Genome-wide association study identifies multiple susceptibility loci for pulmonary fibrosis

Brent S. Pedersen | Naftali Kaminski | James D. Crapo | Yoichiro Kamatani | Elizabeth A. Regan | Elissa Murphy | David A. Schwartz | David Lynch | Kevin K. Brown | Keith Smith | Joy D. Cogan | Athol U. Wells | Kenneth B. Beckman | Tasha E. Fingerlin | Philip L. Molyneaux | Toby M. Maher | James E. Loyd | Gregory P. Cosgrove | Barry J. Make | Annie Pardo | Weiming Zhang | E. Regan | D. Lynch | B. Make | J. Crapo | H. Collard | Y. Kamatani | M. Lathrop | D. Zélénika | K. Beckman | D. Schwartz | N. Kaminski | M. Moffatt | G. Gudmundsson | D. McKean | R. D. du Bois | M. Selman | K. Brown | M. Steele | S. Groshong | A. Pardo | P. Wolters | A. Wells | T. Fingerlin | J. Cogan | K. Gibson | Elissa Murphy | Weiming Zhang | A. Peljto | J. Loyd | G. Cosgrove | W. Bradford | K. Kossen | S. Seiwert | C. Garcia | M. Devine | H. Isaksson | Yingze Zhang | L. Lancaster | W. Mason | T. Maher | P. Molyneaux | D. S. Kim | Dinesha S. Walek | J. Daniel | Keith Smith | Janet L. Talbert | Ravin N. Kidd | C. Markin | M. Schwarz | David F McKean | Mark Lathrop | Yingze Zhang | Diana Zelenika | Anna L Peljto | Miriam F. Moffatt | Moises Selman | Paul J. Wolters | Gunnar Gudmundsson | Dong Soon Kim | Marvin I. Schwarz | Harold R. Collard | Scott D. Seiwert | Karl Kossen | Mark P. Steele | Steve Groshong | Helgi J. Isaksson | Anna L. Peljto | Williamson Z. Bradford | Roland M. du Bois | Christine Kim Garcia | Megan S. Devine | Kevin F. Gibson | Lisa H. Lancaster | Wendi R. Mason | Jerry J. Daniel | David McKean | Janet Talbert | Cheryl R. Markin | Kenneth B. Beckman | A. Pardo | Marvin I. Schwarz | J. Crapo | Mark Lathrop | Kevin K. Brown | Miriam F. Moffatt | P. Molyneaux | Moisés Selman | Weiming Zhang | Mark P. Steele | James E. Loyd | Gregory P. Cosgrove | David Lynch | Steve Groshong | P. Wolters | Williamson Z. Bradford | Roland M. du Bois | Christine Kim Garcia | Gunnar Gudmundsson | Naftali Kaminski | Yingze Zhang | Lisa H. Lancaster | Athol U. Wells | Dong Soon Kim | Elizabeth A. Regan | Brent S. Pedersen | Ravin N. Kidd | David A. Schwartz | R. du Bois | Naftali Kaminski | M. Lathrop

[1]  P. Donnelly,et al.  A new multipoint method for genome-wide association studies by imputation of genotypes , 2007, Nature Genetics.

[2]  M. Saarma,et al.  A novel gene family encoding leucine-rich repeat transmembrane proteins differentially expressed in the nervous system. , 2003, Genomics.

[3]  E. Crouch,et al.  Pathobiology of pulmonary fibrosis. , 1990, The American journal of physiology.

[4]  B. Hansen,et al.  Optimal Full Matching and Related Designs via Network Flows , 2006 .

[5]  V. Poletti,et al.  Aberrant Wnt/ (cid:1) -Catenin Pathway Activation in Idiopathic Pulmonary Fibrosis , 2003 .

[6]  P. Donnelly,et al.  A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies , 2009, PLoS genetics.

[7]  C. Guillouf,et al.  Spi-1/PU.1 Oncoprotein Affects Splicing Decisions in a Promoter Binding-dependent Manner* , 2006, Journal of Biological Chemistry.

[8]  P. D. de Jong,et al.  Surfactant protein C mutations are the basis of a significant portion of adult familial pulmonary fibrosis in a dutch cohort. , 2010, American journal of respiratory and critical care medicine.

[9]  S. Heath,et al.  Investigation of the fine structure of European populations with applications to disease association studies , 2008, European Journal of Human Genetics.

[10]  D. Reich,et al.  Population Structure and Eigenanalysis , 2006, PLoS genetics.

[11]  M. Stephens,et al.  Genome-wide Efficient Mixed Model Analysis for Association Studies , 2012, Nature Genetics.

[12]  C. Nguyên,et al.  Inhibition of Wnt/β-catenin/CREB binding protein (CBP) signaling reverses pulmonary fibrosis , 2010, Proceedings of the National Academy of Sciences.

