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Integrative genotyping of cancer and immune phenotypes by long-read sequencing

ABSTRACT: Single-cell transcriptomics has become the definitive method for classifying cell types and states, and can be augmented with genotype information to improve cell lineage identification. Due to constraints of short-read sequencing, current methods to detect natural genetic barcodes often require cumbersome primer panels and early commitment to targets. Here we devise a flexible long-read sequencing workflow and analysis pipeline, termed nanoranger, that starts from intermediate single-cell cDNA libraries to detect cell lineage-defining features, including single-nucleotide variants, fusion genes, isoforms, sequences of chimeric antigen and TCRs. Through systematic analysis of these classes of natural ‘barcodes’, we define the optimal targets for nanoranger, namely those loci close to the 5’ end of highly expressed genes with transcript lengths shorter than 4 kB. As proof-of-concept, we apply nanoranger to longitudinal tracking of subclones of acute myeloid leukemia (AML) and describe the heterogeneous isoform landscape of thousands of marrow-infiltrating immune cells. We propose that enhanced cellular genotyping using nanoranger can improve the tracking of single-cell tumor and immune cell co-evolution.

ORGANISM(S): Homo sapiens

PROVIDER: GSE243227 | GEO | 2023/10/31

REPOSITORIES: GEO

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Longitudinal single-cell dynamics of mitochondrial mutations in chronic lymphocytic leukemia mirror disease history

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Homo sapiens

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2019-04-20 | GSE130065 | GEO

Clonal diversity of mTORC high and low AML before and after chemotherapy

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2021-05-06 | E-MTAB-10349 | biostudies-arrayexpress

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2013-10-17 | E-GEOD-48933 | biostudies-arrayexpress

Pre-T cells from control and Zfp36l1, Zfp36l2 double conditional knockout mice. [iCLIP]

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