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High-throughput single-cell DNA sequencing of AML tumors with droplet microfluidics

Maurizio Pellegrino, Adam Sciambi, Sebastian Treusch, Robert Durruthy-Durruthy, Kaustubh Gokhale, Jose Jacob, Tina X. Chen, William Oldham, Jairo Matthews, Hagop Kantarjian, P. Andrew Futreal, Keyur Patel, Keith W. Jones, Koichi Takahashi, Dennis J. Eastburn
doi: https://doi.org/10.1101/203158
Maurizio Pellegrino
1Mission Bio, Inc., San Francisco, CA, USA
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Adam Sciambi
1Mission Bio, Inc., San Francisco, CA, USA
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Sebastian Treusch
1Mission Bio, Inc., San Francisco, CA, USA
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Robert Durruthy-Durruthy
1Mission Bio, Inc., San Francisco, CA, USA
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Kaustubh Gokhale
1Mission Bio, Inc., San Francisco, CA, USA
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Jose Jacob
1Mission Bio, Inc., San Francisco, CA, USA
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Tina X. Chen
1Mission Bio, Inc., San Francisco, CA, USA
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William Oldham
1Mission Bio, Inc., San Francisco, CA, USA
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Jairo Matthews
2Department of Leukemia and The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Hagop Kantarjian
2Department of Leukemia and The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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P. Andrew Futreal
3Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Keyur Patel
4Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Keith W. Jones
1Mission Bio, Inc., San Francisco, CA, USA
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Koichi Takahashi
2Department of Leukemia and The University of Texas MD Anderson Cancer Center, Houston, TX, USA
3Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Dennis J. Eastburn
1Mission Bio, Inc., San Francisco, CA, USA
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ABSTRACT

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. Using this approach, we sequenced longitudinally collected 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 tumor cells during complete remission and uncovered complex clonal evolution within AML tumors that was not observable with bulk sequencing. We anticipate that this approach will make feasible the routine analysis of heterogeneity in AML leading to improved stratification and therapy selection for the disease.

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Posted November 03, 2017.
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High-throughput single-cell DNA sequencing of AML tumors with droplet microfluidics
Maurizio Pellegrino, Adam Sciambi, Sebastian Treusch, Robert Durruthy-Durruthy, Kaustubh Gokhale, Jose Jacob, Tina X. Chen, William Oldham, Jairo Matthews, Hagop Kantarjian, P. Andrew Futreal, Keyur Patel, Keith W. Jones, Koichi Takahashi, Dennis J. Eastburn
bioRxiv 203158; doi: https://doi.org/10.1101/203158
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High-throughput single-cell DNA sequencing of AML tumors with droplet microfluidics
Maurizio Pellegrino, Adam Sciambi, Sebastian Treusch, Robert Durruthy-Durruthy, Kaustubh Gokhale, Jose Jacob, Tina X. Chen, William Oldham, Jairo Matthews, Hagop Kantarjian, P. Andrew Futreal, Keyur Patel, Keith W. Jones, Koichi Takahashi, Dennis J. Eastburn
bioRxiv 203158; doi: https://doi.org/10.1101/203158

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