Correcting PCR amplification errors in unique molecular identifiers to generate accurate numbers of sequencing molecules.

High-Throughput Nucleotide Sequencing Sequence Analysis, RNA Nucleotides Oligonucleotides / genetics Polymerase Chain Reaction

Journal

Nature methods
ISSN: 1548-7105
Titre abrégé: Nat Methods
Pays: United States
ID NLM: 101215604

Informations de publication

Date de publication:
Mar 2024
Historique:
received: 08 04 2023
accepted: 04 01 2024
medline: 13 3 2024
pubmed: 6 2 2024
entrez: 5 2 2024
Statut: ppublish

Résumé

Unique molecular identifiers are random oligonucleotide sequences that remove PCR amplification biases. However, the impact that PCR associated sequencing errors have on the accuracy of generating absolute counts of RNA molecules is underappreciated. We show that PCR errors are a source of inaccuracy in both bulk and single-cell sequencing data, and synthesizing unique molecular identifiers using homotrimeric nucleotide blocks provides an error-correcting solution that allows absolute counting of sequenced molecules.

Identifiants

DOI: 10.1038/s41592-024-02168-y PMID: 38317008 PMC: PMC10927542
pubmed: 38317008
doi: 10.1038/s41592-024-02168-y
pii: 10.1038/s41592-024-02168-y
pmc: PMC10927542
doi:

Substances chimiques

Nucleotides 0
Oligonucleotides 0

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

401-405

Subventions

Organisme : RCUK | Medical Research Council (MRC)
ID : MR/V010182/1

Informations de copyright

© 2024. The Author(s).

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Auteurs

Jianfeng Sun (J)

Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, UK.
ORCID: 0000-0002-1274-5080

Martin Philpott (M)

Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, UK.

Danson Loi (D)

Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, UK.
ORCID: 0000-0003-0137-9094

Shuang Li (S)

Gene Center, Ludwig-Maximilians University of Munich, Munich, Germany.
ORCID: 0009-0001-7932-9436

Pablo Monteagudo-Mesas (P)

Gene Center, Ludwig-Maximilians University of Munich, Munich, Germany.
ORCID: 0000-0002-8706-4079

Gabriela Hoffman (G)

ATDBio Ltd (now part of Biotage), Magdalen Centre, Oxford Science Park, Oxford, UK.

Jonathan Robson (J)

ATDBio Ltd (now part of Biotage), Magdalen Centre, Oxford Science Park, Oxford, UK.
ORCID: 0000-0002-0670-5875

Neelam Mehta (N)

Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, UK.

Vicki Gamble (V)

Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, UK.

Tom Brown (T)

ATDBio Ltd (now part of Biotage), Magdalen Centre, Oxford Science Park, Oxford, UK.
ORCID: 0000-0002-8607-1226

Tom Brown (T)

Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK.
ORCID: 0000-0002-6538-3036

Stefan Canzar (S)

Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, USA.
Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.
ORCID: 0000-0003-4719-8010

Udo Oppermann (U)

Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, UK.
Oxford Centre for Translational Myeloma Research, University of Oxford, Oxford, UK.

Adam P Cribbs (AP)

Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, UK. adam.cribbs@ndorms.ox.ac.uk.
Oxford Centre for Translational Myeloma Research, University of Oxford, Oxford, UK. adam.cribbs@ndorms.ox.ac.uk.
ORCID: 0000-0001-5288-3077

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Classifications MeSH

Recherchemedicale.com › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Séquençage nucléotidique à haut débit › Correcting PCR amplification errors in unique...
Recherchemedicale.com › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ARN › Correcting PCR amplification errors in unique...
Recherchemedicale.com › Acides nucléiques, nucléotides et nucléosides › Nucléotides › Correcting PCR amplification errors in unique...
Recherchemedicale.com › Acides nucléiques, nucléotides et nucléosides › Nucléotides › Polynucléotides › Oligonucléotides › Correcting PCR amplification errors in unique...
Recherchemedicale.com › Techniques d'investigation › Techniques génétiques › Techniques d'amplification d'acides nucléiques › Réaction de polymérisation en chaîne › Correcting PCR amplification errors in unique...