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Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants

science (New York, N.Y.) 2025年第6734期387卷 eadp4753页

作者： Liu, Hongbo Abedini, Amin Ha, Eunji Ma, Ziyuan Sheng, Xin Dumoulin, Bernhard Qiu, Chengxiang Aranyi, Tamas Li, Shen Dittrich, Nicole Chen, Hua-Chang Tao, Ran Tarng, Der-Cherng Hsieh, Feng-Jen Chen, Shih-Ann Yang, Shun-Fa Lee, Mei-Yueh Kwok, Pui-Yan Wu, Jer-Yuarn Chen, Chien-Hsiun Khan, Atlas Limdi, Nita A. Wei, Wei-Qi Walunas, Theresa L. Karlson, Elizabeth W. Kenny, Eimear E. Luo, Yuan Kottyan, Leah Connolly, John J. Jarvik, Gail P. Weng, Chunhua Shang, Ning Cole, Joanne B. Mercader, Josep M. Mandla, Ravi Majarian, Timothy D. Florez, Jose C. Haas, Mary E. Lotta, Luca A. Drivas, Theodore G. Vy, Ha My T Nadkarni, Girish N. Wiley, Laura K. Wilson, Melissa P. Gignoux, Christopher R. Rasheed, Humaira Thomas, Laurent F. Åsvold, Bjørn Olav Brumpton, Ben M. Hallan, Stein I. Hveem, Kristian Zheng, Jie Hellwege, Jacklyn N. Zawistowski, Matthew Zöllner, Sebastian Franceschini, Nora Hu, Hailong Zhou, Jianfu Kiryluk, Krzysztof Ritchie, Marylyn D. Palmer, Matthew Edwards, Todd L. Voight, Benjamin F. Hung, Adriana M. Susztak, Katalin Department of Medicine Renal Electrolyte and Hypertension Division University of Pennsylvania Philadelphia PA United States Institute of Diabetes Obesity and Metabolism University of Pennsylvania Philadelphia PA United States Department of Genetics University of Pennsylvania Philadelphia PA United States Penn-CHOP Kidney Innovation Center University of Pennsylvania Philadelphia PA United States Liangzhu Laboratory Zhejiang University 1369 West Wenyi Road Hangzhou Zhejiang China Department of Nephrology Children' Hospital Zhejiang University School of Medicine National Clinical Research Center for Child Health Hangzhou Zhejiang China Institute of Molecular Life Sciences HUN-REN Research Center for Natural Sciences Budapest Hungary Department of Molecular Biology Semmelweis University Budapest Hungary Department of Medicine Federal University of São Paulo São Paulo Brazil Department of Biostatistics Vanderbilt University Medical Center Nashville TN United States Vanderbilt Genetics Institute Vanderbilt University Medical Center Nashville TN United States Institute of Clinical Medicine School of Medicine National Yang Ming Chiao Tung University ROC Taipei Taiwan Division of Nephrology Department of Medicine Taipei Veterans General Hospital ROC Taipei Taiwan Institute of Biomedical Sciences Academia Sinica ROC Taipei Taiwan Cardiovascular Center Taichung Veterans General Hospital Taichung Taiwan ROC National Chung Hsing University Taichung Taiwan ROC Heart Rhythm Center Division of Cardiology Department of Medicine Taipei Veterans General Hospital ROC Taipei Taiwan Department of Internal Medicine College of Medicine National Yang Ming Chiao Tung University ROC Taipei Taiwan Institute of Medicine Chung Shan Medical University Taichung Taiwan ROC Department of Medical Research Chung Shan Medical University Hospital Taichung Taiwan ROC Division of Endocrinology and Metabolism Department of Internal Medicine Kaohsiung Medical Universit

Kidney dysfunction is a major cause of mortality, but its genetic architecture remains elusive. In this study, we conducted a multiancestry genome-wide association study in 2.2 million individuals and identified 1026 (97 previously unknown) independent loci. Ancestry-specific analysis indicated an attenuation of newly identified signals on common variants in European ancestry populations and the power of population diversity for further discoveries. We defined genotype effects on allele-specific gene expression and regulatory circuitries in more than 700 human kidneys and 237,000 cells. We found 1363 coding variants disrupting 782 genes, with 601 genes also targeted by regulatory variants and convergence in 161 genes. Integrating 32 types of genetic information, we present the "Kidney Disease Genetic Scorecard" for prioritizing potentially causal genes, cell types, and druggable targets for kidney disease.

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P052 A novel algorithm for KIR copy number imputation by KIBAG and consolidation of population specific KIR references in HKimpNet (HLA & KIR imputation network)

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Human Immunology 2019年 80卷 93-93页

作者： Seik-Soon Khor Xiuwen Zheng Akiko Ishitani Fumihiro Azuma Chul-Woo Pyo Yosuke Omae Toshio Yabe Daniel Geraghty Mary Carrington Katsushi Tokunaga HLA & KIR Imputation Network (HKimpnet) The University of Tokyo Tokyo Japan Toyama Genome Medical Science Project National Center for Global Health and Medicine Tokyo Japan University of Washington Seattle WA United States Nara Medical University Nara Japan Japanese Red Cross Kanto-Koshinetsu Block Blood Center Tokyo Japan Clinical Research Division Fred Hutchinson Cancer Research Center Seattle WA United States Scisco Genetics Inc Seattle WA United States Basic Science Program Frederick National Laboratory for Cancer Research Frederick MD United States Ragon Institute of the Massachusetts General Hospital Massachusetts Institute of Technology and Harvard University Boston MA United States

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Author Correction: Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

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Nature genetics 2018年第12期50卷 1754页

作者： Huipeng Li Elise T Courtois Debarka Sengupta Yuliana Tan Kok Hao Chen Jolene Jie Lin Goh Say Li Kong Clarinda Chua Lim Kiat Hon Wah Siew Tan Mark Wong Igor Cima Min-Han Tan Lawrence J K Wee Axel M Hillmer Iain Beehuat Tan Paul Robson Shyam Prabhakar Computational and Systems Biology Genome Institute of Singapore Singapore Singapore. Developmental Cellomics Laboratory Genome Institute of Singapore Singapore Singapore. Department of Computer Science and Engineering and Center for Computational Biology Indraprastha Institute of Information Technology Delhi India. Synthetic Biology Genome Institute of Singapore Singapore Singapore. Cancer Therapeutics and Stratified Oncology Genome Institute of Singapore Singapore Singapore. Department of Medical Oncology National Cancer Centre Singapore Singapore Singapore. Department of Pathology Singapore General Hospital Singapore Singapore. Department of Colorectal Surgery Singapore General Hospital Singapore Singapore. Institute of Bioengineering and Nanotechnology Singapore Singapore. Data Analytics Department Institute for Infocomm Research Singapore Singapore. Cancer Therapeutics and Stratified Oncology Genome Institute of Singapore Singapore Singapore. iain.tan.b.h@singhealth.com.sg. Department of Medical Oncology National Cancer Centre Singapore Singapore Singapore. iain.tan.b.h@singhealth.com.sg. Program in Cancer and Stem Cell Biology Duke-NUS Medical School Singapore Singapore. iain.tan.b.h@singhealth.com.sg. Developmental Cellomics Laboratory Genome Institute of Singapore Singapore Singapore. paul.robson@***. The Jackson Laboratory for Genomic Medicine Farmington Connecticut USA. paul.robson@***. Department of Genetics and Genome Sciences Institute for Systems Genomics University of Connecticut Farmington Connecticut USA. paul.robson@***. Department of Biological Sciences National University of Singapore Singapore Singapore. paul.robson@***. Computational and Systems Biology Genome Institute of Singapore Singapore Singapore. prabhakars@gis.a-star.edu.sg.

In the version of the article published, the author list is not accurate. Igor Cima and Min-Han Tan should have been authors, appearing after Mark Wong in the author list, while Paul Jongjoon Choi should not have been listed as an author. Igor Cima and Min-Han Tan both have the affiliation Institute of Bioengineering and Nanotechnology, Singapore, Singapore, and their contributions should have been noted in the Author Contributions section as "I.C. preprocessed Primary Cell Atlas data with inputs from M.-H.T." The following description of the contribution of Paul Jongjoon Choi should not have appeared: "P.J.C. supported the smFISH experiments." In the 'RCA: global panel' section of the Online Methods, the following sentence should have appeared as the second sentence, "An expression atlas of human primary cells (the Primary Cell Atlas) was preprocessed similarly to in ref. 55," with new reference 55 (Cima, I. et al. Tumor-derived circulating endothelial cell clusters in colorectal cancer. science Transl. Med. 8, 345ra89, 2016).

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Erratum to: Identifying candidate positive selection genes in Korean imported pig breeds

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Genes & Genomics 2017年第6期39卷 687-687页

作者： Wonseok Lee Mengistie Taye Taehyung Kwon Joon Yoon Dongsung Jang Shunsuke Suzuki Heebal Kim Department of Agricultural Biotechnology Animal Biotechnology and Research Institute of Agriculture and Life Sciences Seoul National University Seoul Republic of Korea Bahir Dar University College of Agriculture and Environmental Sciences Bahir Dar Ethiopia Department of Natural Science Interdisciplinary Program in Bioinformatics Seoul National University Seoul Republic of Korea Interdisciplinary Program in Agricultural Genomics Seoul National University Seoul Republic of Korea Epigenomics Division Frontier Agriscience and Technology Center Faculty of Agriculture Shinshu University Kami‑Ina Japan Department of Interdisciplinary Genome Sciences and Cell Metabolism Institute for Biomedical Sciences Interdisciplinary Cluster for Cutting Edge Research Shinshu University Kami‑Ina Japan Institute for Biomedical Sciences Shinshu University Kami‑Ina Japan

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Merit of integrating in situ transcriptomics and anatomical information for cell annotation and lineage construction in single-cell analyses of Populus

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genome biology 2024年第1期25卷 85页

作者： Ying-Lan Chen Jo-Wei Allison Hsieh Shang-Che Kuo Chung-Ting Kao Chia-Chun Tung Jhong-He Yu Tien-Hsien Chang Chuan Ku Jianbo Xie Deqiang Zhang Quanzi Li Ying-Chung Jimmy Lin Department of Biotechnology and Bioindustry Sciences College of Bioscience and Biotechnology National Cheng Kung University Tainan Taiwan. cyl0828@gs.ncku.edu.tw. Department of Life Science National Taiwan University Taipei Taiwan. Genome and Systems Biology Degree Program National Taiwan University and Academia Sinica Taipei Taiwan. Institute of Plant Biology National Taiwan University Taipei Taiwan. Genomics Research Center Academia Sinica Taipei Taiwan. Institute of Plant and Microbial Biology Academia Sinica Taipei Taiwan. National Engineering Laboratory for Tree Breeding College of Biological Sciences and Technology Beijing Forestry University Beijing China. Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants Ministry of Education College of Biological Sciences and Technology Beijing Forestry University Beijing China. State Key Laboratory of Tree Genetics and Breeding Chinese Academy of Forestry Beijing China. Department of Life Science National Taiwan University Taipei Taiwan. YCJimmyLin@ntu.edu.tw. Genome and Systems Biology Degree Program National Taiwan University and Academia Sinica Taipei Taiwan. YCJimmyLin@ntu.edu.tw. Institute of Plant Biology National Taiwan University Taipei Taiwan. YCJimmyLin@ntu.edu.tw.

Cell type annotation and lineage construction are two of the most critical tasks conducted in the analyses of single-cell RNA sequencing (scRNA-seq). Four recent scRNA-seq studies of differentiating xylem propose four models on differentiating xylem development in Populus. The differences are mostly caused by the use of different strategies for cell type annotation and subsequent lineage interpretation. Here, we emphasize the necessity of using in situ transcriptomes and anatomical information to construct the most plausible xylem development model.

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Publisher Correction: Paternal restraint stress affects offspring metabolism via ATF-2 dependent mechanisms in Drosophila melanogaster germ cells

Communications biology

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Communications biology 2020年第1期3卷 251页

作者： Ki-Hyeon Seong Nhung Hong Ly Yuki Katou Naoko Yokota Ryuichiro Nakato Shinnosuke Murakami Akiyoshi Hirayama Shinji Fukuda Siu Kang Tomoyoshi Soga Katsuhiko Shirahige Shunsuke Ishii RIKEN Cluster for Pioneering Research Tsukuba Ibaraki Japan. ki-hyeon.seong@riken.jp. PRESTO Japan Science and Technology Agency Kawaguchi Japan. ki-hyeon.seong@riken.jp. RIKEN Cluster for Pioneering Research Tsukuba Ibaraki Japan. Laboratory of Genome Structure and Function Institute for Quantitative Biosciences University of Tokyo Tokyo Japan. Laboratory of Computational Genomics Institute for Quantitative Biosciences University of Tokyo Tokyo Japan. Institute for Advanced Biosciences Keio University Tsuruoka Yamagata Japan. Systems Biology Program Graduate School of Media and Governance Keio University Fujisawa Kanagawa Japan. PRESTO Japan Science and Technology Agency Kawaguchi Japan. Transborder Medical Research Center University of Tsukuba Tsukuba Ibaraki Japan. Department of Bio-Systems Engineering Graduate School of Science and Engineering Yamagata University Yonezawa Yamagata Japan. RIKEN Cluster for Pioneering Research Tsukuba Ibaraki Japan. sishii@riken.jp.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Author Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers

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Nature genetics 2023年第6期55卷 1078页

作者： Yuan Yuan Young Seok Ju Youngwook Kim Jun Li Yumeng Wang Christopher J Yoon Yang Yang Inigo Martincorena Chad J Creighton John N Weinstein Yanxun Xu Leng Han Hyung-Lae Kim Hidewaki Nakagawa Keunchil Park Peter J Campbell Han Liang Department of Bioinformatics and Computational Biology The University of Texas MD Anderson Cancer Center Houston TX USA. Cancer Genome Project Wellcome Trust Sanger Institute Hinxton UK. Graduate School of Medical Science and Engineering Korea Advanced Institute of Science and Technology Daejeon Korea. Department of Health Science and Technology Samsung Advanced Institute for Health Science and Technology Sungkyunkwan University School of Medicine Seoul Korea. Samsung Genome Institute Samsung Medical Center Seoul Korea. Quantitative and Computational Biosciences Graduate Program Baylor College of Medicine Houston TX USA. Division of Biostatistics The University of Texas Health Science Center at Houston School of Public Health Houston TX USA. Department of Medicine and Dan L. Duncan Cancer Center Division of Biostatistics Baylor College of Medicine Houston TX USA. Department of Systems Biology The University of Texas MD Anderson Cancer Center Houston TX USA. Department of Applied Mathematics and Statistics Johns Hopkins University Baltimore MD USA. Department of Biochemistry and Molecular Biology The University of Texas Health Science Center at Houston McGovern Medical School Houston TX USA. Department of Biochemistry Ewha Womans University School of Medicine Seoul Korea. Laboratory for Cancer Genomics RIKEN Center for Integrative Medical Sciences Yokohama Japan. Division of Hematology/Oncology Samsung Medical Center Sungkyunkwan University School of Medicine Seoul Korea. kpark@skku.edu. Samsung Advanced Institute for Health Sciences and Technology Sungkyunkwan University School of Medicine Seoul South Korea. kpark@skku.edu. Cancer Genome Project Wellcome Trust Sanger Institute Hinxton UK. pc8@sanger.ac.uk. Department of Haematology University of Cambridge Cambridge UK. pc8@sanger.ac.uk. Department of Bioinformatics and Computational Biology The University of Texas MD Anderson Cancer Center Houston TX USA. hliang1@mdanderson.org. Quantitative and Comp

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Artificial Intelligence, Bioinformatics, and Pathology

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Advances in Molecular Pathology 2022年第1期5卷 e1-e24页

作者： Joshua Levy Yunrui Lu Marietta Montivero Ojas Ramwala Jason McFadden Carly Miles Adam Gilbert Diamond Ramya Reddy Ram Reddy Taylor Hudson Zarif Azher Akash Pamal Sameer Gabbita Tess Cronin Abdol Aziz Ould Ismail Tarushii Goel Sanjay Jacob Anish Suvarna Sumanth Ratna Jason Zavras Louis Vaickus Department of Pathology and Laboratory Medicine Emerging Diagnostic and Investigative Technologies Dartmouth Health Lebanon NH USA Department of Dermatology Dartmouth Health Lebanon NH USA Department of Epidemiology Dartmouth College Geisel School of Medicine Hanover NH USA Program in Quantitative Biomedical Sciences Dartmouth College Geisel School of Medicine Hanover NH USA Dartmouth College Geisel School of Medicine Hanover NH USA Department of Biomedical Informatics and Medical Education University of Washington Seattle WA USA Undiagnosed Diseases Program National Human Genome Research Institute Bethesda MD USA Department of Computer Science University of Michigan Ann Arbor MI USA Hanover High School Hanover NH USA Thomas Jefferson High School for Science and Technology Alexandria VA USA Department of Computer Science University of Virginia Charlottesville VA USA University of New Hampshire Durham NH USA White River Junction VA Medical Center White River Junction VT USA Massachusetts Institute of Technology Cambridge MA USA Case Western Reserve University Cleveland OH USA Yale University New Haven CT USA Broad Institute of MIT and Harvard Cambridge MA USA

The advent of complex molecular assays and anatomic imaging platforms has enabled unprecedented characterization of disease pathogenesis. However, challenges remain in formulating diagnostic and prognostic tests that can effectively navigate and synthesize the massive treasure troves of information now available in modern pathology laboratories. Artificial intelligence (AI), and, in particular, machine learning, are pattern mining algorithms that can efficiently uncover biomarkers and risk factors personalized to the individual. These technologies will also have the benefit of providing efficiency gains, resolving ambiguity, and reducing the unnecessary resource expenditures in the Pathology setting. Adoption of AI technologies in these settings can be improved by engaging pathologists on how AI can be meaningfully used in their practice and through dissemination and communication of these core concepts and their potential benefits. In this work, we summarize emerging application areas for AI in the fields of Anatomic and Molecular Pathology.

