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.
Subject(s)
Idiopathic Pulmonary Fibrosis , Humans , Idiopathic Pulmonary Fibrosis/genetics , Whole Genome Sequencing , ExomeABSTRACT
This review provides an updated approach to the diagnosis and management of hypersensitivity pneumonitis (HP). The importance of using a multidisciplinary discussion to increase diagnostic and treatment confidence is emphasized. The role of Bayesian reasoning is highlighted throughout, underscoring the importance of hypothesis generation (differential diagnosis) and diagnostic test interpretation based on the probability of HP. Probability estimates of diagnostic certainty (i.e., a confident versus a working diagnosis) and treatment thresholds are carefully examined.Therapeutically, beyond antigen avoidance and newly available antifibrotic therapy for patients with a progressive fibrosing phenotype; the role, timing, and expected response to anti-inflammatory therapy in individual patients are unanswered questions. Since the evidence and validation of testing generally performed during the diagnostic work-up and longitudinal monitoring of HP is feeble at best, the viewpoints discussed are not intended to resolve current controversies but rather to provide a conceptual framework for evaluating discordant information when evaluating and caring for patients with HP.
Subject(s)
Alveolitis, Extrinsic Allergic/diagnosis , Alveolitis, Extrinsic Allergic/therapy , Clinical Decision-Making , Alveolitis, Extrinsic Allergic/classification , Alveolitis, Extrinsic Allergic/pathology , Diagnosis, Differential , Disease Progression , Humans , Occupational Exposure/adverse effects , Pulmonary Fibrosis/etiology , Risk FactorsABSTRACT
In 2015, a multidisciplinary task force comprising pulmonologists, rheumatologists, pathologists, and radiologists representing the European Respiratory Society and American Thoracic Society published a diagnostic classification schema for individuals with interstitial lung disease and autoimmune features who did not meet criteria for a defined connective tissue disease. The term interstitial pneumonia with autoimmune features (IPAF) was applied. Classification criteria are often nonspecific, but up to 90% of subjects with IPAF have serological evidence for autoimmunity (particularly (+) antinuclear antibodies). Distinguishing patients with IPAF from idiopathic pulmonary disorders may be difficult. The natural history and appropriate management of IPAF have not been clarified, as data are largely limited to retrospective studies. In this review, we discuss the salient clinical, serologic, histologic, and radiographic features of IPAF and discuss an approach to management.
