检索结果-内蒙古大学图书馆

SSRN 2023年

作者： Indrati, Niken Sirisarn, Wanchat Nuanpirom, Jiratchaya Yodsawat, Prasert Wanna, Warapond Prombutara, Pinidphon Phonsatta, Natthaporn Panya, Atikorn Maneerat, Suppasil Poungsombat, Patcha Khoomrung, Sakda Sumpavapol, Punnanee Food Microbiology and Safety Laboratory Food Science and Technology Program Faculty of Agro-Industry Prince of Songkla University Songkhla90110 Thailand Center of Genomics and Bioinformatics Research Faculty of Science Prince of Songkla University Songkhla90110 Thailand Omics Sciences and Bioinformatics Center Faculty of Science Chulalongkorn University Bangkok10330 Thailand Thailand Science Park Pathumthani12120 Thailand Center of Excellence in Innovative Biotechnology for Sustainable Utilization of Bioresources Faculty of Agro-Industry Prince of Songkla University Songkhla90110 Thailand Metabolomics and Systems Biology Department of Biochemistry Faculty of Medicine Siriraj Hospital Mahidol University Bangkok10700 Thailand Siriraj Metabolomics and Phenomics Center Faculty of Medicine Siriraj Hospital Mahidol University Bangkok10700 Thailand Faculty of Science Mahidol University Bangkok10400 Thailand Faculty of Science and Technology Songkhla Rajabhat University Songkhla90000 Thailand

Southern Thailand's traditional sweet pickled mango, known as Ma-Muang Bao Chae-Im (MBC), holds an important place in the local community. Several immersion processes, including brining and submersion in a hypertonic sugar solution, have been employed in the MBC production process. The occurrence of microbial succession during the production process affects its flavor due to the produced metabolites. However, microbial succession during the production process has received inadequate research. Therefore, this study aimed to (i) understand the microbiome alteration and (ii) investigate the functional profiling (metabolic pathways) during MBC production process. Through shotgun metagenomics, the microbial succession was shifting from bacteria in raw mango to fungi in MBC, with Ascomycota as the dominant phylum and Hanseniaspora as the dominant genus in MBC. The abundance of biosynthesis pathways was in line with the occurrence of microbial growth throughout the production process and prolonged storage. Polymyxin resistance was found as a significant pathway during brining 1 (B1-RM) and brining 2 (B2-B1). Mixed acid fermentation pathway and glyoxylate cycle were suggested to have a role in the aroma development of MBC by synthesizing metabolites related to the acidic and alcoholic aroma. © 2023, The Authors. All rights reserved.

关键词： Brining

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Molecular and clinical epidemiology of carbapenem-resistant Enterobacterales in the USA (CRACKLE-2): a prospective cohort study (vol 20, pg 731, 2020)

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LANCET INFECTIOUS DISEASES 2020年第6期20卷 E116-E116页

作者： van Duin, D. Arias, C. A. Komarow, L. [a]Division of Infectious Diseases University of North Carolina Chapel Hill NC USA [b]Division of Infectious Diseases and Center for Antimicrobial Resistance and Microbial Genomics UTHealth Houston TX USA [c]Center for Infectious Diseases UTHealth Houston TX USA [d]Molecular Genetics and Antimicrobial Resistance Unit International Center for Microbial Genomics Universidad El Bosque Bogota Colombia [e]The Biostatistics Center The George Washington University Rockville MD USA [f]Center for Discovery and Innovation Hackensack Meridian Health Nutley NJ USA [g]Division of Infectious Diseases Department of Medicine Montefiore Medical Center Albert Einstein College of Medicine Bronx NY USA [h]Department of Infectious Diseases Cleveland Clinic Cleveland OH USA [i]Department of Pathology and Laboratory Medicine David Geffen School of Medicine at the University of California Los Angeles CA USA [j]Division of Infectious Diseases Department of Medicine Emory University School of Medicine Atlanta GA USA [k]Division of Infectious Diseases Weill Cornell Medicine New York-Presbyterian Hospital New York NY USA [l]Department of Medicine Division of Infectious Diseases Stony Brook University Stony Brook NY USA [m]Department of Infectious Diseases Ochsner Clinic Foundation New Orleans LA USA [n]Division of Infectious Diseases University of Pittsburgh School of Medicine Pittsburgh PA USA [o]Departments of Microbiology and Infectious Diseases Fujita Health University School of Medicine Aichi Japan [p]Division of Infectious Diseases Detroit Medical Center Wayne State University Detroit MI USA [q]Division of Infectious Diseases University of Michigan Ann Arbor MI USA [r]Louis Stokes Cleveland Department of Veterans Affairs Medical Center Cleveland OH USA [s]Department of Medicine Case Western Reserve University School of Medicine Cleveland OH USA [t]Institute of Antibiotics Huashan Hospital Fudan University Shanghai China [u]University of Queensland Cent

Summary Background Carbapenem-resistant Enterobacterales (CRE) are a global threat. We aimed to describe the clinical and molecular characteristics of Centers for Disease Control and Prevention (CDC)-defined CRE in the *** CRACKLE-2 is a prospective, multicentre, cohort study. Patients hospitalised in 49 US hospitals, with clinical cultures positive for CDC-defined CRE between April 30, 2016, and Aug 31, 2017, were included. There was no age exclusion. The primary outcome was desirability of outcome ranking (DOOR) at 30 days after index culture. Clinical data and bacteria were collected, and whole genome sequencing was done. This trial is registered with ***, number *** 1040 patients with unique isolates were included, 449 (43%) with infection and 591 (57%) with colonisation. The CDC-defined CRE admission rate was 57 per 100 000 admissions (95% CI 45-71). Three subsets of CDC-defined CRE were identified: carbapenemase-producing Enterobacterales (618 [59%] of 1040), non-carbapenemase-producing Enterobacterales (194 [19%]), and unconfirmed CRE (228 [22%]; initially reported as CRE, but susceptible to carbapenems in two central laboratories). Klebsiella pneumoniae carbapenemase-producing clonal group 258 K pneumoniae was the most common carbapenemase-producing Enterobacterales. In 449 patients with CDC-defined CRE infections, DOOR outcomes were not significantly different in patients with carbapenemase-producing Enterobacterales, non-carbapenemase-producing Enterobacterales, and unconfirmed CRE. At 30 days 107 (24%, 95% CI 20-28) of these patients had *** Among patients with CDC-defined CRE, similar outcomes were observed among three subgroups, including the novel unconfirmed CRE group. CDC-defined CRE represent diverse bacteria, whose spread might not respond to interventions directed to carbapenemase-producing *** National Institutes of Health.

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Clinical Features and Outcomes of Primary Breast Diffuse Large B-Cell Lymphoma: A Matched-Pair Study

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Clinical medicine Insights: Oncology 2023年 17卷

作者： Teng, Ling-Chiao Liao, Yu-Min Gau, Jyh-Pyng Hsiao, Tzu-Hung Chen, Tsung-Chih Chen, Mei-Hui Yeh, Su-Peng Teng, Chieh-Lin Jerry Division of Hematology/Medical Oncology Department of Medicine Taichung Veterans General Hospital Taichung Taiwan Department of Hematology and Oncology China Medical University Hospital Taichung Taiwan Division of Hematology and Oncology Department of Medicine Taipei Medical University Hospital Taipei City Taiwan Department of Medical Research Taichung Veterans General Hospital Taichung Taiwan Department of Chemical Engineering National Tsing Hua University Hsinchu Taiwan Department of Public Health Fu Jen Catholic University New Taipei City Taiwan Institute of Genomics and Bioinformatics National Chung Hsing University Taichung Taiwan Department of Nursing Taichung Veterans General Hospital Taichung Taiwan College of Nursing Hung Kuang University Taichung Taiwan School of Medicine China Medical University Taichung Taiwan Department of Post-Baccalaureate Medicine College of Medicine National Chung Hsing University Taichung Taiwan Department of Life Science Tunghai University Taichung Taiwan School of Medicine Chung Shan Medical University Taichung Taiwan Ph.D. Program in Translational Medicine National Chung Hsing University Taichung Taiwan Rong Hsing Research Center for Translational Medicine National Chung Hsing University Taichung Taiwan

Background: The influence of the breast as the primary site on the outcome of diffuse large B-cell lymphoma (DLBCL) and further changes in therapeutic strategies remain unclear. We aimed to compare the outcomes between primary breast and non-breast DLBCL and analyze the genetic profiles of some of the study cohorts using next-generation sequencing. Methods: This matched-pair study reviewed the medical records of 19 patients with stage I and II primary breast DLBCL diagnosed between January 2005 and December 2021 on the basis of the Wiseman and Liao criteria, and we used 1:4 propensity score matching to identify patients with non-breast DLBCL as the control group. The overall response rate, progression-free survival (PFS), and overall survival (OS) were the outcome measures. Results: Patients with primary breast and non-breast DLBCL had a 5-year PFS of 72.6% and 86.9%, respectively (P =.206). These 2 groups also had comparable 5-year OS (86.9% vs 87.8%;P =.772). The breast as the primary site was not associated with inferior PFS (hazard ratio [HR]: 2.14;95% CI: 0.66-6.96;P =.206) and OS (HR: 1.26;95% CI: 0.27-5.93;P =.772). Conclusion: Patients with primary breast DLBCL and those with non-breast DLBCL had comparable PFS and OS under rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) or R-CHOP-like regimens. Further investigations of the mutation profile, its clinical impact, potential central nervous system relapse, and prognosis of primary breast DLBCL are required. © The Author(s) 2023.

关键词： breast DLBCL NGS OS PFS

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GREGoR: Accelerating genomics for Rare Diseases

arXiv

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arXiv 2024年

作者： Dawood, Moez Heavner, Ben Wheeler, Marsha M. Ungar, Rachel A. LoTempio, Jonathan Wiel, Laurens Berger, Seth Bernstein, Jonathan A. Chong, Jessica X. Délot, Emmanuèle C. Eichler, Evan E. Gibbs, Richard A. Lupski, James R. Shojaie, Ali Talkowski, Michael E. Wagner, Alex H. Wei, Chia-Lin Wellington, Christopher Wheeler, Matthew T. Carvalho, Claudia M.B. Gifford, Casey A. May, Susanne Miller, Danny E. Rehm, Heidi L. Sedlazeck, Fritz J. Vilain, Eric O'Donnell-Luria, Anne Posey, Jennifer E. Chadwick, Lisa H. Bamshad, Michael J. Montgomery, Stephen B. Human Genome Sequencing Center Baylor College of Medicine HoustonTX United States Department of Molecular and Human Genetics Baylor College of Medicine HoustonTX United States Medical Scientist Training Program Baylor College of Medicine HoustonTX United States Department of Biostatistics University of Washington SeattleWA United States Department of Genetics School of Medicine Stanford University StanfordCA United States Department of Pathology School of Medicine Stanford University Stanford CA United States Stanford Center for Biomedical Ethics School of Medicine Stanford University Stanford CA United States Institute for Clinical and Translational Science University of California IrvineCA United States Division of Cardiovascular Medicine School of Medicine Stanford University Stanford CA United States Division of Genetics and Metabolism Children’s National Rare Disease Institute WashingtonDC United States Center for Genetic Medicine Research Children’s National Rare Disease Institute WashingtonDC United States Department of Genomics and Precision Medicine George Washington University WashingtonDC United States Department of Pediatrics School of Medicine Stanford University Stanford CA United States Department of Pediatrics Dvision of Genetic Medicine University of Washington SeattleWA United States Brotman Baty Institute for Precision Medicine University of Washington SeattleWA United States Department of Genome Sciences University of Washington SeattleWA United States Howard Hughes Medical Institute University of Washington SeattleWA United States Department of Pediatrics Baylor College of Medicine HoustonTX United States Center for Genomic Medicine Massachusetts General Hospital BostonMA United States Program in Medical and Population Genetics Broad Institute of MIT and Harvard BostonMA United States Department of Neurology Massachusetts General Hospital Harvard Medical School BostonMA United States Stanley Center for

Rare diseases are collectively common, affecting approximately one in twenty individuals worldwide. In recent years, rapid progress has been made in rare disease diagnostics due to advances in DNA sequencing, development of new computational and experimental approaches to prioritize genes and genetic variants, and increased global exchange of clinical and genetic data. However, more than half of individuals suspected to have a rare disease lack a genetic diagnosis. The genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium was initiated to study thousands of challenging rare disease cases and families and apply, standardize, and evaluate emerging genomics technologies and analytics to accelerate their adoption in clinical practice. Further, all data generated, currently representing ~7500 individuals from ~3000 families, is rapidly made available to researchers worldwide via the Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) to catalyze global efforts to develop approaches for genetic diagnoses in rare diseases (https://***/data). The majority of these families have undergone prior clinical genetic testing but remained unsolved, with most being exome-negative. Here, we describe the collaborative research framework, datasets, and discoveries comprising GREGoR that will provide foundational resources and substrates for the future of rare disease genomics. © 2024, CC BY.

关键词： Genome

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An atlas of dynamic chromatin landscapes in mouse fetal development (vol 583, pg 744, 2020)

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NATURE 2021年第7842期589卷 E4-E4页

作者： Gorkin, David U. Barozzi, Iros Zhao, Yuan Zhang, Yanxiao Huang, Hui Lee, Ah Young Li, Bin Chiou, Joshua Wildberg, Andre Ding, Bo Zhang, Bo Wang, Mengchi Strattan, J. Seth Davidson, Jean M. Qiu, Yunjiang Afzal, Veena Akiyama, Jennifer A. Plajzer-Frick, Ingrid Novak, Catherine S. Kato, Momoe Garvin, Tyler H. Pham, Quan T. Harrington, Anne N. Mannion, Brandon J. Lee, Elizabeth A. Fukuda-Yuzawa, Yoko He, Yupeng Preissl, Sebastian Chee, Sora Han, Jee Yun Williams, Brian A. Trout, Diane Amrhein, Henry Yang, Hongbo Cherry, J. Michael Wang, Wei Gaulton, Kyle Ecker, Joseph R. Shen, Yin Dickel, Diane E. Visel, Axel Pennacchio, Len A. Ren, Bing Ludwig Institute for Cancer Research La Jolla CA USA Center for Epigenomics University of California San Diego School of Medicine La Jolla CA USA Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla CA USA Biomedical Sciences Graduate Program University of California San Diego School of Medicine La Jolla CA USA Department of Cellular and Molecular Medicine University of California San Diego School of Medicine La Jolla CA USA Institute of Genomic Medicine University of California San Diego School of Medicine La Jolla CA USA Moores Cancer Center University of California San Diego School of Medicine La Jolla CA USA Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley CA USA Department of Surgery and Cancer Imperial College London London UK US Department of Energy Joint Genome Institute Berkeley CA USA School of Natural Sciences University of California Merced Merced CA USA Comparative Biochemistry Program University of California Berkeley Berkeley CA USA Genomic Analysis Laboratory Salk Institute for Biological Studies La Jolla CA USA Department of Pediatrics University of California San Diego School of Medicine La Jolla CA USA Department of Biochemistry and Molecular Biology Penn State School of Medicine Hershey PA USA Stanford University School of Medicine Department of Genetics Stanford CA USA Howard Hughes Medical Institute Salk Institute for Biological Studies La Jolla CA USA Division of Biology and Biological Engineering California Institute of Technology Pasadena CA USA Institute for Human Genetics and University of California San Francisco San Francisco CA USA Department of Neurology University of California San Francisco San Francisco CA USA

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New candidate genes potentially involved in Zika virus teratogenesis

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Computers in Biology and medicine 2024年 173卷 108259-108259页

作者： Ferrão Maciel-Fiuza, Miriãn Rengel, Bruna Duarte Wachholz, Gabriela Elis do Amaral Gomes, Julia de Oliveira, Maikel Rosa Kowalski, Thayne Woycinck Roehe, Paulo Michel Luiz Vianna, Fernanda Sales Schüler-Faccini, Lavínia Mayer, Fabiana Quoos Varela, Ana Paula Muterle Fraga, Lucas Rosa Graduate Program in Genetics and Molecular Biology Universidade Federal do Rio Grande do Sul Porto Alegre Brazil Instituto Nacional de Genética Médica Populacional Porto Alegre Brazil Genomics Medicine Laboratory Center of Experimental Research Hospital de Clínicas de Porto Alegre Porto Alegre Brazil Department of Morphological Sciences Institute of Health Sciences Universidade Federal do Rio Grande do Sul Porto Alegre Brazil Graduate Program in Medicine: Medical Sciences Universidade Federal do Rio Grande do Sul Porto Alegre Brazil Teratogen Information System Medical Genetics Service Hospital de Clínicas de Porto Alegre Porto Alegre Brazil Bioinformatics Core Hospital de Clínicas de Porto Alegre Porto Alegre Brazil Centro Universitário CESUCA Cachoeirinha Brazil Department of Microbiology Immunology and Parasitology Institute of Health Sciences Universidade Federal do Rio Grande do Sul Porto Alegre Brazil Graduate Program in Molecular and Cellular Biology Biotechnology Center Universidade Federal do Rio Grande do Sul Porto Alegre Brazil Graduate Program in Biosciences Universidade Federal de Ciências da Saúde de Porto Alegre Porto Alegre Brazil

Despite efforts to elucidate Zika virus (ZIKV) teratogenesis, still several issues remain unresolved, particularly on the molecular mechanisms behind the pathogenesis of Congenital Zika Syndrome (CZS). To answer this question, we used bioinformatics tools, animal experiments and human gene expression analysis to investigate genes related to brain development potentially involved in CZS. Searches in databases for genes related to brain development and CZS were performed, and a protein interaction network was created. The expression of these genes was analyzed in a CZS animal model and secondary gene expression analysis (DGE) was performed in human cells exposed to ZIKV. A total of 2610 genes were identified in the databases, of which 1013 were connected. By applying centrality statistics of the global network, 36 candidate genes were identified, which, after selection resulted in nine genes. Gene expression analysis revealed distinctive expression patterns for PRKDC, PCNA, ATM, SMC3 as well as for FGF8 and SHH in the CZS model. Furthermore, DGE analysis altered expression of ATM, PRKDC, PCNA. In conclusion, systems biology are helpful tools to identify candidate genes to be validated in vitro and in vivo. PRKDC, PCNA, ATM, SMC3, FGF8 and SHH have altered expression in ZIKV-induced brain malformations. © Elsevier Ltd

关键词： Viruses

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Author Correction: SARS-CoV-2 infection engenders heterogeneous ribonucleoprotein interactions to impede translation elongation in the lungs

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EXPERIMENTAL AND MOLECULAR medicine 2023年第12期55卷 2609-2609页

作者： Kim, Junsoo Youn, Daehwa Choi, Seunghoon Lee, Youn Woo Sumberzul, Dulguun Yoon, Jeongeun Lee, Hanju Bae, Jong Woo Noh, Hyuna On, Dain Hong, Seung-Min An, Se-Hee Jang, Hui Jeong Kim, Seo Yeon Kim, Young Been Hwang, Ji-Yeon Lee, Hyo-Jung Kim, Hong Bin Park, Jun Won Yun, Jun-Won Shin, Jeon-Soo Seo, Jun-Young Nam, Ki Taek Choi, Kang-Seuk Lee, Ho-Young Chang, Hyeshik Seong, Je Kyung Cho, Jun Center for RNA Research Institute for Basic Science (IBS) Seoul National University Seoul Republic of Korea Interdisciplinary Program in Bioinformatics Seoul National University Seoul Republic of Korea Department of Biomedical Science and Engineering Gwangju Institute of Science and Technology (GIST) Gwangju Republic of Korea Korea Mouse Phenotyping Center (KMPC) Seoul National University Seoul Republic of Korea Laboratory of Developmental Biology and Genomics Research Institute for Veterinary Science and BK 21 PLUS Program for Creative Veterinary Science Research College of Veterinary Medicine Seoul National University Seoul Republic of Korea Department of Nuclear Medicine Seoul National University Bundang Hospital Seongnam Republic of Korea School of Biological Sciences Seoul National University Seoul Republic of Korea Laboratory of Avian Diseases Research Institute for Veterinary Science and BK 21 PLUS Program for Creative Veterinary Science Research College of Veterinary Medicine Seoul National University Seoul Republic of Korea Preclinical Research Center Seoul National University Bundang Hospital Seongnam Republic of Korea Department of Periodontology Section of Dentistry Seoul National University Bundang Hospital Seongnam Republic of Korea Department of Internal Medicine Seoul National University Bundang Hospital Seoul National University College of Medicine Seongnam Republic of Korea Division of Biomedical Convergence College of Biomedical Science Kangwon National University ChunCheon Republic of Korea Laboratory of Veterinary Toxicology College of Veterinary Medicine Seoul National University Seoul Republic of Korea Severance Biomedical Science Institute Graduate School of Medical Science Brain Korea 21 Project Yonsei University College of Medicine Seoul Republic of Korea Department of Nuclear Medicine Seoul National University College of Medicine Seoul Republic of Korea Interdisciplinary Program and BIO MAX Institute Seoul National University

