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. 2023 May 1;207(9):1194-1202.
doi: 10.1164/rccm.202207-1331OC.

Idiopathic Pulmonary Fibrosis Is Associated with Common Genetic Variants and Limited Rare Variants

Anna L Peljto  1 Rachel Z Blumhagen  1   2 Avram D Walts  2 Jonathan Cardwell  1 Julia Powers  1 Tamera J Corte  3 Joanne L Dickinson  4 Ian Glaspole  5 Yuben P Moodley  6 Martina Koziar Vasakova  7 Elisabeth Bendstrup  8   9 Jesper R Davidsen  10 Raphael Borie  11 Bruno Crestani  11   12 Philippe Dieude  13 Francesco Bonella  14 Ulrich Costabel  14 Gunnar Gudmundsson  15   16 Seamas C Donnelly  17 Jim Egan  18 Michael T Henry  19 Michael P Keane  20 Marcus P Kennedy  19 Cormac McCarthy  20 Aoife N McElroy  17 Joshua A Olaniyi  17 Katherine M A O'Reilly  21 Luca Richeldi  22   23 Paolo M Leone  22   23 Venerino Poletti  24   25 Francesco Puppo  26 Sara Tomassetti  27 Valentina Luzzi  28 Nurdan Kokturk  29 Nesrin Mogulkoc  30 Christine A Fiddler  31 Nikhil Hirani  32 R Gisli Jenkins  33 Toby M Maher  33   34 Philip L Molyneaux  33 Helen Parfrey  31 Rebecca Braybrooke  35 Timothy S Blackwell  36 Peter D Jackson  37 Steven D Nathan  38 Mary K Porteous  39 Kevin K Brown  2 Jason D Christie  40 Harold R Collard  41 Oliver Eickelberg  42 Elena E Foster  43 Kevin F Gibson  42 Marilyn Glassberg  44 Daniel J Kass  42 Jonathan A Kropski  36 David Lederer  45 Angela L Linderholm  46 Jim Loyd  36 Susan K Mathai  47 Sydney B Montesi  48 Imre Noth  49 Justin M Oldham  50 Amy J Palmisciano  51 Cristina A Reichner  52 Mauricio Rojas  53 Jesse Roman  54 Neil Schluger  55 Barry S Shea  51 Jeffrey J Swigris  2 Paul J Wolters  41 Yingze Zhang  42 Cecilia M A Prele  56 Juan I Enghelmayer  57   58 Maria Otaola  59 Christopher J Ryerson  60 Mauricio Salinas  61 Martina Sterclova  8 Tewodros H Gebremariam  62 Marjukka Myllärniemi  63 Roberto G Carbone  26 Haruhiko Furusawa  64 Masaki Hirose  65 Yoshikazu Inoue  65 Yasunari Miyazaki  64 Ken Ohta  66 Shin Ohta  67 Tsukasa Okamoto  64 Dong Soon Kim  68 Annie Pardo  69 Moises Selman  70 Alvaro U Aranda  71 Moo Suk Park  72 Jong Sun Park  73 Jin Woo Song  68 Maria Molina-Molina  74 Lurdes Planas-Cerezales  75 Gunilla Westergren-Thorsson  76 Albert V Smith  77 Ani W Manichaikul  78 John S Kim  49 Stephen S Rich  78   79 Elizabeth C Oelsner  80 R Graham Barr  80 Jerome I Rotter  81 Josee Dupuis  82   83 George O'Connor  84 Ramachandran S Vasan  85 Michael H Cho  86 Edwin K Silverman  86 Marvin I Schwarz  1 Mark P Steele  1 Joyce S Lee  1 Ivana V Yang  1 Tasha E Fingerlin  2 David A Schwartz  1
Affiliations

Idiopathic Pulmonary Fibrosis Is Associated with Common Genetic Variants and Limited Rare Variants

Anna L Peljto et al. Am J Respir Crit Care Med. .

Erratum in

Abstract

Rationale: Idiopathic pulmonary fibrosis (IPF) is a rare, irreversible, and progressive disease of the lungs. Common genetic variants, in addition to nongenetic factors, have been consistently associated with IPF. Rare variants identified by candidate gene, family-based, and exome studies have also been reported to associate with IPF. However, the extent to which rare variants, genome-wide, may contribute to the risk of IPF remains unknown. Objectives: We used whole-genome sequencing to investigate the role of rare variants, genome-wide, on IPF risk. Methods: As part of the Trans-Omics for Precision Medicine Program, we sequenced 2,180 cases of IPF. Association testing focused on the aggregated effect of rare variants (minor allele frequency ⩽0.01) within genes or regions. We also identified individual rare variants that are influential within genes and estimated the heritability of IPF on the basis of rare and common variants. Measurements and Main Results: Rare variants in both TERT and RTEL1 were significantly associated with IPF. A single rare variant in each of the TERT and RTEL1 genes was found to consistently influence the aggregated test statistics. There was no significant evidence of association with other previously reported rare variants. The SNP heritability of IPF was estimated to be 32% (SE = 3%). Conclusions: Rare variants within the TERT and RTEL1 genes and well-established common variants have the largest contribution to IPF risk overall. Efforts in risk profiling or the development of therapies for IPF that focus on TERT, RTEL1, common variants, and environmental risk factors are likely to have the largest impact on this complex disease.

Keywords: TOPMed; genetic association studies; interstitial lung disease; telomerase; whole-genome sequencing.

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Figures

Figure 1.
Figure 1.
Manhattan plot for rare loss-of-function variants (A) and loss-of-function and missense variants (B), aggregated by gene, in the discovery cohort. Horizontal lines represent the genome-wide significance thresholds adjusted for the effective number of tests (solid) and the total number of tests (dashed).
Figure 2.
Figure 2.
Manhattan plots for meta-analysis with rare loss-of-function variants (A) and loss-of-function and missense variants (B). Horizontal lines represent the genome-wide significance thresholds adjusted for the total number of tests.

Comment in

References

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