Comparison of primary neuroblastoma tumors and derivative early-passage cell lines using genome-wide SNP array analysis

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

ORGANISM(S): Homo sapiens

SUBMITTER: Samuel Volchenboum 

PROVIDER: E-GEOD-14656 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress