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EpiSort: Enumeration of cell types using targeted bisulfite sequencing

View ORCID ProfileDvir Aran, Ron S. Dover, Karen E. Lundy, Michael D. Leipold, Ji Xuhuai, Shana L. McDevitt, Mark M. Davis, Atul J. Butte
doi: https://doi.org/10.1101/677211
Dvir Aran
1Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, 94158, USA
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  • ORCID record for Dvir Aran
Ron S. Dover
2Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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Karen E. Lundy
3California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, 94720, USA
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Michael D. Leipold
4Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, CA, 94305, USA
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Ji Xuhuai
4Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, CA, 94305, USA
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Shana L. McDevitt
3California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, 94720, USA
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Mark M. Davis
2Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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Atul J. Butte
1Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, 94158, USA
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  • For correspondence: dvir.aran@ucsf.edu
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Abstract

The cellular composition of tumors is now recognized as an essential phenotype, with implications to diagnostic, progression and therapy efficacy. A tool for accurate profiling of the tumor microenvironment is lacking, as single-cell methods and computational approaches are not applicable or suffer from low accuracy. Here we present EpiSort, a novel strategy based on targeted bisulfite sequencing, which allows the accurate enumeration of 23 cell types and may be applicable to cancer studies.

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Posted June 21, 2019.
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EpiSort: Enumeration of cell types using targeted bisulfite sequencing
Dvir Aran, Ron S. Dover, Karen E. Lundy, Michael D. Leipold, Ji Xuhuai, Shana L. McDevitt, Mark M. Davis, Atul J. Butte
bioRxiv 677211; doi: https://doi.org/10.1101/677211
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EpiSort: Enumeration of cell types using targeted bisulfite sequencing
Dvir Aran, Ron S. Dover, Karen E. Lundy, Michael D. Leipold, Ji Xuhuai, Shana L. McDevitt, Mark M. Davis, Atul J. Butte
bioRxiv 677211; doi: https://doi.org/10.1101/677211

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