Novel candidate susceptibility genes for idiopathic pulmonary fibrosis in Han Chinese families identified via the T2T-YAO reference Genome

Genetic factors contribute to familial idiopathic pulmonary fibrosis (FIPF) susceptibility and progression. However, genetic studies have relied on reference genomes derived predominantly from individuals of European ancestry (e.g. GRCh38 and T2T-CHM13). T2T-YAO, the first gapless diploid reference genome of Han Chinese origin, exhibits substantial sequence divergence from these references, providing a basis for improved variant calling. We performed whole-genome sequencing of 18 individuals from an extended Han Chinese family with FIPF. Mapping quality and variant calling accuracy were compared across three reference genomes (T2T-YAO, T2T-CHM13, and GRCh38). Candidate variants were validated by Sanger sequencing in three independent cohorts: an IPF cohort ( n = 40), which was further categorized into IPF-only (without lung cancer, n = 27) and IPF with lung cancer (IPF-LC, n = 13) subgroups; a control cohort ( n = 40); and a LC cohort ( n = 43). Bioinformatics analysis and gene expression profiling were used for functional characterization. Compared with GRCh38, T2T-YAO yielded 312.79 Mb of additional mapped reads and 22.7% lower error rates. Compared with T2T-CHM13, T2T-YAO substantially reduced false-positive calls for population-specific variants, particularly homozygous variants (31.6% reduction). In two patients with IPF complicated by LC, we identified the homozygous missense mutations PITRM1 c·2906C > T (p.Pro969Leu) and CFAP54 c·6875C > G (p.Ser2292Cys). Heterozygous PITRM1 mutations were significantly enriched in patients with IPF-LC (61.5%) compared with those in the LC cohort (18.6%, p = 0.003), control cohort (2%, p = 0.004), and IPF-only group (patients without LC in the IPF cohort, 18.5%, p = 0.008). Both mutations were predicted to be deleterious and were associated with decreased mRNA expression in patients. We identified PITRM1 and CFAP54 as novel susceptibility genes for FIPF in a Han Chinese family. Notably, the significant enrichment of heterozygous PITRM1 mutations in patients with IPF-LC suggests a shared genetic basis between pulmonary fibrosis and carcinogenesis. These findings highlight the value of population-matched reference genomes for novel variant discovery.