Automated cell type discovery and classification through knowledge transfer.
BACKGROUND
Recent advances in mass cytometry allow simultaneous measurements of up to 50 markers at single-cell resolution. However, the high dimensionality of mass cytometry data introduces computational challenges for automated data analysis and hinders translation of new biological understanding into clinical applications. Previous studies have applied machine learning to facilitate processing of mass cytometry data. However, manual inspection is still inevitable and becoming the barrier to reliable large-scale analysis.


RESULTS
We present a new algorithm called utomated ell-type iscovery and lassification (ACDC) that fully automates the classification of canonical cell populations and highlights novel cell types in mass cytometry data. Evaluations on real-world data show ACDC provides accurate and reliable estimations compared to manual gating results. Additionally, ACDC automatically classifies previously ambiguous cell types to facilitate discovery. Our findings suggest that ACDC substantially improves both reliability and interpretability of results obtained from high-dimensional mass cytometry profiling data.


METHODS
A Python package (Python 3) and analysis scripts for reproducing the results are availability on https://bitbucket.org/dudleylab/acdc .


BACKGROUND
brian.kidd@mssm.edu or joel.dudley@mssm.edu.


BACKGROUND
Supplementary data are available at Bioinformatics online.
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.|Icahn School of Medicine at Mt. Sinai, Institute for Next Generation Healthcare, New York, NY, USA.
Hao-Chih
HC
Lee
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.
Roman
R
Kosoy
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.|Icahn School of Medicine at Mt. Sinai, Institute for Next Generation Healthcare, New York, NY, USA.
Christine E
CE
Becker
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.|Icahn School of Medicine at Mt. Sinai, Institute for Next Generation Healthcare, New York, NY, USA.
Joel T
JT
Dudley
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.|Icahn School of Medicine at Mt. Sinai, Institute for Next Generation Healthcare, New York, NY, USA.
Brian A
BA
Kidd
D000818:Animals; D015415:Biomarkers / Q000032:analysis*; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D003592:Cytophotometry / Q000379:methods*; D006801:Humans; D007962:Leukocytes / Q000145:classification; D000069550:Machine Learning; D015203:Reproducibility of Results; D059010:Single-Cell Analysis / Q000379:methods*
D015415:Biomarkers