1
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Hickey G, Monlong J, Ebler J, Novak AM, Eizenga JM, Gao Y, Marschall T, Li H, Paten B, Abel HJ, Antonacci-Fulton LL, Asri M, Baid G, Baker CA, Belyaeva A, Billis K, Bourque G, Buonaiuto S, Carroll A, Chaisson MJP, Chang PC, Chang XH, Cheng H, Chu J, Cody S, Colonna V, Cook DE, Cook-Deegan RM, Cornejo OE, Diekhans M, Doerr D, Ebert P, Ebler J, Eichler EE, Eizenga JM, Fairley S, Fedrigo O, Felsenfeld AL, Feng X, Fischer C, Flicek P, Formenti G, Frankish A, Fulton RS, Gao Y, Garg S, Garrison E, Garrison NA, Giron CG, Green RE, Groza C, Guarracino A, Haggerty L, Hall IM, Harvey WT, Haukness M, Haussler D, Heumos S, Hickey G, Hoekzema K, Hourlier T, Howe K, Jain M, Jarvis ED, Ji HP, Kenny EE, Koenig BA, Kolesnikov A, Korbel JO, Kordosky J, Koren S, Lee H, Lewis AP, Li H, Liao WW, Lu S, Lu TY, Lucas JK, Magalhães H, Marco-Sola S, Marijon P, Markello C, Marschall T, Martin FJ, McCartney A, McDaniel J, Miga KH, Mitchell MW, Monlong J, Mountcastle J, Munson KM, Mwaniki MN, Nattestad M, Novak AM, Nurk S, Olsen HE, Olson ND, Paten B, Pesout T, Phillippy AM, Popejoy AB, Porubsky D, Prins P, Puiu D, Rautiainen M, Regier AA, Rhie A, Sacco S, Sanders AD, Schneider VA, Schultz BI, Shafin K, Sibbesen JA, Sirén J, Smith MW, Sofia HJ, Tayoun ANA, Thibaud-Nissen F, Tomlinson C, Tricomi FF, Villani F, Vollger MR, Wagner J, Walenz B, Wang T, Wood JMD, Zimin AV, Zook JM. Pangenome graph construction from genome alignments with Minigraph-Cactus. Nat Biotechnol 2024; 42:663-673. [PMID: 37165083 PMCID: PMC10638906 DOI: 10.1038/s41587-023-01793-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 04/18/2023] [Indexed: 05/12/2023]
Abstract
Pangenome references address biases of reference genomes by storing a representative set of diverse haplotypes and their alignment, usually as a graph. Alternate alleles determined by variant callers can be used to construct pangenome graphs, but advances in long-read sequencing are leading to widely available, high-quality phased assemblies. Constructing a pangenome graph directly from assemblies, as opposed to variant calls, leverages the graph's ability to represent variation at different scales. Here we present the Minigraph-Cactus pangenome pipeline, which creates pangenomes directly from whole-genome alignments, and demonstrate its ability to scale to 90 human haplotypes from the Human Pangenome Reference Consortium. The method builds graphs containing all forms of genetic variation while allowing use of current mapping and genotyping tools. We measure the effect of the quality and completeness of reference genomes used for analysis within the pangenomes and show that using the CHM13 reference from the Telomere-to-Telomere Consortium improves the accuracy of our methods. We also demonstrate construction of a Drosophila melanogaster pangenome.
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Affiliation(s)
- Glenn Hickey
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
- These authors contributed equally: Glenn Hickey, Jean Monlong
| | - Jean Monlong
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
- These authors contributed equally: Glenn Hickey, Jean Monlong
| | - Jana Ebler
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Adam M. Novak
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Jordan M. Eizenga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Yan Gao
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Tobias Marschall
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | | | - Haley J. Abel
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Mobin Asri
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | | | - Carl A. Baker
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Canadian Center for Computational Genomics, McGill University, Montreal, QC, Canada
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Silvia Buonaiuto
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
| | | | - Mark J. P. Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | | | - Xian H. Chang
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Haoyu Cheng
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Justin Chu
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sarah Cody
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Vincenza Colonna
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | | | - Robert M. Cook-Deegan
- Arizona State University, Barrett and O’Connor Washington Center, Washington, DC, USA
| | - Omar E. Cornejo
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Daniel Doerr
- Center for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Peter Ebert
- Center for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Core Unit Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jana Ebler
- Center for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Jordan M. Eizenga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Susan Fairley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Olivier Fedrigo
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Adam L. Felsenfeld
- National Institutes of Health (NIH)–National Human Genome Research Institute, Bethesda, MD, USA
| | - Xiaowen Feng
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Christian Fischer
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Robert S. Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Yan Gao
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shilpa Garg
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Copenhagen, Denmark
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Nanibaa’ A. Garrison
- Institute for Society and Genetics, College of Letters and Science, University of California, Los Angeles, Los Angeles, CA, USA
- Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Division of General Internal Medicine and Health Services Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Carlos Garcia Giron
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Richard E. Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
- Dovetail Genomics, Scotts Valley, CA, USA
| | - Cristian Groza
- Quantitative Life Sciences, McGill University, Montreal, QC, Canada
| | - Andrea Guarracino
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Genomics Research Centre, Human Technopole, Milan, Italy
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ira M. Hall
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Genomic Health, Yale University School of Medicine, New Haven, CT, USA
| | - William T. Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Marina Haukness
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - David Haussler
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Simon Heumos
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
- Biomedical Data Science, Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Glenn Hickey
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
- These authors contributed equally: Glenn Hickey, Jean Monlong
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Miten Jain
- Northeastern University, Boston, MA, USA
| | - Erich D. Jarvis
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Hanlee P. Ji
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Eimear E. Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Barbara A. Koenig
- Program in Bioethics and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | | | - Jan O. Korbel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Jennifer Kordosky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - HoJoon Lee
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Alexandra P. Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Wen-Wei Liao
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Genomic Health, Yale University School of Medicine, New Haven, CT, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Shuangjia Lu
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Tsung-Yu Lu
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Julian K. Lucas
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Hugo Magalhães
- Center for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Santiago Marco-Sola
- Computer Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
- Departament d’Arquitectura de Computadors i Sistemes Operatius, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Pierre Marijon
- Center for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Charles Markello
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Tobias Marschall
- Center for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Fergal J. Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ann McCartney
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer McDaniel
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Karen H. Miga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | | | - Jean Monlong
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
- These authors contributed equally: Glenn Hickey, Jean Monlong
| | | | - Katherine M. Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | | | - Adam M. Novak
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Sergey Nurk
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hugh E. Olsen
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Nathan D. Olson
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Trevor Pesout
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Adam M. Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alice B. Popejoy
- Department of Public Health Sciences, University of California, Davis, Davis, CA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Pjotr Prins
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Daniela Puiu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Mikko Rautiainen
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Allison A. Regier
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Ashley D. Sanders
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Valerie A. Schneider
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Baergen I. Schultz
- National Institutes of Health (NIH)–National Human Genome Research Institute, Bethesda, MD, USA
| | | | - Jonas A. Sibbesen
- Center for Health Data Science, University of Copenhagen, Copenhagen, Denmark
| | - Jouni Sirén
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Michael W. Smith
- National Institutes of Health (NIH)–National Human Genome Research Institute, Bethesda, MD, USA
| | - Heidi J. Sofia
- National Institutes of Health (NIH)–National Human Genome Research Institute, Bethesda, MD, USA
| | - Ahmad N. Abou Tayoun
- Al Jalila Genomics Center of Excellence, Al Jalila Children’s Specialty Hospital, Dubai, UAE
- Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Francesca Floriana Tricomi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Flavia Villani
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Mitchell R. Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
| | - Justin Wagner
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Brian Walenz
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ting Wang
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Aleksey V. Zimin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Justin M. Zook
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
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2
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Liao WW, Asri M, Ebler J, Doerr D, Haukness M, Hickey G, Lu S, Lucas JK, Monlong J, Abel HJ, Buonaiuto S, Chang XH, Cheng H, Chu J, Colonna V, Eizenga JM, Feng X, Fischer C, Fulton RS, Garg S, Groza C, Guarracino A, Harvey WT, Heumos S, Howe K, Jain M, Lu TY, Markello C, Martin FJ, Mitchell MW, Munson KM, Mwaniki MN, Novak AM, Olsen HE, Pesout T, Porubsky D, Prins P, Sibbesen JA, Sirén J, Tomlinson C, Villani F, Vollger MR, Antonacci-Fulton LL, Baid G, Baker CA, Belyaeva A, Billis K, Carroll A, Chang PC, Cody S, Cook DE, Cook-Deegan RM, Cornejo OE, Diekhans M, Ebert P, Fairley S, Fedrigo O, Felsenfeld AL, Formenti G, Frankish A, Gao Y, Garrison NA, Giron CG, Green RE, Haggerty L, Hoekzema K, Hourlier T, Ji HP, Kenny EE, Koenig BA, Kolesnikov A, Korbel JO, Kordosky J, Koren S, Lee H, Lewis AP, Magalhães H, Marco-Sola S, Marijon P, McCartney A, McDaniel J, Mountcastle J, Nattestad M, Nurk S, Olson ND, Popejoy AB, Puiu D, Rautiainen M, Regier AA, Rhie A, Sacco S, Sanders AD, Schneider VA, Schultz BI, Shafin K, Smith MW, Sofia HJ, Abou Tayoun AN, Thibaud-Nissen F, Tricomi FF, Wagner J, Walenz B, Wood JMD, Zimin AV, Bourque G, Chaisson MJP, Flicek P, Phillippy AM, Zook JM, Eichler EE, Haussler D, Wang T, Jarvis ED, Miga KH, Garrison E, Marschall T, Hall IM, Li H, Paten B. A draft human pangenome reference. Nature 2023; 617:312-324. [PMID: 37165242 PMCID: PMC10172123 DOI: 10.1038/s41586-023-05896-x] [Citation(s) in RCA: 163] [Impact Index Per Article: 163.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 02/28/2023] [Indexed: 05/12/2023]
Abstract
Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.
