title: Quantification of normal cell fraction and copy number neutral LOH in clinical lung cancer samples using SNP array data.
abstract: BACKGROUND
  Technologies 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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  Genome-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.
authors: Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
authors: Hanna
authors: H
authors: Göransson
authors: Karolina
authors: K
authors: Edlund
authors: Maria
authors: M
authors: Rydåker
authors: Markus
authors: M
authors: Rasmussen
authors: Johan
authors: J
authors: Winquist
authors: Simon
authors: S
authors: Ekman
authors: Michael
authors: M
authors: Bergqvist
authors: Andrew
authors: A
authors: Thomas
authors: Mats
authors: M
authors: Lambe
authors: Richard
authors: R
authors: Rosenquist
authors: Lars
authors: L
authors: Holmberg
authors: Patrick
authors: P
authors: Micke
authors: Johan
authors: J
authors: Botling
authors: Anders
authors: A
authors: Isaksson
mesh_terms: D000483:Alleles; D002289:Carcinoma, Non-Small-Cell Lung / Q000235:genetics* / Q000378:metabolism; D045744:Cell Line, Tumor; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic; D005838:Genotype; D006579:Heterozygote; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D007834:Lasers; D019656:Loss of Heterozygosity; D008175:Lung Neoplasms / Q000235:genetics* / Q000378:metabolism; D042282:Microdissection; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide