ArticleNature communications2024
Allele-specific transcriptional effects of subclonal copy number alterations enable genotype-phenotype mapping in cancer cells.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 16 citations in OpenAlex.
- A single-cell lens into the co-evolution of genotypes and phenotypes in cancer.Nature reviews. Cancer · 2026Review
- CNVeil resolves haplotype-specific copy number and uncovers subclonal architecture hidden from total copy number profiling in single-cell cancer genomes.bioRxiv : the preprint server for biology · 2026Article
- Quantitative coupling of clonal CNV evolution and spatially restricted malignant states identifies MFGE8 as a candidate late-state-associated target in breast cancer.Journal of translational medicine · 2026Article
- Leveraging AI and integrated genomic-enviromic prediction for intelligent sugarcane breeding.Plant communications · 2026Review
- Inferring tumor absolute copy number and clonal substructure from single-cell chromatin accessibility.Briefings in bioinformatics · 2026Article
- Extending differential gene expression testing to handle genome aneuploidy in cancer.PLoS computational biology · 2026Article
- Single-cell aneuploidy and chromosomal arm imbalances define subclones with divergent transcriptomic phenotypes.NAR genomics and bioinformatics · 2025Article
- Article
- Inferring active mutational processes in cancer using single cell sequencing and evolutionary constraints.bioRxiv : the preprint server for biology · 2025Article
- Inferring Phenotypes of Copy Number Clones in Cancer Populations Using TreeAlign.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Luminal breast epithelial cells of BRCA1 or BRCA2 mutation carriers and noncarriers harbor common breast cancer copy number alterations.Nature genetics · 2024Article
- Inferring replication timing and proliferation dynamics from single-cell DNA sequencing data.Nature communications · 2024Article
- Tracking clonal evolution of drug resistance in ovarian cancer patients by exploiting structural variants in cfDNA.bioRxiv : the preprint server for biology · 2024Article
- Single-cell mtDNA dynamics in tumors is driven by coregulation of nuclear and mitochondrial genomes.Nature genetics · 2024Article
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6 authors at 1 institution in 1 country.
Funding
Abstract
Subclonal copy number alterations are a prevalent feature in tumors with high chromosomal instability and result in heterogeneous cancer cell populations with distinct phenotypes. However, the extent to which subclonal copy number alterations contribute to clone-specific phenotypes remains poorly understood. We develop TreeAlign, which computationally integrates independently sampled single-cell DNA and RNA sequencing data from the same cell population. TreeAlign accurately encodes dosage effects from subclonal copy number alterations, the impact of allelic imbalance on allele-specific transcription, and obviates the need to define genotypic clones from a phylogeny a priori, leading to highly granular definitions of clones with distinct expression programs. These improvements enable clone-clone gene expression comparisons with higher resolution and identification of expression programs that are genomically independent. Our approach sets the stage for dissecting the relative contribution of fixed genomic alterations and dynamic epigenetic processes on gene expression programs in cancer.
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