ArticleGenome biology2011
Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity.
Article in Genome biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers, 1 of them a synthesis that pooled it.
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Who cites it
54 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure.Briefings in bioinformatics · 2022Pooled it
- Transcriptomic Subgroups in Soft Tissue Tumors Correlate with Morphologic Subtype, Genomic Features, and Outcome.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Article
- Multiomics assessment of lung adenocarcinoma subtypes defined through tumor purity-adjusted DNA methylation.Genome medicine · 2026Article
- The Role of RB1 and Secondary Genomic Changes in the Development of Spindle Cell and Pleomorphic Lipomas.Genes, chromosomes & cancer · 2025Article
- Tracing metastatic spread in pediatric solid tumors using copy number and targeted deep sequencing.The Journal of pathology · 2025Article
- Reliable on-treatment prognostication and target identification with a customized assay for circulating tumor DNA in patients with newly diagnosed pancreatic cancer.Scientific reports · 2025Observational
- Bladder cancer subtypes exhibit limited plasticity across different microenvironments and in metastases.Experimental hematology & oncology · 2025Article
- Early evolutionary branching across spatial domains predisposes to clonal replacement under chemotherapy in neuroblastoma.Nature communications · 2024Article
- CDK4 is co-amplified with either TP53 promoter gene fusions or MDM2 through distinct mechanisms in osteosarcoma.NPJ genomic medicine · 2024Article
- MDM2 amplification in rod-shaped chromosomes provides clues to early stages of circularized gene amplification in liposarcoma.Communications biology · 2024Article
- Resolving the Pathogenesis of Anaplastic Wilms Tumors through Spatial Mapping of Cancer Cell Evolution.Clinical cancer research : an official journal of the American Association for Cancer Research · 2023Article
- Clonal origin and development of high hyperdiploidy in childhood acute lymphoblastic leukaemia.Nature communications · 2023Article
- Widespread hypertranscription in aggressive human cancers.Science advances · 2022Article
- Clinically relevant treatment of PDX models reveals patterns of neuroblastoma chemoresistance.Science advances · 2022Article
- The diagnostic utility of DNA copy number analysis of core needle biopsies from soft tissue and bone tumors.Laboratory investigation; a journal of technical methods and pathology · 2022Article
- Branching Copy-Number Evolution and Parallel Immune Profiles across the Regional Tumor Space of Resected Pancreatic Cancer.Molecular cancer research : MCR · 2022Article
- Article
- Tracing the evolution of aneuploid cancers by multiregional sequencing with CRUST.Briefings in bioinformatics · 2021Article
- Somatic Hypomethylation of Pericentromeric SST1 Repeats and Tetraploidization in Human Colorectal Cancer Cells.Cancers · 2021Article
- Sister chromatid cohesion defects are associated with chromosomal copy number heterogeneity in high hyperdiploid childhood acute lymphoblastic leukemia.Genes, chromosomes & cancer · 2021Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We describe a bioinformatic tool, Tumor Aberration Prediction Suite (TAPS), for the identification of allele-specific copy numbers in tumor samples using data from Affymetrix SNP arrays. It includes detailed visualization of genomic segment characteristics and iterative pattern recognition for copy number identification, and does not require patient-matched normal samples. TAPS can be used to identify chromosomal aberrations with high sensitivity even when the proportion of tumor cells is as low as 30%. Analysis of cancer samples indicates that TAPS is well suited to investigate samples with aneuploidy and tumor heterogeneity, which is commonly found in many types of solid tumors.
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