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Article

Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics.

Nature methods - 1 Dec 2024

Ma Cong, Balaban Metin, Liu Jingxian, Chen Siqi, Wilson Michael J, Sun Christopher H, Ding Li, Raphael Benjamin J

Abstract excerpt

Analyzing somatic evolution within a tumor over time and across space is a key challenge in cancer research. Spatially resolved transcriptomics (SRT) measures gene expression at thousands of spatial locations in a tumor, but does not directly reveal genomic aberrations. We introduce CalicoST, an algorithm to simultaneously infer allele-specific copy number aberrations (CNAs) and reconstruct spatial tumor...

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PMID: 39478176
DOI: 10.1038/s41592-024-02438-9
PMCID: PMC11621028

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