Abstract Clonal genetic diversity is a hallmark of tumor biology. In many cancers, clonal evolution has been implicated as a driver of tumor initiation, progression, and relapse, and can be a prognostic indicator of disease outcome. Cancer cells are also phenotypically heterogeneous, constituting features which can enable intravasation and metastasis, or which can impart immunoevasive capabilities. Clinically, a combination of single-cell genotype and phenotype data from cancer biopsies could provide valuable insights into oncological disease states, such as metastatic risk or drug response. Here we present a multiomic technology for the simultaneous, high-throughput capture of DNA genotype and protein information from single cells, demonstrated through the analysis of acute myeloid leukemia (AML) derived cell lines. The experimental workflow leverages the high-throughput single-cell microfluidic droplet technology on the Mission Bio Tapestri platform, a system optimized to conduct multiplex targeted genomic DNA amplification from >50 AML-associated loci. In our modified workflow, cells are stained with a pool of monoclonal antibodies conjugated with barcoded oligonucleotides, enabling a sequencing-based readout of single-cell protein signatures. The sequencing data is analyzed with a bioinformatic pipeline that separates antibody signal from targeted genotyping data on a cell-by-cell basis. We find that on a mixed population of myelogenous leukemia cells and B-cells, single-cell genotype information effectively distinguishes between cell lines, while the protein data independently recapitulates the biological signal from conventional flow cytometric methods. In conclusion, this technology opens up a new era for discovery using multiomic analysis of the complex relationships between genotype and phenotype in cancer, paving the way for future studies analyzing primary tissue samples. Citation Format: Benjamin Demaree, Cyrille Delley, David Ruff, Sebastian Treusch, Dennis Eastburn, Keith Jones, Adam Abate. Combined high-throughput DNA genotyping and protein quantification in single cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3527.