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Smail C, Ge B, Keever-Keigher MR, Schwendinger-Schreck C, Cheung WA, Johnston JJ, Barrett C, Feldman K, Cohen ASA, Farrow EG, Thiffault I, Grundberg E, Pastinen T. Complex trait associations in rare diseases and impacts on Mendelian variant interpretation. Nat Commun 2024; 15:8196. [PMID: 39294130 PMCID: PMC11411080 DOI: 10.1038/s41467-024-52407-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 09/05/2024] [Indexed: 09/20/2024] Open
Abstract
Emerging evidence implicates common genetic variation - aggregated into polygenic scores (PGS) - in the onset and phenotypic presentation of rare diseases. Here, we comprehensively map individual polygenic liability for 1102 open-source PGS in a cohort of 3059 probands enrolled in the Genomic Answers for Kids (GA4K) rare disease study, revealing widespread associations between rare disease phenotypes and PGSs for common complex diseases and traits, blood protein levels, and brain and other organ morphological measurements. Using this resource, we demonstrate increased polygenic liability in probands with an inherited candidate disease variant (VUS) compared to unaffected carrier parents. Further, we show an enrichment for large-effect rare variants in putative core PGS genes for associated complex traits. Overall, our study supports and expands on previous findings of complex trait associations in rare diseases, implicates polygenic liability as a potential mechanism underlying variable penetrance of candidate causal variants, and provides a framework for identifying novel candidate rare disease genes.
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Affiliation(s)
- Craig Smail
- Genomic Medicine Center, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, USA.
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, USA.
| | - Bing Ge
- Department of Human Genetics, McGill University, Montreal, Canada
| | - Marissa R Keever-Keigher
- Genomic Medicine Center, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, USA
| | | | - Warren A Cheung
- Genomic Medicine Center, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, USA
| | - Jeffrey J Johnston
- Genomic Medicine Center, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, USA
| | - Cassandra Barrett
- Genomic Medicine Center, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, USA
| | - Keith Feldman
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, USA
- Health Outcomes and Health Services Research, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, USA
| | - Ana S A Cohen
- Genomic Medicine Center, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, USA
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, USA
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, USA
| | - Emily G Farrow
- Genomic Medicine Center, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, USA
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, USA
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, USA
| | - Isabelle Thiffault
- Genomic Medicine Center, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, USA
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, USA
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, USA
| | - Elin Grundberg
- Genomic Medicine Center, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, USA
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, USA
| | - Tomi Pastinen
- Genomic Medicine Center, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, USA.
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, USA.
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Smail C, Ge B, Keever-Keigher MR, Schwendinger-Schreck C, Cheung W, Johnston JJ, Barrett C, Feldman K, Cohen AS, Farrow EG, Thiffault I, Grundberg E, Pastinen T. Complex trait associations in rare diseases and impacts on Mendelian variant interpretation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.10.24301111. [PMID: 38260377 PMCID: PMC10802745 DOI: 10.1101/2024.01.10.24301111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Emerging evidence implicates common genetic variation - aggregated into polygenic scores (PGS) - impacting the onset and phenotypic presentation of rare diseases. In this study, we quantified individual polygenic liability for 1,151 previously published PGS in a cohort of 2,374 probands enrolled in the Genomic Answers for Kids (GA4K) rare disease study, revealing widespread associations between rare disease phenotypes and PGSs for common complex diseases and traits, blood protein levels, and brain and other organ morphological measurements. We observed increased polygenic burden in probands with variants of unknown significance (VUS) compared to unaffected carrier parents. We further observed an enrichment in overlap between diagnostic and candidate rare disease genes and large-effect PGS genes. Overall, our study supports and expands on previous findings of complex trait associations in rare disease phenotypes and provides a framework for identifying novel candidate rare disease genes and in understanding variable penetrance of candidate Mendelian disease variants.
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Affiliation(s)
- Craig Smail
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
| | - Bing Ge
- Department of Human Genetics, McGill University, Montreal, Canada
| | - Marissa R. Keever-Keigher
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Carl Schwendinger-Schreck
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Warren Cheung
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Jeffrey J. Johnston
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Cassandra Barrett
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | | | - Keith Feldman
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
- Health Outcomes and Health Services Research, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Ana S.A. Cohen
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
- Department of Pathology and Laboratory Medicine, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Emily G. Farrow
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
- Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Isabelle Thiffault
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
- Department of Pathology and Laboratory Medicine, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Elin Grundberg
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
| | - Tomi Pastinen
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
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