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Jin J, Zhan J, Zhang J, Zhao R, O’Connell J, Jiang Y, Buyske S, Gignoux C, Haiman C, Kenny EE, Kooperberg C, North K, Koelsch BL, Wojcik G, Zhang H, Chatterjee N. MUSSEL: Enhanced Bayesian Polygenic Risk Prediction Leveraging Information across Multiple Ancestry Groups. bioRxiv 2023:2023.04.12.536510. [PMID: 37090648 PMCID: PMC10120638 DOI: 10.1101/2023.04.12.536510] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Polygenic risk scores (PRS) are now showing promising predictive performance on a wide variety of complex traits and diseases, but there exists a substantial performance gap across different populations. We propose MUSSEL, a method for ancestry-specific polygenic prediction that borrows information in the summary statistics from genome-wide association studies (GWAS) across multiple ancestry groups. MUSSEL conducts Bayesian hierarchical modeling under a MUltivariate Spike-and-Slab model for effect-size distribution and incorporates an Ensemble Learning step using super learner to combine information across different tuning parameter settings and ancestry groups. In our simulation studies and data analyses of 16 traits across four distinct studies, totaling 5.7 million participants with a substantial ancestral diversity, MUSSEL shows promising performance compared to alternatives. The method, for example, has an average gain in prediction R2 across 11 continuous traits of 40.2% and 49.3% compared to PRS-CSx and CT-SLEB, respectively, in the African Ancestry population. The best-performing method, however, varies by GWAS sample size, target ancestry, underlying trait architecture, and the choice of reference samples for LD estimation, and thus ultimately, a combination of methods may be needed to generate the most robust PRS across diverse populations.
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Affiliation(s)
- Jin Jin
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Jingning Zhang
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Ruzhang Zhao
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | | | | | - Steven Buyske
- Department of Statistics, Rutgers University, New Brunswick, NJ, USA
| | - Christopher Gignoux
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Christopher Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Eimear E. Kenny
- Icahn Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Kari North
- Department of Epidemiology, University of North Carolina Chapel Hill, Chapel Hill, NC, USA
| | | | - Genevieve Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Haoyu Zhang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Nilanjan Chatterjee
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
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Akiyama M, Miyake M, Momozawa Y, Arakawa S, Maruyama-Inoue M, Endo M, Iwasaki Y, Ishigaki K, Matoba N, Okada Y, Yasuda M, Oshima Y, Yoshida S, Nakao SY, Morino K, Mori Y, Kido A, Kato A, Yasukawa T, Obata R, Nagai Y, Takahashi K, Fujisawa K, Miki A, Nakamura M, Honda S, Ushida H, Yasuma T, Nishiguchi KM, Mori R, Tanaka K, Wakatsuki Y, Yamashiro K, Kadonosono K, Terao C, Ishibashi T, Tsujikawa A, Sonoda KH, Kubo M, Kamatani Y. Genome-Wide Association Study of Age-Related Macular Degeneration Reveals 2 New Loci Implying Shared Genetic Components with Central Serous Chorioretinopathy. Ophthalmology 2023; 130:361-372. [PMID: 36423732 DOI: 10.1016/j.ophtha.2022.10.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/27/2022] [Accepted: 10/17/2022] [Indexed: 11/23/2022] Open
Abstract
PURPOSE To investigate the genetic architecture of age-related macular degeneration (AMD) in a Japanese population. DESIGN Genome-wide association study (GWAS). PARTICIPANTS Three thousand seven hundred seventy-two patients with AMD and 16 770 control participants from the Japanese population were enrolled in the association analyses. METHODS We conducted a meta-analysis of 2 independent GWASs that included a total of 2663 patients with AMD and 9471 control participants using the imputation reference panel for genotype imputation specified for the Japanese population (n = 3541). A replication study was performed using an independent set of 1109 patients with AMD and 7299 control participants. MAIN OUTCOME MEASURES Associations of genetic variants with AMD. RESULTS A meta-analysis of the 2 GWASs identified 6 loci significantly associated with AMD (P < 5.0 × 10-8). Of these loci, 4 were known to be associated with AMD (CFH, C2/FB, TNFRSF10A, and ARMS2), and 2 were novel (rs4147157 near WBP1L and rs76228488 near GATA5). The newly identified associations were confirmed in a replication study (P < 0.01). After the meta-analysis of all datasets, we observed strong associations in these loci (P = 1.88 × 10-12 and P = 1.35 × 10-9 for meta-analysis for rs4147157 and rs76228488, respectively). When we looked up the associations in the reported central serous chorioretinopathy (CSC) GWAS conducted in the Japanese population, both loci were associated significantly with CSC (P = 4.86 × 10-3 and P = 4.28 × 10-3 for rs4147157 and rs76228488, respectively). We performed a genetic colocalization analysis for these loci and estimated that the posterior probabilities of shared causal variants between AMD and CSC were 0.39 and 0.60 for WBP1L and GATA5, respectively. Genetic correlation analysis focusing on the epidemiologically suggested clinical risk factors implicated shared polygenic architecture between AMD and smoking cessation (rg [the measure of genetic correlation] = -0.33; P = 0.01; false discovery rate, 0.099). CONCLUSIONS Our findings imply shared genetic components conferring the risk of both AMD and CSC. FINANCIAL DISCLOSURE(S) Proprietary or commercial disclosure may be found after the references.