关键词： Artificial intelligence technologies Artificial neural networks Machine learning algorithms Virtual staining Spatial omics Bioinformatics Image analysis

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Author Correction: The high-dimensional space of human diseases built from diagnosis records and mapped to genetic loci

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Nature computational science 2023年第7期3卷 658页

作者： Gengjie Jia Yu Li Xue Zhong Kanix Wang Milton Pividori Rabab Alomairy Aniello Esposito Hatem Ltaief Chikashi Terao Masato Akiyama Koichi Matsuda David E Keyes Hae Kyung Im Takashi Gojobori Yoichiro Kamatani Michiaki Kubo Nancy J Cox James Evans Xin Gao Andrey Rzhetsky Shenzhen Branch Guangdong Laboratory of Lingnan Modern Agriculture Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China. jiagengjie@***. Computational Bioscience Research Center King Abdullah University of Science and Technology Thuwal Saudi Arabia. Computer Science Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal Saudi Arabia. Department of Computer Science and Engineering The Chinese University of Hong Kong Hong Kong People's Republic of China. Department of Medicine and Vanderbilt Genetics Institute Vanderbilt University Medical Center Nashville TN US. Department of Medicine Institute of Genomics and Systems Biology Committee on Genomics Genetics and Systems Biology University of Chicago Chicago IL US. Department of Operations Business Analytics and Information Systems University of Cincinnati Cincinnati OH US. Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine University of Pennsylvania Philadelphia PA US. Extreme Computing Research Center Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal Saudi Arabia. College of Computer Science and Engineering University of Jeddah Jeddah Saudi Arabia. HPE HPC/AI EMEA Research Laboratory Bristol UK. RIKEN Center for Integrative Medical Sciences Yokohama Japan. Clinical Research Center Shizuoka General Hospital Shizuoka Japan. Department of Applied Genetics The School of Pharmaceutical Sciences University of Shizuoka Shizuoka Japan. Department of Ophthalmology Graduate School of Medical Sciences Kyushu University Fukuoka Japan. Department of Computational Biology and Medical Sciences Graduate School of Frontier Sciences The University of Tokyo Tokyo Japan. Biological and Environmenta

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Correction to: Stage-dependent piRNAs in chicken implicated roles in modulating male germ cell development

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BMC genomics 2018年第1期19卷 480页

作者： Kai-Wei Chang Yen-Tzu Tseng Yi-Chen Chen Chih-Yun Yu Hung-Fu Liao Yi-Chun Chen Yu-Fan Evan Tu Shinn-Chih Wu I-Hsuan Liu Marina Pinskaya Antonin Morillon Bertrand Pain Shau-Ping Lin Genome and Systems Biology Degree Program National Taiwan University Taipei 106 Taiwan. Present Address: Graduate Institute of Brain and Mind Sciences College of Medicine National Taiwan University Taipei 10051 Taiwan. Institute of Biotechnology National Taiwan University Taipei 106 Taiwan. Department of Animal Science and Technology National Taiwan University Taipei 106 Taiwan. Univ Lyon Université Lyon 1 INSERM INRA Stem Cell and Brain Research Institute U1208 USC1361 F-69500 Bron France. ncRNA epigenetic and genome fluidity Institut Curie Centre de Recherche CNRS UMR 3244 PSL Research University Université Pierre et Marie Curie F-75005 Paris France. Genome and Systems Biology Degree Program National Taiwan University Taipei 106 Taiwan. shaupinglin@ntu.edu.tw. Institute of Biotechnology National Taiwan University Taipei 106 Taiwan. shaupinglin@ntu.edu.tw. Research Center for Developmental Biology and Regenerative Medicine National Taiwan University Taipei 106 Taiwan. shaupinglin@ntu.edu.tw. Agricultural Biotechnology Research Centre Academia Sinica Taipei 106 Taiwan. shaupinglin@ntu.edu.tw. Center for Systems Biology National Taiwan University Taipei 106 Taiwan. shaupinglin@ntu.edu.tw.

Following publication of the original article [1], the authors reported that one of the authors' names is spelled incorrectly.

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