Linked-read analysis identifies mutations in single-cell DNA-sequencing data.

DNA Mutational Analysis / methods Heterozygote Humans Mutation / genetics Mutation Rate Polymorphism, Single Nucleotide / genetics Sequence Analysis, DNA / methods Single-Cell Analysis / methods Whole Genome Sequencing / methods

Journal

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

Informations de publication

Date de publication:
04 2019
Historique:
received: 22 01 2018
accepted: 01 02 2019
pubmed: 20 3 2019
medline: 20 4 2019
entrez: 20 3 2019
Statut: ppublish

Résumé

Whole-genome sequencing of DNA from single cells has the potential to reshape our understanding of mutational heterogeneity in normal and diseased tissues. However, a major difficulty is distinguishing amplification artifacts from biologically derived somatic mutations. Here, we describe linked-read analysis (LiRA), a method that accurately identifies somatic single-nucleotide variants (sSNVs) by using read-level phasing with nearby germline heterozygous polymorphisms, thereby enabling the characterization of mutational signatures and estimation of somatic mutation rates in single cells.

Identifiants

DOI: 10.1038/s41588-019-0366-2 PMID: 30886424 PMC: PMC6900933
pubmed: 30886424
doi: 10.1038/s41588-019-0366-2
pii: 10.1038/s41588-019-0366-2
pmc: PMC6900933
mid: NIHMS1061349
doi:

Types de publication

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

Langues

eng

Sous-ensembles de citation

IM

Pagination

749-754

Subventions

Organisme : NINDS NIH HHS
ID : R01 NS032457
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM007753
Pays : United States
Organisme : NHGRI NIH HHS
ID : T32 HG002295
Pays : United States
Organisme : NIMH NIH HHS
ID : U01 MH106883
Pays : United States

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Auteurs

Craig L Bohrson (CL)

Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Bioinformatics and Integrative Genomics PhD Program, Harvard Medical School, Boston, MA, USA.

Alison R Barton (AR)

Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Bioinformatics and Integrative Genomics PhD Program, Harvard Medical School, Boston, MA, USA.

Michael A Lodato (MA)

Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA.
Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA.
Broad Institute, Cambridge, MA, USA.

Rachel E Rodin (RE)

Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA.
Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA.
Broad Institute, Cambridge, MA, USA.
Program in Neuroscience and Harvard/MIT MD-PHD Program, Harvard Medical School, Boston, MA, USA.

Lovelace J Luquette (LJ)

Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Bioinformatics and Integrative Genomics PhD Program, Harvard Medical School, Boston, MA, USA.

Vinay V Viswanadham (VV)

Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Bioinformatics and Integrative Genomics PhD Program, Harvard Medical School, Boston, MA, USA.

Doga C Gulhan (DC)

Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.

Isidro Cortés-Ciriano (I)

Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK.
ORCID: 0000-0002-2036-494X

Maxwell A Sherman (MA)

Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.

Minseok Kwon (M)

Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.

Michael E Coulter (ME)

Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA.
Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA.
Broad Institute, Cambridge, MA, USA.
Program in Neuroscience and Harvard/MIT MD-PHD Program, Harvard Medical School, Boston, MA, USA.

Alon Galor (A)

Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.

Christopher A Walsh (CA)

Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA.
Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA.
Broad Institute, Cambridge, MA, USA.
ORCID: 0000-0002-0156-2238

Peter J Park (PJ)

Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA. peter_park@hms.harvard.edu.
ORCID: 0000-0001-9378-960X

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Classifications MeSH

questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ADN › Analyse de mutations d'ADN › Linked-read analysis identifies mutations in...
questionsmedicales.fr › Phénomènes génétiques › Génotype › Hétérozygote › Linked-read analysis identifies mutations in...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Linked-read analysis identifies mutations in...
questionsmedicales.fr › Phénomènes génétiques › Variation génétique › Mutation › Linked-read analysis identifies mutations in...
questionsmedicales.fr › Phénomènes biologiques › Évolution biologique › Évolution moléculaire › Taux de mutation › Linked-read analysis identifies mutations in...
questionsmedicales.fr › Phénomènes génétiques › Variation génétique › Polymorphisme génétique › Polymorphisme de nucléotide simple › Linked-read analysis identifies mutations in...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ADN › Linked-read analysis identifies mutations in...
questionsmedicales.fr › Techniques d'investigation › Techniques cytologiques › Analyse sur cellule unique › Linked-read analysis identifies mutations in...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ADN › Séquençage du génome entier › Linked-read analysis identifies mutations in...