction in the composite cardiovascular endpoint with dalcetrapib compared with placebo (hazard ratio, 0.61; 95% confidence interval, 0.41-0.92). In patients with genotype GG, there was a 27% increase in events with dalcetrapib versus placebo. Ten single-nucleotide polymorphism in the ADCY9 gene, the majority in linkage disequilibrium with rs1967309, were associated with the effect of dalcetrapib on intima-media thickness (P<0.05). Marker rs2238448 in ADCY9, in linkage disequilibrium with rs1967309 (r(2)=0.8), was associated with both the effects of dalcetrapib on intima-media thickness in dal-PLAQUE-2 (P=0.009) and events in dal-OUTCOMES (P=8.88×10(-8); hazard ratio, 0.67; 95% confidence interval, 0.58-0.78). CONCLUSIONS The effects of dalcetrapib on atherosclerotic outcomes are determined by correlated polymorphisms in the ADCY9 gene. CLINICAL TRIAL INFORMATION URL: http://www.clinicaltrials.gov. Unique identifiers: NCT00658515 and NCT01059682.
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Affiliation(s)
- Jean-Claude Tardif
- Montreal Heart Institute (J.-C.T., E.R., L.-P.L.P., J.C.G., Y.F.Z., G.A., S.P., A.B., D.R., P.L.L'., R.I., M.-C.G., I.M., M.-P.D.), Université de Montréal (J.-C.T., E.R., J.C.G., P.L.L'., R.I., M.-P.D.), Université de Montréal Beaulieu-Saucier Pharmacogenomics, Centre Montreal, Quebec, Canada (L.-P.L.P., Y.F.Z., G.A., S.P., A.B., I.M., M.-P.D.), Montreal Health Innovations Coordinating Centre (MHICC) (M.-C.G.), Montreal, Quebec, Canada; Stockholm Heart Center, Stockholm, Sweden (A.G.O.); Veterans Affairs Medical Center, University of Colorado, Denver (G.G.S.); and F. Hoffmann-La Roche, Basel, Switzerland (R.U., E.J.N., R.B., G.S., F.L.-T.).
| | - Eric Rhéaume
- Montreal Heart Institute (J.-C.T., E.R., L.-P.L.P., J.C.G., Y.F.Z., G.A., S.P., A.B., D.R., P.L.L'., R.I., M.-C.G., I.M., M.-P.D.), Université de Montréal (J.-C.T., E.R., J.C.G., P.L.L'., R.I., M.-P.D.), Université de Montréal Beaulieu-Saucier Pharmacogenomics, Centre Montreal, Quebec, Canada (L.-P.L.P., Y.F.Z., G.A., S.P., A.B., I.M., M.-P.D.), Montreal Health Innovations Coordinating Centre (MHICC) (M.-C.G.), Montreal, Quebec, Canada; Stockholm Heart Center, Stockholm, Sweden (A.G.O.); Veterans Affairs Medical Center, University of Colorado, Denver (G.G.S.); and F. Hoffmann-La Roche, Basel, Switzerland (R.U., E.J.N., R.B., G.S., F.L.-T.)
| | - Louis-Philippe Lemieux Perreault
- Montreal Heart Institute (J.-C.T., E.R., L.-P.L.P., J.C.G., Y.F.Z., G.A., S.P., A.B., D.R., P.L.L'., R.I., M.-C.G., I.M., M.-P.D.), Université de Montréal (J.-C.T., E.R., J.C.G., P.L.L'., R.I., M.-P.D.), Université de Montréal Beaulieu-Saucier Pharmacogenomics, Centre Montreal, Quebec, Canada (L.-P.L.P., Y.F.Z., G.A., S.P., A.B., I.M., M.-P.D.), Montreal Health Innovations Coordinating Centre (MHICC) (M.-C.G.), Montreal, Quebec, Canada; Stockholm Heart Center, Stockholm, Sweden (A.G.O.); Veterans Affairs Medical Center, University of Colorado, Denver (G.G.S.); and F. Hoffmann-La Roche, Basel, Switzerland (R.U., E.J.N., R.B., G.S., F.L.-T.)