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Affiliation(s)
- Wen-Wei Liao
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Genomic Health, Yale University School of Medicine, New Haven, CT, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Mobin Asri
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Jana Ebler
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - Daniel Doerr
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - Marina Haukness
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Glenn Hickey
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Shuangjia Lu
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Center for Genomic Health, Yale University School of Medicine, New Haven, CT, USA
| | - Julian K Lucas
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Jean Monlong
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Haley J Abel
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Silvia Buonaiuto
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
| | - Xian H Chang
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Haoyu Cheng
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Justin Chu
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Vincenza Colonna
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jordan M Eizenga
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Xiaowen Feng
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Christian Fischer
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Robert S Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Shilpa Garg
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Copenhagen, Denmark
| | - Cristian Groza
- Quantitative Life Sciences, McGill University, Montréal, Québec, Canada
| | - Andrea Guarracino
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Genomics Research Centre, Human Technopole, Milan, Italy
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Simon Heumos
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
- Biomedical Data Science, Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Miten Jain
- Northeastern University, Boston, MA, USA
| | - Tsung-Yu Lu
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Charles Markello
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Adam M Novak
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Hugh E Olsen
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Trevor Pesout
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Pjotr Prins
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jonas A Sibbesen
- Center for Health Data Science, University of Copenhagen, Copenhagen, Denmark
| | - Jouni Sirén
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Flavia Villani
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Mitchell R Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
| | | | | | - Carl A Baker
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | | | - Sarah Cody
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Robert M Cook-Deegan
- Barrett and O'Connor Washington Center, Arizona State University, Washington, DC, USA
| | - Omar E Cornejo
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Mark Diekhans
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Peter Ebert
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany
- Core Unit Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Susan Fairley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Olivier Fedrigo
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Adam L Felsenfeld
- National Institutes of Health (NIH)-National Human Genome Research Institute, Bethesda, MD, USA
| | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yan Gao
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nanibaa' A Garrison
- Institute for Society and Genetics, College of Letters and Science, University of California, Los Angeles, CA, USA
- Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Division of General Internal Medicine and Health Services Research, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Carlos Garcia Giron
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
- Dovetail Genomics, Scotts Valley, CA, USA
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Hanlee P Ji
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Barbara A Koenig
- Program in Bioethics and Institute for Human Genetics, University of California, San Francisco, CA, USA
| | | | - Jan O Korbel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jennifer Kordosky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - HoJoon Lee
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Hugo Magalhães
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - Santiago Marco-Sola
- Computer Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
- Departament d'Arquitectura de Computadors i Sistemes Operatius, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Pierre Marijon
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - Ann McCartney
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer McDaniel
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | | | - Sergey Nurk
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nathan D Olson
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Alice B Popejoy
- Department of Public Health Sciences, University of California, Davis, CA, USA
| | - Daniela Puiu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Mikko Rautiainen
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Allison A Regier
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Ashley D Sanders
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Valerie A Schneider
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Baergen I Schultz
- National Institutes of Health (NIH)-National Human Genome Research Institute, Bethesda, MD, USA
| | | | - Michael W Smith
- National Institutes of Health (NIH)-National Human Genome Research Institute, Bethesda, MD, USA
| | - Heidi J Sofia
- National Institutes of Health (NIH)-National Human Genome Research Institute, Bethesda, MD, USA
| | - Ahmad N Abou Tayoun
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai, UAE
- Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Francesca Floriana Tricomi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Justin Wagner
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Brian Walenz
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Aleksey V Zimin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Canadian Center for Computational Genomics, McGill University, Montréal, Québec, Canada
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Mark J P Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Justin M Zook
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - David Haussler
- Genomics Institute, University of California, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Ting Wang
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Erich D Jarvis
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Karen H Miga
- Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
| | - Tobias Marschall
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany.
- Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany.
| | - Ira M Hall
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
- Center for Genomic Health, Yale University School of Medicine, New Haven, CT, USA.
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Benedict Paten
- Genomics Institute, University of California, Santa Cruz, CA, USA.
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3
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Byrska-Bishop M, Evani US, Zhao X, Basile AO, Abel HJ, Regier AA, Corvelo A, Clarke WE, Musunuri R, Nagulapalli K, Fairley S, Runnels A, Winterkorn L, Lowy E, Paul Flicek, Germer S, Brand H, Hall IM, Talkowski ME, Narzisi G, Zody MC. High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios. Cell 2022; 185:3426-3440.e19. [PMID: 36055201 PMCID: PMC9439720 DOI: 10.1016/j.cell.2022.08.004] [Citation(s) in RCA: 201] [Impact Index Per Article: 100.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 06/21/2022] [Accepted: 08/03/2022] [Indexed: 01/05/2023]
Abstract
The 1000 Genomes Project (1kGP) is the largest fully open resource of whole-genome sequencing (WGS) data consented for public distribution without access or use restrictions. The final, phase 3 release of the 1kGP included 2,504 unrelated samples from 26 populations and was based primarily on low-coverage WGS. Here, we present a high-coverage 3,202-sample WGS 1kGP resource, which now includes 602 complete trios, sequenced to a depth of 30X using Illumina. We performed single-nucleotide variant (SNV) and short insertion and deletion (INDEL) discovery and generated a comprehensive set of structural variants (SVs) by integrating multiple analytic methods through a machine learning model. We show gains in sensitivity and precision of variant calls compared to phase 3, especially among rare SNVs as well as INDELs and SVs spanning frequency spectrum. We also generated an improved reference imputation panel, making variants discovered here accessible for association studies.
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Affiliation(s)
| | | | - Xuefang Zhao
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | | | - Haley J. Abel
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA,Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Allison A. Regier
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA,Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Wayne E. Clarke
- New York Genome Center, New York, NY 10013, USA,Outlier Informatics Inc., Saskatoon, SK S7H 1L4, Canada
| | | | | | - Susan Fairley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | | | - Ernesto Lowy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Harrison Brand
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ira M. Hall
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA,Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA,Center for Genomic Health, Yale University School of Medicine, New Haven, CT 06510, USA,Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Michael E. Talkowski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA,Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Michael C. Zody
- New York Genome Center, New York, NY 10013, USA,Corresponding author
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4
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Borrie A, Fairley S, Harding SA. Initial clinical experience with a new sheathless guiding catheter designed for direct insertion. Eur Heart J 2022. [DOI: 10.1093/eurheartj/ehab849.131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Funding Acknowledgements
Type of funding sources: None.
Background
Radial access for percutaneous coronary intervention (PCI) is growing rapidly as this approach has been shown to improve patient comfort and reduce complications. Use of a sheathless guiding catheter for transradial PCI has the potential reduce trauma to the radial artery and to further expand the type of cases where this approach can be utilised. The new Sheathless Hyperion system allows direct insertion of the Sheathless Hyperion guiding catheter using a 20 G needle or IV cannula, a 0.25" Silverway wire and a custom dilator.
Purpose
We report the first clinical experience with the new Sheathless Hyperion guiding catheter designed for direct insertion.
Methods
We prospectively evaluated outcomes in consecutive patients who underwent PCI using the Sheathless Hyperion catheter at our institution between June 2020 and March 2021. All procedures were performed via radial access. There were no exclusion criteria.
Results
Eighty one patients were included with 99 lesion being treated using 85 Sheathless Hyperion catheters. Mean age 67.7 ± 11.8 years, 77.8% male, 22.2% diabetic and 38.8% had acute coronary syndromes. The Sheathless Hyperion was inserted directly into the radial artery in 46 (54.1%) cases with 100% success rate and inserted following initial sheath insertion for the remaining 39 (45.9%). Of the Sheathless Hyperion catheters used 30 (35.3%) were 6F in 55 (64.7%) were 7F. The Sheathless Hyperion was passed into the ascending aorta successfully in all cases. The target coronary artery was successfully engaged in 85 (98.8%). In one case the coronary could not be engaged because of excessive brachiocephalic tortuosity and conversion to femoral access occurred. In 4 cases the Sheathless Hyperion catheter had to be exchanged for one with a small curve. The majority of lesions were complex: 18.2% CTO, 39.4% heavily calcified, 44.4% long lesions and 31.3% bifurcation lesions. Adjunctive devices included rotational atherectomy (12.1%), intravascular lithotripsy 14.1%, IVUS (56.6%) and OCT (28.3%). Angiographic success was achieved in 100%. Peri-procedural non-ST-elevation myocardial infarctions defined by the 4th Universal definition occurred in 3 (3.7%) patients. No patient meet the SCAI criteria for periprocedural MI. There was no in-hospital target vessel revascularisation or death. Radial artery occlusion was infrequent occurring in one patient. No major haematomas or vascular complications occurred.
Conclusion
First clinical experience with the Sheathless Hyperion demonstrates that direct insertion is safe and effective and that it allows complex interventions to be undertaken transradially with a high success rate.
