A multicenter study benchmarking single-cell RNA sequencing technologies using reference samples.

Algorithms B-Lymphocytes Benchmarking Breast Neoplasms Cell Line, Tumor Datasets as Topic Female Gene Expression Profiling / methods Humans Sequence Analysis, RNA / methods Single-Cell Analysis / 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: 10 05 2019
accepted: 22 10 2020
pubmed: 23 12 2020
medline: 23 9 2021
entrez: 22 12 2020
Statut: ppublish

Résumé

Comparing diverse single-cell RNA sequencing (scRNA-seq) datasets generated by different technologies and in different laboratories remains a major challenge. Here we address the need for guidance in choosing algorithms leading to accurate biological interpretations of varied data types acquired with different platforms. Using two well-characterized cellular reference samples (breast cancer cells and B cells), captured either separately or in mixtures, we compared different scRNA-seq platforms and several preprocessing, normalization and batch-effect correction methods at multiple centers. Although preprocessing and normalization contributed to variability in gene detection and cell classification, batch-effect correction was by far the most important factor in correctly classifying the cells. Moreover, scRNA-seq dataset characteristics (for example, sample and cellular heterogeneity and platform used) were critical in determining the optimal bioinformatic method. However, reproducibility across centers and platforms was high when appropriate bioinformatic methods were applied. Our findings offer practical guidance for optimizing platform and software selection when designing an scRNA-seq study.

Identifiants

DOI: 10.1038/s41587-020-00748-9 PMID: 33349700
pubmed: 33349700
doi: 10.1038/s41587-020-00748-9
pii: 10.1038/s41587-020-00748-9
doi:

Types de publication

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

Langues

eng

Sous-ensembles de citation

IM

Pagination

1103-1114

Subventions

Organisme : NIH HHS
ID : S10 OD019960
Pays : United States
Organisme : U.S. Department of Health & Human Services | NIH | NIH Office of the Director (OD)
ID : S10OD019960

Informations de copyright

© 2020. The Author(s), under exclusive licence to Springer Nature America, Inc.

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Auteurs

Wanqiu Chen (W)

Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, USA.

Yongmei Zhao (Y)

CCR-SF Bioinformatics Group, Advanced Biomedical and Computational Sciences, Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
Sequencing Facility, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.

Xin Chen (X)

Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, USA.
Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA.

Zhaowei Yang (Z)

Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, USA.
Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China.
ORCID: 0000-0002-1805-4360

Xiaojiang Xu (X)

Integrative Bioinformatics Support Group, National Institute of Environment Health Sciences, Research Triangle Park, NC, USA.

Yingtao Bi (Y)

Abbvie Cambridge Research Center, Cambridge, MA, USA.

Vicky Chen (V)

CCR-SF Bioinformatics Group, Advanced Biomedical and Computational Sciences, Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
Sequencing Facility, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.

Jing Li (J)

Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA.
Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China.

Hannah Choi (H)

Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, USA.

Ben Ernest (B)

Digicon Corporation, McLean, VA, USA.

Bao Tran (B)

Sequencing Facility, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.

Monika Mehta (M)

Sequencing Facility, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
ORCID: 0000-0003-3928-3733

Parimal Kumar (P)

Sequencing Facility, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.

Andrew Farmer (A)

Takara Bio USA, Inc., Mountain View, CA, USA.

Alain Mir (A)

Takara Bio USA, Inc., Mountain View, CA, USA.

Urvashi Ann Mehra (UA)

Digicon Corporation, McLean, VA, USA.

Jian-Liang Li (JL)

Integrative Bioinformatics Support Group, National Institute of Environment Health Sciences, Research Triangle Park, NC, USA.
ORCID: 0000-0002-6487-081X

Malcolm Moos (M)

Center for Biologics Evaluation and Research & Division of Cellular and Gene Therapies, U.S. Food and Drug Administration, Silver Spring, MD, USA.

Wenming Xiao (W)

The Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, MD, USA. wenming.xiao@fda.hhs.gov.

Charles Wang (C)

Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, USA. oxwang@gmail.com.
Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA. oxwang@gmail.com.
ORCID: 0000-0001-8861-2121

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