[13]  S. Kudoh,et al.  A genome-wide association study identifies an association of a common variant in TERT with susceptibility to idiopathic pulmonary fibrosis , 2008, Journal of Medical Genetics.

[14]  J. Marchini,et al.  Genotype imputation for genome-wide association studies , 2010, Nature Reviews Genetics.

[15]  N. Kaminski,et al.  Idiopathic Pulmonary Fibrosis: Aberrant Recapitulation of Developmental Programs? , 2008, PLoS medicine.

[16]  M. Mareel,et al.  alphaT-catenin: a novel tissue-specific beta-catenin-binding protein mediating strong cell-cell adhesion. , 2001, Journal of cell science.

[17]  V. Poletti,et al.  Aberrant Wnt/beta-catenin pathway activation in idiopathic pulmonary fibrosis. , 2003, The American journal of pathology.

[18]  H. Calkins,et al.  Mechanisms of Disease: molecular genetics of arrhythmogenic right ventricular dysplasia/cardiomyopathy , 2008, Nature Clinical Practice Cardiovascular Medicine.

[19]  P. Lansdorp,et al.  Telomerase mutations in families with idiopathic pulmonary fibrosis. , 2007, The New England journal of medicine.

[20]  Christoph Lange,et al.  Variants in FAM13A are associated with chronic obstructive pulmonary disease , 2010, Nature Genetics.

[21]  N. Grishin,et al.  Genetic defects in surfactant protein A2 are associated with pulmonary fibrosis and lung cancer. , 2009, American journal of human genetics.

[22]  I. Petersen,et al.  Desmoplakin acts as a tumor suppressor by inhibition of the Wnt/β-catenin signaling pathway in human lung cancer. , 2012, Carcinogenesis.

[23]  Corinna Cortes,et al.  Support-Vector Networks , 1995, Machine Learning.

[24]  Michael Boehnke,et al.  LocusZoom: regional visualization of genome-wide association scan results , 2010, Bioinform..

[25]  S. Sahn,et al.  Effect of interferon gamma-1b on survival in patients with idiopathic pulmonary fibrosis (INSPIRE): a multicentre, randomised, placebo-controlled trial , 2009, The Lancet.

[26]  P. Visscher,et al.  GCTA: a tool for genome-wide complex trait analysis. , 2011, American journal of human genetics.

[27]  Hugh Calkins,et al.  Desmosomal Dysfunction due to Mutations in Desmoplakin Causes Arrhythmogenic Right Ventricular Dysplasia/Cardiomyopathy , 2006, Circulation research.

[28]  A. Nicholson,et al.  Mucin 5B promoter polymorphism is associated with idiopathic pulmonary fibrosis but not with development of lung fibrosis in systemic sclerosis or sarcoidosis , 2013, Thorax.

[29]  T. King,et al.  An immunohistochemical study of architectural remodeling and connective tissue synthesis in pulmonary fibrosis. , 1989, The American review of respiratory disease.

[30]  Jonathan Haines,et al.  Heterozygosity for a surfactant protein C gene mutation associated with usual interstitial pneumonitis and cellular nonspecific interstitial pneumonitis in one kindred. , 2002, American journal of respiratory and critical care medicine.

[31]  M. Mareel,et al.  αT-Catenin: a novel tissue-specific β-catenin-binding protein mediating strong cell-cell adhesion , 2001 .

[32]  E. Zeggini,et al.  Synthetic associations in the context of genome-wide association scan signals , 2010, Human molecular genetics.

[33]  David B. Goldstein,et al.  Rare Variants Create Synthetic Genome-Wide Associations , 2010, PLoS biology.

[34]  I. D. Johnston,et al.  Exposure to commonly prescribed drugs and the etiology of cryptogenic fibrosing alveolitis: a case-control study. , 1998, American journal of respiratory and critical care medicine.

[35]  J. McGrath,et al.  Compound heterozygosity for non-sense and mis-sense mutations in desmoplakin underlies skin fragility/woolly hair syndrome. , 2002, The Journal of investigative dermatology.

[36]  J. Whitsett,et al.  ABCA3 gene mutations in newborns with fatal surfactant deficiency. , 2004, The New England journal of medicine.

[37]  M. Katoh,et al.  Hedgehog signaling pathway and gastric cancer , 2005, Cancer biology & therapy.

[38]  Ivana V. Yang,et al.  A common MUC5B promoter polymorphism and pulmonary fibrosis. , 2011, The New England journal of medicine.

[39]  T. Colby,et al.  Usual interstitial pneumonia in an adolescent with ABCA3 mutations. , 2008, Chest.

[40]  O. Delaneau,et al.  Supplementary Information for ‘ Improved whole chromosome phasing for disease and population genetic studies ’ , 2012 .

[41]  R. Boucher.  Idiopathic pulmonary fibrosis--a sticky business. , 2011, The New England journal of medicine.

