ArticleProceedings of the National Academy of Sciences of the United States of America2010
Allele-specific copy number analysis of tumors.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 801 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
801 citing papers in PubMed, 2 syntheses or guidelines pooled it, 1,309 citations in OpenAlex.
- Meta-analysis reveals differences in somatic alterations by genetic ancestry across common cancers.Nature genetics · 2025Pooled it
- Clinical application of tumour-in-normal contamination assessment from whole genome sequencing.Nature communications · 2024Pooled it
- Association of HRD Score With Efficacy of Neoadjuvant Short-Course Radiotherapy Plus Sequential Chemoimmunotherapy in pMMR Locally Advanced Rectal Cancer.Cancer reports (Hoboken, N.J.) · 2026Trial
- Tumor-Informed ctDNA in Guiding First-Line Immunochemotherapy in Advanced Non-Small Cell Lung Cancers.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Trial
- Trial
- Genomic and Epigenomic ctDNA Profiling in Liquid Biopsies from Heavily Pretreated Patients with DNA Damage Response-Deficient Tumors.Clinical cancer research : an official journal of the American Association for Cancer Research · 2025Trial
- Multi-omics analysis reveals the attenuation of the interferon pathway as a driver of chemo-refractory ovarian cancer.Cell reports. Medicine · 2025Trial
- RNASEH2B loss and PARP inhibition in advanced prostate cancer.The Journal of clinical investigation · 2024Trial
- Functional and omics-based rationale for the induction of BRCAness by androgen receptor pathway inhibitors to sensitize prostate cancer to PARP inhibition, regardless of HRR status.British journal of cancer · 2026Article
- FFPE-CUTAC: A Single Assay, Multiple Layers.bioRxiv : the preprint server for biology · 2026Article
- Integrated multi-omics and single-cell analysis of galectins and immune associations in triple-negative breast cancer.Translational oncology · 2026Article
- STK11 Mutations and Deletions Define an Aggressive Molecular Subgroup of Cervical Adenocarcinoma.Cancer medicine · 2026Article
- Article
- Somatic mutational landscape in von Hippel-Lindau familial hemangioblastoma.Molecular oncology · 2026Article
- 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
- Analysis of a large osteosarcoma sequencing data set elucidates patterns of genomic alterations.Cancer · 2026Article
- [The problem of determining tumor cell content].Pathologie (Heidelberg, Germany) · 2026Article
- Transcriptomic analysis of tissue-resident memory T cells of the fallopian tube reveals a precursor immune surveillance network for ovarian cancer prevention.Nature communications · 2026Article
- AI-Based Analysis of Tumor-Infiltrating Lymphocytes and Homologous Recombination in Ovarian Cancer: JGOG3025-A1 Study.Cancer science · 2026Article
- Variable latency between the founder genetic event and rhabdoid tumor expansion.bioRxiv : the preprint server for biology · 2026Article
741 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors at 5 institutions in 4 countries.
Funding
Abstract
We present an allele-specific copy number analysis of the in vivo breast cancer genome. We describe a unique bioinformatics approach, ASCAT (allele-specific copy number analysis of tumors), to accurately dissect the allele-specific copy number of solid tumors, simultaneously estimating and adjusting for both tumor ploidy and nonaberrant cell admixture. This allows calculation of "ASCAT profiles" (genome-wide allele-specific copy-number profiles) from which gains, losses, copy number-neutral events, and loss of heterozygosity (LOH) can accurately be determined. In an early-stage breast carcinoma series, we observe aneuploidy (>2.7n) in 45% of the cases and an average nonaberrant cell admixture of 49%. By aggregation of ASCAT profiles across our series, we obtain genomic frequency distributions of gains and losses, as well as genome-wide views of LOH and copy number-neutral events in breast cancer. In addition, the ASCAT profiles reveal differences in aberrant tumor cell fraction, ploidy, gains, losses, LOH, and copy number-neutral events between the five previously identified molecular breast cancer subtypes. Basal-like breast carcinomas have a significantly higher frequency of LOH compared with other subtypes, and their ASCAT profiles show large-scale loss of genomic material during tumor development, followed by a whole-genome duplication, resulting in near-triploid genomes. Finally, from the ASCAT profiles, we construct a genome-wide map of allelic skewness in breast cancer, indicating loci where one allele is preferentially lost, whereas the other allele is preferentially gained. We hypothesize that these alternative alleles have a different influence on breast carcinoma development.
Indexed as
Identifiers
What OpenQuestion holds
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.