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Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data

Research Square

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Research Square 2021年

作者： Zhang, Martin Jinye Hou, Kangcheng Pasaniuc, Bogdan Price, Alkes L. Dey, Kushal K. Jagadeesh, Karthik A. Weinand, Kathryn Sakaue, Saori Taychameekiatchai, Aris Rao, Poorvi Pisco, Angela Oliveira Zou, James Wang, Bruce Gandal, Michael Raychaudhuri, Soumya Harvard University United States Osaka University Japan Department of Epidemiology Harvard T.H. Chan School of Public Health BostonMA United States Program in Medical and Population Genetics Broad Institute of MIT and Harvard CambridgeMA United States Bioinformatics Interdepartmental Program University of California Los Angeles Los AngelesCA United States Department of Pathology and Laboratory Medicine David Geffen School of Medicine University of California Los Angeles Los AngelesCA United States Department of Computational Medicine David Geffen School of Medicine University of California Los Angeles Los AngelesCA United States Center for Data Sciences Brigham and Women’s Hospital BostonMA United States Division of Genetics Department of Medicine Brigham and Women’s Hospital Harvard Medical School BostonMA United States Division of Rheumatology Inflammation and Immunity Department of Medicine Brigham and Women’s Hospital Harvard Medical School BostonMA United States Department of Biomedical Informatics Harvard Medical School BostonMA United States Department of Medicine and Liver Center University of California San Francisco San FranciscoCA United States Developmental and Stem Cell Biology Graduate Program University of California San Francisco San FranciscoCA United States Chan Zuckerberg Biohub San FranciscoCA United States Department of Electrical Engineering Stanford University Palo AltoCA United States Department of Biomedical Data Science Stanford University Palo AltoCA United States Department of Psychiatry David Geffen School of Medicine University of California Los Angeles Los AngelesCA United States Department of Human Genetics David Geffen School of Medicine University of California Los Angeles Los AngelesCA United States Program in Neurobehavioral Genetics Semel Institute David Geffen School of Medicine University of California Los Angeles Los AngelesCA United States Versus Arthritis Centre for Genetics and Genomic

Gene expression at the individual cell-level resolution, as quantified by single-cell RNA-sequencing (scRNA-seq), can provide unique insights into the pathology and cellular origin of diseases and complex traits. Here, we introduce single-cell Disease Relevance Score (scDRS), an approach that links scRNA-seq with polygenic risk of disease at individual cell resolution;scDRS identifies individual cells that show excess expression levels for genes in a disease-specific gene set constructed from GWAS data. We determined via simulations that scDRS is well-calibrated and powerful in identifying individual cells associated to disease. We applied scDRS to GWAS data from 74 diseases and complex traits (average N =341K) in conjunction with 16 scRNA-seq data sets spanning 1.3 million cells from 31 tissues and organs. At the cell type level, scDRS broadly recapitulated known links between classical cell types and disease, and also produced novel biologically plausible findings. At the individual cell level, scDRS identified subpopulations of disease-associated cells that are not captured by existing cell type labels, including subpopulations of CD4+ T cells associated with inflammatory bowel disease, partially characterized by their effector-like states;subpopulations of hippocampal CA1 pyramidal neurons associated with schizophrenia, partially characterized by their spatial location at the proximal part of the hippocampal CA1 region;and subpopulations of hepatocytes associated with triglyceride levels, partially characterized by their higher ploidy levels. At the gene level, we determined that genes whose expression across individual cells was correlated with the scDRS score (thus reflecting co-expression with GWAS disease genes) were strongly enriched for gold-standard drug target and Mendelian disease genes. © 2021, CC BY.