[42]  I. Leigh,et al.  Erratum: Haploinsufficiency of desmoplakin causes a striate subtype of palmoplantar keratoderma (Human Molecular Genetics (1999) 8 (143-148)) , 1999 .

[43]  N. Heisterkamp,et al.  Resistance to farnesyltransferase inhibitors in Bcr/Abl-positive lymphoblastic leukemia by increased expression of a novel ABC transporter homolog ATP11a. , 2005, Blood.

[44]  A. Kowalczyk,et al.  The desmosome. , 2009, Cold Spring Harbor perspectives in biology.

[45]  Kenneth K. Kidd,et al.  Structural Diversity and African Origin of the 17q21.31 Inversion Polymorphism , 2012, Nature Genetics.

[46]  G. Raghu.  Idiopathic pulmonary fibrosis: new evidence and an improved standard of care in 2012 , 2012, The Lancet.

[47]  E. Puré,et al.  Fibroblast activation protein: a serine protease expressed at the remodeling interface in idiopathic pulmonary fibrosis. , 2006, Human pathology.

[48]  P. Lansdorp,et al.  Short telomeres are a risk factor for idiopathic pulmonary fibrosis , 2008, Proceedings of the National Academy of Sciences.

[49]  G. McCaughan,et al.  DP8 and DP9 have extra-enzymatic roles in cell adhesion, migration and apoptosis. , 2006, Advances in experimental medicine and biology.

[50]  Yun Li,et al.  METAL: fast and efficient meta-analysis of genomewide association scans , 2010, Bioinform..

[51]  I. Noth,et al.  A variant in the promoter of MUC5B and idiopathic pulmonary fibrosis. , 2011, The New England journal of medicine.

[52]  E. Regan,et al.  Genetic Epidemiology of COPD (COPDGene) Study Design , 2011, COPD.

[53]  G. Hunninghake,et al.  Idiopathic pulmonary fibrosis. , 2001, The New England journal of medicine.

[54]  V. Ambrosini,et al.  Genetic mutations in surfactant protein C are a rare cause of sporadic cases of IPF , 2004, Thorax.

[55]  I. Leigh,et al.  Haploinsufficiency of desmoplakin causes a striate subtype of palmoplantar keratoderma. , 1999, Human molecular genetics.

[56]  C. Ruppert,et al.  Epithelial endoplasmic reticulum stress and apoptosis in sporadic idiopathic pulmonary fibrosis. , 2008, American journal of respiratory and critical care medicine.

[57]  J. Voynow,et al.  Respiratory tract mucin genes and mucin glycoproteins in health and disease. , 2006, Physiological reviews.

[58]  Andrew D. Johnson,et al.  Genome-wide association identifies OBFC1 as a locus involved in human leukocyte telomere biology , 2010, Proceedings of the National Academy of Sciences.

[59]  M. Nalls,et al.  Genome-wide meta-analysis points to CTC1 and ZNF676 as genes regulating telomere homeostasis in humans , 2012, Human molecular genetics.

[60]  J. Whitsett,et al.  ABCA3 mutations associated with pediatric interstitial lung disease. , 2005, American journal of respiratory and critical care medicine.

[61]  Marta E Alarcón-Riquelme,et al.  Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci , 2008, Nature Genetics.

[62]  J. McGrath,et al.  Striate palmoplantar keratoderma resulting from desmoplakin haploinsufficiency. , 1999, The Journal of investigative dermatology.

[63]  Paul J. Friedman,et al.  American Thoracic Society/European Respiratory Society International Multidisciplinary Consensus Classification of the Idiopathic Interstitial Pneumonias. This joint statement of the American Thoracic Society (ATS), and the European Respiratory Society (ERS) was adopted by the ATS board of directors , 2002, American journal of respiratory and critical care medicine.

[64]  O. Delaneau,et al.  A linear complexity phasing method for thousands of genomes , 2011, Nature Methods.

[65]  R. Handsaker,et al.  Structural haplotypes and recent evolution of the human 17q21.31 region , 2012, Nature Genetics.

[66]  H Page McAdams,et al.  Clinical and pathologic features of familial interstitial pneumonia. , 2005, American journal of respiratory and critical care medicine.

[67]  O. Khalifa,et al.  Novel homozygous mutation in DSP causing skin fragility–woolly hair syndrome: report of a large family and review of the desmoplakin‐related phenotypes , 2011, Clinical genetics.

[68]  Christian Gieger,et al.  Genome-wide association and large scale follow-up identifies 16 new loci influencing lung function , 2011, Nature Genetics.

[69]  N. Morton.  Genetic epidemiology , 1997, International Journal of Obesity.

[70]  Chao Xing,et al.  Adult-onset pulmonary fibrosis caused by mutations in telomerase , 2007, Proceedings of the National Academy of Sciences.

[71]  J. Marchini,et al.  Genotype Imputation with Thousands of Genomes , 2011, G3: Genes | Genomes | Genetics.