Genome-wide imputation study identifies novel HLA locus for pulmonary fibrosis and potential role for auto-immunity in fibrotic idiopathic interstitial pneumonia

Tasha E. Fingerlin, Weiming Zhang, Ivana V. Yang, Hannah C. Ainsworth, Pamela H. Russell, Rachel Z. Blumhagen, Marvin I. Schwarz, Kevin K. Brown, Mark P. Steele, James E. Loyd, Gregory P. Cosgrove, David A. Lynch, Steve Groshong, Harold R. Collard, Paul J. Wolters, Williamson Z. Bradford, Karl Kossen, Scott D. Seiwert, Roland M. Bois, Christine Kim GarciaMegan S. Devine, Gunnar Gudmundsson, Helgi J. Isaksson, Naftali Kaminski, Yingze Zhang, Kevin F. Gibson, Lisa H. Lancaster, Toby M. Maher, Philip L. Molyneaux, Athol U. Wells, Miriam F. Moffatt, Moises Selman, Annie Pardo, Dong Soon Kim, James D. Crapo, Barry J. Make, Elizabeth A. Regan, Dinesha S. Walek, Jerry J. Daniel, Yoichiro Kamatani, Diana Zelenika, Elissa Murphy, Keith Smith, David McKean, Brent S. Pedersen, Janet Talbert, Julia Powers, Cheryl R. Markin, Kenneth B. Beckman, Mark Lathrop, Brian Freed, Carl D. Langefeld, David A. Schwartz

Research output: Contribution to journalArticlepeer-review


Fibrotic idiopathic interstitial pneumonias (fIIP) are a group of fatal lung diseases with largely unknown etiology and without definitive treatment other than lung transplant to prolong life. There is strong evidence for the importance of both rare and common genetic risk alleles in familial and sporadic disease. We have previously used genome-wide single nucleotide polymorphism data to identify 10 risk loci for fIIP. Here we extend that work to imputed genome-wide genotypes and conduct new RNA sequencing studies of lung tissue to identify and characterize new fIIP risk loci. Results: We performed genome-wide genotype imputation association analyses in 1616 non-Hispanic white (NHW) cases and 4683 NHW controls followed by validation and replication (878 cases, 2017 controls) genotyping and targeted gene expression in lung tissue. Following meta-analysis of the discovery and replication populations, we identified a novel fIIP locus in the HLA region of chromosome 6 (rs7887 Pmeta = 3.7 × 10-09). Imputation of classic HLA alleles identified two in high linkage disequilibrium that are associated with fIIP (DRB1 15:01 P = 1.3 × 10-7 and DQB1 06:02 P = 6.1 × 10-8). Targeted RNA-sequencing of the HLA locus identified 21 genes differentially expressed between fibrotic and control lung tissue (Q < 0.001), many of which are involved in immune and inflammatory response regulation. In addition, the putative risk alleles, DRB1 15:01 and DQB1 06:02, are associated with expression of the DQB1 gene among fIIP cases (Q < 1 × 10-16).

Original languageEnglish (US)
Article number74
JournalBMC genetics
Issue number1
StatePublished - 2016
Externally publishedYes

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)


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