Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study.

Base Pair Mismatch Benchmarking DNA / genetics DNA, Bacterial / genetics Genome, Bacterial Genome, Human High-Throughput Nucleotide Sequencing / methods Humans Sequence Analysis, DNA / methods

Journal

Nature biotechnology
ISSN: 1546-1696
Titre abrégé: Nat Biotechnol
Pays: United States
ID NLM: 9604648

Informations de publication

Date de publication:
09 2021
Historique:
received: 31 07 2020
accepted: 05 08 2021
entrez: 10 9 2021
pubmed: 11 9 2021
medline: 23 9 2021
Statut: ppublish

Résumé

Assessing the reproducibility, accuracy and utility of massively parallel DNA sequencing platforms remains an ongoing challenge. Here the Association of Biomolecular Resource Facilities (ABRF) Next-Generation Sequencing Study benchmarks the performance of a set of sequencing instruments (HiSeq/NovaSeq/paired-end 2 × 250-bp chemistry, Ion S5/Proton, PacBio circular consensus sequencing (CCS), Oxford Nanopore Technologies PromethION/MinION, BGISEQ-500/MGISEQ-2000 and GS111) on human and bacterial reference DNA samples. Among short-read instruments, HiSeq 4000 and X10 provided the most consistent, highest genome coverage, while BGI/MGISEQ provided the lowest sequencing error rates. The long-read instrument PacBio CCS had the highest reference-based mapping rate and lowest non-mapping rate. The two long-read platforms PacBio CCS and PromethION/MinION showed the best sequence mapping in repeat-rich areas and across homopolymers. NovaSeq 6000 using 2 × 250-bp read chemistry was the most robust instrument for capturing known insertion/deletion events. This study serves as a benchmark for current genomics technologies, as well as a resource to inform experimental design and next-generation sequencing variant calling.

Identifiants

DOI: 10.1038/s41587-021-01049-5 PMID: 34504351 PMC: PMC8985210
pubmed: 34504351
doi: 10.1038/s41587-021-01049-5
pii: 10.1038/s41587-021-01049-5
pmc: PMC8985210
mid: NIHMS1782172
doi:

Substances chimiques

DNA, Bacterial 0
DNA 9007-49-2

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Validation Study

Langues

eng

Sous-ensembles de citation

IM

Pagination

1129-1140

Subventions

Organisme : NIAID NIH HHS
ID : R01 AI125416
Pays : United States
Organisme : NIEHS NIH HHS
ID : R01 ES021006
Pays : United States
Organisme : NIAID NIH HHS
ID : R21 AI129851
Pays : United States
Organisme : NIDA NIH HHS
ID : U01 DA053941
Pays : United States
Organisme : NIMH NIH HHS
ID : R01 MH117406
Pays : United States
Organisme : NIBIB NIH HHS
ID : R25 EB020393
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI151059
Pays : United States
Organisme : NINDS NIH HHS
ID : R01 NS076465
Pays : United States
Organisme : NHGRI NIH HHS
ID : UM1 HG008898
Pays : United States

Commentaires et corrections

Type : ErratumIn

Informations de copyright

© 2021. The Author(s), under exclusive licence to Springer Nature America, Inc.

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Auteurs

Jonathan Foox (J)

Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.

Scott W Tighe (SW)

University of Vermont Cancer Center, Vermont Integrative Genomics Resource, University of Vermont, Burlington, VT, USA.
ORCID: 0000-0002-3988-0741

Charles M Nicolet (CM)

Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.

Justin M Zook (JM)

Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA.
ORCID: 0000-0003-2309-8402

Marta Byrska-Bishop (M)

New York Genome Center, New York, NY, USA.
ORCID: 0000-0002-9118-1032

Wayne E Clarke (WE)

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

Michael M Khayat (MM)

Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
ORCID: 0000-0001-5452-3147

Medhat Mahmoud (M)

Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
ORCID: 0000-0002-2553-4231

Phoebe K Laaguiby (PK)

University of Vermont Cancer Center, Vermont Integrative Genomics Resource, University of Vermont, Burlington, VT, USA.

Zachary T Herbert (ZT)

Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA, USA.
ORCID: 0000-0001-9401-2464

Derek Warner (D)

DNA Sequencing Core, University of Utah, Salt Lake City, UT, USA.

George S Grills (GS)

Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA.

Jin Jen (J)

Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.

Shawn Levy (S)

HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
ORCID: 0000-0002-1369-5740

Jenny Xiang (J)

Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.

Alicia Alonso (A)

Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.

Xia Zhao (X)

BGI-Shenzhen, Shenzhen, China.
MGI, BGI-Shenzhen, Shenzhen, China.

Wenwei Zhang (W)

BGI-Shenzhen, Shenzhen, China.

Fei Teng (F)

BGI-Shenzhen, Shenzhen, China.
ORCID: 0000-0003-4913-7094

Yonggang Zhao (Y)

BGI-Shenzhen, Shenzhen, China.
Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.

Haorong Lu (H)

BGI-Shenzhen, Shenzhen, China.
Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China.
ORCID: 0000-0003-0132-8166

Gary P Schroth (GP)

Illumina, Inc., San Diego, CA, USA.
ORCID: 0000-0002-3055-056X

Giuseppe Narzisi (G)

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

William Farmerie (W)

Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA.
ORCID: 0000-0002-1627-8774

Fritz J Sedlazeck (FJ)

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

Don A Baldwin (DA)

Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA, USA. donald.baldwin@fccc.edu.
ORCID: 0000-0002-1853-9253

Christopher E Mason (CE)

Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA. chm2042@med.cornell.edu.
The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA. chm2042@med.cornell.edu.
The Feil Family Brain and Mind Research Institute, New York, NY, USA. chm2042@med.cornell.edu.
The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA. chm2042@med.cornell.edu.
ORCID: 0000-0002-1850-1642

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Classifications MeSH

questionsmedicales.fr › Phénomènes génétiques › Variation génétique › Mutation › Mésappariement de bases › Performance assessment of DNA sequencing...
questionsmedicales.fr › Qualité, accès, évaluation des soins de santé › Qualité des soins de santé › Mécanismes d'évaluation des soins de santé › Évaluation de programme › Référenciation › Performance assessment of DNA sequencing...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ADN › Performance assessment of DNA sequencing...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ADN › ADN bactérien › Performance assessment of DNA sequencing...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome microbien › Génome bactérien › Performance assessment of DNA sequencing...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome humain › Performance assessment of DNA sequencing...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Séquençage nucléotidique à haut débit › Performance assessment of DNA sequencing...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Performance assessment of DNA sequencing...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ADN › Performance assessment of DNA sequencing...