Rare variant analysis of 4241 pulmonary arterial hypertension cases from an international consortium implicates FBLN2, PDGFD, and rare de novo variants in PAH
Authors: Na Zhu, Emilia M. Swietlik, Carrie L. Welch, Michael W. Pauciulo, Jacob J. Hagen, Xueya Zhou, Yicheng Guo, Johannes Karten, Divya Pandya, Tobias Tilly, Katie A. Lutz, Jennifer M. Martin, Carmen M. Treacy, Erika B. Rosenzweig, Usha Krishnan, Anna W. Coleman, Claudia Gonzaga-Jauregui, Allan Lawrie, Richard C. Trembath, Martin R. Wilkins, Russel Hirsch, R. James White, Marc Simon, David Badesch, Erika Rosenzweig, Charles Burger, Murali Chakinala, Thenappan Thenappan, Greg Elliott, Robert Simms, Harrison Farber, Robert Frantz, Jean Elwing, Nicholas Hill, Dunbar Ivy, James Klinger, Steven Nathan, Ronald Oudiz, Ivan Robbins, Robert Schilz, Terry Fortin, Jeffrey Wilt, Delphine Yung, Eric Austin, Ferhaan Ahmad, Nitin Bhatt, Tim Lahm, Adaani Frost, Zeenat Safdar, Zia Rehman, Robert Walter, Fernando Torres, Sahil Bakshi, Stephen Archer, Rahul Argula, Christopher Barnett, Raymond Benza, Ankit Desai, Veeranna Maddipati, Harm J. Bogaard, Colin Church, Gerry Coghlin, Robin Condliffe, Mélanie Eyries, Henning Gall, Stefano Ghio, Barbara Girerd, Simon Holden, Luke Howard, Marc Humbert, David G. Kiely, Gabor Kovacs, Jim Lordan, Rajiv D. Machado, Robert V. MacKenzie Ross, Colm McCabe, Jennifer M. Martin, Shahin Moledina, David Montani, Horst Olschewski, Christopher J. Penkett, Joanna Pepke-Zaba, Laura Price, Christopher J. Rhodes, Werner Seeger, Florent Soubrier, Laura Southgate, Jay Suntharalingam, Andrew J. Swift, Mark R. Toshner, Carmen M. Treacy, Anton Vonk Noordegraaf, John Wharton, Jim Wild, Stephen John Wort, Harm J. Bogaard, Colin Church, Gerry Coghlin, Robin Condliffe, Mélanie Eyries, Henning Gall, Stefano Ghio, Barbara Girerd, Simon Holden, Luke Howard, Marc Humbert, David G. Kiely, Gabor Kovacs, Jim Lordan, Rajiv D. Machado, Robert V. MacKenzie Ross, Colm McCabe, Jennifer M. Martin, Shahin Moledina, David Montani, Horst Olschewski, Christopher J. Penkett, Joanna Pepke-Zaba, Laura Price, Christopher J. Rhodes, Werner Seeger, Florent Soubrier, Laura Southgate, Jay Suntharalingam, Andrew J. Swift, Mark R. Toshner, Carmen M. Treacy, Anton Vonk Noordegraaf, John Wharton, Jim Wild, Stephen John Wort, Nicholas W. Morrell, Yufeng Shen, Stefan Gräf, William C. Nichols, Wendy K. Chung
Journal: Genome Medicine (2021)

Abstract Background Pulmonary arterial hypertension (PAH) is a lethal vasculopathy characterized by pathogenic remodeling of pulmonary arterioles leading to increased pulmonary pressures, right ventricular hypertrophy, and heart failure. PAH can be associated with other diseases (APAH: connective tissue diseases, congenital heart disease, and others) but often the etiology is idiopathic (IPAH). Mutations in bone morphogenetic protein receptor 2 ( BMPR2 ) are the cause of most heritable cases but the vast majority of other cases are genetically undefined. Methods To identify new risk genes, we utilized an international consortium of 4241 PAH cases with exome or genome sequencing data from the National Biological Sample and Data Repository for PAH, Columbia University Irving Medical Center, and the UK NIHR BioResource – Rare Diseases Study. The strength of this combined cohort is a doubling of the number of IPAH cases compared to either national cohort alone. We identified protein-coding variants and performed rare variant association analyses in unrelated participants of European ancestry, including 1647 IPAH cases and 18,819 controls. We also analyzed de novo variants in 124 pediatric trios enriched for IPAH and APAH-CHD. Results Seven genes with rare deleterious variants were associated with IPAH with false discovery rate smaller than 0.1: three known genes ( BMPR2 , GDF2 , and TBX4 ), two recently identified candidate genes ( SOX17 , KDR ), and two new candidate genes (fibulin 2, FBLN2 ; platelet-derived growth factor D, PDGFD ). The new genes were identified based solely on rare deleterious missense variants, a variant type that could not be adequately assessed in either cohort alone. The candidate genes exhibit expression patterns in lung and heart similar to that of known PAH risk genes, and most variants occur in conserved protein domains. For pediatric PAH, predicted deleterious de novo variants exhibited a significant burden compared to the background mutation rate (2.45×, p = 2.5e−5). At least eight novel pediatric candidate genes carrying de novo variants have plausible roles in lung/heart development. Conclusions Rare variant analysis of a large international consortium identified two new candidate genes— FBLN2 and PDGFD . The new genes have known functions in vasculogenesis and remodeling. Trio analysis predicted that ~ 15% of pediatric IPAH may be explained by de novo variants.