| | - Jean C Grégoire
- Montreal Heart Institute (J.-C.T., E.R., L.-P.L.P., J.C.G., Y.F.Z., G.A., S.P., A.B., D.R., P.L.L'., R.I., M.-C.G., I.M., M.-P.D.), Université de Montréal (J.-C.T., E.R., J.C.G., P.L.L'., R.I., M.-P.D.), Université de Montréal Beaulieu-Saucier Pharmacogenomics, Centre Montreal, Quebec, Canada (L.-P.L.P., Y.F.Z., G.A., S.P., A.B., I.M., M.-P.D.), Montreal Health Innovations Coordinating Centre (MHICC) (M.-C.G.), Montreal, Quebec, Canada; Stockholm Heart Center, Stockholm, Sweden (A.G.O.); Veterans Affairs Medical Center, University of Colorado, Denver (G.G.S.); and F. Hoffmann-La Roche, Basel, Switzerland (R.U., E.J.N., R.B., G.S., F.L.-T.)
| | - Yassamin Feroz Zada
- Montreal Heart Institute (J.-C.T., E.R., L.-P.L.P., J.C.G., Y.F.Z., G.A., S.P., A.B., D.R., P.L.L'., R.I., M.-C.G., I.M., M.-P.D.), Université de Montréal (J.-C.T., E.R., J.C.G., P.L.L'., R.I., M.-P.D.), Université de Montréal Beaulieu-Saucier Pharmacogenomics, Centre Montreal, Quebec, Canada (L.-P.L.P., Y.F.Z., G.A., S.P., A.B., I.M., M.-P.D.), Montreal Health Innovations Coordinating Centre (MHICC) (M.-C.G.), Montreal, Quebec, Canada; Stockholm Heart Center, Stockholm, Sweden (A.G.O.); Veterans Affairs Medical Center, University of Colorado, Denver (G.G.S.); and F. Hoffmann-La Roche, Basel, Switzerland (R.U., E.J.N., R.B., G.S., F.L.-T.)
| | - Géraldine Asselin
- Montreal Heart Institute (J.-C.T., E.R., L.-P.L.P., J.C.G., Y.F.Z., G.A., S.P., A.B., D.R., P.L.L'., R.I., M.-C.G., I.M., M.-P.D.), Université de Montréal (J.-C.T., E.R., J.C.G., P.L.L'., R.I., M.-P.D.), Université de Montréal Beaulieu-Saucier Pharmacogenomics, Centre Montreal, Quebec, Canada (L.-P.L.P., Y.F.Z., G.A., S.P., A.B., I.M., M.-P.D.), Montreal Health Innovations Coordinating Centre (MHICC) (M.-C.G.), Montreal, Quebec, Canada; Stockholm Heart Center, Stockholm, Sweden (A.G.O.); Veterans Affairs Medical Center, University of Colorado, Denver (G.G.S.); and F. Hoffmann-La Roche, Basel, Switzerland (R.U., E.J.N., R.B., G.S., F.L.-T.)
| | - Sylvie Provost
- Montreal Heart Institute (J.-C.T., E.R., L.-P.L.P., J.C.G., Y.F.Z., G.A., S.P., A.B., D.R., P.L.L'., R.I., M.-C.G., I.M., M.-P.D.), Université de Montréal (J.-C.T., E.R., J.C.G., P.L.L'., R.I., M.-P.D.), Université de Montréal Beaulieu-Saucier Pharmacogenomics, Centre Montreal, Quebec, Canada (L.-P.L.P., Y.F.Z., G.A., S.P., A.B., I.M., M.-P.D.), Montreal Health Innovations Coordinating Centre (MHICC) (M.-C.G.), Montreal, Quebec, Canada; Stockholm Heart Center, Stockholm, Sweden (A.G.O.); Veterans Affairs Medical Center, University of Colorado, Denver (G.G.S.); and F. Hoffmann-La Roche, Basel, Switzerland (R.U., E.J.N., R.B., G.S., F.L.-T.)
| | - Amina Barhdadi
- Montreal Heart Institute (J.-C.T., E.R., L.-P.L.P., J.C.G., Y.F.Z., G.A., S.P., A.B., D.R., P.L.L'., R.I., M.-C.G., I.M., M.-P.D.), Université de Montréal (J.-C.T., E.R., J.C.G., P.L.L'., R.I., M.-P.D.), Université de Montréal Beaulieu-Saucier Pharmacogenomics, Centre Montreal, Quebec, Canada (L.-P.L.P., Y.F.Z., G.A., S.P., A.B., I.M., M.-P.D.), Montreal Health Innovations Coordinating Centre (MHICC) (M.-C.G.), Montreal, Quebec, Canada; Stockholm Heart Center, Stockholm, Sweden (A.G.O.); Veterans Affairs Medical Center, University of Colorado, Denver (G.G.S.); and F. Hoffmann-La Roche, Basel, Switzerland (R.U., E.J.N., R.B., G.S., F.L.-T.)
