Annotation of loci from genome-wide association studies using tissue-specific quantitative interaction proteomics.

PubWeight™: 0.86‹?›

🔗 View Article (PMC 4117722)

Published in Nat Methods on June 22, 2014

Authors

Alicia Lundby1, Elizabeth J Rossin2, Annette B Steffensen3, Moshe Rav Acha4, Christopher Newton-Cheh5, Arne Pfeufer6, Stacey N Lynch4, QT Interval International GWAS Consortium (QT-IGC), Søren-Peter Olesen3, Søren Brunak7, Patrick T Ellinor4, J Wouter Jukema8, Stella Trompet9, Ian Ford10, Peter W Macfarlane11, Bouwe P Krijthe12, Albert Hofman12, André G Uitterlinden13, Bruno H Stricker14, Hendrik M Nathoe15, Wilko Spiering16, Mark J Daly17, Folkert W Asselbergs18, Pim van der Harst19, David J Milan4, Paul I W de Bakker20, Kasper Lage21, Jesper V Olsen22

Author Affiliations

1: 1] Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA. [2] Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark. [3] The Danish National Research Foundation Centre for Cardiac Arrhythmia, University of Copenhagen, Copenhagen, Denmark.
2: 1] The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA. [2] Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA. [3] MD/PhD Program and Health Sciences and Technology Program, Harvard Medical School, Boston, USA. [4].
3: The Danish National Research Foundation Centre for Cardiac Arrhythmia, Copenhagen, Denmark.
4: 1] Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA. [2] Center for Human Genetics Research, Massachusetts General Hospital, Boston, Massachusetts, USA.
5: 1] The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA. [2] Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA. [3] Center for Human Genetics Research, Massachusetts General Hospital, Boston, Massachusetts, USA.
6: Institute of Human Genetics, Technical University of Munich, Munich, Germany.
7: 1] Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark. [2] Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark.
8: 1] Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands. [2] Durrer Center for Cardiogenetic Research, ICIN - Netherlands Heart Institute, Utrecht, the Netherlands.
9: 1] Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands. [2] Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands.
10: Robertson Centre for Biostatistics, University of Glasgow, Glasgow, UK.
11: Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK.
12: 1] Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands. [2] Netherlands Consortium for Healthy Aging (NCHA), Leiden, the Netherlands.
13: 1] Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands. [2] Netherlands Consortium for Healthy Aging (NCHA), Leiden, the Netherlands. [3] Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands.
14: 1] Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands. [2] Netherlands Consortium for Healthy Aging (NCHA), Leiden, the Netherlands. [3] Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands. [4] Inspectorate for Health Care, The Hague, the Netherlands. [5] Department of Medical Informatics, Erasmus Medical Center, Rotterdam, the Netherlands. [6] Department of Vascular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands.
15: Department of Cardiology, Division of Heart and Lungs, University Medical Center Utrecht, Utrecht, the Netherlands.
16: Department of Vascular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands.
17: 1] The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA. [2] Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA.
18: 1] Durrer Center for Cardiogenetic Research, ICIN - Netherlands Heart Institute, Utrecht, the Netherlands. [2] Department of Cardiology, Division of Heart and Lungs, University Medical Center Utrecht, Utrecht, the Netherlands. [3] Faculty of Population Health Sciences, Institute of Cardiovascular Science, University College London, London, UK.
19: University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
20: 1] Department of Epidemiology, University Medical Center Utrecht, Utrecht, the Netherlands. [2] Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands.
21: 1] Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark. [2] The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA. [3] Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA. [4] Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark. [5] Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, Massachusetts, USA. [6].
22: 1] Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark. [2].

Articles cited by this

PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet (2007) 209.92

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol (2008) 38.00

Proteome survey reveals modularity of the yeast cell machinery. Nature (2006) 20.77

Pravastatin in elderly individuals at risk of vascular disease (PROSPER): a randomised controlled trial. Lancet (2002) 17.19

Practical aspects of imputation-driven meta-analysis of genome-wide association studies. Hum Mol Genet (2008) 13.26

Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat Protoc (2007) 10.71

Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap. Mol Cell Proteomics (2005) 10.60

A molecular basis for cardiac arrhythmia: HERG mutations cause long QT syndrome. Cell (1995) 10.18

A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol (2007) 9.90

Ca(V)1.2 calcium channel dysfunction causes a multisystem disorder including arrhythmia and autism. Cell (2004) 7.45

Positional cloning of a novel potassium channel gene: KVLQT1 mutations cause cardiac arrhythmias. Nat Genet (1996) 7.35

Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology. PLoS Genet (2011) 6.20

Common variants at ten loci influence QT interval duration in the QTGEN Study. Nat Genet (2009) 5.20

Higher-energy C-trap dissociation for peptide modification analysis. Nat Methods (2007) 5.04

A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed. Mol Cell Proteomics (2009) 4.75

Common variants at ten loci modulate the QT interval duration in the QTSCD Study. Nat Genet (2009) 4.10

Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions. J Cell Biol (2010) 3.61

A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes. Proc Natl Acad Sci U S A (2008) 3.57