关键词： RNA

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The LSC17 Leukemic Stem Cell Signature Predicts Outcome in Pediatric Acute Myeloid Leukemia

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BLOOD 2017年 130卷 24-24页

作者： Smith, Jenny L. Ries, Rhonda E. Kolb, Anders Alonzo, Todd A. Gerbing, Robert B. Ma, Yussanne Marra, Marco A. Bolouri, Hamid Meshinchi, Soheil Clinical Research Division Fred Hutchinson Cancer Research Center Seattle WA Applied Bioinformatics and Genomics Program University of Oregon Eugene OR Nemours Center for Cancer and Blood Disorders Alfred I. duPont Hospital for Children Wilmington DE Children's Oncology Group Monrovia CA Univ. of Southern California Keck School of Med. Monrovia CA Department of Preventive Medicine University of Southern California Los Angeles CA Canada's Michael Smith Genome Sciences Centre British Columbia Cancer Agency Vancouver Canada Human Biology Division Fred Hutchinson Cancer Research Center Seattle Department of Pediatrics University of Washington Seattle Clinical Research Division Fred Hutchinson Cancer Rsrch. Ctr. Seattle WA

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Identification of rare coding variants associated with Alzheimer’s disease.

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Alzheimer's & Dementia 2023年第S12期19卷

作者： Zainab Khurshid Lindsay A. Farrer Xiaoling Zhang Eden R. Martin Amanda B Kuzma John Farrell Tong Tong Congcong Zhu Adam C. Naj Laura B Cantwell Otto Valladares Li-San Wang Kathryn L. Lunetta Gerald D. Schellenberg Jonathan L. Haines Yuk Yee Leung Margaret A. Pericak-Vance Boston University Chobanian & Avedisian School of Medicine Boston MA USA Boston University Bioinformatics Program Boston MA USA John P. Hussman Institute for Human Genomics Miller School of Medicine Miami FL USA Penn Neurodegeneration Genomics Center Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Department of Medicine (Biomedical Genetics) Boston University Chobanian & Avedisian School of Medicine Boston MA USA Penn Neurodegeneration Genomics Center Department of Pathology and Laboratory Medicine University of Pennsylvania Perelman School of Medicine Philadelphia PA USA University of Pennsylvania Perelman School of Medicine Philadelphia PA USA Penn Neurodegeneration Genomics Center University of Pennsylvania Perelman School of Medicine Philadelphia PA USA Department of Biostatistics Boston University School of Public Health Boston MA USA Department of Genetics and Genome Sciences Case Western Reserve University School of Medicine Cleveland OH USA University of Miami Miller School of Medicine Miami FL USA

Background Previous whole exome sequencing (WES) studies of Alzheimer’s disease (AD) have identified genome-wide significant associations with rare variants in several novel genes and highlighted the need for investigations in larger samples. We combined WES and whole genome sequencing (WGS) data assembled by the Alzheimer Disease Sequencing Project (ADSP) to increase the power for detecting associations of AD with rare variants in gene coding regions. Method We developed an efficient computational pipeline to perform both pre-merging and post-merging genotype, variant and sample-level quality control (QC) on WGS data containing 16,905 individuals and WES data for 20,504 individuals. The resultant sample included participants from European (EA, 11,279 AD cases, 8,924 controls), African American (AA, 2,757 AD cases, 4,336 controls), and Caribbean Hispanic (CH 1,438 AD cases, 3,256 controls) ancestries. We employed GENESIS to test association of AD with 250,465 bi-allelic QC’d variants using a logistic model including covariates for age, sex, exome capture kit, read length, and ancestry principal components (PCs). Result In the total sample, variants from APOE and other known AD genes including SORL1 (P = 5.30×10-7), NECTIN2 (P = 6.94×10-7), and TREM2 R47H (P = 2.34×10-13) crossed or neared the study-wide significance (SWS) threshold of P = 2.00×10-7 (0.05/250,465). SWS or borderline significant associations were also found with variants in several novel loci including TKTL2 (P = 2.35×10-8), D2HGDH , (P = 1.09×10-7) , CECR1 (P = 4.02×10-7), PDHA2 (P = 2.76×10-7), GOLGA1 (P = 1.72×10-7), CYLD (P = 1.84×10-7), and RP11-243M5.4 (P = 1.37×10-7). PSEN1 missense mutation G206A (rs63750082) previously associated with early onset AD in the CH group, was significantly associated with late onset AD in the same population (P = 1.58×10-13). SWS association of AD with APOE was observed in all groups. Significant associations were also observed with variants in SERPINB8 (P = 3.77×1

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