ArticleGenome biology2009
Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays.
Article in Genome biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 106 papers.
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Who cites it
106 citing papers in PubMed.
- High-resolution analysis of DNA copy number alterations in rectal cancer: correlation with metastasis, survival, and mRNA expression.Strahlentherapie und Onkologie : Organ der Deutschen Rontgengesellschaft ... [et al] · 2014Trial
- Randomised proof-of-concept phase II trial comparing targeted therapy based on tumour molecular profiling vs conventional therapy in patients with refractory cancer: results of the feasibility part of the SHIVA trial.British journal of cancer · 2014Trial
- An ANOCEF genomic and transcriptomic microarray study of the response to irinotecan and bevacizumab in recurrent glioblastomas.BioMed research international · 2014Trial
- Genomic characterization of aggressiveness in pituitary neuroendocrine tumors.Neuro-oncology · 2026Article
- Pivotal role of biallelic frequency analysis in identifying copy number alterations using genome-wide methods in tumors with a high level of aneuploidy.Journal of applied genetics · 2026Article
- Overcoming intra-tumoral heterogeneity for biomarker discovery in the high-grade serous ovarian cancer proteome.NPJ precision oncology · 2025Article
- High level of aneuploidy and recurrent loss of chromosome 11 as relevant features of somatotroph pituitary tumors.Journal of translational medicine · 2024Article
- Expanding a precision medicine platform for malignant peripheral nerve sheath tumors: New patient-derived orthotopic xenografts, cell lines and tumor entities.Molecular oncology · 2024Article
- Preclinical evaluation of CDK4 phosphorylation predicts high sensitivity of pleural mesotheliomas to CDK4/6 inhibition.Molecular oncology · 2024Article
- Homologous recombination deficiency derived from whole-genome sequencing predicts platinum response in triple-negative breast cancers.Nature communications · 2023Article
- Article
- A new tumorgraft panel to accelerate precision medicine in prostate cancer.Frontiers in oncology · 2023Article
- Oligosarcomas, IDH-mutant are distinct and aggressive.Acta neuropathologica · 2022Article
- Patient-derived xenograft models capture genomic heterogeneity in endometrial cancer.Genome medicine · 2022Article
- Integrated Genomic Analysis Identifies Driver Genes and Cisplatin-Resistant Progenitor Phenotype in Pediatric Liver Cancer.Cancer discovery · 2021Article
- A high-risk retinoblastoma subtype with stemness features, dedifferentiated cone states and neuronal/ganglion cell gene expression.Nature communications · 2021Article
- Chromosomal translocations inactivating CDKN2A support a single path for malignant peripheral nerve sheath tumor initiation.Human genetics · 2021Article
- Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL.Nature biotechnology · 2021Article
- RNA-sequencing of IDH-wild-type glioblastoma with chromothripsis identifies novel gene fusions with potential oncogenic properties.Translational oncology · 2021Article
- PLK1 inhibition exhibits strong anti-tumoral activity in CCND1-driven breast cancer metastases with acquired palbociclib resistance.Nature communications · 2020Article
46 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
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We describe a method for automatic detection of absolute segmental copy numbers and genotype status in complex cancer genome profiles measured with single-nucleotide polymorphism (SNP) arrays. The method is based on pattern recognition of segmented and smoothed copy number and allelic imbalance profiles. Assignments were verified by DNA indexes of primary tumors and karyotypes of cell lines. The method performs well even for poor-quality data, low tumor content, and highly rearranged tumor genomes.
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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.