Journal
NATURE COMMUNICATIONS
Volume 12, Issue 1, Pages -Publisher
NATURE PORTFOLIO
DOI: 10.1038/s41467-021-25957-x
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Funding
- National Institutes of Health [1UH2AR067677, U19 AI111224, U01 HG009379, 1R01AR073833, R01AR063759]
- National Institute of General Medical Sciences [T32GM007753]
- National Institute of Arthritis and Musculoskeletal and Skin Diseases [T32AR007530]
- National Human Genome Research Institute [5T32HG002295-17]
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Recent advances in single-cell technologies and integration algorithms have made it possible to construct comprehensive reference atlases. Symphony is an algorithm for building large-scale, integrated reference atlases in a convenient, portable format that enables efficient query mapping within seconds.
Recent advances in single-cell technologies and integration algorithms make it possible to construct comprehensive reference atlases encompassing many donors, studies, disease states, and sequencing platforms. Much like mapping sequencing reads to a reference genome, it is essential to be able to map query cells onto complex, multimillion-cell reference atlases to rapidly identify relevant cell states and phenotypes. We present Symphony (), an algorithm for building large-scale, integrated reference atlases in a convenient, portable format that enables efficient query mapping within seconds. Symphony localizes query cells within a stable low-dimensional reference embedding, facilitating reproducible downstream transfer of reference-defined annotations to the query. We demonstrate the power of Symphony in multiple real-world datasets, including (1) mapping a multi-donor, multi-species query to predict pancreatic cell types, (2) localizing query cells along a developmental trajectory of fetal liver hematopoiesis, and (3) inferring surface protein expression with a multimodal CITE-seq atlas of memory T cells. The number of single-cell RNA-seq datasets generated is increasing rapidly, making methods that map cell types to well-curated references increasingly important. Here, the authors propose an accurate method for mapping single cells onto a reference atlas in seconds.
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