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Polygenic prediction via Bayesian regression and continuous shrinkage priors

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Cited by:

  1. Alexandra Barry & Michelle T. McNulty & Xiaoyuan Jia & Yask Gupta & Hanna Debiec & Yang Luo & China Nagano & Tomoko Horinouchi & Seulgi Jung & Manuela Colucci & Dina F. Ahram & Adele Mitrotti & Aditi , 2023. "Multi-population genome-wide association study implicates immune and non-immune factors in pediatric steroid-sensitive nephrotic syndrome," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
  2. Bingxin Zhao & Yujue Li & Zirui Fan & Zhenyi Wu & Juan Shu & Xiaochen Yang & Yilin Yang & Xifeng Wang & Bingxuan Li & Xiyao Wang & Carlos Copana & Yue Yang & Jinjie Lin & Yun Li & Jason L. Stein & Joa, 2024. "Eye-brain connections revealed by multimodal retinal and brain imaging genetics," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
  3. Clara Albiñana & Zhihong Zhu & Andrew J. Schork & Andrés Ingason & Hugues Aschard & Isabell Brikell & Cynthia M. Bulik & Liselotte V. Petersen & Esben Agerbo & Jakob Grove & Merete Nordentoft & David , 2023. "Multi-PGS enhances polygenic prediction by combining 937 polygenic scores," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
  4. Junyang Qian & Yosuke Tanigawa & Wenfei Du & Matthew Aguirre & Chris Chang & Robert Tibshirani & Manuel A Rivas & Trevor Hastie, 2020. "A fast and scalable framework for large-scale and ultrahigh-dimensional sparse regression with application to the UK Biobank," PLOS Genetics, Public Library of Science, vol. 16(10), pages 1-30, October.
  5. Magdalena Zimoń & Yunfeng Huang & Anthi Trasta & Aliaksandr Halavatyi & Jimmy Z. Liu & Chia-Yen Chen & Peter Blattmann & Bernd Klaus & Christopher D. Whelan & David Sexton & Sally John & Wolfgang Hube, 2021. "Pairwise effects between lipid GWAS genes modulate lipid plasma levels and cellular uptake," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
  6. Yi-Jia Huang & Chun-houh Chen & Hsin-Chou Yang, 2024. "AI-enhanced integration of genetic and medical imaging data for risk assessment of Type 2 diabetes," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  7. Jingning Zhang & Jianan Zhan & Jin Jin & Cheng Ma & Ruzhang Zhao & Jared O’Connell & Yunxuan Jiang & Bertram L. Koelsch & Haoyu Zhang & Nilanjan Chatterjee, 2024. "An ensemble penalized regression method for multi-ancestry polygenic risk prediction," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  8. Kenichi Yamamoto & Kyuto Sonehara & Shinichi Namba & Takahiro Konuma & Hironori Masuko & Satoru Miyawaki & Yoichiro Kamatani & Nobuyuki Hizawa & Keiichi Ozono & Loic Yengo & Yukinori Okada, 2023. "Genetic footprints of assortative mating in the Japanese population," Nature Human Behaviour, Nature, vol. 7(1), pages 65-73, January.
  9. Song Zhai & Hong Zhang & Devan V. Mehrotra & Judong Shen, 2022. "Pharmacogenomics polygenic risk score for drug response prediction using PRS-PGx methods," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
  10. Karlsson Linnér, Richard & Koellinger, Philipp D., 2022. "Genetic risk scores in life insurance underwriting," Journal of Health Economics, Elsevier, vol. 81(C).
  11. Yanyi Song & Xiang Zhou & Min Zhang & Wei Zhao & Yongmei Liu & Sharon L. R. Kardia & Ana V. Diez Roux & Belinda L. Needham & Jennifer A. Smith & Bhramar Mukherjee, 2020. "Bayesian shrinkage estimation of high dimensional causal mediation effects in omics studies," Biometrics, The International Biometric Society, vol. 76(3), pages 700-710, September.
