ArticleGenome research2004
High-resolution analysis of DNA copy number using oligonucleotide microarrays.
Article in Genome research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 122 papers.
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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
122 citing papers in PubMed.
- Genomic structural variants analysis in leukemia by a novel cytogenetic technique: Optical genome mapping.Cancer science · 2024Review
- Evaluation and Analysis of Absence of Homozygosity (AOH) Using Chromosome Analysis by Medium Coverage Whole Genome Sequencing (CMA-seq) in Prenatal Diagnosis.Diagnostics (Basel, Switzerland) · 2023Article
- Cancer Genetics and Clinical Research.Journal of personalized medicine · 2022Article
- Progress in Methods for Copy Number Variation Profiling.International journal of molecular sciences · 2022Review
- Deep whole-genome sequencing of 3 cancer cell lines on 2 sequencing platforms.Scientific reports · 2019Article
- High-Density RNA Microarrays Synthesized In Situ by Photolithography.Angewandte Chemie (International ed. in English) · 2018Article
- Prenatal diagnosis by chromosomal microarray analysis.Fertility and sterility · 2018Review
- Exploring the key genes and pathways in enchondromas using a gene expression microarray.Oncotarget · 2017Article
- aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations.PloS one · 2017Article
- Copy number variation in archival melanoma biopsies versus benign melanocytic lesions.Cancer biomarkers : section A of Disease markers · 2016Article
- Computational characterisation of cancer molecular profiles derived using next generation sequencing.Contemporary oncology (Poznan, Poland) · 2015Review
- ENVE: a novel computational framework characterizes copy-number mutational landscapes in colorectal cancers from African American patients.Genome medicine · 2015Article
- Somatic mosaicism in the human genome.Genes · 2014Review
- Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity.Bioinformatics (Oxford, England) · 2014Article
- Cell line modeling for systems medicine in cancers (review).International journal of oncology · 2014Review
- Progenetix: 12 years of oncogenomic data curation.Nucleic acids research · 2014Article
- Evaluation of real-time quantitative PCR as a standard cytogenetic diagnostic tool for confirmation of microarray (aCGH) results and determination of inheritance.Genetic testing and molecular biomarkers · 2013Article
- Genomic approaches to chronic lymphocytic leukemia.Hematology/oncology clinics of North America · 2013Review
- Patchwork: allele-specific copy number analysis of whole-genome sequenced tumor tissue.Genome biology · 2013Article
- Overview of DNA microarrays: types, applications, and their future.Current protocols in molecular biology · 2013Article
62 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genomic copy number alterations are a feature of many human diseases including cancer. We have evaluated the effectiveness of an oligonucleotide array, originally designed to detect single-nucleotide polymorphisms, to assess DNA copy number. We first showed that fluorescent signal from the oligonucleotide array varies in proportion to both decreases and increases in copy number. Subsequently we applied the system to a series of 20 cancer cell lines. All of the putative homozygous deletions (10) and high-level amplifications (12; putative copy number >4) tested were confirmed by PCR (either qPCR or normal PCR) analysis. Low-level copy number changes for two of the lines under analysis were compared with BAC array CGH; 77% (n = 44) of the autosomal chromosomes used in the comparison showed consistent patterns of LOH (loss of heterozygosity) and low-level amplification. Of the remaining 10 comparisons that were discordant, eight were caused by low SNP densities and failed in both lines. The studies demonstrate that combining the genotype and copy number analyses gives greater insight into the underlying genetic alterations in cancer cells with identification of complex events including loss and reduplication of loci.
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