Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods

Drew Neavin; Anne Senabouth; Himanshi Arora; Jimmy Tsz Hang Lee; Aida Ripoll-Cladellas; sc-eQTLGen Consortium; Lude Franke; Shyam Prabhakar; Chun Jimmie Ye; Davis J McCarthy; Marta Melé; Martin Hemberg; Joseph E Powell

doi:10.1186/s13059-024-03224-8

Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods

Genome Biol. 2024 Apr 15;25(1):94. doi: 10.1186/s13059-024-03224-8.

Authors

Drew Neavin¹, Anne Senabouth², Himanshi Arora^{2

3}, Jimmy Tsz Hang Lee⁴, Aida Ripoll-Cladellas⁵; sc-eQTLGen Consortium; Lude Franke⁶, Shyam Prabhakar^{7

8

9}, Chun Jimmie Ye^{10

11

12

13}, Davis J McCarthy^{14

15}, Marta Melé⁵, Martin Hemberg¹⁶, Joseph E Powell^{17

18}

Affiliations

¹ Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute for Medical Research, Darlinghurst, NSW, Australia. d.neavin@garvan.org.au.
² Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute for Medical Research, Darlinghurst, NSW, Australia.
³ Present address: Statewide Genomics at NSW Health Pathology, Sydney, NSW, Australia.
⁴ Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
⁵ Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, Spain.
⁶ Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
⁷ Spatial and Single Cell Systems Domain, Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.
⁸ Population and Global Health, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Republic of Singapore.
⁹ Cancer Science Institute of Singapore, National University of Singapore, Singapore, Republic of Singapore.
¹⁰ Bakar Institute for Computational Health Sciences, University of California, San Francisco, CA, USA.
¹¹ Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
¹² Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
¹³ Chan Zuckerberg Biohub, San Francisco, CA, USA.
¹⁴ Bioinformatics and Cellular Genomics, St Vincent's Institute of Medical Research, Fitzroy, Australia.
¹⁵ Melbourne Integrative Genomics, School of BioSciences-School of Mathematics & Statistics, Faculty of Science, University of Melbourne, Melbourne, Australia.
¹⁶ Present address: The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
¹⁷ Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute for Medical Research, Darlinghurst, NSW, Australia. j.powell@garvan.org.au.
¹⁸ UNSW Cellular Genomics Futures Institute, University of New South Wales, Kensington, NSW, Australia. j.powell@garvan.org.au.

Abstract

Recent innovations in single-cell RNA-sequencing (scRNA-seq) provide the technology to investigate biological questions at cellular resolution. Pooling cells from multiple individuals has become a common strategy, and droplets can subsequently be assigned to a specific individual by leveraging their inherent genetic differences. An implicit challenge with scRNA-seq is the occurrence of doublets-droplets containing two or more cells. We develop Demuxafy, a framework to enhance donor assignment and doublet removal through the consensus intersection of multiple demultiplexing and doublet detecting methods. Demuxafy significantly improves droplet assignment by separating singlets from doublets and classifying the correct individual.

Keywords: Doublet detecting; Genetic demultiplexing; Single-cell analysis.

MeSH terms

Humans
Sequence Analysis, RNA / methods
Single-Cell Analysis* / methods