  12. Chachrit Khunsriraksakul & Qinmengge Li & Havell Markus & Matthew T. Patrick & Renan Sauteraud & Daniel McGuire & Xingyan Wang & Chen Wang & Lida Wang & Siyuan Chen & Ganesh Shenoy & Bingshan Li & Xue, 2023. "Multi-ancestry and multi-trait genome-wide association meta-analyses inform clinical risk prediction for systemic lupus erythematosus," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
  13. Danielle Rasooly & Gina M. Peloso & Alexandre C. Pereira & Hesam Dashti & Claudia Giambartolomei & Eleanor Wheeler & Nay Aung & Brian R. Ferolito & Maik Pietzner & Eric H. Farber-Eger & Quinn Stanton , 2023. "Genome-wide association analysis and Mendelian randomization proteomics identify drug targets for heart failure," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
  14. Rita Dias Pereira & Pietro Biroli & Titus Galama & Stephanie von Hinke & Hans van Kippersluis & Cornelius A. Rietveld & Kevin Thom, 2022. "Gene-Environment Interplay in the Social Sciences," Papers 2203.02198, arXiv.org, revised Aug 2022.
  15. Lucía de Hoyos & Maria T. Barendse & Fenja Schlag & Marjolein M. J. van Donkelaar & Ellen Verhoef & Chin Yang Shapland & Alexander Klassmann & Jan Buitelaar & Brad Verhulst & Simon E. Fisher & Dheeraj, 2024. "Structural models of genome-wide covariance identify multiple common dimensions in autism," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  16. Tzu-Ting Chen & Jaeyoung Kim & Max Lam & Yi-Fang Chuang & Yen-Ling Chiu & Shu-Chin Lin & Sang-Hyuk Jung & Beomsu Kim & Soyeon Kim & Chamlee Cho & Injeong Shim & Sanghyeon Park & Yeeun Ahn & Aysu Okbay, 2024. "Shared genetic architectures of educational attainment in East Asian and European populations," Nature Human Behaviour, Nature, vol. 8(3), pages 562-575, March.
  17. Niloy Biswas & Anirban Bhattacharya & Pierre E. Jacob & James E. Johndrow, 2022. "Coupling‐based convergence assessment of some Gibbs samplers for high‐dimensional Bayesian regression with shrinkage priors," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 84(3), pages 973-996, July.
  18. Bingxin Zhao & Fei Zou & Hongtu Zhu, 2023. "Cross‐trait prediction accuracy of summary statistics in genome‐wide association studies," Biometrics, The International Biometric Society, vol. 79(2), pages 841-853, June.
  19. Rikifumi Ohta & Yosuke Tanigawa & Yuta Suzuki & Manolis Kellis & Shinichi Morishita, 2024. "A polygenic score method boosted by non-additive models," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
  20. Yosuke Tanigawa & Junyang Qian & Guhan Venkataraman & Johanne Marie Justesen & Ruilin Li & Robert Tibshirani & Trevor Hastie & Manuel A Rivas, 2022. "Significant sparse polygenic risk scores across 813 traits in UK Biobank," PLOS Genetics, Public Library of Science, vol. 18(3), pages 1-21, March.
  21. Beomsu Kim & Dan Say Kim & Joong-Gon Shin & Sangseob Leem & Minyoung Cho & Hanji Kim & Ki-Nam Gu & Jung Yeon Seo & Seung Won You & Alicia R. Martin & Sun Gyoo Park & Yunkwan Kim & Choongwon Jeong & Na, 2024. "Mapping and annotating genomic loci to prioritize genes and implicate distinct polygenic adaptations for skin color," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
  22. Geyu Zhou & Hongyu Zhao, 2021. "A fast and robust Bayesian nonparametric method for prediction of complex traits using summary statistics," PLOS Genetics, Public Library of Science, vol. 17(7), pages 1-17, July.
