A strategy for building and using a human reference pangenome.

Graph Genome Hackathon Pangenome RNAseq Structural Variant

Journal

F1000Research
ISSN: 2046-1402
Titre abrégé: F1000Res
Pays: England
ID NLM: 101594320

Informations de publication

Date de publication:
2019
Historique:
accepted: 23 07 2021
entrez: 16 8 2021
pubmed: 14 10 2019
medline: 14 10 2019
Statut: epublish

Résumé

In March 2019, 45 scientists and software engineers from around the world converged at the University of California, Santa Cruz for the first pangenomics codeathon. The purpose of the meeting was to propose technical specifications and standards for a usable human pangenome as well as to build relevant tools for genome graph infrastructures. During the meeting, the group held several intense and productive discussions covering a diverse set of topics, including advantages of graph genomes over a linear reference representation, design of new methods that can leverage graph-based data structures, and novel visualization and annotation approaches for pangenomes. Additionally, the participants self-organized themselves into teams that worked intensely over a three-day period to build a set of pipelines and tools for specific pangenomic applications. A summary of the questions raised and the tools developed are reported in this manuscript.

Identifiants

DOI: 10.12688/f1000research.19630.2 PMID: 34386196 PMC: PMC8350888.2
pubmed: 34386196
doi: 10.12688/f1000research.19630.2
pmc: PMC8350888.2
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

1751

Subventions

Organisme : NHGRI NIH HHS
ID : U41 HG007234
Pays : United States
Organisme : NHGRI NIH HHS
ID : UM1 HG008898
Pays : United States

Informations de copyright

Copyright: © 2021 Llamas B et al.

Déclaration de conflit d'intérêts

No competing interests were disclosed.

Auteurs

Bastien Llamas (B)

Australian Centre for Ancient DNA, School of Biological Sciences, Environment Institute, The University of Adelaide, Adelaide, South Australia, 5005, Australia.

Giuseppe Narzisi (G)

New York Genome Center, New York, NY, 10013, USA.
ORCID: 0000-0003-1118-8849

Valerie Schneider (V)

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.

Peter A Audano (PA)

Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA.

Evan Biederstedt (E)

Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02215, USA.

Lon Blauvelt (L)

Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA.

Peter Bradbury (P)

Robert W. Holley Center, USDA-ARS, Ithaca, NY, 14853, USA.
ORCID: 0000-0003-3825-8480

Xian Chang (X)

Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA.

Chen-Shan Chin (CS)

DNAnexus, Mountain View, CA, 94040, USA.

Arkarachai Fungtammasan (A)

DNAnexus, Mountain View, CA, 94040, USA.

Wayne E Clarke (WE)

New York Genome Center, New York, NY, 10013, USA.

Alan Cleary (A)

National Center for Genome Resources 87505, Santa Fe, NM, 87505, USA.

Jana Ebler (J)

Max Planck Institute for Informatics, Saarbrücken, Germany.

Jordan Eizenga (J)

Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA.

Jonas A Sibbesen (JA)

Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA.

Charles J Markello (CJ)

Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA.

Erik Garrison (E)

Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA.

Shilpa Garg (S)

Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.

Glenn Hickey (G)

Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA.

Gerard R Lazo (GR)

Western Regional Research Center, USDA-ARS, Albany, CA, 94710-1105, USA.

Michael F Lin (MF)

mlin.net LLC, San Jose, CA, 95113, USA.

Medhat Mahmoud (M)

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX, TX, 77030, USA.

Tobias Marschall (T)

Max Planck Institute for Informatics, Saarbrücken, Germany.

Ilia Minkin (I)

Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, 16802, USA.

Jean Monlong (J)

Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA.

Rajeeva L Musunuri (RL)

New York Genome Center, New York, NY, 10013, USA.

Sagayamary Sagayaradj (S)

Genome Center, University of California, Davis, Davis, CA, USA.
BASF, West Sacramento, CA, USA.

Adam M Novak (AM)

Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA.
ORCID: 0000-0001-5828-047X

Mikko Rautiainen (M)

Max Planck Institute for Informatics, Saarbrücken, Germany.

Allison Regier (A)

McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, 63108, USA.
ORCID: 0000-0002-1932-8714

Fritz J Sedlazeck (FJ)

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX, TX, 77030, USA.
ORCID: 0000-0001-6040-2691

Jouni Siren (J)

Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA.

Yassine Souilmi (Y)

Australian Centre for Ancient DNA, School of Biological Sciences, Environment Institute, The University of Adelaide, Adelaide, South Australia, 5005, Australia.
ORCID: 0000-0001-7543-4864

Justin Wagner (J)

Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA.

Travis Wrightsman (T)

Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14853, USA.

Toshiyuki T Yokoyama (TT)

Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.

Qiandong Zeng (Q)

Laboratory Corporation of America Holdings, Westborough, MA, 01581, USA.
ORCID: 0000-0002-1885-7892

Justin M Zook (JM)

Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA.

Benedict Paten (B)

Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA.

Ben Busby (B)

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
ORCID: 0000-0001-5267-4988

Classifications MeSH