Assembly of a pan-genome from deep sequencing of 910 humans of African descent.

Black People / genetics Genome, Human / genetics High-Throughput Nucleotide Sequencing / methods Humans Sequence Analysis, DNA / methods

Journal

Nature genetics
ISSN: 1546-1718
Titre abrégé: Nat Genet
Pays: United States
ID NLM: 9216904

Informations de publication

Date de publication:
01 2019
Historique:
received: 20 11 2017
accepted: 08 10 2018
pubmed: 21 11 2018
medline: 25 4 2019
entrez: 21 11 2018
Statut: ppublish

Résumé

We used a deeply sequenced dataset of 910 individuals, all of African descent, to construct a set of DNA sequences that is present in these individuals but missing from the reference human genome. We aligned 1.19 trillion reads from the 910 individuals to the reference genome (GRCh38), collected all reads that failed to align, and assembled these reads into contiguous sequences (contigs). We then compared all contigs to one another to identify a set of unique sequences representing regions of the African pan-genome missing from the reference genome. Our analysis revealed 296,485,284 bp in 125,715 distinct contigs present in the populations of African descent, demonstrating that the African pan-genome contains ~10% more DNA than the current human reference genome. Although the functional significance of nearly all of this sequence is unknown, 387 of the novel contigs fall within 315 distinct protein-coding genes, and the rest appear to be intergenic.

Identifiants

DOI: 10.1038/s41588-018-0273-y PMID: 30455414 PMC: PMC6309586
pubmed: 30455414
doi: 10.1038/s41588-018-0273-y
pii: 10.1038/s41588-018-0273-y
pmc: PMC6309586
mid: NIHMS1509230
doi:

Types de publication

Journal Article Research Support, N.I.H., Extramural

Langues

eng

Sous-ensembles de citation

IM

Pagination

30-35

Subventions

Organisme : NHGRI NIH HHS
ID : R01 HG006677
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL129239
Pays : United States
Organisme : NIGMS NIH HHS
ID : U54 GM115428
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL104608
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI132476
Pays : United States

Commentaires et corrections

Type : ErratumIn
Type : CommentIn

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Auteurs

Rachel M Sherman (RM)

Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA. rsherman@jhu.edu.
Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA. rsherman@jhu.edu.
ORCID: 0000-0003-1750-8428

Juliet Forman (J)

Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
Departments of Computer Science, Biology, and Mathematics, Harvey Mudd College, Claremont, CA, USA.

Valentin Antonescu (V)

Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.

Daniela Puiu (D)

Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.

Michelle Daya (M)

Department of Medicine, University of Colorado Denver, Aurora, CO, USA.

Nicholas Rafaels (N)

Department of Medicine, University of Colorado Denver, Aurora, CO, USA.

Meher Preethi Boorgula (MP)

Department of Medicine, University of Colorado Denver, Aurora, CO, USA.

Sameer Chavan (S)

Department of Medicine, University of Colorado Denver, Aurora, CO, USA.

Candelaria Vergara (C)

Department of Medicine, Johns Hopkins University, Baltimore, MD, USA.
ORCID: 0000-0003-3297-8057

Victor E Ortega (VE)

Department of Internal Medicine, Section on Pulmonary, Critical Care, Allergy and Immunologic Diseases, Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA.

Albert M Levin (AM)

Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, USA.

Celeste Eng (C)

Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.

Maria Yazdanbakhsh (M)

Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands.
ORCID: 0000-0002-7666-1441

James G Wilson (JG)

Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA.

Javier Marrugo (J)

Institute for Immunological Research, Universidad de Cartagena, Cartagena, Colombia.

Leslie A Lange (LA)

Department of Medicine, University of Colorado Denver, Aurora, CO, USA.

L Keoki Williams (LK)

Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA.

Harold Watson (H)

Faculty of Medical Sciences Cave Hill Campus, The University of the West Indies, Bridgetown, Barbados.

Lorraine B Ware (LB)

Department of Medicine, Vanderbilt University, Nashville, TN, USA.

Christopher O Olopade (CO)

Department of Medicine and Center for Global Health, University of Chicago, Chicago, IL, USA.

Olufunmilayo Olopade (O)

Department of Medicine, University of Chicago, Chicago, IL, USA.

Ricardo R Oliveira (RR)

Laboratório de Patologia Experimental, Centro de Pesquisas Gonçalo Moniz, Salvador, Brazil.

Carole Ober (C)

Department of Human Genetics, University of Chicago, Chicago, IL, USA.

Dan L Nicolae (DL)

Department of Medicine, University of Chicago, Chicago, IL, USA.

Deborah A Meyers (DA)

Department of Medicine, University of Arizona College of Medicine, Tucson, AZ, USA.

Alvaro Mayorga (A)

Centro de Neumologia y Alergias, San Pedro Sula, Honduras.

Jennifer Knight-Madden (J)

Caribbean Institute for Health Research, The University of the West Indies, Kingston, Jamaica.

Tina Hartert (T)

Department of Medicine, Vanderbilt University, Nashville, TN, USA.

Nadia N Hansel (NN)

Department of Medicine, Johns Hopkins University, Baltimore, MD, USA.

Marilyn G Foreman (MG)

Pulmonary and Critical Care Medicine, Morehouse School of Medicine, Atlanta, GA, USA.

Jean G Ford (JG)

Department of Medicine, Einstein Medical Center, Philadelphia, PA, USA.

Mezbah U Faruque (MU)

National Human Genome Center, Howard University College of Medicine, Washington, DC, USA.

Georgia M Dunston (GM)

Department of Microbiology, Howard University College of Medicine, Washington, DC, USA.

Luis Caraballo (L)

Institute for Immunological Research, Universidad de Cartagena, Cartagena, Colombia.

Esteban G Burchard (EG)

Departments of Bioengineering & Therapeutic Sciences and Medicine, University of California, San Francisco, San Francisco, CA, USA.

Eugene R Bleecker (ER)

Department of Medicine, University of Arizona College of Medicine, Tucson, AZ, USA.

Maria I Araujo (MI)

Immunology Service, Universidade Federal da Bahia, Salvador, Brazil.

Edwin F Herrera-Paz (EF)

Facultad de Ciencias Médicas, Universidad Tecnológica Centroamericana (UNITEC), Tegucigalpa, Honduras.
ORCID: 0000-0001-9437-6620

Monica Campbell (M)

Department of Medicine, University of Colorado Denver, Aurora, CO, USA.

Cassandra Foster (C)

Department of Medicine, Johns Hopkins University, Baltimore, MD, USA.

Margaret A Taub (MA)

Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.

Terri H Beaty (TH)

Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
ORCID: 0000-0002-7644-1705

Ingo Ruczinski (I)

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.

Rasika A Mathias (RA)

Department of Medicine, Johns Hopkins University, Baltimore, MD, USA.
Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.

Kathleen C Barnes (KC)

Department of Medicine, University of Colorado Denver, Aurora, CO, USA.

Steven L Salzberg (SL)

Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA. salzberg@jhu.edu.
Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA. salzberg@jhu.edu.
Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA. salzberg@jhu.edu.
Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA. salzberg@jhu.edu.
ORCID: 0000-0002-8859-7432

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Classifications MeSH

questionsmedicales.fr › Personnes › Noirs › Assembly of a pan-genome from deep sequencing...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome humain › Assembly of a pan-genome from deep sequencing...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Séquençage nucléotidique à haut débit › Assembly of a pan-genome from deep sequencing...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Assembly of a pan-genome from deep sequencing...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ADN › Assembly of a pan-genome from deep sequencing...