Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA112343 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description: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 cell lines compared to the matched tumor samples (mean increase 3.2% ± 1.9%). We have developed an algorithm that shows that the presence of stroma contributes to under-reporting of LOH and copy number loss (CNL). Notable findings in this sample set were uniparental disomy (UPD) of chromosome arms 11p, 1q, 14q, and 15q and a novel area of amplification on chromosome band 11p15. Our analysis demonstrates that LOH was identified significantly more often in derived cell lines compared to the original tumor samples. While these may in part be due to clonal selection during adaptation to tissue culture, our study indicates contamination by normal stromal elements may be a major contributing factor in underestimation of LOH and CNL events. Keywords: genome wide SNP analysis Nine human neuroblastoma tumor samples with paired blood samples and derivative cell lines
2009-01-31 | E-GEOD-14656 | biostudies-arrayexpress
Project description: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 cell lines compared to the matched tumor samples (mean increase 3.2% ± 1.9%). We have developed an algorithm that shows that the presence of stroma contributes to under-reporting of LOH and copy number loss (CNL). Notable findings in this sample set were uniparental disomy (UPD) of chromosome arms 11p, 1q, 14q, and 15q and a novel area of amplification on chromosome band 11p15. Our analysis demonstrates that LOH was identified significantly more often in derived cell lines compared to the original tumor samples. While these may in part be due to clonal selection during adaptation to tissue culture, our study indicates contamination by normal stromal elements may be a major contributing factor in underestimation of LOH and CNL events. Keywords: genome wide SNP analysis
2009-01-31 | GSE14656 | GEO
Project description:<p>Early passage breast cancer xenografts have been proposed as alternatives to cell lines as model systems for studying the basic biology of tumors and for advancing therapy development. This study explores the relatedness of primary disease genomes to their matched xenotransplants. Using paired-end massively parallel sequencing 17 matched progenitor tumor, xenograft and normal trios were sequenced to at least 30-fold coverage with diploid coverage of at least 95% of the genome as determined by SNP array concordance. RNA sequence was generated from the xenograft tumors. The xenografts were derived from a spectrum of tumor samples from patients with both early and advanced breast cancer.</p>
| phs000611 | dbGaP
Project description:microRNA array of 4 cell lines: WI-38 primary fibroblasts (“Control”), slow growers (early passage after immortalization, Slow), fast growers (extensive passaging after immortalization) and fast growers transformed by constitutively activated mutant H-RasV12 (“Ras”)
2016-01-29 | GSE77338 | GEO
Project description:Reports on common mutations in neuroendocrine tumors (NET) are rare and clonality of NET metastases has not been investigated in this tumor entity yet. We selected a NET and a the corresponding lymph node and liver metastases as well as the derivative cell lines to screen for somatic mutations in the primary NET and to track the fate of genetic changes (by Affymetrix SNP 6.0 micorarray and targeted resequencing by 454 GS FLX) and during metastasis and in vitro progression. using Affymetrix SNP 6.0 Arrays.
2012-07-17 | GSE39371 | GEO
Project description:TERT promoter muatations occur frequently in tumors of various origin. We here accessed the frequency of TERT pomoter mutations in 131 human primary neuroblastomas and 20 human neuroblastoma cell lines. No TERT promoter mutations were found in the 131 primary neuroblastomas. However, in the three cell lines SH-SY5Y, SH-EP and SK-N-SH a TERT promoter mutation was detected. Sanger sequencing indicated a homozygous mutation. To confirm loss of heterozygosity (LOH) we performed Affymetrix CytoScanHD SNP arrays. Indeed LOH could be confirmed.
2015-03-03 | GSE66422 | GEO
Project description:Expression profiling in Neuroblastoma Primary tumors and Cell lines
| PRJNA120953 | ENA
Project description:Reports on common mutations in neuroendocrine tumors (NET) are rare and clonality of NET metastases has not been investigated in this tumor entity yet. We selected a NET and a the corresponding lymph node and liver metastases as well as the derivative cell lines to screen for somatic mutations in the primary NET and to track the fate of genetic changes (by Affymetrix SNP 6.0 micorarray and targeted resequencing by 454 GS FLX) and during metastasis and in vitro progression. using Affymetrix SNP 6.0 Arrays. Affymetrix SNP 6.0 arrays were performed according to the manufacturer's directions on DNA extracted from cryo material or cell lines. Copy number analysis of Affymetrix SNP 6.0 arrays was performed for 4 samples. 60 samples from HapMap database were used as references for copy number inference.
2012-07-16 | E-GEOD-39371 | biostudies-arrayexpress