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Affiliation(s)
- A Borrie
- Wellington Hospital, Wellington, New Zealand
| | - S Fairley
- Wellington Hospital, Wellington, New Zealand
| | - S A Harding
- Wellington Hospital, Wellington, New Zealand
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5
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Rehm HL, Page AJ, Smith L, Adams JB, Alterovitz G, Babb LJ, Barkley MP, Baudis M, Beauvais MJ, Beck T, Beckmann JS, Beltran S, Bernick D, Bernier A, Bonfield JK, Boughtwood TF, Bourque G, Bowers SR, Brookes AJ, Brudno M, Brush MH, Bujold D, Burdett T, Buske OJ, Cabili MN, Cameron DL, Carroll RJ, Casas-Silva E, Chakravarty D, Chaudhari BP, Chen SH, Cherry JM, Chung J, Cline M, Clissold HL, Cook-Deegan RM, Courtot M, Cunningham F, Cupak M, Davies RM, Denisko D, Doerr MJ, Dolman LI, Dove ES, Dursi LJ, Dyke SO, Eddy JA, Eilbeck K, Ellrott KP, Fairley S, Fakhro KA, Firth HV, Fitzsimons MS, Fiume M, Flicek P, Fore IM, Freeberg MA, Freimuth RR, Fromont LA, Fuerth J, Gaff CL, Gan W, Ghanaim EM, Glazer D, Green RC, Griffith M, Griffith OL, Grossman RL, Groza T, Guidry Auvil JM, Guigó R, Gupta D, Haendel MA, Hamosh A, Hansen DP, Hart RK, Hartley DM, Haussler D, Hendricks-Sturrup RM, Ho CW, Hobb AE, Hoffman MM, Hofmann OM, Holub P, Hsu JS, Hubaux JP, Hunt SE, Husami A, Jacobsen JO, Jamuar SS, Janes EL, Jeanson F, Jené A, Johns AL, Joly Y, Jones SJ, Kanitz A, Kato K, Keane TM, Kekesi-Lafrance K, Kelleher J, Kerry G, Khor SS, Knoppers BM, Konopko MA, Kosaki K, Kuba M, Lawson J, Leinonen R, Li S, Lin MF, Linden M, Liu X, Liyanage IU, Lopez J, Lucassen AM, Lukowski M, Mann AL, Marshall J, Mattioni M, Metke-Jimenez A, Middleton A, Milne RJ, Molnár-Gábor F, Mulder N, Munoz-Torres MC, Nag R, Nakagawa H, Nasir J, Navarro A, Nelson TH, Niewielska A, Nisselle A, Niu J, Nyrönen TH, O’Connor BD, Oesterle S, Ogishima S, Ota Wang V, Paglione LA, Palumbo E, Parkinson HE, Philippakis AA, Pizarro AD, Prlic A, Rambla J, Rendon A, Rider RA, Robinson PN, Rodarmer KW, Rodriguez LL, Rubin AF, Rueda M, Rushton GA, Ryan RS, Saunders GI, Schuilenburg H, Schwede T, Scollen S, Senf A, Sheffield NC, Skantharajah N, Smith AV, Sofia HJ, Spalding D, Spurdle AB, Stark Z, Stein LD, Suematsu M, Tan P, Tedds JA, Thomson AA, Thorogood A, Tickle TL, Tokunaga K, Törnroos J, Torrents D, Upchurch S, Valencia A, Guimera RV, Vamathevan J, Varma S, Vears DF, Viner C, Voisin C, Wagner AH, Wallace SE, Walsh BP, Williams MS, Winkler EC, Wold BJ, Wood GM, Woolley JP, Yamasaki C, Yates AD, Yung CK, Zass LJ, Zaytseva K, Zhang J, Goodhand P, North K, Birney E. GA4GH: International policies and standards for data sharing across genomic research and healthcare. Cell Genom 2021; 1:100029. [PMID: 35072136 PMCID: PMC8774288 DOI: 10.1016/j.xgen.2021.100029] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.
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Affiliation(s)
- Heidi L. Rehm
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Angela J.H. Page
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Global Alliance for Genomics and Health, Toronto, ON, Canada
| | - Lindsay Smith
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jeremy B. Adams
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Gil Alterovitz
- Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | | | - Michael Baudis
- University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Michael J.S. Beauvais
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- McGill University, Montreal, QC, Canada
| | - Tim Beck
- University of Leicester, Leicester, UK
| | | | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
| | - David Bernick
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Tiffany F. Boughtwood
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | - Guillaume Bourque
- McGill University, Montreal, QC, Canada
- Canadian Center for Computational Genomics, Montreal, QC, Canada
| | | | | | - Michael Brudno
- Canadian Center for Computational Genomics, Montreal, QC, Canada
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
- Canadian Distributed Infrastructure for Genomics (CanDIG), Toronto, ON, Canada
| | | | - David Bujold
- McGill University, Montreal, QC, Canada
- Canadian Center for Computational Genomics, Montreal, QC, Canada
- Canadian Distributed Infrastructure for Genomics (CanDIG), Toronto, ON, Canada
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | - Daniel L. Cameron
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | | | | | | | - Bimal P. Chaudhari
- Nationwide Children’s Hospital, Columbus, OH, USA
- The Ohio State University, Columbus, OH, USA
| | - Shu Hui Chen
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Justina Chung
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Melissa Cline
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | | | | | - Mélanie Courtot
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | | | | | | | | | - L. Jonathan Dursi
- University Health Network, Toronto, ON, Canada
- Canadian Distributed Infrastructure for Genomics (CanDIG), Toronto, ON, Canada
| | | | | | | | | | - Susan Fairley
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Khalid A. Fakhro
- Sidra Medicine, Doha, Qatar
- Weill Cornell Medicine - Qatar, Doha, Qatar
| | - Helen V. Firth
- Wellcome Sanger Institute, Hinxton, UK
- Addenbrooke’s Hospital, Cambridge, UK
| | | | | | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Ian M. Fore
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mallory A. Freeberg
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | - Lauren A. Fromont
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Clara L. Gaff
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Weiniu Gan
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elena M. Ghanaim
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - David Glazer
- Verily Life Sciences, South San Francisco, CA, USA
| | - Robert C. Green
- Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Malachi Griffith
- Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Obi L. Griffith
- Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | | | | | | | - Roderic Guigó
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Dipayan Gupta
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | - Ada Hamosh
- Johns Hopkins University, Baltimore, MD, USA
| | - David P. Hansen
- Australian Genomics, Parkville, VIC, Australia
- The Australian e-Health Research Centre, CSIRO, Herston, QLD, Australia
| | - Reece K. Hart
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Invitae, San Francisco, CA, USA
- MyOme, Inc, San Bruno, CA, USA
| | | | - David Haussler
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California, Santa Cruz, CA, USA
| | | | | | | | - Michael M. Hoffman
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
| | - Oliver M. Hofmann
- University of Toronto, Toronto, ON, Canada
- University of Melbourne, Melbourne, VIC, Australia
| | - Petr Holub
- BBMRI-ERIC, Graz, Austria
- Masaryk University, Brno, Czech Republic
| | | | | | - Sarah E. Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Ammar Husami
- Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | | | - Saumya S. Jamuar
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Republic of Singapore
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Republic of Singapore
| | - Elizabeth L. Janes
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- University of Waterloo, Waterloo, ON, Canada
| | | | - Aina Jené
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Amber L. Johns
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Yann Joly
- McGill University, Montreal, QC, Canada
| | - Steven J.M. Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Alexander Kanitz
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Thomas M. Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- University of Nottingham, Nottingham, UK
| | - Kristina Kekesi-Lafrance
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- McGill University, Montreal, QC, Canada
| | | | - Giselle Kerry
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Seik-Soon Khor
- National Center for Global Health and Medicine Hospital, Tokyo, Japan
- University of Tokyo, Tokyo, Japan
| | | | | | | | | | | | - Rasko Leinonen
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Stephanie Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Global Alliance for Genomics and Health, Toronto, ON, Canada
| | | | - Mikael Linden
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | | | - Isuru Udara Liyanage
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | | | - Alice L. Mann
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Wellcome Sanger Institute, Hinxton, UK
| | | | | | | | - Anna Middleton
- Wellcome Connecting Science, Hinxton, UK
- University of Cambridge, Cambridge, UK
| | - Richard J. Milne
- Wellcome Connecting Science, Hinxton, UK
- University of Cambridge, Cambridge, UK
| | | | - Nicola Mulder
- H3ABioNet, Computational Biology Division, IDM, Faculty of Health Sciences, Cape Town, South Africa
| | | | - Rishi Nag
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Hidewaki Nakagawa
- Japan Agency for Medical Research & Development (AMED), Tokyo, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Arcadi Navarro
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain
| | | | - Ania Niewielska
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Amy Nisselle
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
- Human Genetics Society of Australasia Education, Ethics & Social Issues Committee, Alexandria, NSW, Australia
| | - Jeffrey Niu
- University Health Network, Toronto, ON, Canada
| | - Tommi H. Nyrönen
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | | | - Sabine Oesterle
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Vivian Ota Wang
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Emilio Palumbo
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Helen E. Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | | | - Jordi Rambla
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Renee A. Rider
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peter N. Robinson
- The Jackson Laboratory, Farmington, CT, USA
- University of Connecticut, Farmington, CT, USA
| | - Kurt W. Rodarmer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Alan F. Rubin
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Manuel Rueda
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | | | | | - Helen Schuilenburg
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Torsten Schwede
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University of Basel, Basel, Switzerland
| | | | | | | | - Neerjah Skantharajah
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Heidi J. Sofia
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dylan Spalding
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | | | - Zornitza Stark
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Lincoln D. Stein
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | | | - Patrick Tan
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Republic of Singapore
- Precision Health Research Singapore, Singapore, Republic of Singapore
- Genome Institute of Singapore, Singapore, Republic of Singapore
| | | | - Alastair A. Thomson
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Adrian Thorogood
- McGill University, Montreal, QC, Canada
- University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | - Katsushi Tokunaga
- University of Tokyo, Tokyo, Japan
- National Center for Global Health and Medicine, Tokyo, Japan
| | - Juha Törnroos
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | - David Torrents
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Barcelona Supercomputing Center, Barcelona, Spain
| | - Sean Upchurch
- California Institute of Technology, Pasadena, CA, USA
| | - Alfonso Valencia
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Barcelona Supercomputing Center, Barcelona, Spain
| | | | - Jessica Vamathevan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Susheel Varma
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- Health Data Research UK, London, UK
| | - Danya F. Vears
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
- Human Genetics Society of Australasia Education, Ethics & Social Issues Committee, Alexandria, NSW, Australia
- Melbourne Law School, University of Melbourne, Parkville, VIC, Australia
| | - Coby Viner
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
| | | | - Alex H. Wagner
- Nationwide Children’s Hospital, Columbus, OH, USA
- The Ohio State University, Columbus, OH, USA
| | | | | | | | - Eva C. Winkler
- Section of Translational Medical Ethics, University Hospital Heidelberg, Heidelberg, Germany
| | | | | | | | | | - Andrew D. Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Christina K. Yung
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Indoc Research, Toronto, ON, Canada
| | - Lyndon J. Zass
- H3ABioNet, Computational Biology Division, IDM, Faculty of Health Sciences, Cape Town, South Africa
| | - Ksenia Zaytseva
- McGill University, Montreal, QC, Canada
- Canadian Centre for Computational Genomics, Montreal, QC, Canada
| | - Junjun Zhang
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Peter Goodhand
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Kathryn North
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Toronto, Toronto, ON, Canada
- University of Melbourne, Melbourne, VIC, Australia
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- European Molecular Biology Laboratory, Heidelberg, Germany
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6
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Lowy E, Fairley S, Flicek P. Variant calling across 505 openly consented samples from four Gambian populations on GRCh38. Wellcome Open Res 2021. [DOI: 10.12688/wellcomeopenres.17001.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The International Genome Sample Resource (IGSR) repository was established to maximise the utility of human genetic data derived from openly consented samples within the research community. Here we describe variant detection in 505 samples from four populations in The Gambia, using the GRCh38 reference genome, adding to the range of populations for which this has been done and, importantly, making allele frequencies available. A multi-caller site discovery process was applied along with imputation and phasing to produce a phased biallelic single nucleotide variant (SNV) and insertion/deletion (INDEL) call set. Variation had not previously been explored on the GRCh38 human genome assembly for 387 of the samples. Compared to our previous work with the 1000 Genomes Project data on GRCh38, we identified over nine million novel SNVs and over 870 thousand novel INDELs.