  23. Andras Gezsi & Sandra Auwera & Hannu Mäkinen & Nora Eszlari & Gabor Hullam & Tamas Nagy & Sarah Bonk & Rubèn González-Colom & Xenia Gonda & Linda Garvert & Teemu Paajanen & Zsofia Gal & Kevin Kirchner, 2024. "Unique genetic and risk-factor profiles in clusters of major depressive disorder-related multimorbidity trajectories," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  24. Young Jin Kim & Sanghoon Moon & Mi Yeong Hwang & Sohee Han & Hye-Mi Jang & Jinhwa Kong & Dong Mun Shin & Kyungheon Yoon & Sung Min Kim & Jong-Eun Lee & Anubha Mahajan & Hyun-Young Park & Mark I. McCar, 2022. "The contribution of common and rare genetic variants to variation in metabolic traits in 288,137 East Asians," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
  25. Mingyang Li & Xixi Dang & Yiwei Chen & Zhifan Chen & Xinyi Xu & Zhiyong Zhao & Dan Wu, 2024. "Cognitive processing speed and accuracy are intrinsically different in genetic architecture and brain phenotypes," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
  26. Kenichi Yamamoto & Shinichi Namba & Kyuto Sonehara & Ken Suzuki & Saori Sakaue & Niall P. Cooke & Shinichi Higashiue & Shuzo Kobayashi & Hisaaki Afuso & Kosho Matsuura & Yojiro Mitsumoto & Yasuhiko Fu, 2024. "Genetic legacy of ancient hunter-gatherer Jomon in Japanese populations," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  27. Ana Maria Portugal & Charlotte Viktorsson & Mark J. Taylor & Luke Mason & Kristiina Tammimies & Angelica Ronald & Terje Falck-Ytter, 2024. "Infants’ looking preferences for social versus non-social objects reflect genetic variation," Nature Human Behaviour, Nature, vol. 8(1), pages 115-124, January.
  28. Jiacheng Miao & Hanmin Guo & Gefei Song & Zijie Zhao & Lin Hou & Qiongshi Lu, 2023. "Quantifying portable genetic effects and improving cross-ancestry genetic prediction with GWAS summary statistics," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
  29. Yash Patel & Jean Shin & Eeva Sliz & Ariana Tang & Aniket Mishra & Rui Xia & Edith Hofer & Hema Sekhar Reddy Rajula & Ruiqi Wang & Frauke Beyer & Katrin Horn & Max Riedl & Jing Yu & Henry Völzke & Rob, 2024. "Genetic risk factors underlying white matter hyperintensities and cortical atrophy," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
  30. Chamlee Cho & Beomsu Kim & Dan Say Kim & Mi Yeong Hwang & Injeong Shim & Minku Song & Yeong Chan Lee & Sang-Hyuk Jung & Sung Kweon Cho & Woong-Yang Park & Woojae Myung & Bong-Jo Kim & Ron Do & Hyon K., 2024. "Large-scale cross-ancestry genome-wide meta-analysis of serum urate," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
  31. Priya Gupta & Marco Galimberti & Yue Liu & Sarah Beck & Aliza Wingo & Thomas Wingo & Keyrun Adhikari & Henry R. Kranzler & Murray B. Stein & Joel Gelernter & Daniel F. Levey, 2024. "A genome-wide investigation into the underlying genetic architecture of personality traits and overlap with psychopathology," Nature Human Behaviour, Nature, vol. 8(11), pages 2235-2249, November.
  32. Alexander T. Williams & Jing Chen & Kayesha Coley & Chiara Batini & Abril Izquierdo & Richard Packer & Erik Abner & Stavroula Kanoni & David J. Shepherd & Robert C. Free & Edward J. Hollox & Nigel J. , 2023. "Genome-wide association study of thyroid-stimulating hormone highlights new genes, pathways and associations with thyroid disease," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
  33. Bussu, Giorgia & Taylor, Mark & Tammimies, Kristiina & Ronald, Angelica & Falck-Ytter, Terje, 2023. "The latent structure of emerging cognitive abilities: An infant twin study," Intelligence, Elsevier, vol. 99(C).
