Comparison of primary neuroblastoma tumors and derivative early-passage cell lines using genome-wide single nucleotide polymorphism array analysis.

ABSTRACT: Stromal contamination is one of the major confounding factors in the analysis of solid tumor samples by single nucleotide polymorphism (SNP) arrays. As we propose to use genome-wide SNP microarray analysis as a diagnostic platform for neuroblastoma, the sensitivity, specificity, and accuracy of these studies must be optimized. To investigate the effects of stromal contamination, we derived early-passage cell lines from nine primary tumors and compared their genomic signature with that of the primary tumors using 100K SNP arrays. The average concordance between tumor and cell line for raw loss of heterozygosity (LOH) calls was 96% (range, 91-99%) and for raw copy number alterations, 71% (range, 43-87%). In general, there were a larger number of LOH events identified in the cell lines compar

SUBMITTER: Volchenboum SL 

PROVIDER: S-EPMC2739280 | biostudies-literature | 2009 May

REPOSITORIES: biostudies-literature