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7
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Ebert P, Audano PA, Zhu Q, Rodriguez-Martin B, Porubsky D, Bonder MJ, Sulovari A, Ebler J, Zhou W, Serra Mari R, Yilmaz F, Zhao X, Hsieh P, Lee J, Kumar S, Lin J, Rausch T, Chen Y, Ren J, Santamarina M, Höps W, Ashraf H, Chuang NT, Yang X, Munson KM, Lewis AP, Fairley S, Tallon LJ, Clarke WE, Basile AO, Byrska-Bishop M, Corvelo A, Evani US, Lu TY, Chaisson MJP, Chen J, Li C, Brand H, Wenger AM, Ghareghani M, Harvey WT, Raeder B, Hasenfeld P, Regier AA, Abel HJ, Hall IM, Flicek P, Stegle O, Gerstein MB, Tubio JMC, Mu Z, Li YI, Shi X, Hastie AR, Ye K, Chong Z, Sanders AD, Zody MC, Talkowski ME, Mills RE, Devine SE, Lee C, Korbel JO, Marschall T, Eichler EE. Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Science 2021; 372:eabf7117. [PMID: 33632895 PMCID: PMC8026704 DOI: 10.1126/science.abf7117] [Citation(s) in RCA: 270] [Impact Index Per Article: 90.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/09/2021] [Indexed: 12/14/2022]
Abstract
Long-read and strand-specific sequencing technologies together facilitate the de novo assembly of high-quality haplotype-resolved human genomes without parent-child trio data. We present 64 assembled haplotypes from 32 diverse human genomes. These highly contiguous haplotype assemblies (average minimum contig length needed to cover 50% of the genome: 26 million base pairs) integrate all forms of genetic variation, even across complex loci. We identified 107,590 structural variants (SVs), of which 68% were not discovered with short-read sequencing, and 278 SV hotspots (spanning megabases of gene-rich sequence). We characterized 130 of the most active mobile element source elements and found that 63% of all SVs arise through homology-mediated mechanisms. This resource enables reliable graph-based genotyping from short reads of up to 50,340 SVs, resulting in the identification of 1526 expression quantitative trait loci as well as SV candidates for adaptive selection within the human population.
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Affiliation(s)
- Peter Ebert
- Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany
| | - Peter A Audano
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA
| | - Qihui Zhu
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA
| | - Bernardo Rodriguez-Martin
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA
| | - Marc Jan Bonder
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Arvis Sulovari
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA
| | - Jana Ebler
- Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany
| | - Weichen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Rebecca Serra Mari
- Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany
| | - Feyza Yilmaz
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA
| | - Xuefang Zhao
- Center for Genomic Medicine, Massachusetts General Hospital, Department of Neurology, Harvard Medical School, Boston, MA 02114, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - PingHsun Hsieh
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA
| | - Joyce Lee
- Bionano Genomics, San Diego, CA 92121, USA
| | - Sushant Kumar
- Program in Computational Biology and Bioinformatics, Yale University, BASS 432 and 437, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Jiadong Lin
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Tobias Rausch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Yu Chen
- Department of Genetics and Informatics Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jingwen Ren
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Martin Santamarina
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Department of Zoology, Genetics, and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Wolfram Höps
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Hufsah Ashraf
- Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany
| | - Nelson T Chuang
- Institute for Genome Sciences, University of Maryland School of Medicine, 670 W Baltimore Street, Baltimore, MD 21201, USA
| | - Xiaofei Yang
- School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA
| | - Susan Fairley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Luke J Tallon
- Institute for Genome Sciences, University of Maryland School of Medicine, 670 W Baltimore Street, Baltimore, MD 21201, USA
| | | | | | | | | | | | - Tsung-Yu Lu
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Mark J P Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Junjie Chen
- Department of Computer and Information Sciences, Temple University, Philadelphia, PA 19122, USA
| | - Chong Li
- Department of Computer and Information Sciences, Temple University, Philadelphia, PA 19122, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Department of Neurology, Harvard Medical School, Boston, MA 02114, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aaron M Wenger
- Pacific Biosciences of California, Menlo Park, CA 94025, USA
| | - Maryam Ghareghani
- Max Planck Institute for Informatics, Saarland Informatics Campus E1.4, 66123 Saarbrücken, Germany
- Saarbrücken Graduate School of Computer Science, Saarland University, Saarland Informatics Campus E1.3, 66123 Saarbrücken, Germany
- Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA
| | - Benjamin Raeder
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Patrick Hasenfeld
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Allison A Regier
- Department of Medicine, Washington University, St. Louis, MO 63108, USA
| | - Haley J Abel
- Department of Medicine, Washington University, St. Louis, MO 63108, USA
| | - Ira M Hall
- Department of Genetics, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Oliver Stegle
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Mark B Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, BASS 432 and 437, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Jose M C Tubio
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Department of Zoology, Genetics, and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Zepeng Mu
- Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Yang I Li
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Xinghua Shi
- Department of Computer and Information Sciences, Temple University, Philadelphia, PA 19122, USA
| | | | - Kai Ye
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
- Department of Human Genetics, University of Michigan, 1241 E. Catherine Street, Ann Arbor, MI 48109, USA
| | - Zechen Chong
- Department of Genetics and Informatics Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ashley D Sanders
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | | | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Department of Neurology, Harvard Medical School, Boston, MA 02114, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ryan E Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
- Department of Human Genetics, University of Michigan, 1241 E. Catherine Street, Ann Arbor, MI 48109, USA
| | - Scott E Devine
- Institute for Genome Sciences, University of Maryland School of Medicine, 670 W Baltimore Street, Baltimore, MD 21201, USA
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA.
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, China
- Department of Graduate Studies-Life Sciences, Ewha Womans University, Ewhayeodae-gil, Seodaemun-gu, Seoul 120-750, South Korea
| | - Jan O Korbel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tobias Marschall
- Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany.
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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8
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Borrie A, Shi B, Zebrauskaite A, Ranchord A, Fairley S, Harding S. Outcomes of a New-Generation Polymer-Free Amphilimus-Eluting Stent in Complex Coronary Lesions. Heart Lung Circ 2021. [DOI: 10.1016/j.hlc.2021.06.495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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9
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Fairley S, Lowy-Gallego E, Perry E, Flicek P. The International Genome Sample Resource (IGSR) collection of open human genomic variation resources. Nucleic Acids Res 2020; 48:D941-D947. [PMID: 31584097 PMCID: PMC6943028 DOI: 10.1093/nar/gkz836] [Citation(s) in RCA: 159] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/06/2019] [Accepted: 09/30/2019] [Indexed: 12/21/2022] Open
Abstract
To sustain and develop the largest fully open human genomic resources the International Genome Sample Resource (IGSR) (https://www.internationalgenome.org) was established. It is built on the foundation of the 1000 Genomes Project, which created the largest openly accessible catalogue of human genomic variation developed from samples spanning five continents. IGSR (i) maintains access to 1000 Genomes Project resources, (ii) updates 1000 Genomes Project resources to the GRCh38 human reference assembly, (iii) adds new data generated on 1000 Genomes Project cell lines, (iv) shares data from samples with a similarly open consent to increase the number of samples and populations represented in the resources and (v) provides support to users of these resources. Among recent updates are the release of variation calls from 1000 Genomes Project data calculated directly on GRCh38 and the addition of high coverage sequence data for the 2504 samples in the 1000 Genomes Project phase three panel. The data portal, which facilitates web-based exploration of the IGSR resources, has been updated to include samples which were not part of the 1000 Genomes Project and now presents a unified view of data and samples across almost 5000 samples from multiple studies. All data is fully open and publicly accessible.
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Affiliation(s)
- Susan Fairley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ernesto Lowy-Gallego
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Emily Perry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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10
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Borrie A, Zebrauskaite A, Fairley S, Ranchord A, Harding S. 777 A New Generation Polymer-Free Amphilimus Eluting Stent in Complex PCI: A Single Centre Experience. Heart Lung Circ 2020. [DOI: 10.1016/j.hlc.2020.09.784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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11
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Lowy-Gallego E, Fairley S, Zheng-Bradley X, Ruffier M, Clarke L, Flicek P. Variant calling on the GRCh38 assembly with the data from phase three of the 1000 Genomes Project. Wellcome Open Res 2019; 4:50. [PMID: 32175479 PMCID: PMC7059836 DOI: 10.12688/wellcomeopenres.15126.2] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/17/2019] [Indexed: 12/20/2022] Open
Abstract
We present a set of biallelic SNVs and INDELs, from 2,548 samples spanning 26 populations from the 1000 Genomes Project, called
de novo on GRCh38. We believe this will be a useful reference resource for those using GRCh38. It represents an improvement over the “lift-overs” of the 1000 Genomes Project data that have been available to date by encompassing all of the GRCh38 primary assembly autosomes and pseudo-autosomal regions, including novel, medically relevant loci. Here, we describe how the data set was created and benchmark our call set against that produced by the final phase of the 1000 Genomes Project on GRCh37 and the lift-over of that data to GRCh38.