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Affiliation(s)
- Masato Akiyama
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Department of Ocular Pathology and Imaging Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan; Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
| | - Masahiro Miyake
- Department of Ophthalmology and Visual Sciences, Kyoto University, Graduate School of Medicine, Kyoto, Japan; Center for Genomic Medicine, Kyoto University, Graduate School of Medicine, Kyoto, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Satoshi Arakawa
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan; Japan Community Health care Organization Kyushu Hospital, Fukuoka, Japan; Arakawa Eye Clinic, Fukuoka, Japan
| | - Maiko Maruyama-Inoue
- Department of Ophthalmology and Micro-technology, Yokohama City University, Yokohama, Japan
| | - Mikiko Endo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Yusuke Iwasaki
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Kazuyoshi Ishigaki
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Nana Matoba
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan; Department of Genome Informatics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan; Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Miho Yasuda
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan; Kurakazu Eye Clinic, Fukuoka, Japan
| | - Yuji Oshima
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan; Section of Ophthalmology, Department of Medicine, Fukuoka Dental College, Fukuoka, Japan
| | - Shigeo Yoshida
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan; Department of Ophthalmology, Kurume University School of Medicine, Fukuoka, Japan
| | - Shin-Ya Nakao
- Department of Ophthalmology and Visual Sciences, Kyoto University, Graduate School of Medicine, Kyoto, Japan
| | - Kazuya Morino
- Department of Ophthalmology and Visual Sciences, Kyoto University, Graduate School of Medicine, Kyoto, Japan
| | - Yuki Mori
- Department of Ophthalmology and Visual Sciences, Kyoto University, Graduate School of Medicine, Kyoto, Japan
| | - Ai Kido
- Department of Ophthalmology and Visual Sciences, Kyoto University, Graduate School of Medicine, Kyoto, Japan
| | - Aki Kato
- Department of Ophthalmology and Visual Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Tsutomu Yasukawa
- Department of Ophthalmology and Visual Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Ryo Obata
- Department of Ophthalmology, University of Tokyo School of Medicine, Tokyo, Japan
| | - Yoshimi Nagai
- Department of Ophthalmology, Kansai Medical University, Osaka, Japan
| | - Kanji Takahashi
- Department of Ophthalmology, Kansai Medical University, Osaka, Japan
| | - Kimihiko Fujisawa
- Japan Community Health care Organization Kyushu Hospital, Fukuoka, Japan
| | - Akiko Miki
- Department of Surgery, Division of Ophthalmology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Makoto Nakamura
- Department of Surgery, Division of Ophthalmology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Shigeru Honda
- Department of Surgery, Division of Ophthalmology, Kobe University Graduate School of Medicine, Kobe, Japan; Department of Ophthalmology and Visual Sciences, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
| | - Hiroaki Ushida
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tetsuhiro Yasuma
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Koji M Nishiguchi
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Ryusaburo Mori
- Division of Ophthalmology, Nihon University School of Medicine, Tokyo, Japan
| | - Koji Tanaka
- Division of Ophthalmology, Nihon University School of Medicine, Tokyo, Japan
| | - Yu Wakatsuki
- Division of Ophthalmology, Nihon University School of Medicine, Tokyo, Japan
| | - Kenji Yamashiro
- Department of Ophthalmology and Visual Sciences, Kyoto University, Graduate School of Medicine, Kyoto, Japan; Department of Ophthalmology and Visual Science, Kochi Medical School, Kochi University, Kochi, Japan
| | - Kazuaki Kadonosono
- Department of Ophthalmology and Micro-technology, Yokohama City University, Yokohama, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tatsuro Ishibashi
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Akitaka Tsujikawa
- Department of Ophthalmology and Visual Sciences, Kyoto University, Graduate School of Medicine, Kyoto, Japan
| | - Koh-Hei Sonoda
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
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