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Rare penetrant mutations confer severe risk of common diseases.

ABSTRACT: We examined 454,712 exomes for genes associated with a wide spectrum of complex traits and common diseases and observed that rare, penetrant mutations in genes implicated by genome-wide association studies confer ∼10-fold larger effects than common variants in the same genes. Consequently, an individual at the phenotypic extreme and at the greatest risk for severe, early-onset disease is better identified by a few rare penetrant variants than by the collective action of many common variants with weak effects. By combining rare variants across phenotype-associated genes into a unified genetic risk model, we demonstrate superior portability across diverse global populations compared to common variant polygenic risk scores, greatly improving the clinical utility of genetic-based risk prediction.

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Rare variant polygenic risk scores identify individuals with outlier phenotypes in common human diseases and complex traits.

SUBMITTER: Fiziev P

PROVIDER: S-EPMC10187340 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature

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Rare penetrant mutations confer severe risk of common diseases.

Fiziev Petko P McRae Jeremy J Ulirsch Jacob C JC Dron Jacqueline S JS Hamp Tobias T Yang Yanshen Y Wainschtein Pierrick P Ni Zijian Z Schraiber Joshua G JG Gao Hong H Cable Dylan D Field Yair Y Aguet Francois F Fasnacht Marc M Metwally Ahmed A Rogers Jeffrey J Marques-Bonet Tomas T Rehm Heidi L HL O'Donnell-Luria Anne A Khera Amit V AV Kai-How Farh Kyle K

medRxiv : the preprint server for health sciences 20230508

We examined 454,712 exomes for genes associated with a wide spectrum of complex traits and common diseases and observed that rare, penetrant mutations in genes implicated by genome-wide association studies confer ∼10-fold larger effects than common variants in the same genes. Consequently, an individual at the phenotypic extreme and at the greatest risk for severe, early-onset disease is better identified by a few rare penetrant variants than by the collective action of many common variants with ...[more]

PMID: 37205493

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Project description:BackgroundNasopharyngeal carcinoma (NPC) exhibits significant familial aggregation; however, its susceptibility genes are largely unknown. Thus, this study aimed to identify germline mutations that might contribute to the risk of familial NPC, and explore their biological functions.MethodsWhole-exome sequencing was performed in 13 NPC pedigrees with multiple cases. Mutations co-segregated with disease status were further validated in a cohort composed of 563 probands from independent families, 2,953 sporadic cases, and 3,175 healthy controls. Experimental studies were used to explore the functions of susceptibility genes and their disease-related mutations.FindingsThe three rare missense mutations in POLN (DNA polymerase nu) gene, P577L, R303Q, and F545C, were associated with familial NPC risk (5/576 [0·87%] in cases vs. 2/3374 [0·059%] in healthy controls with an adjusted OR of 44·84 [95% CI:3·91-514·34, p = 2·25 × 10-3]). POLN was involved in Epstein-Barr virus (EBV) lytic replication in NPC cells in vitro. POLN promoted viral DNA replication, immediate-early and late lytic gene expression, and progeny viral particle production, ultimately affecting the proliferation of host cells. The three mutations were located in two pivotal functional domains and were predicted to alter the protein stability of POLN in silico. Further assays demonstrated that POLN carrying any of the three mutations displayed reduced protein stability and decreased expression levels, thereby impairing its ability to promote complete EBV lytic replication and facilitate cell survival.InterpretationWe identified a susceptibility gene POLN for familial NPC and elucidated its function.FundingThis study was funded by the National Key Research and Development Program of China (2021YFC2500400); the National Key Research and Development Program of China (2020YFC1316902); the Basic and Applied Basic Research Foundation of Guangdong Province, China (2021B1515420007); the National Natural Science Foundation of China (81973131); the National Natural Science Foundation of China (82003520); the National Natural Science Foundation of China (81903395).

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Rare penetrant mutations confer severe risk of common diseases.

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Publications

Rare penetrant mutations confer severe risk of common diseases.

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