Mutant caveolin-3 induces persistent late sodium current and is associated with long-QT syndrome. Circulation (2006) 3.50

The Rotterdam Study: 2010 objectives and design update. Eur J Epidemiol (2009) 3.44

Syntrophin mutation associated with long QT syndrome through activation of the nNOS-SCN5A macromolecular complex. Proc Natl Acad Sci U S A (2008) 2.79

Universal risk factors for multifactorial diseases: LifeLines: a three-generation population-based study. Eur J Epidemiol (2007) 2.18

The design of a prospective study of Pravastatin in the Elderly at Risk (PROSPER). PROSPER Study Group. PROspective Study of Pravastatin in the Elderly at Risk. Am J Cardiol (1999) 2.18

The QT syndromes: long and short. Lancet (2008) 2.10

Quantitative proteomics of the Cav2 channel nano-environments in the mammalian brain. Proc Natl Acad Sci U S A (2010) 1.85

Identification of heart rate-associated loci and their effects on cardiac conduction and rhythm disorders. Nat Genet (2013) 1.72

Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues. Nat Commun (2012) 1.72

Drug-sensitized zebrafish screen identifies multiple genes, including GINS3, as regulators of myocardial repolarization. Circulation (2009) 1.41

KCNQ1 mutation Q147R is associated with atrial fibrillation and prolonged QT interval. Heart Rhythm (2007) 1.39

Second manifestations of ARTerial disease (SMART) study: rationale and design. Eur J Epidemiol (1999) 1.35

In vivo phosphoproteomics analysis reveals the cardiac targets of β-adrenergic receptor signaling. Sci Signal (2013) 1.22

Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization. Nat Genet (2014) 1.17

Impaired Ca2+ store functions in skeletal and cardiac muscle cells from sarcalumenin-deficient mice. J Biol Chem (2004) 1.05

Separate Na,K-ATPase genes are required for otolith formation and semicircular canal development in zebrafish. Dev Biol (2006) 0.97

Obstructive hypertrophic cardiomyopathy is associated with reduced expression of vinculin in the intercalated disc. Biochem Biophys Res Commun (2006) 0.90

In-vivo characterization of human dilated cardiomyopathy genes in zebrafish. Biochem Biophys Res Commun (2009) 0.89

GeLCMS for in-depth protein characterization and advanced analysis of proteomes. Methods Mol Biol (2011) 0.88

Patients with coronary, cerebrovascular or peripheral arterial obstructive disease differ in risk for new vascular events and mortality: the SMART study. Eur J Cardiovasc Prev Rehabil (2010) 0.78

Articles by these authors

Defining the role of common variation in the genomic and biological architecture of adult human height. Nat Genet (2014) 5.78

Association between alcohol and cardiovascular disease: Mendelian randomisation analysis based on individual participant data. BMJ (2014) 4.69

HMG-coenzyme A reductase inhibition, type 2 diabetes, and bodyweight: evidence from genetic analysis and randomised trials. Lancet (2014) 3.94

Metformin for non-diabetic patients with coronary heart disease (the CAMERA study): a randomised controlled trial. Lancet Diabetes Endocrinol (2013) 1.95

The effect of statin therapy on heart failure events: a collaborative meta-analysis of unpublished data from major randomized trials. Eur Heart J (2015) 1.83

Prognostic significance of infarct core pathology revealed by quantitative non-contrast in comparison with contrast cardiac magnetic resonance imaging in reperfused ST-elevation myocardial infarction survivors. Eur Heart J (2015) 1.62

The effect of QRS duration on cardiac resynchronization therapy in patients with a narrow QRS complex: a subgroup analysis of the EchoCRT trial. Eur Heart J (2015) 1.45

Bradycardia and atrial fibrillation in patients with stable coronary artery disease treated with ivabradine: an analysis from the SIGNIFY study. Eur Heart J (2015) 1.42

Genome-wide association study identifies multiple susceptibility loci for diffuse large B cell lymphoma. Nat Genet (2014) 1.41

The importance of patient-reported outcomes: a call for their comprehensive integration in cardiovascular clinical trials. Eur Heart J (2014) 1.40

Association of Cardiometabolic Multimorbidity With Mortality. JAMA (2015) 1.32

Trans-ancestry genome-wide association study identifies 12 genetic loci influencing blood pressure and implicates a role for DNA methylation. Nat Genet (2015) 1.28

Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization. Nat Genet (2014) 1.17

Assessing methods to specify the target difference for a randomised controlled trial: DELTA (Difference ELicitation in TriAls) review. Health Technol Assess (2014) 1.16

Fine mapping in the MHC region accounts for 18% additional genetic risk for celiac disease. Nat Genet (2015) 1.09

Common variants in the HLA-DQ region confer susceptibility to idiopathic achalasia. Nat Genet (2014) 1.04

Genome-wide meta-analysis identifies multiple novel associations and ethnic heterogeneity of psoriasis susceptibility. Nat Commun (2015) 0.93

