检索结果-内蒙古大学图书馆

Genome-wide association studies identify susceptibility loci for epithelial ovarian cancer in east Asian women

Gynecologic oncology 2019年第2期153卷 343-355页

作者： Kate Lawrenson Fengju Song Dennis J Hazelett Siddhartha P Kar Jonathan Tyrer Catherine M Phelan Rosario I Corona Norma I Rodríguez-Malavé Ji-Hei Seo Emily Adler Simon G Coetzee Felipe Segato Marcos A S Fonseca Christopher I Amos Michael E Carney Georgia Chenevix-Trench Jiyeob Choi Jennifer A Doherty Weihua Jia Gang J Jin Byoung-Gie Kim Nhu D Le Juyeon Lee Lian Li Boon K Lim Noor A Adenan Mika Mizuno Boyoung Park Celeste L Pearce Kang Shan Yongyong Shi Xiao-Ou Shu Weiva Sieh Pamela J Thompson Lynne R Wilkens Qingyi Wei Yin L Woo Li Yan Beth Y Karlan Matthew L Freedman Houtan Noushmehr Ellen L Goode Andrew Berchuck Thomas A Sellers Soo-Hwang Teo Wei Zheng Keitaro Matsuo Sue Park Kexin Chen Paul D P Pharoah Simon A Gayther Marc T Goodman Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute Cedars-Sinai Medical Center 8700 Beverly Boulevard Suite 290W Los Angeles CA USA Center for Bioinformatics and Functional Genomics Cedars Sinai Genomics Core Cedars-Sinai Medical Center Los Angeles CA USA. Electronic address: kate.lawrenson@***. National Clinical Research Center for Cancer Tianjin Medical University Cancer Institute and Hospital Tianjin China Department of Epidemiology and Biostatistics Key Laboratory of Cancer Prevention and Therapy Tianjin China. Center for Bioinformatics and Functional Genomics Cedars Sinai Genomics Core Cedars-Sinai Medical Center Los Angeles CA USA. Department of Oncology Centre for Cancer Genetic Epidemiology University of Cambridge Strangeways Research Laboratory Cambridge UK. Department of Gynecologic Oncology Moffitt Cancer Center Tampa FL USA Department of Cancer Epidemiology Moffitt Cancer Center Tampa FL USA. Center for Bioinformatics and Functional Genomics Cedars Sinai Genomics Core Cedars-Sinai Medical Center Los Angeles CA USA. Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA. Department of Preventive Medicine University of Southern California Keck School of Medicine 1450 Biggy Street Los Angeles CA USA. Department of Genetics Ribeirão Preto Medical School University of São Paulo 14049-900 Brazil. Institute for Clinical and Translational Research Department of Medicine Baylor School of Medicine HoustonTX USA. Department of Obstetrics and Gynecology John A. Burns School of Medicine University of Hawaii Honolulu HI USA. Genetics and Computational Biology Department QIMR Berghofer Medical Research Institute 300 Herston Road Herston QLD 4006 Australia. Department of Preventive Medicine Seoul National University College of Medicine Seoul Republic of Korea Cancer Research Institute Seoul National University Seoul Republic of Korea Department of Biomedical Science Graduate School Seoul National Un

OBJECTIVE:Genome-wide association studies (GWASs) for epithelial ovarian cancer (EOC) have focused largely on populations of European ancestry. We aimed to identify common germline variants associated with EOC risk in Asian women. METHODS:Genotyping was performed as part of the OncoArray project. Samples with >60% Asian ancestry were included in the analysis. Genotyping was performed on 533,631 SNPs in 3238 Asian subjects diagnosed with invasive or borderline EOC and 4083 unaffected controls. After imputation, genotypes were available for 11,595,112 SNPs to identify associations. RESULTS:At chromosome 6p25.2, SNP rs7748275 was associated with risk of serous EOC (odds ratio [OR] = 1.34, P = 8.7 × 10) and high-grade serous EOC (HGSOC) (OR = 1.34, P = 4.3 × 10). SNP rs6902488 at 6p25.2 (r = 0.97 with rs7748275) lies in an active enhancer and is predicted to impact binding of STAT3, P300 and ELF1. We identified additional risk loci with low Bayesian false discovery probability (BFDP) scores, indicating they are likely to be true risk associations (BFDP <10%). At chromosome 20q11.22, rs74272064 was associated with HGSOC risk (OR = 1.27, P = 9.0 × 10). Overall EOC risk was associated with rs10260419 at chromosome 7p21.3 (OR = 1.33, P = 1.2 × 10) and rs74917072 at chromosome 2q37.3 (OR = 1.25, P = 4.7 × 10). At 2q37.3, expression quantitative trait locus analysis in 404 HGSOC tissues identified ESPNL as a putative candidate susceptibility gene (P = 1.2 × 10). CONCLUSION:While some risk loci were shared between East Asian and European populations, others were population-specific, indicating that the landscape of EOC risk in Asian women has both shared and unique features compared to women of European ancestry.

关键词： Asian ancestry Enhancer Epithelial ovarian cancer Gene regulation Genome-wide association study eQTL

来源：评论

学校读者我要写书评

暂无评论

Genome-wide association study of long COVID

引用

Nature Genetics 2025年 1-16页

作者： Vilma Lammi Tomoko Nakanishi Samuel E. Jones Juha Karjalainen Martin Broberg Hele H. Haapaniemi Matti Pirinen Mari E. K. Niemi Mattia Cordioli Mark J. Daly Andrea Ganna Hanna M. Ollila J. Brent Richards Yukinori Okada Shea J. Andrews Beatriz Cortés Rafael de Cid Susana Iraola-Guzmán Natalia Blay Xavier Farré Heath E. O’Brien Thompson Hannah Patrick J. Short Ana Ochoa-Guzman Michelle Duran-Gomez Brian E. Fulton-Howard Masahiro Kanai Axel Schmidt Daniella Balla Julia Heggemann Sonja Schultz Pari Behzad Markus M. Nöthen Abigail Miller Kerstin U. Ludwig Ruth E. Mitchell George Davey Smith Nicholas J. Timpson Abdou Mousas Evangelos Evangelou Evangelia Ntzani Konstantinos K. Tsilidis Massimo Mangino Alicia Huerta-Chagoya Nasa Sinnott-Armstrong Elizabeth T. Cirulli Francisco Tanudjaja Efren Sandoval Nicole L. Washington Simon White Alexandre Bolze Kelly M. Schiabor Barrett Marc Vaudel Alex S. F. Kwong Amit K. Maiti Minttu M. Marttila Daniel C. Posner Alexis A. Rodriguez Chiara Batini Beatriz Guillen-Guio Olivia C. Leavy Anna L. Guyatt Catherine John Louise V. Wain Francesca Minnai Anna R. Dearman Benedict Hignell Meena Kumari C. A. Robert Warmerdam Lude H. Franke Celia B. Sequeros Søren Brunak David Westergaard Karina Banasik Thomas W. Winkler Iris M. Heid Daniel M. Jordan Ryan C. Thompson Alexander W. Charney Laura G. Sloofman Nicole W. Simons Noam D. Beckmann Raimonds Rešcenko Vita Rovite Peculis Raitis Monta Briviba Janis Klovinš Laura Ansone Lorenzo Miano Flora Peyvandi Francesco Malvestiti Nicola Montano Alessandra Bandera Francesco Bruno Arturo Blasi Jacqueline M. Lane Jakob M. Cherry Ryan K. Chung Laura Carvajal-Silva Kevin Aguilar-Valdés Leslie C. Cerpa Tamara V. Arévalo Eduardo Lamoza Alicia Colombo Ricardo A. Verdugo Erika Frangione Xu Xinyi Jennifer Taher Jordan Lerner-Ellis Lindsay Guare Shefali S. Verma Ekaterina Vergasova Michil Trofimov Layal Shaheen Nikolay Plotnikov Anna Kim Dmitrii Kharitonov Alexei Kamelin Alexander Rakitko Eirini Marouli Pasquale Striano Ummu Afeera Zainulabid Ashutosh Kumar Hajar Fa Institute for Molecular Medicine Finland (FIMM) Helsinki Institute of Life Science (HiLIFE) University of Helsinki Helsinki Finland Department of Human Genetics McGill University Montreal Quebec Canada Centre for Clinical Epidemiology Department of Medicine Lady Davis Institute Jewish General Hospital McGill University Montreal Quebec Canada Kyoto-McGill International Collaborative Program in Genomic Medicine Graduate School of Medicine Kyoto University Kyoto Japan Department of Genome Informatics Graduate School of Medicine the University of Tokyo Tokyo Japan Research Fellow Japan Society for the Promotion of Science Tokyo Japan Program in Medical and Population Genetics Broad Institute of Harvard and MIT Cambridge MA USA Stanley Center for Psychiatric Research Broad Institute of Harvard and MIT Cambridge MA USA Analytic and Translational Genetics Unit Massachusetts General Hospital Boston MA USA Department of Mathematics and Statistics University of Helsinki Helsinki Finland Department of Public Health University of Helsinki Helsinki Finland Broad Institute Cambridge MA USA Analytical and Translational Genetics Unit Massachusetts General Hospital Harvard Medical School Boston MA USA Center for Genomic Medicine Massachusetts General Hospital Boston MA USA Anesthesia Critical Care and Pain Medicine Massachusetts General Hospital and Harvard Medical School Boston MA USA Broad Institute of MIT and Harvard Cambridge MA USA Department of Twin Research King’s College London London UK 5 Prime Sciences Inc Montreal Quebec Canada Department of Epidemiology Biostatistics and Occupational Health McGill University Montreal Quebec Canada Department of Statistical Genetics Osaka University Graduate School of Medicine Suita Japan Laboratory for Systems Genetics RIKEN Center for Integrative Medical Sciences Yokohama Japan Laboratory of Statistical Immunology Immunology Frontier Research Center (WPI-IFReC) Osaka University Suita Japan Departmen

Infections can lead to persistent symptoms and diseases such as shingles after varicella zoster or rheumatic fever after streptococcal infections. Similarly, severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) infection can result in long coronavirus disease (COVID), typically manifesting as fatigue, pulmonary symptoms and cognitive dysfunction. The biological mechanisms behind long COVID remain unclear. We performed a genome-wide association study for long COVID including up to 6,450 long COVID cases and 1,093,995 population controls from 24 studies across 16 countries. We discovered an association ofFOXP4with long COVID, independent of its previously identified association with severe COVID-19. The signal was replicated in 9,500 long COVID cases and 798,835 population controls. Given the transcription factor FOXP4’s role in lung physiology and pathology, our findings highlight the importance of lung function in the pathophysiology of long COVID.

关键词：

来源：评论

学校读者我要写书评

暂无评论

Quantum computing at the frontiers of biological sciences

arXiv

引用

arXiv 2019年

作者： Emani, Prashant S. Warrell, Jonathan Anticevic, Alan Bekiranov, Stefan Gandal, Michael McConnell, Michael J. Sapiro, Guillermo Aspuru-Guzik, Alán Baker, Justin Bastiani, Matteo McClure, Patrick Murray, John Sotiropoulos, Stamatios N. Taylor, Jacob Senthil, Geetha Lehner, Thomas Gerstein, Mark B. Harrow, Aram W. Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States Department of Molecular Biophysics and Biochemistry Yale University New HavenCT06520 United States Yale School of Medicine Department of Psychiatry New HavenCT06511 United States University of Virginia School of Medicine Department of Biochemistry and Molecular Genetics CharlottesvilleVA22903 United States Department of Psychiatry Semel Institute David Geffen School of Medicine University of California–Los Angeles 695 Charles E. Young Drive South Los AngelesCA90095 United States Univ. of Virginia School of Medicine Department of Neuroscience CharlottesvilleVA22903 United States Department of Electrical and Computer Engineering Duke University DurhamNC27708 United States Department of Chemistry University of Toronto 80 St. George Street TorontoONM5S 3H6 Canada TorontoONM5S 1M1 Canada CIFAR Artificial Intelligence Research Chair Vector Institute TorontoONM5S 1M1 Canada Department of Computer Science University of Toronto 40 St. George Street TorontoONM5S 2E4 Canada Schizophrenia and Bipolar Disorder Program McLean Hospital BelmontMA02478 United States Department of Psychiatry Harvard Medical School BostonMA02114 United States Sir Peter Mansfield Imaging Centre School of Medicine University of Nottingham NottinghamNG7 2RD United Kingdom Machine Learning Team National Institute of Mental Health BethesdaMD20892 United States Section on Functional Imaging Methods National Institute of Mental Health BethesdaMD20892 United States Department of Psychiatry Yale University School of Medicine New HavenCT06511 United States Department of Physics Yale University New HavenCT06511 United States Joint Center for Quantum Information and Computer Science University of Maryland College ParkMD20742 United States National Institute of Standards and Technology GaithersburgMD20899 United States Office of Genomics Research Coordination N

The search for meaningful structure in biological data has relied on cutting-edge advances in computational technology and data science methods. However, challenges arise as we push the limits of scale and complexity in biological problems. Innovation in massively parallel, classical computing hardware and algorithms continues to address many of these challenges, but there is a need to simultaneously consider new paradigms to circumvent current barriers to processing speed. Accordingly, we articulate a view towards quantum computation and quantum information science, where algorithms have demonstrated potential polynomial and exponential computational speedups in certain applications, such as machine learning. The maturation of the field of quantum computing, in hardware and algorithm development, also coincides with the growth of several collaborative efforts to address questions across length and time scales, and scientific disciplines. We use this coincidence to explore the potential for quantum computing to aid in one such endeavor: the merging of insights from genetics, genomics, neuroimaging and behavioral phenotyping. By examining joint opportunities for computational innovation across fields, we highlight the need for a common language between biological data analysis and quantum computing. Ultimately, we consider current and future prospects for the employment of quantum computing algorithms in the biological sciences. Copyright © 2019, The Authors. All rights reserved.

关键词： Machine learning

来源：评论

学校读者我要写书评

暂无评论

Lithium response in bipolar disorder is associated with focal adhesion and PI3K-Akt networks: a multi-omics replication study

引用

Translational psychiatry 2024年第1期14卷 109页

作者： Anna H Ou Sara B Rosenthal Mazda Adli Kazufumi Akiyama Nirmala Akula Martin Alda Azmeraw T Amare Raffaella Ardau Bárbara Arias Jean-Michel Aubry Lena Backlund Michael Bauer Bernhard T Baune Frank Bellivier Antonio Benabarre Susanne Bengesser Abesh Kumar Bhattacharjee Joanna M Biernacka Pablo Cervantes Guo-Bo Chen Hsi-Chung Chen Caterina Chillotti Sven Cichon Scott R Clark Francesc Colom David A Cousins Cristiana Cruceanu Piotr M Czerski Clarissa R Dantas Alexandre Dayer Maria Del Zompo Franziska Degenhardt J Raymond DePaulo Bruno Étain Peter Falkai Frederike Tabea Fellendorf Ewa Ferensztajn-Rochowiak Andreas J Forstner Louise Frisén Mark A Frye Janice M Fullerton Sébastien Gard Julie S Garnham Fernando S Goes Maria Grigoroiu-Serbanescu Paul Grof Oliver Gruber Ryota Hashimoto Joanna Hauser Urs Heilbronner Stefan Herms Per Hoffmann Andrea Hofmann Liping Hou Stephane Jamain Esther Jiménez Jean-Pierre Kahn Layla Kassem Tadafumi Kato Sarah Kittel-Schneider Barbara König Po-Hsiu Kuo Ichiro Kusumi Nina Lackner Gonzalo Laje Mikael Landén Catharina Lavebratt Marion Leboyer Susan G Leckband Carlos A López Jaramillo Glenda MacQueen Mario Maj Mirko Manchia Cynthia Marie-Claire Lina Martinsson Manuel Mattheisen Michael J McCarthy Susan L McElroy Francis J McMahon Philip B Mitchell Marina Mitjans Francis M Mondimore Palmiero Monteleone Caroline M Nievergelt Markus M Nöthen Tomas Novák Urban Ösby Norio Ozaki Sergi Papiol Roy H Perlis Claudia Pisanu James B Potash Andrea Pfennig Daniela Reich-Erkelenz Andreas Reif Eva Z Reininghaus Marcella Rietschel Guy A Rouleau Janusz K Rybakowski Martin Schalling Peter R Schofield K Oliver Schubert Thomas G Schulze Barbara W Schweizer Florian Seemüller Giovanni Severino Tatyana Shekhtman Paul D Shilling Kazutaka Shimoda Christian Simhandl Claire M Slaney Alessio Squassina Thomas Stamm Pavla Stopkova Sarah K Tighe Alfonso Tortorella Gustavo Turecki Eduard Vieta Julia Volkert Stephanie Witt Naomi R Wray Adam Wright L Trevor Young Peter P Zandi John R Kelsoe Department of Psychiatry University of California San Diego La Jolla CA USA. Center for Computational Biology and Bioinformatics Department of Medicine University of California San Diego La Jolla CA USA. Department of Psychiatry and Psychotherapy Charité- Universitätsmedizin Berlin Campus Charité Mitte Berlin Germany. Fliedner Klinik Berlin Center for Psychiatry Psychotherapy and Psychosomatic Medicine Berlin Germany. Department of Biological Psychiatry and Neuroscience Dokkyo Medical University School of Medicine Mibu Japan. Intramural Research Program National Institute of Mental Health National Institutes of Health US Department of Health & Human Services Bethesda MD USA. Department of Psychiatry Dalhousie University Halifax NS Canada. National Institute of Mental Health Klecany Czech Republic. Discipline of Psychiatry University of Adelaide Adelaide SA Australia. Unit of Clinical Pharmacology Hospital University Agency of Cagliari Cagliari Italy. Department of Evolutive Biology Ecology and Environmental Sciences Facultat de Biologia and Institut de Biomedicina (IBUB) Universitat de Barcelona Barcelona Spain. CIBER de Salud Mental ISCIII Madrid Barcelona Catalonia Spain. Department of Mental Health and Psychiatry Mood Disorders Unit-Geneva University Hospitals Geneva Switzerland. Department of Molecular Medicine and Surgery Karolinska Institutet and Center for Molecular Medicine Karolinska University Hospital Stockholm Sweden. Department of Psychiatry and Psychotherapy University Hospital Carl Gustav Carus Medical Faculty Technische Universität Dresden Dresden Germany. Department of Psychiatry University of Münster Münster Germany. INSERM UMR-S 1144-Université Paris Cité Département de Psychiatrie et de Médecine Addictologique AP-HP Groupe Hospitalier Lariboisière-F Widal Paris France. Bipolar and Depressive Disorders Unit Institute of Neuroscience Hospital Clinic University of Barcelona IDIBAPS CIBERSAM ISCIII Barcelona Catalonia Spa

Lithium is the gold standard treatment for bipolar disorder (BD). However, its mechanism of action is incompletely understood, and prediction of treatment outcomes is limited. In our previous multi-omics study of the Pharmacogenomics of Bipolar Disorder (PGBD) sample combining transcriptomic and genomic data, we found that focal adhesion, the extracellular matrix (ECM), and PI3K-Akt signaling networks were associated with response to lithium. In this study, we replicated the results of our previous study using network propagation methods in a genome-wide association study of an independent sample of 2039 patients from the International Consortium on Lithium Genetics (ConLiGen) study. We identified functional enrichment in focal adhesion and PI3K-Akt pathways, but we did not find an association with the ECM pathway. Our results suggest that deficits in the neuronal growth cone and PI3K-Akt signaling, but not in ECM proteins, may influence response to lithium in BD.

关键词：

来源：评论

学校读者我要写书评

暂无评论

Author Correction: Genomic analysis of a large set of currently-and historically-important human adenovirus pathogens

引用

Emerging microbes & infections 2018年第1期7卷 208页

作者： Ashrafali M Ismail Tiange Cui Kalpana Dommaraju Gurdeep Singh Shoaleh Dehghan Jason Seto Susmita Shrivastava Nadia B Fedorova Neha Gupta Timothy B Stockwell Rebecca Halpin Ramana Madupu Albert Heim Adriana E Kajon Eric G Romanowski Regis P Kowalski Jambulingam Malathi Kuzhanthai L Therese Hajib Narahari Madhavan Qiwei Zhang Leonardo J Ferreyra Morris S Jones Jaya Rajaiya David W Dyer James Chodosh Donald Seto Department of Ophthalmology Howe Laboratory Massachusetts Eye and Ear Infirmary Harvard Medical School Boston MA 02114 USA. Bioinformatics and Computational Biology Program School of Systems Biology George Mason University Manassas VA 20110 USA. Chemistry Department American University Washington DC 20016 USA. J. Craig Venter Institute Rockville MD 20850 USA. Institut für Virologie Medizinische Hochschule Hannover Hannover 30625 Germany. Lovelace Respiratory Research Institute Albuquerque NM 87108 USA. Charles T. Campbell Ophthalmic Microbiology Laboratory Ear and Eye Institute School of Medicine University of Pittsburgh Pittsburgh PA 15213 USA. L & T Microbiology Research Center Kamalnayan Bajaj Research Center Sankara Nethralaya No. 41 College Road Chennai Tamil Nadu 600006 India. Biosafety Level-3 Laboratory School of Public Health Southern Medical University 510515 Guangzhou China. Institute of Virology "J. M. Vanella" Enfermera Gordillo Gómez s/n Agencia 4 Ciudad Universitaria CP 5016 Córdoba Argentina. School of Public Health University of California Berkeley Berkeley CA 94704 USA. Department of Microbiology and Immunology University of Oklahoma Health Sciences Center Oklahoma City OK 73104 USA. Department of Ophthalmology Howe Laboratory Massachusetts Eye and Ear Infirmary Harvard Medical School Boston MA 02114 USA. james_chodosh@meei.harvard.edu. Bioinformatics and Computational Biology Program School of Systems Biology George Mason University Manassas VA 20110 USA. dseto@gmu.edu.

The original publication of this article [1] was missing the below author that made contributions to the research and the published article.

关键词：

来源：评论

学校读者我要写书评

暂无评论

40. Genomic profiling of lung adenocarcinomas with increased MET copy numbers

引用

Cancer Genetics 2018年 226卷 51-51页

作者： Liu, Ching-Hua (Ruby) Chen, Hui Fang, Lianghua Hu, Peter C. Gu, Jun Zhao, Jin Abraham, Ronald Yao, Hui Singh, Rajesh R. Jeffrey Medeiros, L. Luthra, Rajyalakshimi Lu, Xinyan Department of Hematopathology University of Texas MD Anderson Cancer Center Houston TX United States Master of Science in Diagnostic Genetics Program School of Health Professions University of Texas MD Anderson Cancer Center Houston TX United States Department of Pathology Northwestern University Feinberg School of Medicine Chicago IL United States Department of Pathology University of Texas MD Anderson Cancer Center Houston TX United States Department of Oncology Jiangsu Hospital of Traditional Chinese Medicine Nanjing Jiangsu China Department of Clinical Laboratory Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine Central South University Shangsha Hunan China Department of Bioinformatics and Computational Biology University of Texas MD Anderson Cancer Center Houston TX United States

来源：评论

学校读者我要写书评

暂无评论

The Genomic Landscape of Pediatric Myelodysplastic Syndromes

引用

BLOOD 2016年第22期128卷 956-956页

作者： Schwartz, Jason R. Walsh, Michael P. Ma, Jing Lamprecht, Tamara Wang, Shuoguo Wu, Gang Easton, John Ribeiro, Raul C. Klco, Jeffery M. Department of Oncology St. Jude Children's Research Hospital Memphis TN Department of Pathology St. Jude Children's Research Hospital Memphis TN Department of Computational Biology St. Jude Children's Research Hospital Memphis TN Department of Computational Biology and Bioinformatics St. Jude Children's Research Hospital Memphis TN Department of Oncology and Global Medicine International Outreach Program St. Jude Children's Research Hospital Memphis TN

956

关键词：

来源：评论

学校读者我要写书评

暂无评论

P065 Information theory-based analysis of classical HLA genes

引用

Human Immunology 2016年 77卷 85-85页

作者： Hu Huang Wei Wang Yung-Tsi Bolon Craig Malmberg Caleb Kennedy Martin Maiers University of Minnesota Bioinformatics and Computational Biology Minneapolis MN United States National Marrow Donor Program Bioinformatics Research Minneapolis MN United States

Aim In IMGT/HLA Release 3.24.0, less than 7% of the named classical HLA alleles have curated full-length gene sequences or sequences outside the antigen recognition sites (ARS). This study is to investigate genetic variants, polymorphism, SNPs and linkage disequilibrium (LD) within the entire gene region for the classical HLA genes using information theory. Methods Multiple sequence alignment was performed on full-length HLA Class I alleles (HLA-A, -B, -C) and partial-length (from intron 1 through intron 3) Class II alleles (HLA-DQB1, -DRB1) for 15,865 subjects, followed by a gene annotation pipeline. We analyzed the Shannon entropy of each nucleotide site and mutual information within each of the loci. Conditional asymmetric linkage disequilibrium (ALD) measures were employed to characterize the LD between multiallelic SNPs within a locus. Results For HLA Class I alleles, the untranslated regions generally show high entropy variation. Highly variable sites (entropy >0.01) appear most in the noncoding regions (intron 3 in HLA-A and -B, respectively; intron 4 in HLA-C); while within coding regions, the ARS regions contain the most variants. However, since multiple sequence alignment introduces gaps that are ambiguous, we considered the distribution of variants after removing sites with at least one alignment gap. Consequently, for noncoding regions, intron 5 in HLA-A and -B, respectively, and introns 3 and 4 in HLA-C show the highest entropy variation; for coding regions, ARS regions remain highest entropy variation across all five loci. The ALD measures indicate that highly associated polymorphic sites mostly reside within exons 2, 3 and 4 (ARS regions for class II). Some of these associations also showed high heterogeneity. Conclusions Non-coding regions along with the non-ARS coding regions include many informative sites and the proposed method could be utilized in allele typing, typing validation, SNP association study, as well as matching for stem cell transplan

关键词：

来源：评论

学校读者我要写书评

暂无评论

Author Correction: Multi-ancestry genome-wide association analyses improve resolution of genes and pathways influencing lung function and chronic obstructive pulmonary disease risk

引用

Nature genetics 2023年第10期55卷 1778-1779页

作者： Nick Shrine Abril G Izquierdo Jing Chen Richard Packer Robert J Hall Anna L Guyatt Chiara Batini Rebecca J Thompson Chandan Pavuluri Vidhi Malik Brian D Hobbs Matthew Moll Wonji Kim Ruth Tal-Singer Per Bakke Katherine A Fawcett Catherine John Kayesha Coley Noemi Nicole Piga Alfred Pozarickij Kuang Lin Iona Y Millwood Zhengming Chen Liming Li Sara R A Wijnant Lies Lahousse Guy Brusselle Andre G Uitterlinden Ani Manichaikul Elizabeth C Oelsner Stephen S Rich R Graham Barr Shona M Kerr Veronique Vitart Michael R Brown Matthias Wielscher Medea Imboden Ayoung Jeong Traci M Bartz Sina A Gharib Claudia Flexeder Stefan Karrasch Christian Gieger Annette Peters Beate Stubbe Xiaowei Hu Victor E Ortega Deborah A Meyers Eugene R Bleecker Stacey B Gabriel Namrata Gupta Albert Vernon Smith Jian'an Luan Jing-Hua Zhao Ailin F Hansen Arnulf Langhammer Cristen Willer Laxmi Bhatta David Porteous Blair H Smith Archie Campbell Tamar Sofer Jiwon Lee Martha L Daviglus Bing Yu Elise Lim Hanfei Xu George T O'Connor Gaurav Thareja Omar M E Albagha Karsten Suhre Raquel Granell Tariq O Faquih Pieter S Hiemstra Annelies M Slats Benjamin H Mullin Jennie Hui Alan James John Beilby Karina Patasova Pirro Hysi Jukka T Koskela Annah B Wyss Jianping Jin Sinjini Sikdar Mikyeong Lee Sebastian May-Wilson Nicola Pirastu Katherine A Kentistou Peter K Joshi Paul R H J Timmers Alexander T Williams Robert C Free Xueyang Wang John L Morrison Frank D Gilliland Zhanghua Chen Carol A Wang Rachel E Foong Sarah E Harris Adele Taylor Paul Redmond James P Cook Anubha Mahajan Lars Lind Teemu Palviainen Terho Lehtimäki Olli T Raitakari Jaakko Kaprio Taina Rantanen Kirsi H Pietiläinen Simon R Cox Craig E Pennell Graham L Hall W James Gauderman Chris Brightling James F Wilson Tuula Vasankari Tarja Laitinen Veikko Salomaa Dennis O Mook-Kanamori Nicholas J Timpson Eleftheria Zeggini Josée Dupuis Caroline Hayward Ben Brumpton Claudia Langenberg Stefan Weiss Georg Homuth Carsten Oliver Schmidt Nicole Probst-Hensch Marjo-Riitta Jarvelin Alanna C Morrison Ozren Polasek Igor Department of Population Health Sciences University of Leicester Leicester UK. nick.shrine@leicester.ac.uk. Department of Population Health Sciences University of Leicester Leicester UK. Division of Respiratory Medicine and NIHR Nottingham Biomedical Research Centre University of Nottingham Nottingham UK. Leicester National Institute for Health and Care Research Biomedical Research Centre Glenfield Hospital Leicester UK. Channing Division of Network Medicine Division of Pulmonary and Critical Care Medicine Department of Medicine Brigham and Women's Hospital Boston MA USA. Harvard Medical School Boston MA USA. COPD Foundation Washington DC USA. Department of Clinical Science Unversity of Bergen Bergen Norway. Nuffield Department of Population Health University of Oxford Oxford UK. MRC Population Health Research Unit University of Oxford Oxford UK. Department of Epidemiology and Biostatistics School of Public Health Peking University Health Science Center Beijing China. Department of Respiratory Diseases Ghent Universital Hospital Ghent Belgium. Department of Bioanalysis Faculty of Pharmaceutical Sciences Ghent University Ghent Belgium. Department of Epidemiology Eramus Medical Center Rotterdam The Netherlands. Department of Internal Medicine Eramus Medical Center Rotterdam The Netherlands. Center for Public Health Genomics University of Virginia Charlottesville VA USA. Department of Medicine Columbia University Medical Center New York NY USA. Medical Research Council Human Genetics Unit Institute of Genetics and Cancer University of Edinburgh Edinburgh UK. Human Genetics Center Department of Epidemiology Human Genetics and Environmental Sciences School of Public Health The University of Texas Health Science Center at Houston Houston TX USA. MRC Centre for Environment and Health Department of Epidemiology and Biostatistics School of Public Health Imperial College London London UK. Department of Epidemiology and Public Health Swiss Tropical

来源：评论

学校读者我要写书评

暂无评论

Publisher Correction: Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries

引用

Nature communications 2020年第1期11卷 1715页

作者： Seyedeh M Zekavat Sanni Ruotsalainen Robert E Handsaker Maris Alver Jonathan Bloom Timothy Poterba Cotton Seed Jason Ernst Mark Chaffin Jesse Engreitz Gina M Peloso Ani Manichaikul Chaojie Yang Kathleen A Ryan Mao Fu W Craig Johnson Michael Tsai Matthew Budoff Ramachandran S Vasan L Adrienne Cupples Jerome I Rotter Stephen S Rich Wendy Post Braxton D Mitchell Adolfo Correa Andres Metspalu James G Wilson Veikko Salomaa Manolis Kellis Mark J Daly Benjamin M Neale Steven McCarroll Ida Surakka Tonu Esko Andrea Ganna Samuli Ripatti Sekar Kathiresan Pradeep Natarajan Program in Medical and Population Genetics Broad Institute of MIT and Harvard Cambridge MA 02142 USA. Yale School of Medicine New Haven CT 06510 USA. Department of Computational Biology & Bioinformatics Yale University New Haven CT 06510 USA. Institute for Molecular Medicine University of Helsinki Helsinki Finland. Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge MA 02142 USA. Department of Genetics Harvard Medical School Boston MA 02115 USA. Department of Biotechnology Institute of Molecular and Cell Biology University of Tartu Tartu Estonia. Estonian Genome Center Tallinn Estonia. Analytic and Translational Genetics Unit Boston MA 02142 USA. Department of Biological Chemistry University of California Los Angeles Los Angeles CA 90095 USA. Department of Biostatistics Boston University School of Public Health Boston MA 02118 USA. Center for Public Health Genomics University of Virginia Charlottesville VA 22904 USA. Program in Personalized and Genomic Medicine Division of Endocrinology Diabetes & Nutrition Department of Medicine University of Maryland School of Medicine Baltimore MD 21201 USA. Department of Biostatistics School of Public Health and Community Medicine University of Washington Seattle WA 98195 USA. Department of Laboratory Medicine and Pathology University of Minnesota Minneapolis MN 55455 USA. Division of Cardiology Harbor-UCLA Medical Center Los Angeles Biomedical Research Institute Los Angeles CA 90509 USA. NHLBI Framingham Heart Study Framingham MA 20892 USA. Sections of Preventive medicine and Epidemiology and cardiovascular medicine Departments of Medicine and Epidemiology Boston university Schools of Medicine and Public health Boston MA 02118 USA. Departments of Pediatrics and Medicine The Institute for Translational Genomics and Population Sciences Los Angeles Biomedical Research Institute Harbor-UCLA Medical Center Torrance CA 90509 USA. Division of Cardiology

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

关键词：

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：