Systematic analysis of Mendelian disease-associated gene variants reveals new classes of cancer-predisposing genes

• Published in: Genome medicine 2023-12, Vol.15 (1), p.107-18, Article 107
• Main Authors: Song, Seulki, Koh, Youngil, Kim, Seokhyeon, Lee, Sang Mi, Kim, Hyun Uk, Ko, Jung Min, Lee, Se-Hoon, Yoon, Sung-Soo, Park, Solip
• Format: Article
• Language: English
• Subjects: Annotations; Cancer; Cancer genomics; Cancer predisposition gene; Cell cycle; Comparative analysis; Consortia; Disease; Genes; Genetic aspects; Genetic Predisposition to Disease; Genomes; Genomics; Humans; Medical research; Medicine, Experimental; Mendelian disease-associated gene; Neoplasms - genetics; Pathogenic variant; Phenotype; Phenotypes; Phenylketonuria; Principal components analysis; Risk; Tumorigenesis
• ISSN: 1756-994X; 1756-994X
• DOI: 10.1186/s13073-023-01252-w

Despite the acceleration of somatic driver gene discovery facilitated by recent large-scale tumor sequencing data, the contribution of inherited variants remains largely unexplored, primarily focusing on previously known cancer predisposition genes (CPGs) due to the low statistical power associated with detecting rare pathogenic variant-phenotype associations. Here, we introduce a generalized log-regression model to measure the excess of pathogenic variants within genes in cancer patients compared to control samples. It aims to measure gene-level cancer risk enrichment by collapsing rare pathogenic variants after controlling the population differences across samples. In this study, we investigate whether pathogenic variants in Mendelian disease-associated genes (OMIM genes) are enriched in cancer patients compared to controls. Utilizing data from PCAWG and the 1,000 Genomes Project, we identify 103 OMIM genes demonstrating significant enrichment of pathogenic variants in cancer samples (FDR 20%). Through an integrative approach considering three distinct properties, we classify these CPG-like OMIM genes into four clusters, indicating potential diverse mechanisms underlying tumor progression. Further, we explore the function of PAH (a key metabolic enzyme associated with Phenylketonuria), the gene exhibiting the highest prevalence of pathogenic variants in a pan-cancer (1.8%) compared to controls (0.6%). Our findings suggest a possible cancer progression mechanism through metabolic profile alterations. Overall, our data indicates that pathogenic OMIM gene variants contribute to cancer progression and introduces new CPG classifications potentially underpinning diverse tumorigenesis mechanisms.