PCSK9 genetic variants and risk of type 2 diabetes: a mendelian randomisation study. Lancet Diabetes Endocrinol (2016) 0.92

Population-specific genotype imputations using minimac or IMPUTE2. Nat Protoc (2015) 0.88

The incidence and risk factors for new onset atrial fibrillation in the PROSPER study. Europace (2011) 0.86

Cardiovascular and metabolic effects of metformin in patients with type 1 diabetes (REMOVAL): a double-blind, randomised, placebo-controlled trial. Lancet Diabetes Endocrinol (2017) 0.83

Endovascular therapy for acute ischaemic stroke: the Pragmatic Ischaemic Stroke Thrombectomy Evaluation (PISTE) randomised, controlled trial. J Neurol Neurosurg Psychiatry (2016) 0.83

Heavier smoking may lead to a relative increase in waist circumference: evidence for a causal relationship from a Mendelian randomisation meta-analysis. The CARTA consortium. BMJ Open (2015) 0.80

Rare genetic variants previously associated with congenital forms of long QT syndrome have little or no effect on the QT interval. Eur Heart J (2015) 0.80

Renal Denervation in a Real Life Setting: A Gradual Decrease in Home Blood Pressure. PLoS One (2016) 0.79

Protocol of the Febuxostat versus Allopurinol Streamlined Trial (FAST): a large prospective, randomised, open, blinded endpoint study comparing the cardiovascular safety of allopurinol and febuxostat in the management of symptomatic hyperuricaemia. BMJ Open (2014) 0.78

Traditional and new composite endpoints in heart failure clinical trials: facilitating comprehensive efficacy assessments and improving trial efficiency. Eur J Heart Fail (2016) 0.77

52 Genetic Loci Influencing Myocardial Mass. J Am Coll Cardiol (2016) 0.77

Methods of a large prospective, randomised, open-label, blinded end-point study comparing morning versus evening dosing in hypertensive patients: the Treatment In Morning versus Evening (TIME) study. BMJ Open (2016) 0.76

Monotherapy versus dual therapy for the initial treatment of hypertension (PATHWAY-1): a randomised double-blind controlled trial. BMJ Open (2015) 0.76

SurgiCal Obesity Treatment Study (SCOTS): protocol for a national prospective cohort study of patients undergoing bariatric surgery in Scotland. BMJ Open (2015) 0.75

Use of Antihypertensive Drugs and Ischemic Stroke Severity - Is There a Role for Angiotensin-II? PLoS One (2016) 0.75

Study protocol; Thyroid hormone Replacement for Untreated older adults with Subclinical hypothyroidism - a randomised placebo controlled Trial (TRUST). BMC Endocr Disord (2017) 0.75

The Effects of Renal Denervation on Renal Hemodynamics and Renal Vasculature in a Porcine Model. PLoS One (2015) 0.75

Electronic health records to facilitate clinical research. Clin Res Cardiol (2016) 0.75

Exome-wide association study of plasma lipids in >300,000 individuals. Nat Genet (2017) 0.75

Erratum to "Traditional and new composite endpoints in heart failure clinical trials: facilitating comprehensive efficacy assessments and improving trial efficiency" [Eur J Heart Fail 2016;18:482-489]. Eur J Heart Fail (2016) 0.75

Prognostic implications of left ventricular global longitudinal strain in heart failure patients with narrow QRS complex treated with cardiac resynchronization therapy: a subanalysis of the randomized EchoCRT trial. Eur Heart J (2017) 0.75

Association between GDF-15 levels and changes in vascular and physical function in older patients with hypertension. Aging Clin Exp Res (2016) 0.75

LDL-Cholesterol Lowering for the Primary Prevention of Cardiovascular Disease Among Men with Primary Elevations of LDL-Cholesterol Levels of 190 mg/dL or Above: Analyses from the WOSCOPS 5-year Randomised Trial and 20-year Observational Follow-Up. Circulation (2017) 0.75

Liver enzymes are not directly involved in atrial fibrillation: a prospective cohort study. Eur J Clin Invest (2017) 0.75

Duration of chronic heart failure affects outcomes with preserved effects of heart rate reduction with ivabradine: findings from SHIFT. Eur J Heart Fail (2017) 0.75

Nicorandil, Gastrointestinal Adverse Drug Reactions and Ulcerations: A Systematic Review. Adv Ther (2016) 0.75

Non-adherence to ivabradine and placebo and outcomes in chronic heart failure: an analysis from SHIFT. Eur J Heart Fail (2016) 0.75

Independent academic Data Monitoring Committees for clinical trials in cardiovascular and cardiometabolic diseases. Eur J Heart Fail (2017) 0.75

Primary care-led weight management for remission of type 2 diabetes (DiRECT): an open-label, cluster-randomised trial. Lancet (2017) 0.75

Comparison of the spatial QRS-T angle derived from digital ECGs recorded using conventional electrode placement with that derived from Mason-Likar electrode position. J Electrocardiol (2016) 0.75

Renal denervation beyond the bifurcation: The effect of distal ablation placement on safety and blood pressure. J Clin Hypertens (Greenwich) (2017) 0.75