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Affiliation(s)
- Ernesto Lowy-Gallego
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Susan Fairley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Xiangqun Zheng-Bradley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Magali Ruffier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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12
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Lowy-Gallego E, Fairley S, Zheng-Bradley X, Ruffier M, Clarke L, Flicek P. Variant calling on the GRCh38 assembly with the data from phase three of the 1000 Genomes Project. Wellcome Open Res 2019; 4:50. [DOI: 10.12688/wellcomeopenres.15126.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2019] [Indexed: 01/07/2023] Open
Abstract
We present biallelic SNVs called from 2,548 samples across 26 populations from the 1000 Genomes Project, called directly on GRCh38. We believe this will be a useful reference resource for those using GRCh38, representing an improvement over the “lift-overs” of the 1000 Genomes Project data that have been available to date and providing a resource necessary for the full adoption of GRCh38 by the community. Here, we describe how the call set was created and provide benchmarking data describing how our call set compares to that produced by the final phase of the 1000 Genomes Project on GRCh37.
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13
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Norton GJ, Travis AJ, Douglas A, Fairley S, Alves EDP, Ruang-areerate P, Naredo MEB, McNally KL, Hossain M, Islam MR, Price AH. Genome Wide Association Mapping of Grain and Straw Biomass Traits in the Rice Bengal and Assam Aus Panel (BAAP) Grown Under Alternate Wetting and Drying and Permanently Flooded Irrigation. Front Plant Sci 2018; 9:1223. [PMID: 30233605 PMCID: PMC6129953 DOI: 10.3389/fpls.2018.01223] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/31/2018] [Indexed: 05/21/2023]
Abstract
Growing demand for staple crops like rice will need to be achieved predominately through agricultural intensification and more efficient use of inputs. To meet this demand it is essential that the genetic diversity within rice is fully utilized. The aus subpopulation is considered an underappreciated resource within that diversity. A new rice panel, the Bengal and Assam Aus Panel (BAAP) of 266 aus accessions was generated with ∼2 million informative SNPs obtained using skim sequencing at ∼4× depth. The BAAP was grown in the field in Bangladesh in the 'boro' season under both continuously flooded and Alternate Wetting and Drying (AWD) irrigation during 2013 and 2014 in Mymensingh and during 2014 in Madhupur. Heading date, grain mass, straw biomass and harvest index were measured. The majority (94%) of BAAP accessions flowered within a relatively small window of 10 days. The AWD irrigation treatment generally caused an increase in grain mass, but no significant genotype by treatment interactions were detected for this trait. Shoot biomass was the only trait that showed evidence of genotype by treatment interaction. The average LD (Linkage Disequilibrium) decay across the genome was 243 Kbp. Genome wide association mapping revealed 115 quantitative trait loci (QTLs). There was little evidence of QTLs specific to the irrigation treatment, and only a few QTLs co-localized with known genes. However, some QTLs were detected across multiple sites and years. These QTLs should be targets for breeding, and include a region around 2.2 Mbp on chromosome 1, a large region in the middle of chromosome 7 and two regions on chromosome 11 (∼10 Mbp and ∼29 Mbp). The BAAP appears to be a valuable addition to the growing collection of GWA mapping populations of rice.
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Affiliation(s)
- Gareth J. Norton
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Anthony J. Travis
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Alex Douglas
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Susan Fairley
- Centre for Genome Enabled Biology and Medicine, University of Aberdeen, Aberdeen, United Kingdom
| | - Eduardo De Paiva Alves
- Centre for Genome Enabled Biology and Medicine, University of Aberdeen, Aberdeen, United Kingdom
| | - Panthita Ruang-areerate
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | | | | | - Mahmud Hossain
- Department of Soil Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md. Rafiqul Islam
- Department of Soil Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Adam H. Price
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
- *Correspondence: Adam H. Price,
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Fairley S, Harding S. Spontaneous Coronary Artery Dissection as a Cause of Acute Coronary Syndromes: A Bigger Problem Than We Thought? Heart Lung Circ 2018. [DOI: 10.1016/j.hlc.2018.06.1034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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15
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Cox R, Roche E, Fairley S. Novel oral anticoagulant drugs and severe oesophagitis dissecans. Intern Med J 2017; 46:1456-1457. [PMID: 27981772 DOI: 10.1111/imj.13275] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 09/16/2016] [Indexed: 11/28/2022]
Affiliation(s)
- R Cox
- Department of Gastroenterology, The Townsville Hospital, Townsville, Queensland, Australia
| | - E Roche
- Department of Gastroenterology, The Townsville Hospital, Townsville, Queensland, Australia
| | - S Fairley
- Department of Gastroenterology, The Townsville Hospital, Townsville, Queensland, Australia
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16
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Zheng-Bradley X, Streeter I, Fairley S, Richardson D, Clarke L, Flicek P. Alignment of 1000 Genomes Project reads to reference assembly GRCh38. Gigascience 2017; 6:1-8. [PMID: 28531267 PMCID: PMC5522380 DOI: 10.1093/gigascience/gix038] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/29/2017] [Accepted: 05/19/2017] [Indexed: 12/30/2022] Open
Abstract
The 1000 Genomes Project produced more than 100 trillion basepairs of short read sequence from more than 2600 samples in 26 populations over a period of five years. In its final phase, the project released over 85 million genotyped and phased variants on human reference genome assembly GRCh37. An updated reference assembly, GRCh38, was released in late 2013, but there was insufficient time for the final phase of the project analysis to change to the new assembly. Although it is possible to lift the coordinates of the 1000 Genomes Project variants to the new assembly, this is a potentially error-prone process as coordinate remapping is most appropriate only for non-repetitive regions of the genome and those that did not see significant change between the two assemblies. It will also miss variants in any region that was newly added to GRCh38. Thus, to produce the highest quality variants and genotypes on GRCh38, the best strategy is to realign the reads and recall the variants based on the new alignment. As the first step of variant calling for the 1000 Genomes Project data, we have finished remapping all of the 1000 Genomes sequence reads to GRCh38 with alternative scaffold-aware BWA-MEM. The resulting alignments are available as CRAM, a reference-based sequence compression format. The data have been released on our FTP site and are also available from European Nucleotide Archive to facilitate researchers discovering variants on the primary sequences and alternative contigs of GRCh38.
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Affiliation(s)
- Xiangqun Zheng-Bradley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ian Streeter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Susan Fairley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - David Richardson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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17
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Holley A, Wilkins B, Fairley S, Ranchord A, Larsen P, Harding S. Prior Myocardial Infarction an Independent Predictor of Adverse Cardiovascular Events. Heart Lung Circ 2017. [DOI: 10.1016/j.hlc.2017.06.110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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18
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Harding S, Holley A, Fairley S, Wilkins B, Simmonds M, Larsen P. Contemporary Antiplatelet Therapy in Acute Coronary Syndromes: Are There Differences in Outcomes and Complications Between Clopidogrel and Ticagrelor? Heart Lung Circ 2017. [DOI: 10.1016/j.hlc.2017.06.576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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19
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Toribio AL, Alako B, Amid C, Cerdeño-Tarrága A, Clarke L, Cleland I, Fairley S, Gibson R, Goodgame N, Ten Hoopen P, Jayathilaka S, Kay S, Leinonen R, Liu X, Martínez-Villacorta J, Pakseresht N, Rajan J, Reddy K, Rosello M, Silvester N, Smirnov D, Vaughan D, Zalunin V, Cochrane G. European Nucleotide Archive in 2016. Nucleic Acids Res 2016; 45:D32-D36. [PMID: 27899630 PMCID: PMC5210577 DOI: 10.1093/nar/gkw1106] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 10/25/2016] [Accepted: 10/31/2016] [Indexed: 02/07/2023] Open
Abstract
The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) offers a rich platform for data sharing, publishing and archiving and a globally comprehensive data set for onward use by the scientific community. With a broad scope spanning raw sequencing reads, genome assemblies and functional annotation, the resource provides extensive data submission, search and download facilities across web and programmatic interfaces. Here, we outline ENA content and major access modalities, highlight major developments in 2016 and outline a number of examples of data reuse from ENA.
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Affiliation(s)
- Ana Luisa Toribio
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Blaise Alako
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Clara Amid
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ana Cerdeño-Tarrága
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Iain Cleland
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Susan Fairley
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Richard Gibson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Neil Goodgame
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Petra Ten Hoopen
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Suran Jayathilaka
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Simon Kay
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rasko Leinonen
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Xin Liu
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Josué Martínez-Villacorta
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nima Pakseresht
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jeena Rajan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kethi Reddy
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marc Rosello
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nicole Silvester
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Dmitriy Smirnov
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel Vaughan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Vadim Zalunin
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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20
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Clarke L, Fairley S, Zheng-Bradley X, Streeter I, Perry E, Lowy E, Tassé AM, Flicek P. The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data. Nucleic Acids Res 2016; 45:D854-D859. [PMID: 27638885 PMCID: PMC5210610 DOI: 10.1093/nar/gkw829] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 09/08/2016] [Indexed: 01/09/2023] Open
Abstract
The International Genome Sample Resource (IGSR; http://www.internationalgenome.org) expands in data type and population diversity the resources from the 1000 Genomes Project. IGSR represents the largest open collection of human variation data and provides easy access to these resources. IGSR was established in 2015 to maintain and extend the 1000 Genomes Project data, which has been widely used as a reference set of human variation and by researchers developing analysis methods. IGSR has mapped all of the 1000 Genomes sequence to the newest human reference (GRCh38), and will release updated variant calls to ensure maximal usefulness of the existing data. IGSR is collecting new structural variation data on the 1000 Genomes samples from long read sequencing and other technologies, and will collect relevant functional data into a single comprehensive resource. IGSR is extending coverage with new populations sequenced by collaborating groups. Here, we present the new data and analysis that IGSR has made available. We have also introduced a new data portal that increases discoverability of our data—previously only browseable through our FTP site—by focusing on particular samples, populations or data sets of interest.