  34. Junhao Wen & Bingxin Zhao & Zhijian Yang & Guray Erus & Ioanna Skampardoni & Elizabeth Mamourian & Yuhan Cui & Gyujoon Hwang & Jingxuan Bao & Aleix Boquet-Pujadas & Zhen Zhou & Yogasudha Veturi & Mary, 2024. "The genetic architecture of multimodal human brain age," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  35. Yunfeng Huang & Dora Bodnar & Chia-Yen Chen & Gabriela Sanchez-Andrade & Mark Sanderson & Jun Shi & Katherine G. Meilleur & Matthew E. Hurles & Sebastian S. Gerety & Ellen A. Tsai & Heiko Runz, 2023. "Rare genetic variants impact muscle strength," Nature Communications, Nature, vol. 14(1), pages 1-8, December.
  36. Lida Wang & Chachrit Khunsriraksakul & Havell Markus & Dieyi Chen & Fan Zhang & Fang Chen & Xiaowei Zhan & Laura Carrel & Dajiang. J. Liu & Bibo Jiang, 2024. "Integrating single cell expression quantitative trait loci summary statistics to understand complex trait risk genes," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
  37. Wei Jiang & Ling Chen & Matthew J. Girgenti & Hongyu Zhao, 2024. "Tuning parameters for polygenic risk score methods using GWAS summary statistics from training data," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  38. Anders M. Fjell & Øystein Sørensen & Yunpeng Wang & Inge K. Amlien & William F. C. Baaré & David Bartrés-Faz & Lars Bertram & Carl-Johan Boraxbekk & Andreas M. Brandmaier & Ilja Demuth & Christian A. , 2023. "No phenotypic or genotypic evidence for a link between sleep duration and brain atrophy," Nature Human Behaviour, Nature, vol. 7(11), pages 2008-2022, November.
  39. Bryan R. Gorman & Sun-Gou Ji & Michael Francis & Anoop K. Sendamarai & Yunling Shi & Poornima Devineni & Uma Saxena & Elizabeth Partan & Andrea K. DeVito & Jinyoung Byun & Younghun Han & Xiangjun Xiao, 2024. "Multi-ancestry GWAS meta-analyses of lung cancer reveal susceptibility loci and elucidate smoking-independent genetic risk," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
  40. Ruoyu Tian & Tian Ge & Hyeokmoon Kweon & Daniel B. Rocha & Max Lam & Jimmy Z. Liu & Kritika Singh & Daniel F. Levey & Joel Gelernter & Murray B. Stein & Ellen A. Tsai & Hailiang Huang & Christopher F., 2024. "Whole-exome sequencing in UK Biobank reveals rare genetic architecture for depression," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
  41. Qile Dai & Geyu Zhou & Hongyu Zhao & Urmo Võsa & Lude Franke & Alexis Battle & Alexander Teumer & Terho Lehtimäki & Olli T. Raitakari & Tõnu Esko & Michael P. Epstein & Jingjing Yang, 2023. "OTTERS: a powerful TWAS framework leveraging summary-level reference data," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
  42. Carla Márquez-Luna & Steven Gazal & Po-Ru Loh & Samuel S. Kim & Nicholas Furlotte & Adam Auton & Alkes L. Price, 2021. "Incorporating functional priors improves polygenic prediction accuracy in UK Biobank and 23andMe data sets," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
  43. Maria Niarchou & Daniel E. Gustavson & J. Fah Sathirapongsasuti & Manuel Anglada-Tort & Else Eising & Eamonn Bell & Evonne McArthur & Peter Straub & J. Devin McAuley & John A. Capra & Fredrik Ullén & , 2022. "Genome-wide association study of musical beat synchronization demonstrates high polygenicity," Nature Human Behaviour, Nature, vol. 6(9), pages 1292-1309, September.
  44. Tuomo Hartonen & Bradley Jermy & Hanna Sõnajalg & Pekka Vartiainen & Kristi Krebs & Andrius Vabalas & Tuija Leino & Hanna Nohynek & Jonas Sivelä & Reedik Mägi & Mark Daly & Hanna M. Ollila & Lili Mila, 2023. "Nationwide health, socio-economic and genetic predictors of COVID-19 vaccination status in Finland," Nature Human Behaviour, Nature, vol. 7(7), pages 1069-1083, July.
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