ArticlePloS one2009
Quantification of normal cell fraction and copy number neutral LOH in clinical lung cancer samples using SNP array data.
Article in PloS one, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 27 citations in OpenAlex.
- RefCell: multi-dimensional analysis of image-based high-throughput screens based on 'typical cells'.BMC bioinformatics · 2018Article
- Three dimensional microfluidic cell arrays for ex vivo drug screening with mimicked vascular flow.Analytical chemistry · 2014Article
- Article
- TAGCNA: a method to identify significant consensus events of copy number alterations in cancer.PloS one · 2012Article
- Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity.Genome biology · 2011Article
- Array-based genomic screening at diagnosis and during follow-up in chronic lymphocytic leukemia.Haematologica · 2011Article
- Renal cell carcinoma primary cultures maintain genomic and phenotypic profile of parental tumor tissues.BMC cancer · 2011Article
- BACOM: in silico detection of genomic deletion types and correction of normal cell contamination in copy number data.Bioinformatics (Oxford, England) · 2011Article
- High-density screening reveals a different spectrum of genomic aberrations in chronic lymphocytic leukemia patients with 'stereotyped' IGHV3-21 and IGHV4-34 B-cell receptors.Haematologica · 2010Article
- TumorBoost: normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays.BMC bioinformatics · 2010Article
- A statistical approach for detecting genomic aberrations in heterogeneous tumor samples from single nucleotide polymorphism genotyping data.Genome biology · 2010Article
- Article
Corrections and comments
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Authors and funding
14 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTechnologies based on DNA microarrays have the potential to provide detailed information on genomic aberrations in tumor cells. In practice a major obstacle for quantitative detection of aberrations is the heterogeneity of clinical tumor tissue. Since tumor tissue invariably contains genetically normal stromal cells, this may lead to a failure to detect aberrations in the tumor cells. PRINCIPAL FINDING: Using SNP array data from 44 non-small cell lung cancer samples we have developed a bioinformatic algorithm that accurately models the fractions of normal and tumor cells in clinical tumor samples. The proportion of normal cells in combination with SNP array data can be used to detect and quantify copy number neutral loss-of-heterozygosity (CNNLOH) in the tumor cells both in crude tumor tissue and in samples enriched for tumor cells by laser capture microdissection.
conclusionGenome-wide quantitative analysis of CNNLOH using the CNNLOH Quantifier method can help to identify recurrent aberrations contributing to tumor development in clinical tumor samples. In addition, SNP-array based analysis of CNNLOH may become important for detection of aberrations that can be used for diagnostic and prognostic purposes.
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