| | - David Rhainds
- Montreal Heart Institute (J.-C.T., E.R., L.-P.L.P., J.C.G., Y.F.Z., G.A., S.P., A.B., D.R., P.L.L'., R.I., M.-C.G., I.M., M.-P.D.), Université de Montréal (J.-C.T., E.R., J.C.G., P.L.L'., R.I., M.-P.D.), Université de Montréal Beaulieu-Saucier Pharmacogenomics, Centre Montreal, Quebec, Canada (L.-P.L.P., Y.F.Z., G.A., S.P., A.B., I.M., M.-P.D.), Montreal Health Innovations Coordinating Centre (MHICC) (M.-C.G.), Montreal, Quebec, Canada; Stockholm Heart Center, Stockholm, Sweden (A.G.O.); Veterans Affairs Medical Center, University of Colorado, Denver (G.G.S.); and F. Hoffmann-La Roche, Basel, Switzerland (R.U., E.J.N., R.B., G.S., F.L.-T.)
| | - Philippe L L'Allier
- Montreal Heart Institute (J.-C.T., E.R., L.-P.L.P., J.C.G., Y.F.Z., G.A., S.P., A.B., D.R., P.L.L'., R.I., M.-C.G., I.M., M.-P.D.), Université de Montréal (J.-C.T., E.R., J.C.G., P.L.L'., R.I., M.-P.D.), Université de Montréal Beaulieu-Saucier Pharmacogenomics, Centre Montreal, Quebec, Canada (L.-P.L.P., Y.F.Z., G.A., S.P., A.B., I.M., M.-P.D.), Montreal Health Innovations Coordinating Centre (MHICC) (M.-C.G.), Montreal, Quebec, Canada; Stockholm Heart Center, Stockholm, Sweden (A.G.O.); Veterans Affairs Medical Center, University of Colorado, Denver (G.G.S.); and F. Hoffmann-La Roche, Basel, Switzerland (R.U., E.J.N., R.B., G.S., F.L.-T.)
| | - Reda Ibrahim
- Montreal Heart Institute (J.-C.T., E.R., L.-P.L.P., J.C.G., Y.F.Z., G.A., S.P., A.B., D.R., P.L.L'., R.I., M.-C.G., I.M., M.-P.D.), Université de Montréal (J.-C.T., E.R., J.C.G., P.L.L'., R.I., M.-P.D.), Université de Montréal Beaulieu-Saucier Pharmacogenomics, Centre Montreal, Quebec, Canada (L.-P.L.P., Y.F.Z., G.A., S.P., A.B., I.M., M.-P.D.), Montreal Health Innovations Coordinating Centre (MHICC) (M.-C.G.), Montreal, Quebec, Canada; Stockholm Heart Center, Stockholm, Sweden (A.G.O.); Veterans Affairs Medical Center, University of Colorado, Denver (G.G.S.); and F. Hoffmann-La Roche, Basel, Switzerland (R.U., E.J.N., R.B., G.S., F.L.-T.)
| | - Ruchi Upmanyu
- Montreal Heart Institute (J.-C.T., E.R., L.-P.L.P., J.C.G., Y.F.Z., G.A., S.P., A.B., D.R., P.L.L'., R.I., M.-C.G., I.M., M.-P.D.), Université de Montréal (J.-C.T., E.R., J.C.G., P.L.L'., R.I., M.-P.D.), Université de Montréal Beaulieu-Saucier Pharmacogenomics, Centre Montreal, Quebec, Canada (L.-P.L.P., Y.F.Z., G.A., S.P., A.B., I.M., M.-P.D.), Montreal Health Innovations Coordinating Centre (MHICC) (M.-C.G.), Montreal, Quebec, Canada; Stockholm Heart Center, Stockholm, Sweden (A.G.O.); Veterans Affairs Medical Center, University of Colorado, Denver (G.G.S.); and F. Hoffmann-La Roche, Basel, Switzerland (R.U., E.J.N., R.B., G.S., F.L.-T.)