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Affiliation(s)
- Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Susan Fairley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Xiangqun Zheng-Bradley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ian Streeter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Emily Perry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ernesto Lowy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Anne-Marie Tassé
- Public Population Project in Genomics and Society, McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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21
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Aken BL, Ayling S, Barrell D, Clarke L, Curwen V, Fairley S, Fernandez Banet J, Billis K, García Girón C, Hourlier T, Howe K, Kähäri A, Kokocinski F, Martin FJ, Murphy DN, Nag R, Ruffier M, Schuster M, Tang YA, Vogel JH, White S, Zadissa A, Flicek P, Searle SMJ. The Ensembl gene annotation system. Database (Oxford) 2016; 2016:baw093. [PMID: 27337980 PMCID: PMC4919035 DOI: 10.1093/database/baw093] [Citation(s) in RCA: 638] [Impact Index Per Article: 79.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 05/09/2016] [Indexed: 12/12/2022]
Abstract
The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads, to the target genome in order to construct candidate transcript models. Careful assessment and filtering of these candidate transcripts ultimately leads to the final gene set, which is made available on the Ensembl website. Here, we describe the annotation process in detail.Database URL: http://www.ensembl.org/index.html.
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Affiliation(s)
- Bronwen L Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Sarah Ayling
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK Present addresses: The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Daniel Barrell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK Eagle Genomics Ltd, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Laura Clarke
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Valery Curwen
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Susan Fairley
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Julio Fernandez Banet
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK Pfizer Inc, 10646 Science Center Dr, San Diego, CA 92121, USA
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Carlos García Girón
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Kevin Howe
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andreas Kähäri
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK Institutionen för cell-och molekylärbiologi, Uppsala University, Husargatan 3, Uppsala 752 37, Sweden
| | - Felix Kokocinski
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Daniel N Murphy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Rishi Nag
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Magali Ruffier
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Michael Schuster
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna a-1090, Austria
| | - Y Amy Tang
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jan-Hinnerk Vogel
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Simon White
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Amonida Zadissa
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Stephen M J Searle
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, García-Girón C, Gordon L, Hourlier T, Hunt S, Juettemann T, Kähäri AK, Keenan S, Komorowska M, Kulesha E, Longden I, Maurel T, McLaren WM, Muffato M, Nag R, Overduin B, Pignatelli M, Pritchard B, Pritchard E, Riat HS, Ritchie GRS, Ruffier M, Schuster M, Sheppard D, Sobral D, Taylor K, Thormann A, Trevanion S, White S, Wilder SP, Aken BL, Birney E, Cunningham F, Dunham I, Harrow J, Herrero J, Hubbard TJP, Johnson N, Kinsella R, Parker A, Spudich G, Yates A, Zadissa A, Searle SMJ. Ensembl 2013. Nucleic Acids Res 2012. [PMID: 23203987 PMCID: PMC3531136 DOI: 10.1093/nar/gks1236] [Citation(s) in RCA: 787] [Impact Index Per Article: 65.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Ensembl project (http://www.ensembl.org) provides genome information for sequenced chordate genomes with a particular focus on human, mouse, zebrafish and rat. Our resources include evidenced-based gene sets for all supported species; large-scale whole genome multiple species alignments across vertebrates and clade-specific alignments for eutherian mammals, primates, birds and fish; variation data resources for 17 species and regulation annotations based on ENCODE and other data sets. Ensembl data are accessible through the genome browser at http://www.ensembl.org and through other tools and programmatic interfaces.
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Affiliation(s)
- Paul Flicek
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK.
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23
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Groenen MAM, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, Rogel-Gaillard C, Park C, Milan D, Megens HJ, Li S, Larkin DM, Kim H, Frantz LAF, Caccamo M, Ahn H, Aken BL, Anselmo A, Anthon C, Auvil L, Badaoui B, Beattie CW, Bendixen C, Berman D, Blecha F, Blomberg J, Bolund L, Bosse M, Botti S, Bujie Z, Bystrom M, Capitanu B, Carvalho-Silva D, Chardon P, Chen C, Cheng R, Choi SH, Chow W, Clark RC, Clee C, Crooijmans RPMA, Dawson HD, Dehais P, De Sapio F, Dibbits B, Drou N, Du ZQ, Eversole K, Fadista J, Fairley S, Faraut T, Faulkner GJ, Fowler KE, Fredholm M, Fritz E, Gilbert JGR, Giuffra E, Gorodkin J, Griffin DK, Harrow JL, Hayward A, Howe K, Hu ZL, Humphray SJ, Hunt T, Hornshøj H, Jeon JT, Jern P, Jones M, Jurka J, Kanamori H, Kapetanovic R, Kim J, Kim JH, Kim KW, Kim TH, Larson G, Lee K, Lee KT, Leggett R, Lewin HA, Li Y, Liu W, Loveland JE, Lu Y, Lunney JK, Ma J, Madsen O, Mann K, Matthews L, McLaren S, Morozumi T, Murtaugh MP, Narayan J, Nguyen DT, Ni P, Oh SJ, Onteru S, Panitz F, Park EW, Park HS, Pascal G, Paudel Y, Perez-Enciso M, Ramirez-Gonzalez R, Reecy JM, Rodriguez-Zas S, Rohrer GA, Rund L, Sang Y, Schachtschneider K, Schraiber JG, Schwartz J, Scobie L, Scott C, Searle S, Servin B, Southey BR, Sperber G, Stadler P, Sweedler JV, Tafer H, Thomsen B, Wali R, Wang J, Wang J, White S, Xu X, Yerle M, Zhang G, Zhang J, Zhang J, Zhao S, Rogers J, Churcher C, Schook LB. Analyses of pig genomes provide insight into porcine demography and evolution. Nature 2012; 491:393-8. [PMID: 23151582 PMCID: PMC3566564 DOI: 10.1038/nature11622] [Citation(s) in RCA: 947] [Impact Index Per Article: 78.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Accepted: 09/27/2012] [Indexed: 01/03/2023]
Abstract
For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.
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Affiliation(s)
- Martien A M Groenen
- Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands.
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Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri AK, Keefe D, Keenan S, Kinsella R, Komorowska M, Koscielny G, Kulesha E, Larsson P, Longden I, McLaren W, Muffato M, Overduin B, Pignatelli M, Pritchard B, Riat HS, Ritchie GRS, Ruffier M, Schuster M, Sobral D, Tang YA, Taylor K, Trevanion S, Vandrovcova J, White S, Wilson M, Wilder SP, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Harrow J, Herrero J, Hubbard TJP, Parker A, Proctor G, Spudich G, Vogel J, Yates A, Zadissa A, Searle SMJ. Ensembl 2012. Nucleic Acids Res 2011; 40:D84-90. [PMID: 22086963 PMCID: PMC3245178 DOI: 10.1093/nar/gkr991] [Citation(s) in RCA: 806] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The Ensembl project (http://www.ensembl.org) provides genome resources for chordate genomes with a particular focus on human genome data as well as data for key model organisms such as mouse, rat and zebrafish. Five additional species were added in the last year including gibbon (Nomascus leucogenys) and Tasmanian devil (Sarcophilus harrisii) bringing the total number of supported species to 61 as of Ensembl release 64 (September 2011). Of these, 55 species appear on the main Ensembl website and six species are provided on the Ensembl preview site (Pre!Ensembl; http://pre.ensembl.org) with preliminary support. The past year has also seen improvements across the project.
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Affiliation(s)
- Paul Flicek
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK.
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Renfree MB, Papenfuss AT, Deakin JE, Lindsay J, Heider T, Belov K, Rens W, Waters PD, Pharo EA, Shaw G, Wong ESW, Lefèvre CM, Nicholas KR, Kuroki Y, Wakefield MJ, Zenger KR, Wang C, Ferguson-Smith M, Nicholas FW, Hickford D, Yu H, Short KR, Siddle HV, Frankenberg SR, Chew KY, Menzies BR, Stringer JM, Suzuki S, Hore TA, Delbridge ML, Mohammadi A, Schneider NY, Hu Y, O'Hara W, Al Nadaf S, Wu C, Feng ZP, Cocks BG, Wang J, Flicek P, Searle SMJ, Fairley S, Beal K, Herrero J, Carone DM, Suzuki Y, Sugano S, Toyoda A, Sakaki Y, Kondo S, Nishida Y, Tatsumoto S, Mandiou I, Hsu A, McColl KA, Lansdell B, Weinstock G, Kuczek E, McGrath A, Wilson P, Men A, Hazar-Rethinam M, Hall A, Davis J, Wood D, Williams S, Sundaravadanam Y, Muzny DM, Jhangiani SN, Lewis LR, Morgan MB, Okwuonu GO, Ruiz SJ, Santibanez J, Nazareth L, Cree A, Fowler G, Kovar CL, Dinh HH, Joshi V, Jing C, Lara F, Thornton R, Chen L, Deng J, Liu Y, Shen JY, Song XZ, Edson J, Troon C, Thomas D, Stephens A, Yapa L, Levchenko T, Gibbs RA, Cooper DW, Speed TP, Fujiyama A, M Graves JA, O'Neill RJ, Pask AJ, Forrest SM, Worley KC. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development. Genome Biol 2011; 12:R81. [PMID: 21854559 PMCID: PMC3277949 DOI: 10.1186/gb-2011-12-8-r81] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 07/22/2011] [Accepted: 08/19/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. RESULTS The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. CONCLUSIONS Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution.
