TY - JOUR
T1 - Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics
AU - Ma, Cong
AU - Balaban, Metin
AU - Liu, Jingxian
AU - Chen, Siqi
AU - Wilson, Michael J.
AU - Sun, Christopher H.
AU - Ding, Li
AU - Raphael, Benjamin J.
N1 - Publisher Copyright:
© The Author(s), under exclusive licence to Springer Nature America, Inc. 2024.
PY - 2024/12
Y1 - 2024/12
N2 - 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 evolution, or phylogeography, from SRT data. CalicoST identifies important classes of CNAs—including copy-neutral loss of heterozygosity and mirrored subclonal CNAs—that are invisible to total copy number analysis. Using nine patients’ data from the Human Tumor Atlas Network, CalicoST achieves an average accuracy of 86%, approximately 21% higher than existing methods. CalicoST reconstructs a tumor phylogeography in three-dimensional space for two patients with multiple adjacent slices. CalicoST analysis of multiple SRT slices from a cancerous prostate organ reveals mirrored subclonal CNAs on the two sides of the prostate, forming a bifurcating phylogeography in both genetic and physical space.
AB - 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 evolution, or phylogeography, from SRT data. CalicoST identifies important classes of CNAs—including copy-neutral loss of heterozygosity and mirrored subclonal CNAs—that are invisible to total copy number analysis. Using nine patients’ data from the Human Tumor Atlas Network, CalicoST achieves an average accuracy of 86%, approximately 21% higher than existing methods. CalicoST reconstructs a tumor phylogeography in three-dimensional space for two patients with multiple adjacent slices. CalicoST analysis of multiple SRT slices from a cancerous prostate organ reveals mirrored subclonal CNAs on the two sides of the prostate, forming a bifurcating phylogeography in both genetic and physical space.
UR - https://www.scopus.com/pages/publications/85207948152
U2 - 10.1038/s41592-024-02438-9
DO - 10.1038/s41592-024-02438-9
M3 - Article
C2 - 39478176
AN - SCOPUS:85207948152
SN - 1548-7091
VL - 21
SP - 2239
EP - 2247
JO - Nature Methods
JF - Nature Methods
IS - 12
M1 - 130
ER -