Abstract Background: Tumor tissues exhibit cell-specific genetic variations and gene expression profiles critical to disease diagnosis, progression, and treatment outcomes. Single cell sequencing offers detailed insights into the heterogeneity of cancer cells which is pivotal for developing personalized treatment strategies. However, current high-throughput methods primarily detect gene expression levels, lacking information on genetic variants such as mutations or gene fusions. Understanding tumor responses to therapy requires linking cell-type specific mutations with gene expression profiles to understand cancer development and progression. Method: We developed FocuSCOPE, a high-throughput single cell sequencing solution that simultaneously measures gene expression and detects genetic variantion from individual cells. Single cell partitioning is performed using SCOPE-chip®, a portable microwell chip the size of a microscopy slide. The technology utilizes barcoding microbeads conjugated with oligos to efficiently capture mRNA and target sequences. The optimized chemistry facilitates amplification and library construction of both mRNA and target regions, including point mutations, fusion genes, and non-polyadenylated RNAs such as viral RNAs. Results: NB4, CCRF, and K562 cell lines were mixed in equal proportions. Libraries were prepared using the FocuSCOPE Blood Cancer Panel. Experiments demonstrated the specific detection of KRAS and TP53 mutations in mixed cell lines (NB4, CCRF, and K562) using the FocuSCOPE Blood Cancer Panel. The NB4 cell line contained KRAS (A18D) and TP53 (R248Q) mutations, CCRF contained KRAS (G12D) and TP53 (R248Q, R175H), and K562 contained only the BCR-ABL1 fusion gene. Additionally, FocuSCOPE effectively captured PML-RARA and BCR-ABL1 fusion genes with high sensitivity. Conclusion: FocuSCOPE enables comprehensive analysis of gene expression profiles and targeted genetic sequences, capturing driver mutations, fusion genes, and non-polyA sequences such as viral sequences with high sensitivity, thus advancing our understanding of tumor biology and therapeutic responses. This makes it an invaluable tool for personalized medicine, guiding therapeutic decisions and improving patient outcomes. Citation Format: Ankhita Nair, Rachael Lee, Sujatha Narayanankutty, Yingting Wang, Jonathan Scolnick. FocuSCOPE: A Multi-omics Solution to Simultaneously Analyse Genetic Variants and Transcriptome in Single Cells in Leukemia abstract. In: Proceedings of Frontiers in Cancer Science 2024; 2024 Nov 13-15; Singapore. Philadelphia (PA): AACR; Cancer Res 2025;85 (15Suppl): Abstract nr P17.
Nair et al. (Fri,) studied this question.
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