Rare variants in RTEL1 are associated with familial interstitial pneumonia.

RATIONALE: Up to 20% of cases of idiopathic interstitial pneumonia cluster in families, comprising the syndrome of familial interstitial pneumonia (FIP); however, the genetic basis of FIP remains uncertain in most families. OBJECTIVES: To determine if new disease-causing rare genetic variants could be identified using whole-exome sequencing of affected members from FIP families, providing additional insights into disease pathogenesis. METHODS: Affected subjects from 25 kindreds were selected from an ongoing FIP registry for whole-exome sequencing from genomic DNA. Candidate rare variants were confirmed by Sanger sequencing, and cosegregation analysis was performed in families, followed by additional sequencing of affected individuals from another 163 kindreds. MEASUREMENTS AND MAIN RESULTS: We identified a potentially damaging rare variant in the gene encoding for regulator of telomere elongation helicase 1 (RTEL1) that segregated with disease and was associated with very short telomeres in peripheral blood mononuclear cells in 1 of 25 families in our original whole-exome sequencing cohort. Evaluation of affected individuals in 163 additional kindreds revealed another eight families (4.7%) with heterozygous rare variants in RTEL1 that segregated with clinical FIP. Probands and unaffected carriers of these rare variants had short telomeres (<10% for age) in peripheral blood mononuclear cells and increased T-circle formation, suggesting impaired RTEL1 function. CONCLUSIONS: Rare loss-of-function variants in RTEL1 represent a newly defined genetic predisposition for FIP, supporting the importance of telomere-related pathways in pulmonary fibrosis.

Identity-by-descent graphs offer a flexible framework for imputation and both linkage and association analyses.

We demonstrate the flexibility of identity-by-descent (IBD) graphs for genotype imputation and testing relationships between genotype and phenotype. We analyzed chromosome 3 and the first replicate of simulated diastolic blood pressure. IBD graphs were obtained from complete pedigrees and full multipoint marker analysis, facilitating subsequent linkage and other analyses. For rare alleles, pedigree-based imputation using these IBD graphs had a higher call rate than did population-based imputation. Combining the two approaches improved call rates for common alleles. We found it advantageous to incorporate known, rather than estimated, pedigree relationships when testing for association. Replacing missing data with imputed alleles improved association signals as well. Analyses were performed with knowledge of the underlying model.