| | - Eric J Niesor
- Montreal Heart Institute (J.-C.T., E.R., L.-P.L.P., J.C.G., Y.F.Z., G.A., S.P., A.B., D.R., P.L.L'., R.I., M.-C.G., I.M., M.-P.D.), Université de Montréal (J.-C.T., E.R., J.C.G., P.L.L'., R.I., M.-P.D.), Université de Montréal Beaulieu-Saucier Pharmacogenomics, Centre Montreal, Quebec, Canada (L.-P.L.P., Y.F.Z., G.A., S.P., A.B., I.M., M.-P.D.), Montreal Health Innovations Coordinating Centre (MHICC) (M.-C.G.), Montreal, Quebec, Canada; Stockholm Heart Center, Stockholm, Sweden (A.G.O.); Veterans Affairs Medical Center, University of Colorado, Denver (G.G.S.); and F. Hoffmann-La Roche, Basel, Switzerland (R.U., E.J.N., R.B., G.S., F.L.-T.)
| | - Renée Benghozi
- Montreal Heart Institute (J.-C.T., E.R., L.-P.L.P., J.C.G., Y.F.Z., G.A., S.P., A.B., D.R., P.L.L'., R.I., M.-C.G., I.M., M.-P.D.), Université de Montréal (J.-C.T., E.R., J.C.G., P.L.L'., R.I., M.-P.D.), Université de Montréal Beaulieu-Saucier Pharmacogenomics, Centre Montreal, Quebec, Canada (L.-P.L.P., Y.F.Z., G.A., S.P., A.B., I.M., M.-P.D.), Montreal Health Innovations Coordinating Centre (MHICC) (M.-C.G.), Montreal, Quebec, Canada; Stockholm Heart Center, Stockholm, Sweden (A.G.O.); Veterans Affairs Medical Center, University of Colorado, Denver (G.G.S.); and F. Hoffmann-La Roche, Basel, Switzerland (R.U., E.J.N., R.B., G.S., F.L.-T.)
| | - Gabriela Suchankova
- Montreal Heart Institute (J.-C.T., E.R., L.-P.L.P., J.C.G., Y.F.Z., G.A., S.P., A.B., D.R., P.L.L'., R.I., M.-C.G., I.M., M.-P.D.), Université de Montréal (J.-C.T., E.R., J.C.G., P.L.L'., R.I., M.-P.D.), Université de Montréal Beaulieu-Saucier Pharmacogenomics, Centre Montreal, Quebec, Canada (L.-P.L.P., Y.F.Z., G.A., S.P., A.B., I.M., M.-P.D.), Montreal Health Innovations Coordinating Centre (MHICC) (M.-C.G.), Montreal, Quebec, Canada; Stockholm Heart Center, Stockholm, Sweden (A.G.O.); Veterans Affairs Medical Center, University of Colorado, Denver (G.G.S.); and F. Hoffmann-La Roche, Basel, Switzerland (R.U., E.J.N., R.B., G.S., F.L.-T.)
| | - Fouzia Laghrissi-Thode
- Montreal Heart Institute (J.-C.T., E.R., L.-P.L.P., J.C.G., Y.F.Z., G.A., S.P., A.B., D.R., P.L.L'., R.I., M.-C.G., I.M., M.-P.D.), Université de Montréal (J.-C.T., E.R., J.C.G., P.L.L'., R.I., M.-P.D.), Université de Montréal Beaulieu-Saucier Pharmacogenomics, Centre Montreal, Quebec, Canada (L.-P.L.P., Y.F.Z., G.A., S.P., A.B., I.M., M.-P.D.), Montreal Health Innovations Coordinating Centre (MHICC) (M.-C.G.), Montreal, Quebec, Canada; Stockholm Heart Center, Stockholm, Sweden (A.G.O.); Veterans Affairs Medical Center, University of Colorado, Denver (G.G.S.); and F. Hoffmann-La Roche, Basel, Switzerland (R.U., E.J.N., R.B., G.S., F.L.-T.)
| | - Marie-Claude Guertin
- Montreal Heart Institute (J.-C.T., E.R., L.-P.L.P., J.C.G., Y.F.Z., G.A., S.P., A.B., D.R., P.L.L'., R.I., M.-C.G., I.M., M.-P.D.), Université de Montréal (J.-C.T., E.R., J.C.G., P.L.L'., R.I., M.-P.D.), Université de Montréal Beaulieu-Saucier Pharmacogenomics, Centre Montreal, Quebec, Canada (L.-P.L.P., Y.F.Z., G.A., S.P., A.B., I.M., M.-P.D.), Montreal Health Innovations Coordinating Centre (MHICC) (M.-C.G.), Montreal, Quebec, Canada; Stockholm Heart Center, Stockholm, Sweden (A.G.O.); Veterans Affairs Medical Center, University of Colorado, Denver (G.G.S.); and F. Hoffmann-La Roche, Basel, Switzerland (R.U., E.J.N., R.B., G.S., F.L.-T.)
