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

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Authors
Fingerlin, Tasha E
Zhang, Weiming
Yang, Ivana V
Ainsworth, Hannah C
Russell, Pamela H
Blumhagen, Rachel Z
Schwarz, Marvin I
Brown, Kevin K
Steele, Mark P
Loyd, James E
Cosgrove, Gregory P
Lynch, David A
Groshong, Steve
Collard, Harold R
Wolters, Paul J
Bradford, Williamson Z
Kossen, Karl
Seiwert, Scott D
du Bois, Roland M
Garcia, Christine Kim
Devine, Megan S
Gudmundsson, Gunnar
Isaksson, Helgi J
Kaminski, Naftali
Zhang, Yingze
Gibson, Kevin F
Lancaster, Lisa H
Maher, Toby M
Molyneaux, Philip L
Wells, Athol U
Moffatt, Miriam F
Selman, Moises
Pardo, Annie
Kim, Dong Soon
Crapo, James D
Make, Barry J
Regan, Elizabeth A
Walek, Dinesha S
Daniel, Jerry J
Kamatani, Yoichiro
Zelenika, Diana
Murphy, Elissa
Smith, Keith
McKean, David
Pedersen, Brent S
Talbert, Janet
Powers, Julia
Markin, Cheryl R
Beckman, Kenneth B
Lathrop, Mark
Freed, Brian
Langefeld, Carl D
Schwartz, David A
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Issue Date
2016

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Citation
Genome-wide imputation study identifies novel HLA locus for pulmonary fibrosis and potential role for auto-immunity in fibrotic idiopathic interstitial pneumonia. 2016, 17 (1):74 BMC Genet.
Abstract
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.
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 P meta  = 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)).
We have identified a genome-wide significant association between the HLA region and fIIP. Two HLA alleles are associated with fIIP and affect expression of HLA genes in lung tissue, indicating that the potential genetic risk due to HLA alleles may involve gene regulation in addition to altered protein structure. These studies reveal the importance of the HLA region for risk of fIIP and a basis for the potential etiologic role of auto-immunity in fIIP.
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To access publisher's full text version of this article, please click on the hyperlink in Additional Links field or click on the hyperlink at the top of the page marked Files. This article is open access.
Additional Links
http://dx.doi.org/ 10.1186/s12863-016-0377-2
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4895966/
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Archived with thanks to BMC genetics
ae974a485f413a2113503eed53cd6c53
10.1186/s12863-016-0377-2
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