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Affiliation(s)
- Marilyn B Renfree
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Anthony T Papenfuss
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Mathematics and Statistics, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Janine E Deakin
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - James Lindsay
- Department of Molecular and Cell Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, CT 06269, USA
| | - Thomas Heider
- Department of Molecular and Cell Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, CT 06269, USA
| | - Katherine Belov
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Willem Rens
- Department of Veterinary Medicine, University of Cambridge, Madingley Rd, Cambridge, CB3 0ES, UK
| | - Paul D Waters
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Elizabeth A Pharo
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Geoff Shaw
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Emily SW Wong
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Christophe M Lefèvre
- Institute for Technology Research and Innovation, Deakin University, Geelong, Victoria, 3214, Australia
| | - Kevin R Nicholas
- Institute for Technology Research and Innovation, Deakin University, Geelong, Victoria, 3214, Australia
| | - Yoko Kuroki
- RIKEN Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Matthew J Wakefield
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Kyall R Zenger
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
- School of Marine and Tropical Biology, James Cook University, Townsville, Queensland 4811, Australia
| | - Chenwei Wang
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Malcolm Ferguson-Smith
- Department of Veterinary Medicine, University of Cambridge, Madingley Rd, Cambridge, CB3 0ES, UK
| | - Frank W Nicholas
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Danielle Hickford
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Hongshi Yu
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Kirsty R Short
- Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Hannah V Siddle
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Stephen R Frankenberg
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Keng Yih Chew
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Brandon R Menzies
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, Berlin 10315, Germany
| | - Jessica M Stringer
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Shunsuke Suzuki
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Timothy A Hore
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Laboratory of Developmental Genetics and Imprinting, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Margaret L Delbridge
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Amir Mohammadi
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Nanette Y Schneider
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
- Department of Molecular Genetics, German Institute of Human Nutrition, Potsdam-Rehbruecke, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Yanqiu Hu
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - William O'Hara
- Department of Molecular and Cell Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, CT 06269, USA
| | - Shafagh Al Nadaf
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Chen Wu
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Zhi-Ping Feng
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Benjamin G Cocks
- Biosciences Research Division, Department of Primary Industries, Victoria, 1 Park Drive, Bundoora 3083, Australia
| | - Jianghui Wang
- Biosciences Research Division, Department of Primary Industries, Victoria, 1 Park Drive, Bundoora 3083, Australia
| | - Paul Flicek
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stephen MJ Searle
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Susan Fairley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Kathryn Beal
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Javier Herrero
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Dawn M Carone
- Department of Molecular and Cell Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, CT 06269, USA
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Yutaka Suzuki
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8560, Japan
| | - Sumio Sugano
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8560, Japan
| | - Atsushi Toyoda
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yoshiyuki Sakaki
- RIKEN Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Shinji Kondo
- RIKEN Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yuichiro Nishida
- RIKEN Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Shoji Tatsumoto
- RIKEN Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Ion Mandiou
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Arthur Hsu
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Kaighin A McColl
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Benjamin Lansdell
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - George Weinstock
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Elizabeth Kuczek
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
- Westmead Institute for Cancer Research, University of Sydney, Westmead, New South Wales 2145, Australia
| | - Annette McGrath
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Peter Wilson
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Artem Men
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Mehlika Hazar-Rethinam
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Allison Hall
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - John Davis
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - David Wood
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Sarah Williams
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Yogi Sundaravadanam
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Lora R Lewis
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Margaret B Morgan
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Geoffrey O Okwuonu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - San Juana Ruiz
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Jireh Santibanez
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Lynne Nazareth
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrew Cree
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Gerald Fowler
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Christie L Kovar
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Huyen H Dinh
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Vandita Joshi
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Chyn Jing
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Fremiet Lara
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Rebecca Thornton
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Lei Chen
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Jixin Deng
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Yue Liu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Joshua Y Shen
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Xing-Zhi Song
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Janette Edson
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Carmen Troon
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Daniel Thomas
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Amber Stephens
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Lankesha Yapa
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Tanya Levchenko
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Desmond W Cooper
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Terence P Speed
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Asao Fujiyama
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- National Institute of Informatics, 2-1-2 Hitotsubashi, Chiyoda-ku, Tokyo 101-8430, Japan
| | - Jennifer A M Graves
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Rachel J O'Neill
- Department of Molecular and Cell Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, CT 06269, USA
| | - Andrew J Pask
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
- Department of Molecular and Cell Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, CT 06269, USA
| | - Susan M Forrest
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
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Renfree MB, Papenfuss AT, Deakin JE, Lindsay J, Heider T, Belov K, Rens W, Waters PD, Pharo EA, Shaw G, Wong ESW, Lefèvre CM, Nicholas KR, Kuroki Y, Wakefield MJ, Zenger KR, Wang C, Ferguson-Smith M, Nicholas FW, Hickford D, Yu H, Short KR, Siddle HV, Frankenberg SR, Chew KY, Menzies BR, Stringer JM, Suzuki S, Hore TA, Delbridge ML, Patel H, Mohammadi A, Schneider NY, Hu Y, O'Hara W, Al Nadaf S, Wu C, Feng ZP, Cocks BG, Wang J, Flicek P, Searle SMJ, Fairley S, Beal K, Herrero J, Carone DM, Suzuki Y, Sugano S, Toyoda A, Sakaki Y, Kondo S, Nishida Y, Tatsumoto S, Mandiou I, Hsu A, McColl KA, Lansdell B, Weinstock G, Kuczek E, McGrath A, Wilson P, Men A, Hazar-Rethinam M, Hall A, Davis J, Wood D, Williams S, Sundaravadanam Y, Muzny DM, Jhangiani SN, Lewis LR, Morgan MB, Okwuonu GO, Ruiz SJ, Santibanez J, Nazareth L, Cree A, Fowler G, Kovar CL, Dinh HH, Joshi V, Jing C, Lara F, Thornton R, Chen L, Deng J, Liu Y, Shen JY, Song XZ, Edson J, Troon C, Thomas D, Stephens A, Yapa L, Levchenko T, Gibbs RA, Cooper DW, Speed TP, Fujiyama A, M Graves JA, O'Neill RJ, Pask AJ, Forrest SM, Worley KC. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development. Genome Biol 2011. [PMCID: PMC3334613 DOI: 10.1186/gb-2011-12-12-414] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Larsson P, Longden I, McLaren W, Overduin B, Pritchard B, Riat HS, Rios D, Ritchie GRS, Ruffier M, Schuster M, Sobral D, Spudich G, Tang YA, Trevanion S, Vandrovcova J, Vilella AJ, White S, Wilder SP, Zadissa A, Zamora J, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Herrero J, Hubbard TJP, Parker A, Proctor G, Vogel J, Searle SMJ. Ensembl 2011. Nucleic Acids Res 2011; 39:D800-6. [PMID: 21045057 PMCID: PMC3013672 DOI: 10.1093/nar/gkq1064] [Citation(s) in RCA: 564] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 10/13/2010] [Indexed: 11/13/2022] Open
Abstract
The Ensembl project (http://www.ensembl.org) seeks to enable genomic science by providing high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent and accessible infrastructure. All supported species include comprehensive, evidence-based gene annotations and a selected set of genomes includes additional data focused on variation, comparative, evolutionary, functional and regulatory annotation. The most advanced resources are provided for key species including human, mouse, rat and zebrafish reflecting the popularity and importance of these species in biomedical research. As of Ensembl release 59 (August 2010), 56 species are supported of which 5 have been added in the past year. Since our previous report, we have substantially improved the presentation and integration of both data of disease relevance and the regulatory state of different cell types.
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Affiliation(s)
- Paul Flicek
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
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Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, Minx P, Lovell P, Velho TAF, Ferris M, Balakrishnan CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J, Southey B, Gunaratne P, Watson M, Nam K, Backström N, Smeds L, Nabholz B, Itoh Y, Whitney O, Pfenning AR, Howard J, Völker M, Skinner BM, Griffin DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente XS, Olender T, Lancet D, Smit AFA, Hubley R, Konkel MK, Walker JA, Batzer MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J, Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H, Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T, Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, Wilson RK. The genome of a songbird. Nature 2010; 464:757-62. [PMID: 20360741 PMCID: PMC3187626 DOI: 10.1038/nature08819] [Citation(s) in RCA: 597] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Accepted: 01/06/2010] [Indexed: 01/16/2023]
Abstract
The zebra finch is an important model organism in several fields with unique relevance to human neuroscience. Like other songbirds, the zebra finch communicates through learned vocalizations, an ability otherwise documented only in humans and a few other animals and lacking in the chicken-the only bird with a sequenced genome until now. Here we present a structural, functional and comparative analysis of the genome sequence of the zebra finch (Taeniopygia guttata), which is a songbird belonging to the large avian order Passeriformes. We find that the overall structures of the genomes are similar in zebra finch and chicken, but they differ in many intrachromosomal rearrangements, lineage-specific gene family expansions, the number of long-terminal-repeat-based retrotransposons, and mechanisms of sex chromosome dosage compensation. We show that song behaviour engages gene regulatory networks in the zebra finch brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets. We also show evidence for rapid molecular evolution in the songbird lineage of genes that are regulated during song experience. These results indicate an active involvement of the genome in neural processes underlying vocal communication and identify potential genetic substrates for the evolution and regulation of this behaviour.
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Affiliation(s)
- Wesley C Warren
- The Genome Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.
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Flicek P, Aken BL, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Gräf S, Haider S, Hammond M, Howe K, Jenkinson A, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Koscielny G, Kulesha E, Lawson D, Longden I, Massingham T, McLaren W, Megy K, Overduin B, Pritchard B, Rios D, Ruffier M, Schuster M, Slater G, Smedley D, Spudich G, Tang YA, Trevanion S, Vilella A, Vogel J, White S, Wilder SP, Zadissa A, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Herrero J, Hubbard TJP, Parker A, Proctor G, Smith J, Searle SMJ. Ensembl's 10th year. Nucleic Acids Res 2009; 38:D557-62. [PMID: 19906699 PMCID: PMC2808936 DOI: 10.1093/nar/gkp972] [Citation(s) in RCA: 238] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Ensembl (http://www.ensembl.org) integrates genomic information for a comprehensive set of chordate genomes with a particular focus on resources for human, mouse, rat, zebrafish and other high-value sequenced genomes. We provide complete gene annotations for all supported species in addition to specific resources that target genome variation, function and evolution. Ensembl data is accessible in a variety of formats including via our genome browser, API and BioMart. This year marks the tenth anniversary of Ensembl and in that time the project has grown with advances in genome technology. As of release 56 (September 2009), Ensembl supports 51 species including marmoset, pig, zebra finch, lizard, gorilla and wallaby, which were added in the past year. Major additions and improvements to Ensembl since our previous report include the incorporation of the human GRCh37 assembly, enhanced visualisation and data-mining options for the Ensembl regulatory features and continued development of our software infrastructure.
