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High throughput single cell long-read sequencing analyses of same-cell genotypes and phenotypes in human tumors.

ABSTRACT: Single cell Nanopore sequencing of full-length RNAs (scNanoRNAseq) is transforming single cell multi-omics analysis, however it is computationally challenged and relying on paralleled short-read sequencing to curate errors. We developed scNanoGPS to calculate same-cell genotypes-phenotypes from scNanoRNAseq data and eliminate dependance on short-reads guidance. To test its accuracy, robustness and applications, we analyzed 6 single nuclei transcriptomes composited of 4 frozen tumors and 2 cancer cell lines. Our results showed that scNanoGPS accurately deconvoluted raw long-reads into single-cells and single-molecules without short-reads guidance and calculated same-cell gene expressions, isoforms, and mutations and copy numbers simultaneously for thousands of cells. In a kidney tumor, we can identify cell-type-specific alternatively spliced genes enriched in important tumorigenic pathways, in addition to expression levels. Further, we detected transcriptome-wide mutations of each cell-type, enabling direct cell-lineage (genotype) and cell-fate (phenotype) alignment to investigate tumor progression. Together, scNanoGPS addresses major computational challenges and largely simplifies experimental workflow of scNanoRNAseq.

ORGANISM(S): Homo sapiens

PROVIDER: GSE212945 | GEO | 2023/06/03

REPOSITORIES: GEO

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