| | - Anders G Olsson
- Montreal Heart Institute (J.-C.T., E.R., L.-P.L.P., J.C.G., Y.F.Z., G.A., S.P., A.B., D.R., P.L.L'., R.I., M.-C.G., I.M., M.-P.D.), Université de Montréal (J.-C.T., E.R., J.C.G., P.L.L'., R.I., M.-P.D.), Université de Montréal Beaulieu-Saucier Pharmacogenomics, Centre Montreal, Quebec, Canada (L.-P.L.P., Y.F.Z., G.A., S.P., A.B., I.M., M.-P.D.), Montreal Health Innovations Coordinating Centre (MHICC) (M.-C.G.), Montreal, Quebec, Canada; Stockholm Heart Center, Stockholm, Sweden (A.G.O.); Veterans Affairs Medical Center, University of Colorado, Denver (G.G.S.); and F. Hoffmann-La Roche, Basel, Switzerland (R.U., E.J.N., R.B., G.S., F.L.-T.)
| | - Ian Mongrain
- Montreal Heart Institute (J.-C.T., E.R., L.-P.L.P., J.C.G., Y.F.Z., G.A., S.P., A.B., D.R., P.L.L'., R.I., M.-C.G., I.M., M.-P.D.), Université de Montréal (J.-C.T., E.R., J.C.G., P.L.L'., R.I., M.-P.D.), Université de Montréal Beaulieu-Saucier Pharmacogenomics, Centre Montreal, Quebec, Canada (L.-P.L.P., Y.F.Z., G.A., S.P., A.B., I.M., M.-P.D.), Montreal Health Innovations Coordinating Centre (MHICC) (M.-C.G.), Montreal, Quebec, Canada; Stockholm Heart Center, Stockholm, Sweden (A.G.O.); Veterans Affairs Medical Center, University of Colorado, Denver (G.G.S.); and F. Hoffmann-La Roche, Basel, Switzerland (R.U., E.J.N., R.B., G.S., F.L.-T.)
| | - Gregory G Schwartz
- Montreal Heart Institute (J.-C.T., E.R., L.-P.L.P., J.C.G., Y.F.Z., G.A., S.P., A.B., D.R., P.L.L'., R.I., M.-C.G., I.M., M.-P.D.), Université de Montréal (J.-C.T., E.R., J.C.G., P.L.L'., R.I., M.-P.D.), Université de Montréal Beaulieu-Saucier Pharmacogenomics, Centre Montreal, Quebec, Canada (L.-P.L.P., Y.F.Z., G.A., S.P., A.B., I.M., M.-P.D.), Montreal Health Innovations Coordinating Centre (MHICC) (M.-C.G.), Montreal, Quebec, Canada; Stockholm Heart Center, Stockholm, Sweden (A.G.O.); Veterans Affairs Medical Center, University of Colorado, Denver (G.G.S.); and F. Hoffmann-La Roche, Basel, Switzerland (R.U., E.J.N., R.B., G.S., F.L.-T.)
| | - Marie-Pierre Dubé
- Montreal Heart Institute (J.-C.T., E.R., L.-P.L.P., J.C.G., Y.F.Z., G.A., S.P., A.B., D.R., P.L.L'., R.I., M.-C.G., I.M., M.-P.D.), Université de Montréal (J.-C.T., E.R., J.C.G., P.L.L'., R.I., M.-P.D.), Université de Montréal Beaulieu-Saucier Pharmacogenomics, Centre Montreal, Quebec, Canada (L.-P.L.P., Y.F.Z., G.A., S.P., A.B., I.M., M.-P.D.), Montreal Health Innovations Coordinating Centre (MHICC) (M.-C.G.), Montreal, Quebec, Canada; Stockholm Heart Center, Stockholm, Sweden (A.G.O.); Veterans Affairs Medical Center, University of Colorado, Denver (G.G.S.); and F. Hoffmann-La Roche, Basel, Switzerland (R.U., E.J.N., R.B., G.S., F.L.-T.).
