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Correction to: Specific Susceptibility to COVID-19 in Adults with Down Syndrome

Neuromolecular medicine 2021年第4期23卷 572-573页

作者： Tomer Illouz Arya Biragyn Milana Frenkel-Morgenstern Orly Weissberg Alessandro Gorohovski Eugene Merzon Ilan Green Florencia Iulita Lisi Flores-Aguilar Mara Dierssen Ilario De Toma Hefziba Lifshitz Stylianos E Antonarakis Eugene Yu Yann Herault Marie-Claude Potier Alexandra Botté Randall Roper Benjamin Sredni Ronit Sarid Jacqueline London William Mobley Andre Strydom Eitan Okun The Leslie and Susan Gonda Multidisciplinary Brain Research Center Bar-Ilan University 5290002 Ramat-Gan Israel. The Paul Feder Laboratory On Alzheimer's Disease Research Bar-Ilan University 5290002 Ramat-Gan Israel. Laboratory of Molecular Biology and Immunology NIA Baltimore MD 21224 USA. Cancer Genomics and BioComputing of Complex Diseases Lab Azrieli Faculty of Medicine Bar-Ilan University Safed Israel. Leumit Health Services Department of Family Medicine Sackler School of Medicine Tel Aviv University Tel Aviv-Yafo Israel. Sant Pau Memory Unit Department of Neurology Hospital de La Santa Creu I Sant Pau Barcelona Spain. Biomedical Research Institute Sant Pau Universitat Autònoma de Barcelona Barcelona Spain. Center of Biomedical Investigation Network for Neurodegenerative Diseases (CIBERNED) Madrid Spain. Alzheimer-Down Unit Fundación Catalana Síndrome de Down Barcelona Spain. Department of Anatomy and Cell Biology McGill University Montreal Canada. Center for Genomic Regulation The Barcelona Institute for Science and Technology Barcelona Spain. University Pompeu Fabra Barcelona Spain. Biomedical Research Networking Center for Rare Diseases (CIBERER) Barcelona Spain. Cellular & Systems Neurobiology Systems Biology Program The Barcelona Institute of Science and Technology Centre for Genomic Regulation (CRG) Dr. Aiguader 88 08003 Barcelona Spain. Universitat Pompeu Fabra (UPF) Barcelona Spain. Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) Madrid Spain. School of Education Bar-Ilan University 5290002 Ramat-Gan Israel. Department of Genetic Medicine and Development University of Geneva 1211 Geneva Switzerland. Medigenome Swiss Institute of Genomic Medicine 1207 Geneva Switzerland. iGE3 Institute of Genetics and Genomics of Geneva 1211 Geneva Switzerland. The Children's Guild Foundation Down Syndrome Research Program Genetics and Genomics Program and Department of Cancer Genetics and Genomics Roswell Park Comprehensi

A correction to this paper has been published: https://***/10.1007/s12017-021-08657-z

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Comprehensive reanalysis for CNVs in ES data from unsolved rare disease cases results in new diagnoses

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npj Genomic medicine 2024年第1期9卷 49页

作者： Demidov, German Yaldiz, Burcu Garcia-Pelaez, José de Boer, Elke Schuermans, Nika Van de Vondel, Liedewei Paramonov, Ida Johansson, Lennart F. Musacchia, Francesco Benetti, Elisa Bullich, Gemma Sablauskas, Karolis Beltran, Sergi Gilissen, Christian Hoischen, Alexander Ossowski, Stephan de Voer, Richarda Lohmann, Katja Oliveira, Carla Topf, Ana Vissers, Lisenka E. L. M. Zguro, Kristina Zara, Federico Zaganas, Ioannis Yépez, Vicente A. Wirth, Brunhilde Webb, David Verdin, Hannah Van Nieuwenhove, Erika van Montfrans, Joris van Heurck, Roxane van der Veken, Lars Valle, Laura Uva, Paolo Udd, Bjarne Trimouille, Aurelien Thompson, Rachel Tartaglia, Marco Sznajer, Yves Striano, Pasquale Steinke-Lange, Verena Spilioti, Martha Scudieri, Paolo Schröck, Evelin Schon, Katherine Scala, Marcello Savarese, Marco Santen, Gijs W. E. Rump, Andreas Ruivenkamp, Claudia A. L. Roos, Andreas Rooryck, Caroline Riva, Antonella Renieri, Alessandra Ratnaike, Thiloka Radio, Francesca Clementina Privitera, Flavia De la Paz, Manuel Posada Poppe, Bruce Polavarapu, Kiran Platzer, Konrad Peterlin, Borut Pérez-Dueñas, Belén Pauly, Martje Parrini, Elena Olimpio, Catarina Reghan, Mary O. de Benito, Daniel Natera Osorio, Andrés Nascimento Munell, Francina Münchau, Alexander Moortgat, Stéphanie Monestier, Olivier Molnar, Maria Judit Meunier, Colombine Mertes, Christian Mei, Davide Maystadt, Isabelle May, Patrick Maver, Ales Mathioudakis, Lambros Masclaux, Frédéric Mary, Sandrine Delgado, Beatriz Martínez Marcé-Grau, Anna Malaichamy, Sivasankar Macaya, Alfons Luknárová, Rebeka Martín, Estrella López Lochmüller, Hanns Leitão, Elsa Lederer, Damien Leavis, Helen Laner, Andreas Lacombe, Didier Krass, Leon Korff, Christian Kokosali, Evgenia Karakaya, Mert Karadurmus, Deniz Kapaki, Elisabeth Johari, Mridul Iacomino, Michele Huibers, Manon Horvath, Rita Holinski-Feder, Elke Hoffer, Mariette J. V. Herzog, Rebecca Hemelsoet, Dimitri Bouveret, Eva Hammar Haimel, Matthias Hackman, Peter Guerrini, Renzo Grimbacher, Bodo Greally, Marie Ghani, Hamidah Gagneur, Julien Institute of Medical Genetics and Applied Genomics University of Tübingen Tübingen Germany Institute for Bioinformatics and Medical Informatics (IBMI) University of Tübingen Tübingen Germany Department of Human Genetics Radboud University Medical Center Nijmegen Netherlands Department of Clinical Genetics Maastricht University Medical Center Maastricht Netherlands i3S - Instituto de Investigação e Inovação em Saúde Rua Alfredo Allen 208 Porto 4200-135 Portugal IPATIMUP - Institute of Molecular Pathology and Immunology University of Porto Porto Portugal Faculty of Medicine University of Porto Porto Portugal Donders Institute for Brain Cognition and Behaviour Radboud University Nijmegen Netherlands Department of Clinical Genetics Erasmus MC University Medical Center Rotterdam Netherlands Center for Medical Genetics Ghent University Hospital Ghent Belgium Translational Neurosciences Faculty of Medicine and Health Sciences University of Antwerp Antwerp Belgium Laboratory of Neuromuscular Pathology Institute Born-Bunge University of Antwerp Antwerp Belgium Centro Nacional de Análisis Genómico (CNAG) C/Baldiri Reixac 4 Barcelona 08028 Spain Universitat de Barcelona (UB) Barcelona Spain University of Groningen University Medical Center Groningen Department of Genetics Groningen Netherlands Center for Human Technologies Italian Institute of Technology (IIT) Genova Italy Telethon Institute for Genetics and Medicine Pozzuoli (Napoli) 80078 Italy Department of Medical Biotechnologies Med Biotech Hub and Competence Center University of Siena Siena 53100 Italy Institute of Data Science and Digital Technologies Vilnius University Vilnius Lithuania Departament de Genètica Microbiologia i Estadística Facultat de Biologia Universitat de Barcelona (UB) Barcelona Spain Radboud Institute for Molecular Life Sciences Nijmegen Netherlands Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI) Radboud University Medical Center Nijmegen N

We report the results of a comprehensive copy number variant (CNV) reanalysis of 9171 exome sequencing datasets from 5757 families affected by a rare disease (RD). The data reanalysed was extremely heterogeneous, having been generated using 28 different enrichment kits by 42 different research groups across Europe partnering in the Solve-RD project. Each research group had previously undertaken their own analysis of the data but failed to identify disease-causing variants. We applied three CNV calling algorithms to maximise sensitivity, and rare CNVs overlapping genes of interest, provided by four partner European Reference Networks, were taken forward for interpretation by clinical experts. This reanalysis has resulted in a molecular diagnosis being provided to 51 families in this sample, with ClinCNV performing the best of the three algorithms. We also identified partially explanatory pathogenic CNVs in a further 34 individuals. This work illustrates the value of reanalysing ES cold cases for CNVs. © The Author(s) 2024.

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Correction: Robustness of cancer microbiome signals over a broad range of methodological variation

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Oncogene 2024年第20期43卷 1579页

作者： Gregory D Sepich-Poore Daniel McDonald Evguenia Kopylova Caitlin Guccione Qiyun Zhu George Austin Carolina Carpenter Serena Fraraccio Stephen Wandro Tomasz Kosciolek Stefan Janssen Jessica L Metcalf Se Jin Song Jad Kanbar Sandrine Miller-Montgomery Robert Heaton Rana Mckay Sandip Pravin Patel Austin D Swafford Tal Korem Rob Knight Department of Bioengineering University of California San Diego La Jolla CA USA. Micronoma San Diego CA USA. Feinberg School of Medicine Northwestern University Chicago IL USA. Department of Pediatrics University of California San Diego La Jolla CA USA. Clarity Genomics Antwerp Belgium. School of Life Sciences Arizona State University Tempe AZ USA. Department of Biomedical Informatics Columbia University Irving Medical Center New York NY USA. Program for Mathematical Genomics Department of Systems Biology Columbia University Irving Medical Center New York NY USA. Center for Microbiome Innovation University of California San Diego La Jolla CA USA. Malopolska Centre of Biotechnology Jagiellonian University in Kraków Kraków Poland. Algorithmic Bioinformatics Department of Biology and Chemistry Justus Liebig University Gießen Gießen Germany. Department of Animal Sciences Colorado State University Fort Collins CO USA. Department of Medicine University of California San Diego La Jolla CA USA. Department of Psychiatry University of California San Diego La Jolla CA USA. Moores Cancer Center University of California San Diego Health La Jolla CA USA. Department of Obstetrics and Gynecology Columbia University Irving Medical Center New York NY USA. Department of Bioengineering University of California San Diego La Jolla CA USA. rknight@ucsd.edu. Department of Pediatrics University of California San Diego La Jolla CA USA. rknight@ucsd.edu. Center for Microbiome Innovation University of California San Diego La Jolla CA USA. rknight@ucsd.edu. Department of Computer Science and Engineering University of California San Diego La Jolla CA USA. rknight@ucsd.edu.

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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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Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes

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Nature 2022年第7909期605卷 E3页

作者： Jill E Moore Michael J Purcaro Henry E Pratt Charles B Epstein Noam Shoresh Jessika Adrian Trupti Kawli Carrie A Davis Alexander Dobin Rajinder Kaul Jessica Halow Eric L Van Nostrand Peter Freese David U Gorkin Yin Shen Yupeng He Mark Mackiewicz Florencia Pauli-Behn Brian A Williams Ali Mortazavi Cheryl A Keller Xiao-Ou Zhang Shaimae I Elhajjajy Jack Huey Diane E Dickel Valentina Snetkova Xintao Wei Xiaofeng Wang Juan Carlos Rivera-Mulia Joel Rozowsky Jing Zhang Surya B Chhetri Jialing Zhang Alec Victorsen Kevin P White Axel Visel Gene W Yeo Christopher B Burge Eric Lécuyer David M Gilbert Job Dekker John Rinn Eric M Mendenhall Joseph R Ecker Manolis Kellis Robert J Klein William S Noble Anshul Kundaje Roderic Guigó Peggy J Farnham J Michael Cherry Richard M Myers Bing Ren Brenton R Graveley Mark B Gerstein Len A Pennacchio Michael P Snyder Bradley E Bernstein Barbara Wold Ross C Hardison Thomas R Gingeras John A Stamatoyannopoulos Zhiping Weng University of Massachusetts Medical School Program in Bioinformatics and Integrative Biology Worcester MA USA. The Broad Institute of Harvard and MIT Cambridge MA USA. Department of Genetics School of Medicine Stanford University Palo Alto CA USA. Cold Spring Harbor Laboratory Functional Genomics Cold Spring Harbor NY USA. Altius Institute for Biomedical Sciences Seattle WA USA. Department of Medicine University of Washington School of Medicine Seattle WA USA. Department of Cellular and Molecular Medicine Institute for Genomic Medicine Stem Cell Program Sanford Consortium for Regenerative Medicine University of California San Diego La Jolla CA USA. Program in Computational and Systems Biology Massachusetts Institute of Technology Cambridge MA USA. Center for Epigenomics Department of Cellular and Molecular Medicine University of California San Diego La Jolla CA USA. Ludwig Institute for Cancer Research University of California San Diego La Jolla CA USA. Institute for Human Genetics Department of Neurology University of California San Francisco San Francisco CA USA. Genomics Analysis Laboratory The Salk Institute for Biological Studies La Jolla CA USA. HudsonAlpha Institute for Biotechnology Huntsville AL USA. Division of Biology and Biological Engineering California Institute of Technology Pasadena CA USA. Department of Developmental and Cell Biology University of California Irvine Irvine CA USA. Department of Biochemistry and Molecular Biology The Pennsylvania State University University Park PA USA. Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley CA USA. Department of Genetics and Genome Sciences Institute for Systems Genomics UConn Health Farmington CT USA. Département de Biochimie et Médecine Moléculaire Université de Montréal Montréal Quebec Canada. Division of Experimental Medicine McGill University Montreal Quebec Canada. Institut de Recherches Cliniques de Montréal (IR

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Author Correction: A biallelic multiple nucleotide length polymorphism explains functional causality at 5p15.33 prostate cancer risk locus

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Nature communications 2023年第1期14卷 6623页

作者： Sandor Spisak Viktoria Tisza Pier Vitale Nuzzo Ji-Heui Seo Balint Pataki Dezso Ribli Zsofia Sztupinszki Connor Bell Mersedeh Rohanizadegan David R Stillman Sarah Abou Alaiwi Alan H Bartels Marton Papp Anamay Shetty Forough Abbasi Xianzhi Lin Kate Lawrenson Simon A Gayther Mark Pomerantz Sylvan Baca Norbert Solymosi Istvan Csabai Zoltan Szallasi Alexander Gusev Matthew L Freedman Department of Medical Oncology Dana-Farber Cancer Institute Boston MA 02215 USA. Center for Functional Cancer Epigenetics Dana-Farber Cancer Institute Boston MA 02215 USA. Computational Health Informatics Program (CHIP) Boston Children's Hospital Harvard Medical School Boston MA 02215 USA. Institute of Enzymology Research Centre for Natural Sciences Budapest 1117 Hungary. Department of Internal Medicine School of Medicine University of Genoa Genoa Lgo R. Benzi 10 16132 Italy. Department of Physics of Complex Systems ELTE Eötvös Loránd University Pázmány P. s. 1A Budapest 1117 Hungary. Centre for Bioinformatics University of Veterinary Medicine Istvan str. 2 Budapest 1078 Hungary. Division of Genetics Brigham & Women's Hospital Boston MA USA. Women's Cancer Program Samuel Oschin Comprehensive Cancer Institute Cedars-Sinai Medical Center Los Angeles CA 90048 USA. Division of Gynecologic Oncology Department of Obstetrics and Gynecology Cedars-Sinai Medical Center Los Angeles CA 90048 USA. Center for Bioinformatics and Functional Genomics Department of Biomedical Science Cedars-Sinai Medical Center Los Angeles CA 90048 USA. The Eli and Edythe L. Broad Institute Cambridge MA 02142 USA. Department of Bioinformatics Forensic and Insurance Medicine Semmelweis University Budapest Hungary. Danish Cancer Society Research Center Strandboulevarden 49 2100 Copenhagen Denmark. National Korányi Institute of Pulmonology Budapest 1112 Hungary. Department of Medical Oncology Dana-Farber Cancer Institute Boston MA 02215 USA. matthew_freedman@dfci.harvard.edu. Center for Functional Cancer Epigenetics Dana-Farber Cancer Institute Boston MA 02215 USA. matthew_freedman@dfci.harvard.edu. The Eli and Edythe L. Broad Institute Cambridge MA 02142 USA. matthew_freedman@dfci.harvard.edu.

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Distinct modes of mitochondrial metabolism uncouple T cell differentiation and function (vol 571, pg 403, 2019)

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NATURE 2019年第7773期573卷 E2-E2页

作者： Bailis, Will Shyer, Justin A. Zhao, Jun Canaveras, Juan Carlos Garcia Al Khazal, Fatimah J. Qu, Rihao Steach, Holly R. Bielecki, Piotr Khan, Omair Jackson, Ruaidhri Kluger, Yuval Maher, Louis J., III Rabinowitz, Joshua Craft, Joe Flavell, Richard A. Department of Immunobiology Yale School of Medicine New Haven USA Department of Pathology Children’s Hospital of Philadelphia Philadelphia USA Department of Pathology Yale School of Medicine New Haven USA Program of Computational Biology and Bioinformatics Yale University New Haven USA Lewis-Sigler Institute for Integrative Genomics Princeton University Princeton USA Department of Chemistry Princeton University Princeton USA Diabetes Research Center University of Pennsylvania Philadelphia USA Department of Biochemistry and Molecular Biology Mayo Clinic College of Medicine and Science Rochester USA Applied Mathematics Program Yale University New Haven USA Department of Internal Medicine (Rheumatology) Yale School of Medicine New Haven USA Howard Hughes Medical Institute Chevy Chase USA

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: Pathway and network analysis of more than 2500 whole cancer genomes

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Nature communications 2022年第1期13卷 7566页

作者： Matthew A Reyna David Haan Marta Paczkowska Lieven P C Verbeke Miguel Vazquez Abdullah Kahraman Sergio Pulido-Tamayo Jonathan Barenboim Lina Wadi Priyanka Dhingra Raunak Shrestha Gad Getz Michael S Lawrence Jakob Skou Pedersen Mark A Rubin David A Wheeler Søren Brunak Jose M G Izarzugaza Ekta Khurana Kathleen Marchal Christian von Mering S Cenk Sahinalp Alfonso Valencia Jüri Reimand Joshua M Stuart Benjamin J Raphael Department of Computer Science Princeton University Princeton NJ 08540 USA. Department of Biomedical Informatics Emory University Atlanta GA 30322 USA. Department of Biomolecular Engineering and UC Santa Cruz Genomics Institute University of California Santa Cruz Santa Cruz CA 95060 USA. Computational Biology Program Ontario Institute for Cancer Research Toronto Ontario Canada. Department of Information Technology IDLab Ghent University IMEC Ghent the Netherlands. Department of Plant Biotechnology and Bioinformatics Ghent University Ghent the Netherlands. Barcelona Supercomputing Center (BSC) Barcelona 08034 Spain. Department of Clinical and Molecular Medicine Faculty of Medicine and Health Sciences Norwegian University of Science and Technology Trondheim Norway. Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics University of Zurich CH-8057 Zurich Switzerland. Department of Pathology and Molecular Pathology University Hospital Zurich CH-8091 Zurich Switzerland. Department of Physiology and Biophysics Weill Cornell Medicine New York NY 10065 USA. Vancouver Prostate Centre 2660 Oak Street Vancouver BC V6H 3Z6 Canada. The Broad Institute of MIT and Harvard Cambridge MA 02124 USA. Massachusetts General Hospital Center for Cancer Research Charlestown MA 02129 USA. Harvard Medical School 250 Longwood Avenue Boston MA 02115 USA. Massachusetts General Hospital Department of Pathology Boston MA 02114 USA. Department of Molecular Medicine (MOMA) Aarhus University Hospital Aarhus Denmark. Bioinformatics Research Centre (BiRC) Aarhus University Aarhus Denmark. Human Genome Sequencing Center Baylor College of Medicine Houston TX 77030 USA. DTU Bioinformatics Department of Bio and Health Informatics Technical University of Denmark Kemitorvet 2800 Kongens Lyngby Denmark. Novo Nordisk Foundation Center for Protein Research Faculty of Health and Medical Sciences University of Copenhagen 2200 Copenhagen Denmark. De

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Author Correction: Greengenes2 unifies microbial data in a single reference tree

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Nature biotechnology 2024年第5期42卷 813页

