ArticleNucleic acids research2008
Identification of cancer genes using a statistical framework for multiexperiment analysis of nondiscretized array CGH data.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 34 papers, 1 of them a synthesis that pooled it.
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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.
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Who cites it
34 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Comparative oncogenomics identifies combinations of driver genes and drug targets in BRCA1-mutated breast cancer.Nature communications · 2019Pooled it
- FocalScan: Scanning for altered genes in cancer based on coordinated DNA and RNA change.Nucleic acids research · 2016Article
- Article
- BRCA1185delAG tumors may acquire therapy resistance through expression of RING-less BRCA1.The Journal of clinical investigation · 2016Article
- RNF138 interacts with RAD51D and is required for DNA interstrand crosslink repair and maintaining chromosome integrity.DNA repair · 2016Article
- Identification of cancer-driver genes in focal genomic alterations from whole genome sequencing data.Scientific reports · 2016Article
- Identification of Copy Number Aberrations in Breast Cancer Subtypes Using Persistence Topology.Microarrays (Basel, Switzerland) · 2015Article
- Multiscale representation of genomic signals.Nature methods · 2014Article
- A bayesian integrative model for genetical genomics with spatially informed variable selection.Cancer informatics · 2014Article
- Lack of genomic heterogeneity at high-resolution aCGH between primary breast cancers and their paired lymph node metastases.PloS one · 2014Article
- Functional analysis of human cancer-associated genes and their association with the testes and epididymis.Oncology letters · 2013Article
- A scale-space method for detecting recurrent DNA copy number changes with analytical false discovery rate control.Nucleic acids research · 2013Article
- Article
- Copynumber: Efficient algorithms for single- and multi-track copy number segmentation.BMC genomics · 2012Article
- Comparative oncogenomics implicates the neurofibromin 1 gene (NF1) as a breast cancer driver.Genetics · 2012Article
- Genome-wide identification of significant aberrations in cancer genome.BMC genomics · 2012Article
- Matching of array CGH and gene expression microarray features for the purpose of integrative genomic analyses.BMC bioinformatics · 2012Article
- Fenton reaction induced cancer in wild type rats recapitulates genomic alterations observed in human cancer.PloS one · 2012Article
- Comparative analysis of methods for identifying recurrent copy number alterations in cancer.PloS one · 2012Article
- TAGCNA: a method to identify significant consensus events of copy number alterations in cancer.PloS one · 2012Article
Corrections and comments
- Erratum issued
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Tumor formation is in part driven by DNA copy number alterations (CNAs), which can be measured using microarray-based Comparative Genomic Hybridization (aCGH). Multiexperiment analysis of aCGH data from tumors allows discovery of recurrent CNAs that are potentially causal to cancer development. Until now, multiexperiment aCGH data analysis has been dependent on discretization of measurement data to a gain, loss or no-change state. Valuable biological information is lost when a heterogeneous system such as a solid tumor is reduced to these states. We have developed a new approach which inputs nondiscretized aCGH data to identify regions that are significantly aberrant across an entire tumor set. Our method is based on kernel regression and accounts for the strength of a probe's signal, its local genomic environment and the signal distribution across multiple tumors. In an analysis of 89 human breast tumors, our method showed enrichment for known cancer genes in the detected regions and identified aberrations that are strongly associated with breast cancer subtypes and clinical parameters. Furthermore, we identified 18 recurrent aberrant regions in a new dataset of 19 p53-deficient mouse mammary tumors. These regions, combined with gene expression microarray data, point to known cancer genes and novel candidate cancer genes.
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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.