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Affiliation(s)
- Paul Flicek
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
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Hubbard TJP, Aken BL, Ayling S, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Clarke L, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Graf S, Haider S, Hammond M, Holland R, Howe K, Jenkinson A, Johnson N, Kahari A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Rios D, Schuster M, Slater G, Smedley D, Spooner W, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wilder S, Zadissa A, Birney E, Cunningham F, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Kasprzyk A, Proctor G, Smith J, Searle S, Flicek P. Ensembl 2009. Nucleic Acids Res 2008; 37:D690-7. [PMID: 19033362 PMCID: PMC2686571 DOI: 10.1093/nar/gkn828] [Citation(s) in RCA: 683] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases, and other information for chordate, selected model organism and disease vector genomes. As of release 51 (November 2008), Ensembl fully supports 45 species, and three additional species have preliminary support. New species in the past year include orangutan and six additional low coverage mammalian genomes. Major additions and improvements to Ensembl since our previous report include a major redesign of our website; generation of multiple genome alignments and ancestral sequences using the new Enredo-Pecan-Ortheus pipeline and development of our software infrastructure, particularly to support the Ensembl Genomes project (http://www.ensemblgenomes.org/).
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Affiliation(s)
- T J P Hubbard
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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Longbottom D, Fairley S, Chapman S, Psarrou E, Vretou E, Livingstone M. Serological diagnosis of ovine enzootic abortion by enzyme-linked immunosorbent assay with a recombinant protein fragment of the polymorphic outer membrane protein POMP90 of Chlamydophila abortus. J Clin Microbiol 2002; 40:4235-43. [PMID: 12409404 PMCID: PMC139646 DOI: 10.1128/jcm.40.11.4235-4243.2002] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2002] [Revised: 06/19/2002] [Accepted: 07/23/2002] [Indexed: 11/20/2022] Open
Abstract
Ovine enzootic abortion (OEA) resulting from infection of sheep and goats with Chlamydophila abortus is of major economic importance worldwide. Over the last 50 years the serological diagnosis of infection has been based mainly on the complement fixation test (CFT), which lacks both sensitivity and specificity because of cross-reactive antibodies to other gram-negative bacteria, including another common chlamydial pathogen of sheep, Chlamydophila pecorum. In the present study, a series of overlapping recombinant antigens representing the polymorphic outer membrane protein POMP90 of C. abortus was assessed by enzyme-linked immunosorbent assay (ELISA) with a panel of 143 serum samples from sheep experimentally infected with C. abortus, from sheep clinically free of OEA, and from specific-pathogen-free lambs experimentally infected with different subtypes of C. pecorum. The results were compared to those obtained by CFT and another recently described test, an indirect ELISA (iELISA) with the recombinant OMP91B (rOMP91B) fragment (rOMP91B iELISA) (D. Longbottom, E. Psarrou, M. Livingstone, and E. Vretou, FEMS Microbiol. Lett. 195:157-161, 2001). The rOMP90-3 and rOMP90-4 ELISAs were identified as being more sensitive and specific than CFT. Assays with both fragments were evaluated further with a panel of 294 field serum samples from flocks with documented histories of abortion, from flocks with no clinical histories of abortion but which had a high proportion of samples seropositive by CFT, and from animals with no histories of abortion but from which various C. pecorum subtypes had been isolated. ELISAs with both POMP90 fragments outperformed CFT with serum samples from C. pecorum-infected animals, producing no false-positive results. However, the ELISA with the rOMP90-4 fragment appeared to be more sensitive than the one with rOMP90-3, as it identified more of the OEA-positive samples. The ELISA with the rOMP90-4 fragment was also able to identify apparently healthy animals that were infected with an enteric strain of C. abortus in flocks that were probably infected with both enteric C. abortus and C. pecorum strains. The identification of animals infected with enteric C. abortus is extremely important in controlling the spread of OEA. Overall, the new rOMP90-4 ELISA was found to be a more sensitive and specific test than CFT for differentiating animals infected with C. abortus from those infected with C. pecorum.
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Affiliation(s)
- David Longbottom
- Moredun Research Institute, International Research Centre, Pentlands Science Park, Penicuik EH26 0PZ, United Kingdom.
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Abstract
Ileal ulceration is diagnosed commonly at colonoscopy in northeastern Australia. This observation has occurred contemporaneously with the description of a painful enteritis caused through supposedly rare infections by Ancylostoma caninum, the cosmopolitan dog hookworm. In this study, we describe the morphology and prevalence of ileal ulcers and investigate their cause. There were 182 patients with a distinctive aphthous ileitis highlighted by haemorrhage into the tips of surrounding villi. The annual rate reached 4.7% of ileal examinations. Eosinophilic enteritis was the characteristic, but inconsistent, histological appearance. Ulceration was linked to infection by A. caninum through serological testing and, in three patients, by the retrieval of single hookworms. Affected patients were also more likely to own a dog (53%) than the total colonoscopic population (43%; P < 0.02). The monthly rates of diagnosis were related to climate with fewest recordings during winter. Pain was the chief indication for colonoscopy (49%), proportionally higher than in controls (28%; P < 0.0001). Patients with ulcers had increased blood eosinophil, immunoglobulin E and serological values. These results were higher still in the subset with pain compared with the rest. Most patients, however, had colonoscopy performed for unrelated reasons, such as bowel cancer surveillance, and were identified as having subclinical ulceration (rate 3.2%). The findings establish a distinctive aphthous ileitis characterized by tissue eosinophilia. The cause has been tentatively linked to canine hookworms. It is proposed that infection in this geographic region is common and only rarely does a painful enteritis develop as a consequence of hypersensitization.
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Affiliation(s)
- J Croese
- Townsville General Hospital, Queensland, Australia
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Abstract
OBJECTIVE To describe a zoonotic ancylostomiasis (canine), acquired from domestic pets by patients living in developed, urban communities. DESIGN An 8-year, retrospective case study. SETTING A clinical gastroenterologic practice in Townsville and a university parasitology department in Brisbane, Australia. PATIENTS Nine patients, each with enteric hookworm infection diagnosed by finding a single organism in situ; five were treated by us, and the rest were referred to us for parasite identification. MEASUREMENTS Clinical and demographic data, complete blood examinations, total serum immunoglobulin E assay, and serologic testing with enzyme-linked immunosorbent assay and Western blot using excretory-secretory antigens of Ancylostoma caninum. Gut biopsy specimens were examined histologically, and hookworms were identified using morphologic criteria. RESULTS The infections in three of the patients were diagnosed during the initial 6 years and six in the last 2 years. All owned a dog and described activity potentially exposing them to infection with canine hookworm larvae. Three patients had a laparotomy for acute abdominal pain, and six had colonoscopies (five with pain and one without symptoms). Six of the nine had blood eosinophilia (mean, 0.97 x 10(9)/L), and five of eight had elevated immunoglobulin E levels (mean level, 756 micrograms/L); six of eight had eosinophilic inflammation of the gut. In six patients, the worm was identified as A. caninum, whereas in three, damage to the specimen did not allow specific identification; however, they were unlikely to be human parasite species. Although all parasites were in the adult stage, none were sexually mature. Positive serologic findings in seven of the eight patients tested confirmed presence of antibody to the parasite. CONCLUSIONS Human enteric infections with A. caninum are being diagnosed more frequently in northeastern Australia. Although infection may be subclinical, the chief symptom is abdominal pain, sometimes sudden and severe. The pathologic finding is focal or diffuse eosinophilic inflammation caused by a type 1 hypersensitivity response to secreted antigens. Infection by sexually immature worms is scant and nonpatent, indicating poor adaptation to the human host. Serologic testing assists in identification of occult infection. Advanced hygiene and sanitation afford little protection because the parasite reservoir is a large and growing pool of infected domestic pets.
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Affiliation(s)
- J Croese
- University of Queensland, Australia
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Tee W, Fairley S, Smallwood R, Dwyer B. Comparative evaluation of three selective media and a nonselective medium for the culture of Helicobacter pylori from gastric biopsies. J Clin Microbiol 1991; 29:2587-9. [PMID: 1774265 PMCID: PMC270377 DOI: 10.1128/jcm.29.11.2587-2589.1991] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Plating on solid media is the standard technique used in most laboratories for the isolation of Helicobacter pylori from gastric biopsies. Recently, various selective media were developed for this purpose. We compared and evaluated three selective media, Skirrow's, Dent's CP, and modified Glupczynski's Brussels campylobacter charcoal media, and chocolate agar medium for the isolation of H. pylori. Gastric biopsies taken from a total of 203 patients were plated in parallel on all four media. An isolation rate of 51% (104 of 203) was obtained with a combination of all four media. Of the 104, 92 (88%) were positive with Dent's medium and with modified Glupczynski's medium. Skirrow's medium gave the highest isolation rate, 96% (100 of 104). However, growth of H. pylori was scant (only one to five colonies) when growth occurred on Skirrow's medium alone. Overall, modified Glupczynski's medium provided significantly heavier growth. Chocolate agar medium yielded a 76% (79 of 104) positivity rate. We recommend the use of a combination of two selective media for the maximum recovery of H. pylori from antral biopsies.
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Affiliation(s)
- W Tee
- Department of Clinical Pathology, Fairfield Infectious Diseases Hospital, Victoria, Australia
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