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Jin B, Capra JA, Benchek P, Wheeler N, Naj AC, Hamilton-Nelson KL, Farrell JJ, Leung YY, Kunkle B, Vadarajan B, Schellenberg GD, Mayeux R, Wang LS, Farrer LA, Pericak-Vance MA, Martin ER, Haines JL, Crawford DC, Bush WS. Corrigendum: An association test of the spatial distribution of rare missense variants within protein structures identifies Alzheimer's disease–related patterns. Genome Res 2022. [PMCID: PMC9248876 DOI: 10.1101/gr.276900.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Jin B, Capra JA, Benchek P, Wheeler N, Naj AC, Hamilton-Nelson KL, Farrell JJ, Leung YY, Kunkle B, Vadarajan B, Schellenberg GD, Mayeux R, Wang LS, Farrer LA, Pericak-Vance MA, Martin ER, Haines JL, Crawford DC, Bush WS. An association test of the spatial distribution of rare missense variants within protein structures identifies Alzheimer's disease-related patterns. Genome Res 2022; 32:778-790. [PMID: 35210353 PMCID: PMC8997344 DOI: 10.1101/gr.276069.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 02/17/2022] [Indexed: 11/24/2022]
Abstract
More than 90% of genetic variants are rare in most modern sequencing studies, such as the Alzheimer's Disease Sequencing Project (ADSP) whole-exome sequencing (WES) data. Furthermore, 54% of the rare variants in ADSP WES are singletons. However, both single variant and unit-based tests are limited in their statistical power to detect an association between rare variants and phenotypes. To best use missense rare variants and investigate their biological effect, we examine their association with phenotypes in the context of protein structures. We developed a protein structure-based approach, protein optimized kernel evaluation of missense nucleotides (POKEMON), which evaluates rare missense variants based on their spatial distribution within a protein rather than their allele frequency. The hypothesis behind this test is that the three-dimensional spatial distribution of variants within a protein structure provides functional context to power an association test. POKEMON identified three candidate genes (TREM2, SORL1, and EXOC3L4) and another suggestive gene from the ADSP WES data. For TREM2 and SORL1, two known Alzheimer's disease (AD) genes, the signal from the spatial cluster is stable even if we exclude known AD risk variants, indicating the presence of additional low-frequency risk variants within these genes. EXOC3L4 is a novel AD risk gene that has a cluster of variants primarily shared by case subjects around the Sec6 domain. This cluster is also validated in an independent replication data set and a validation data set with a larger sample size.
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Affiliation(s)
- Bowen Jin
- Graduate Program in Systems Biology and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - John A Capra
- The Bakar Computational Health Sciences Institute, Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California 94143, USA
| | - Penelope Benchek
- Cleveland Institute for Computational Biology, Department for Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Nicholas Wheeler
- Cleveland Institute for Computational Biology, Department for Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Adam C Naj
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kara L Hamilton-Nelson
- The John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
| | - John J Farrell
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Yuk Yee Leung
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Brian Kunkle
- The John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
- Dr. John T. Macdonald Foundation, Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
| | - Badri Vadarajan
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Department of Neurology, Gertrude H. Sergievsky Center, Department of Neurology, Columbia University, New York, New York 10032, USA
| | - Gerard D Schellenberg
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Richard Mayeux
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Department of Neurology, Gertrude H. Sergievsky Center, Department of Neurology, Columbia University, New York, New York 10032, USA
| | - Li-San Wang
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Lindsay A Farrer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Margaret A Pericak-Vance
- The John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
- Dr. John T. Macdonald Foundation, Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
| | - Eden R Martin
- The John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
- Dr. John T. Macdonald Foundation, Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
| | - Jonathan L Haines
- Cleveland Institute for Computational Biology, Department for Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Dana C Crawford
- Cleveland Institute for Computational Biology, Department for Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - William S Bush
- Cleveland Institute for Computational Biology, Department for Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio 44106, USA
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