Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations.

DNA, Mitochondrial / genetics High-Throughput Nucleotide Sequencing / methods Humans Mitochondria / genetics Mutation Sequence Analysis, RNA Single-Cell Analysis

Journal

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

Informations de publication

Date de publication:
07 2022
Historique:
received: 06 03 2021
accepted: 06 01 2022
pubmed: 26 2 2022
medline: 20 7 2022
entrez: 25 2 2022
Statut: ppublish

Résumé

The combination of single-cell transcriptomics with mitochondrial DNA variant detection can be used to establish lineage relationships in primary human cells, but current methods are not scalable to interrogate complex tissues. Here, we combine common 3' single-cell RNA-sequencing protocols with mitochondrial transcriptome enrichment to increase coverage by more than 50-fold, enabling high-confidence mutation detection. The method successfully identifies skewed immune-cell expansions in primary human clonal hematopoiesis.

Identifiants

DOI: 10.1038/s41587-022-01210-8 PMID: 35210612 PMC: PMC9288977
pubmed: 35210612
doi: 10.1038/s41587-022-01210-8
pii: 10.1038/s41587-022-01210-8
pmc: PMC9288977
mid: NIHMS1782664
doi:

Substances chimiques

DNA, Mitochondrial 0

Types de publication

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

Langues

eng

Sous-ensembles de citation

IM

Pagination

1030-1034

Subventions

Organisme : NCI NIH HHS
ID : R00 CA218832
Pays : United States
Organisme : NCI NIH HHS
ID : P30 CA014051
Pays : United States
Organisme : NCI NIH HHS
ID : T32 CA009216
Pays : United States
Organisme : NHGRI NIH HHS
ID : T32 HG000044
Pays : United States
Organisme : NIDDK NIH HHS
ID : R01 DK103794
Pays : United States
Organisme : NCI NIH HHS
ID : U01 CA260852
Pays : United States
Organisme : NCI NIH HHS
ID : K99 CA218832
Pays : United States

Informations de copyright

© 2022. The Author(s), under exclusive licence to Springer Nature America, Inc.

Références

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Auteurs

Tyler E Miller (TE)

Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.

Caleb A Lareau (CA)

Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Department of Pathology, Stanford University, Stanford, CA, USA.
Department of Genetics, Stanford University, Stanford, CA, USA.
Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
ORCID: 0000-0003-4179-4807

Julia A Verga (JA)

Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.

Erica A K DePasquale (EAK)

Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Division of Hematology, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA, USA.

Vincent Liu (V)

Department of Pathology, Stanford University, Stanford, CA, USA.
Department of Genetics, Stanford University, Stanford, CA, USA.
ORCID: 0000-0002-6790-6603

Daniel Ssozi (D)

Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Division of Hematology, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA, USA.
ORCID: 0000-0002-1664-2951

Katalin Sandor (K)

Department of Pathology, Stanford University, Stanford, CA, USA.
ORCID: 0000-0003-2892-4865

Yajie Yin (Y)

Department of Pathology, Stanford University, Stanford, CA, USA.
ORCID: 0000-0002-2220-005X

Leif S Ludwig (LS)

Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
ORCID: 0000-0002-2916-2164

Chadi A El Farran (CA)

Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
ORCID: 0000-0002-9374-103X

Duncan M Morgan (DM)

Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
ORCID: 0000-0002-3253-1362

Ansuman T Satpathy (AT)

Department of Pathology, Stanford University, Stanford, CA, USA.
ORCID: 0000-0002-5167-537X

Gabriel K Griffin (GK)

Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.

Andrew A Lane (AA)

Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
ORCID: 0000-0001-7380-0226

J Christopher Love (JC)

Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
ORCID: 0000-0003-0921-3144

Bradley E Bernstein (BE)

Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA.
ORCID: 0000-0002-5726-6278

Vijay G Sankaran (VG)

Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
ORCID: 0000-0003-0044-443X

Peter van Galen (P)

Broad Institute of MIT and Harvard, Cambridge, MA, USA. pvangalen@bwh.harvard.edu.
Division of Hematology, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA, USA. pvangalen@bwh.harvard.edu.
Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA. pvangalen@bwh.harvard.edu.
ORCID: 0000-0002-0735-1570

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Classifications MeSH

questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ADN › ADN mitochondrial › Mitochondrial variant enrichment from...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Séquençage nucléotidique à haut débit › Mitochondrial variant enrichment from...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Mitochondrial variant enrichment from...
questionsmedicales.fr › Cellules › Structures cellulaires › Fractions subcellulaires › Mitochondries › Mitochondrial variant enrichment from...
questionsmedicales.fr › Phénomènes génétiques › Variation génétique › Mutation › Mitochondrial variant enrichment from...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ARN › Mitochondrial variant enrichment from...
questionsmedicales.fr › Techniques d'investigation › Techniques cytologiques › Analyse sur cellule unique › Mitochondrial variant enrichment from...