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Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco; Mission Bio, Inc., San Francisco, CA

High-throughput single-cell DNA sequencing of acute myeloid leukemia tumors with droplet microfluidics

To enable the characterization of genetic heterogeneity in tumor cell populations, we developed a novel microfluidic approach that barcodes amplified genomic DNA from thousands of individual cancer cells confined to droplets. The barcodes are then used to reassemble the genetic profiles of cells from next-generation sequencing data. By using this approach, we sequenced longitudinally collected acute myeloid leukemia (AML) tumor populations from two patients and genotyped up to 62 disease relevant loci across more than 16,000 individual cells. Targeted single-cell sequencing was able to sensitively identify cells harboring pathogenic mutations during complete remission and uncovered complex clonal evolution within AML tumors that were not observable with bulk sequencing. We anticipate that this approach will make feasible the routine analysis of AML heterogeneity, leading to improved stratification and therapy selection for the disease.


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publication
Identification and genetic analysis of cancer cells with PCR-activated cell sorting
Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco; Mission Bio, Inc., San Francisco, CA
Eastburn, D., et al., Nucleic Acids Research (2014)
publication
Microfluidic droplet enrichment for targeted sequencing
Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco; Mission Bio, Inc., San Francisco, CA
Eastburn, D. et. al., Nucleic Acids Research (2015)
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RNA-Seq following PCR-based sorting reveals rare cell transcriptional signatures
Mission Bio, Inc. South San Francisco, CA, USA
Pellegrino, M., et. al., BMC Genomics (2016)
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Differential roles for Lgr5 and Lgr6 in epidermal stem cell lineage selection and squamous tumour development
Helen Diller Family Comprehensive Cancer Center University of California, San Francisco; Genome Institute of Singapore, Singapore
Huang, P., et. al., Nature Genetics (2017)
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