ArticleCell2025
Coalescing single-cell genomes and transcriptomes to decode breast cancer progression.
Article in Cell, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
9 citing papers in PubMed.
- Resolving cell-cell interaction networks and their molecular logic in complex tissues.Nature methods · 2026Article
- Computational approaches for multimodal lineage tracing.Nature reviews. Genetics · 2026Review
- Article
- Unraveling Cell of Origin in Breast Cancer via Joint Profiling of Whole Genome and Transcriptome in Individual Cells.Genomics, proteomics & bioinformatics · 2026Article
- scAmp enables focal gene amplification analysis from single-cell data.Nature communications · 2026Article
- Single-cell multimodal profiling of pan-cancer cell lines uncovers gene regulatory principles underlying intrinsic cell states and environmental features.Nature communications · 2026Article
- Single-cell multimodal profiling of pan-cancer cell lines uncovers gene regulatory principles underlying intrinsic cell states and environmental features.bioRxiv : the preprint server for biology · 2026Article
- Evolution of oncogene amplification across 86,000 cancer cell genomes.bioRxiv : the preprint server for biology · 2026Article
- Network pharmacology approach and experimental verification of Danzhi Xiaoyao Powder for breast cancer treatment based on UHPLC-Q-Orbitrap HRMS.Translational cancer research · 2026Article
Corrections and comments
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Authors and funding
15 authors.
Funding
Abstract
Understanding epithelial lineages of breast cancer and genotype-phenotype relationships requires direct measurements of the genome and transcriptome of the same single cells at scale. To achieve this, we developed wellDR-seq, a high-genomic-resolution, high-throughput method to simultaneously profile the genome and transcriptome of thousands of single cells. We profiled 33,646 single cells from 12 estrogen-receptor-positive breast cancers and identified ancestral subclones in multiple patients that showed a luminal hormone-responsive lineage, indicating a potential cell of origin. In contrast to bulk studies, wellDR-seq enabled the study of subclone-level gene-dosage relationships, which showed near-linear correlations in large chromosomal segments and extensive variation at the single-gene level. We identified dosage-sensitive and dosage-insensitive genes, including many breast cancer genes as well as sporadic copy-number aberrations in non-cancer cells. Overall, these data reveal complex relationships between copy number and gene expression in single cells, improving our understanding of breast cancer progression.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.