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17
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Morris DW, Pearson RD, Cormican P, Kenny EM, O'Dushlaine CT, Perreault LPL, Giannoulatou E, Tropea D, Maher BS, Wormley B, Kelleher E, Fahey C, Molinos I, Bellini S, Pirinen M, Strange A, Freeman C, Thiselton DL, Elves RL, Regan R, Ennis S, Dinan TG, McDonald C, Murphy KC, O'Callaghan E, Waddington JL, Walsh D, O'Donovan M, Grozeva D, Craddock N, Stone J, Scolnick E, Purcell S, Sklar P, Coe B, Eichler EE, Ophoff R, Buizer J, Szatkiewicz J, Hultman C, Sullivan P, Gurling H, Mcquillin A, St Clair D, Rees E, Kirov G, Walters J, Blackwood D, Johnstone M, Donohoe G, O'Neill FA, Kendler KS, Gill M, Riley BP, Spencer CCA, Corvin A. An inherited duplication at the gene p21 Protein-Activated Kinase 7 (PAK7) is a risk factor for psychosis. Hum Mol Genet 2014; 23:3316-26. [PMID: 24474471 PMCID: PMC4030770 DOI: 10.1093/hmg/ddu025] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 12/24/2013] [Accepted: 01/20/2014] [Indexed: 12/14/2022] Open
Abstract
Identifying rare, highly penetrant risk mutations may be an important step in dissecting the molecular etiology of schizophrenia. We conducted a gene-based analysis of large (>100 kb), rare copy-number variants (CNVs) in the Wellcome Trust Case Control Consortium 2 (WTCCC2) schizophrenia sample of 1564 cases and 1748 controls all from Ireland, and further extended the analysis to include an additional 5196 UK controls. We found association with duplications at chr20p12.2 (P = 0.007) and evidence of replication in large independent European schizophrenia (P = 0.052) and UK bipolar disorder case-control cohorts (P = 0.047). A combined analysis of Irish/UK subjects including additional psychosis cases (schizophrenia and bipolar disorder) identified 22 carriers in 11 707 cases and 10 carriers in 21 204 controls [meta-analysis Cochran-Mantel-Haenszel P-value = 2 × 10(-4); odds ratio (OR) = 11.3, 95% CI = 3.7, ∞]. Nineteen of the 22 cases and 8 of the 10 controls carried duplications starting at 9.68 Mb with similar breakpoints across samples. By haplotype analysis and sequencing, we identified a tandem ~149 kb duplication overlapping the gene p21 Protein-Activated Kinase 7 (PAK7, also called PAK5) which was in linkage disequilibrium with local haplotypes (P = 2.5 × 10(-21)), indicative of a single ancestral duplication event. We confirmed the breakpoints in 8/8 carriers tested and found co-segregation of the duplication with illness in two additional family members of one of the affected probands. We demonstrate that PAK7 is developmentally co-expressed with another known psychosis risk gene (DISC1) suggesting a potential molecular mechanism involving aberrant synapse development and plasticity.
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Affiliation(s)
- Derek W Morris
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Richard D Pearson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Paul Cormican
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Elaine M Kenny
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Colm T O'Dushlaine
- Broad Institute and Center for Human Genetics Research of Massachusetts General Hospital, Boston, MA 02142, USA
| | - Louis-Philippe Lemieux Perreault
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK Montreal Heart Institute, Université de Montréal, Montréal, Québec H1T 1C8, Canada
| | - Eleni Giannoulatou
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Daniela Tropea
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Brion S Maher
- Departments of Psychiatry and Human Genetics, Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Brandon Wormley
- Departments of Psychiatry and Human Genetics, Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Eric Kelleher
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Ciara Fahey
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Ines Molinos
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Stefania Bellini
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Matti Pirinen
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Amy Strange
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Colin Freeman
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Dawn L Thiselton
- Departments of Psychiatry and Human Genetics, Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Rachel L Elves
- Departments of Psychiatry and Human Genetics, Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Regina Regan
- School of Medicine and Medical Science, University College Dublin, Ireland
| | - Sean Ennis
- School of Medicine and Medical Science, University College Dublin, Ireland
| | - Timothy G Dinan
- Department of Psychiatry, University College Cork, Cork, Ireland
| | - Colm McDonald
- Department of Psychiatry, National University of Ireland, Galway, University Road, Galway, Ireland
| | - Kieran C Murphy
- Department of Psychiatry, RCSI Education and Research Centre, Beaumont Hospital, Dublin 9, Ireland
| | - Eadbhard O'Callaghan