作者： Daniel McDonald Yueyu Jiang Metin Balaban Kalen Cantrell Qiyun Zhu Antonio Gonzalez James T Morton Giorgia Nicolaou Donovan H Parks Søren M Karst Mads Albertsen Philip Hugenholtz Todd DeSantis Se Jin Song Andrew Bartko Aki S Havulinna Pekka Jousilahti Susan Cheng Michael Inouye Teemu Niiranen Mohit Jain Veikko Salomaa Leo Lahti Siavash Mirarab Rob Knight Department of Pediatrics University of California San Diego School of Medicine La Jolla CA USA. Department of Electrical and Computer Engineering University of California San Diego La Jolla CA USA. Bioinformatics and Systems Biology Program University of California San Diego La Jolla CA USA. Department of Computer Science and Engineering University of California San Diego La Jolla CA USA. School of Life Sciences Arizona State University Tempe AZ USA. Biodesign Center for Fundamental and Applied Microbiomics Arizona State University Tempe AZ USA. Biostatistics & Bioinformatics Branch Eunice Kennedy Shriver National Institute of Child Health and Human Development National Institutes of Health Bethesda MD USA. Halicioglu Data Science Institute University of California San Diego La Jolla CA USA. Australian Centre for Ecogenomics School of Chemistry and Molecular Biosciences The University of Queensland St Lucia Queensland Australia. Department of Obstetrics and Gynecology Columbia University New York NY USA. Department of Chemistry and Bioscience Aalborg University Aalborg Denmark. Department of Informatics Second Genome Brisbane CA USA. Center for Microbiome Innovation Jacobs School of Engineering University of California San Diego La Jolla CA USA. Finnish Institute for Health and Welfare Helsinki Finland. Institute for Molecular Medicine Finland FIMM-HiLIFE Helsinki Finland. Division of Cardiology Brigham and Women's Hospital Boston MA USA. Cedars-Sinai Medical Center Los Angeles CA USA. Cambridge Baker Systems Genomics Initiative Baker Heart and Diabetes Institute Melbourne Victoria Australia. Cambridge Baker Systems Genomics Initiative Department of Public Health and Primary Care University of Cambridge Cambridge UK. Division of Medicine Turku University Hospital and University of Turku Turku Finland. Sapient Bioanalytics LLC San Diego CA USA. Department of Computing University of Turku Turku Finland. Department of Pediatrics Uni

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proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms

arXiv

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arXiv 2021年

作者： LeDuc, Richard D. Deutsch, Eric W. Binz, Pierre-Alain Fellers, Ryan T. Cesnik, Anthony J. Klein, Joshua A. Van Den Bossche, Tim Gabriels, Ralf Yalavarthi, Arshika Perez-Riverol, Yasset Carver, Jeremy Bittremieux, Wout Kawano, Shin Pullman, Benjamin Bandeira, Nuno Kelleher, Neil L. Thomas, Paul M. Vizcaíno, Juan Antonio National Resource for Translational and Developmental Proteomics Northwestern University EvanstonIL60611 United States Institute for Systems Biology SeattleWA98109 United States Clinical Chemistry Service Lausanne University Hospital Lausanne1011 Switzerland Department of Genetics Stanford University StanfordCA94305 United States Chan Zuckerberg Biohub 499 Illinois St San FranciscoCA94158 United States SciLifeLab School of Engineering Sciences in Chemistry Biotechnology and Health KTH-Royal Institute of Technology Stockholm 113 51 SolnaSE-171 21 Sweden Program for Bioinformatics Boston University BostonMA02215 United States VIB-UGent Center for Medical Biotechnology VIB Technologiepark 75-FSVM II Ghent9052 Belgium Department of Biomolecular Medicine Faculty of Medicine and Health Sciences Ghent University Ghent9000 Belgium Cambridge HinxtonCB10 1SD United Kingdom La Jolla CA92093 United States La Jolla CA92093 United States La Jolla CA92093 United States Toyama University of International Studies Toyama Higashikuromaki 6 5-1 Toyama930-1292 Japan Database Center for Life Science Joint Support-Center for Data Science Research Research Organization of Information and Systems Chiba Kashiwa277-0871 Japan

It is important for the proteomics community to have a standardized manner to represent all possible variations of a protein or peptide primary sequence, including natural, chemicallyinduced and artifactualmodifications. The Human Proteome Organization (HUPO) proteomics Standards Initiative (PSI) in collaboration with several members of the Consortium for Top-Down proteomics (CTDP) has developed a standard notation called ProForma 2.0, which is a substantial extension of the original ProForma notation developed by the CTDP. ProForma 2.0 aims to unify the representation of proteoforms and peptidoforms. ProForma 2.0 supports use cases needed for bottom-up and middle-/top-down proteomics approaches and allows the encoding of highly modified proteins and peptides using a humanand machine-readable string. ProForma 2.0 can be used to represent protein modifications in a specified or ambiguous location, designated by mass shifts, chemical formulas, or controlled vocabulary terms, including cross-links (natural and chemical), and atomic isotopes. Notational conventions are based on public controlled vocabularies and ontologies. The most up-to-date full specification document and information about software implementations are available at http://***/proforma. © 2021, CC0.

关键词： Mass spectrometry

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