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

Maurizio Pellegrino; Adam Sciambi; Sebastian Treusch; Robert Durruthy-Durruthy; Kaustubh Gokhale; Jose Jacob; Tina X. Chen; Jennifer A. Geis; William Oldham; Jairo Matthews; Hagop Kantarjian; P. Andrew Futreal; Keyur Patel; Keith W. Jones; Koichi Takahashi; Dennis J. Eastburn

doi:10.1101/gr.232272.117

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

Maurizio Pellegrino, Adam Sciambi, Sebastian Treusch, Robert Durruthy-Durruthy, Kaustubh Gokhale, Jose Jacob, Tina X. Chen, Jennifer A. Geis, William Oldham, Jairo Matthews, Hagop Kantarjian, P. Andrew Futreal, Keyur Patel, Keith W. Jones, Koichi Takahashi, Dennis J. Eastburn

Hematopathology

Research output: Contribution to journal › Article › peer-review

142 Scopus citations

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. 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 was 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.

Original language	English (US)
Pages (from-to)	1345-1352
Number of pages	8
Journal	Genome research
Volume	28
Issue number	9
DOIs	https://doi.org/10.1101/gr.232272.117
State	Published - Sep 2018

ASJC Scopus subject areas

Genetics
Genetics(clinical)

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Pellegrino, M., Sciambi, A., Treusch, S., Durruthy-Durruthy, R., Gokhale, K., Jacob, J., Chen, T. X., Geis, J. A., Oldham, W., Matthews, J., Kantarjian, H., Futreal, P. A., Patel, K., Jones, K. W., Takahashi, K., & Eastburn, D. J. (2018). High-throughput single-cell DNA sequencing of acute myeloid leukemia tumors with droplet microfluidics. Genome research, 28(9), 1345-1352. https://doi.org/10.1101/gr.232272.117

Pellegrino, M, Sciambi, A, Treusch, S, Durruthy-Durruthy, R, Gokhale, K, Jacob, J, Chen, TX, Geis, JA, Oldham, W, Matthews, J, Kantarjian, H , Futreal, PA , Patel, K, Jones, KW, Takahashi, K & Eastburn, DJ 2018, 'High-throughput single-cell DNA sequencing of acute myeloid leukemia tumors with droplet microfluidics', Genome research, vol. 28, no. 9, pp. 1345-1352. https://doi.org/10.1101/gr.232272.117

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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. 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 was 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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note = "Funding Information: We thank Bill Hyun and Hannah Viernes for comments on the manuscript. The study was funded by NIH (National Human Genome Research Institute) grant R44 HG009465 awarded to D.J.E. K.T. was supported by a Khalifa Scholar for Physician Scientist award. Publisher Copyright: {\textcopyright} 2018 Pellegrino et al.",

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AU - Gokhale, Kaustubh

AU - Jacob, Jose

AU - Chen, Tina X.

AU - Geis, Jennifer A.

AU - Oldham, William

AU - Matthews, Jairo

AU - Kantarjian, Hagop

AU - Futreal, P. Andrew

AU - Patel, Keyur

AU - Jones, Keith W.

AU - Takahashi, Koichi

AU - Eastburn, Dennis J.

N1 - Funding Information: We thank Bill Hyun and Hannah Viernes for comments on the manuscript. The study was funded by NIH (National Human Genome Research Institute) grant R44 HG009465 awarded to D.J.E. K.T. was supported by a Khalifa Scholar for Physician Scientist award. Publisher Copyright: © 2018 Pellegrino et al.

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

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