- DETECT Early Intervention in Psychosis Services, Dun Laoghaire, Co. Dublin, Ireland
| | - John L Waddington
- Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Dermot Walsh
- Health Research Board, 73 Lower Baggot St, Dublin 2, Ireland
| | - Michael O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, and Neuroscience and Mental Health Research Institute, Cardiff University, Heath Park, Cardiff CF4 4XN, UK
| | - Detelina Grozeva
- MRC Centre for Neuropsychiatric Genetics and Genomics, and Neuroscience and Mental Health Research Institute, Cardiff University, Heath Park, Cardiff CF4 4XN, UK
| | - Nick Craddock
- MRC Centre for Neuropsychiatric Genetics and Genomics, and Neuroscience and Mental Health Research Institute, Cardiff University, Heath Park, Cardiff CF4 4XN, UK
| | - Jennifer Stone
- Broad Institute and Center for Human Genetics Research of Massachusetts General Hospital, Boston, MA 02142, USA
| | - Ed Scolnick
- Broad Institute and Center for Human Genetics Research of Massachusetts General Hospital, Boston, MA 02142, USA
| | - Shaun Purcell
- Broad Institute and Center for Human Genetics Research of Massachusetts General Hospital, Boston, MA 02142, USA The Mount Sinai Hospital, New York, NY 10029, USA
| | - Pamela Sklar
- Broad Institute and Center for Human Genetics Research of Massachusetts General Hospital, Boston, MA 02142, USA The Mount Sinai Hospital, New York, NY 10029, USA
| | - Bradley Coe
- University of Washington School of Medicine, Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Evan E Eichler
- University of Washington School of Medicine, Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Roel Ophoff
- Department of Human Genetics, UCLA School of Medicine, Los Angeles, CA 90095, USA
| | - Jacobine Buizer
- Rudolf Magnus Institute, University of Utrecht, 3584 CG Utrecht, Netherlands
| | - Jin Szatkiewicz
- University of North Carolina, Chapel Hill, NC 27599-7264, USA
| | - Christina Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | | | - Hugh Gurling
- Molecular Psychiatry Laboratory, Mental Health Sciences Unit, University College London, London WC1E 6BT, UK
| | - Andrew Mcquillin
- Molecular Psychiatry Laboratory, Mental Health Sciences Unit, University College London, London WC1E 6BT, UK
| | - David St Clair
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Elliott Rees
- MRC Centre for Neuropsychiatric Genetics and Genomics, and Neuroscience and Mental Health Research Institute, Cardiff University, Heath Park, Cardiff CF4 4XN, UK
| | - George Kirov
- MRC Centre for Neuropsychiatric Genetics and Genomics, and Neuroscience and Mental Health Research Institute, Cardiff University, Heath Park, Cardiff CF4 4XN, UK
| | - James Walters
- MRC Centre for Neuropsychiatric Genetics and Genomics, and Neuroscience and Mental Health Research Institute, Cardiff University, Heath Park, Cardiff CF4 4XN, UK
| | - Douglas Blackwood
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh EH10 5HF, UK and
| | - Mandy Johnstone
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh EH10 5HF, UK and
| | - Gary Donohoe
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Francis A O'Neill
- Department of Psychiatry, Queen's University, Belfast BT7 1NN, Northern Ireland
| | - Kenneth S Kendler
- Departments of Psychiatry and Human Genetics, Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Michael Gill
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Brien P Riley
- Departments of Psychiatry and Human Genetics, Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Chris C A Spencer
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Aiden Corvin
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 2, Ireland
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18
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Perreault LPL, Legault MA, Barhdadi A, Provost S, Normand V, Tardif JC, Dubé MP. Comparison of genotype clustering tools with rare variants. BMC Bioinformatics 2014; 15:52. [PMID: 24559245 PMCID: PMC3941951 DOI: 10.1186/1471-2105-15-52] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 02/19/2014] [Indexed: 11/15/2022] Open
Abstract
Background Along with the improvement of high throughput sequencing technologies, the genetics community is showing marked interest for the rare variants/common diseases hypothesis. While sequencing can still be prohibitive for large studies, commercially available genotyping arrays targeting rare variants prove to be a reasonable alternative. A technical challenge of array based methods is the task of deriving genotype classes (homozygous or heterozygous) by clustering intensity data points. The performance of clustering tools for common polymorphisms is well established, while their performance when conducted with a large proportion of rare variants (where data points are sparse for genotypes containing the rare allele) is less known. We have compared the performance of four clustering tools (GenCall, GenoSNP, optiCall and zCall) for the genotyping of over 10,000 samples using the Illumina’s HumanExome BeadChip, which includes 247,870 variants, 90% of which have a minor allele frequency below 5% in a population of European ancestry. Different reference parameters for GenCall and different initial parameters for GenoSNP were tested. Genotyping accuracy was assessed using data from the 1000 Genomes Project as a gold standard, and agreement between tools was measured. Results Concordance of GenoSNP’s calls with the gold standard was below expectations and was increased by changing the tool’s initial parameters. While the four tools provided concordance with the gold standard above 99% for common alleles, some of them performed poorly for rare alleles. The reproducibility of genotype calls for each tool was assessed using experimental duplicates which provided concordance rates above 99%. The inter-tool agreement of genotype calls was high for approximately 95% of variants. Most tools yielded similar error rates (approximately 0.02), except for zCall which performed better with a 0.00164 mean error rate. Conclusions The GenoSNP clustering tool could not be run straight “out of the box” with the HumanExome BeadChip, as modification of hard coded parameters was necessary to achieve optimal performance. Overall, GenCall marginally outperformed the other tools for the HumanExome BeadChip. The use of experimental replicates provided a valuable quality control tool for genotyping projects with rare variants.
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Affiliation(s)
- Louis-Philippe Lemieux Perreault
- Beaulieu-Saucier Université de Montréal Pharmacogenomics Center, Montreal Heart Institute Research Center, 5000 Bélanger Street, Montréal, Canada.
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Abstract
Summary: Genetic association studies making use of high-throughput genotyping arrays need to process large amounts of data in the order of millions of markers per experiment. The first step of any analysis with genotyping arrays is typically the conduct of a thorough data clean up and quality control to remove poor quality genotypes and generate metrics to inform and select individuals for downstream statistical analysis. We have developed pyGenClean, a bioinformatics tool to facilitate and standardize the genetic data clean up pipeline with genotyping array data. In conjunction with a source batch-queuing system, the tool minimizes data manipulation errors, accelerates the completion of the data clean up process and provides informative plots and metrics to guide decision making for statistical analysis. Availability and implementation:pyGenClean is an open source Python 2.7 software and is freely available, along with documentation and examples, from http://www.statgen.org. Contact:louis-philippe.lemieux.perreault@umontreal.ca or marie-pierre.dube@statgen.org
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Affiliation(s)
- Louis-Philippe Lemieux Perreault
- Montreal Heart Institute Research Center, Beaulieu-Saucier Université de Montréal Pharmacogenomics Centre, 5000 Bélanger Street, Montréal, Canada.
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20
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Perreault LPL, Andelfinger GU, Asselin G, Dubé MP. Partitioning of copy-number genotypes in pedigrees. BMC Bioinformatics 2010; 11:226. [PMID: 20438641 PMCID: PMC2874807 DOI: 10.1186/1471-2105-11-226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Accepted: 05/03/2010] [Indexed: 01/03/2023] Open
Abstract
Background Copy number variations (CNVs) and polymorphisms (CNPs) have only recently gained the genetic community's attention. Conservative estimates have shown that CNVs and CNPs might affect more than 10% of the genome and that they may be at least as important as single nucleotide polymorphisms in assessing human variability. Widely used tools for CNP analysis have been implemented in Birdsuite and PLINK for the purpose of conducting genetic association studies based on the unpartitioned total number of CNP copies provided by the intensities from Affymetrix's Genome-Wide Human SNP Array. Here, we are interested in partitioning copy number variations and polymorphisms in extended pedigrees for the purpose of linkage analysis on familial data. Results We have developed CNGen, a new software for the partitioning of copy number polymorphism using the integrated genotypes from Birdsuite with the Affymetrix platform. The algorithm applied to familial trios or extended pedigrees can produce partitioned copy number genotypes with distinct parental alleles. We have validated the algorithm using simulations on a complex pedigree structure using frequencies calculated from a real dataset of 300 genotyped samples from 42 pedigrees segregating a congenital heart defect phenotype. Conclusions CNGen is the first published software for the partitioning of copy number genotypes in pedigrees, making possible the use CNPs and CNVs for linkage analysis. It was implemented with the Python interpreter version 2.5.2. It was successfully tested on current Linux, Windows and Mac OS workstations.
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