Sample Type Bias in the Analysis of Cancer Genomes Export

@article{citeulike:5156559, abstract = {There is widespread agreement that cancer gene discovery requires high-quality tumor samples. However, whether primary tumors or cultured samples are superior for cancer genomics has been a longstanding subject of debate. This debate has recently become more important because federally funded cancer genomics has been centralized under The Cancer Genome Atlas, which has chosen to focus exclusively on primary tumors. Here, we provide a data-driven "perspective" on the effect of sample type selection on cancer genomics research. We show that, in the case of glioblastoma multiforme, primary tumors and xenografts are best for the identification of amplifications, whereas xenografts and cell lines are superior for the identification of homozygous deletions. We also note that many of the most important oncogenes and tumor suppressor genes have been discovered through the use of cell lines and xenografts, and highlight the lack of published evidence supporting the dogma that ex vivo culture generates artifactual genetic lesions. Based on this analysis, we suggest that cancer genomics projects such as The Cancer Genome Atlas should include a variety of sample types such as xenografts and cell lines in their integrated genomic analysis of cancer. [Cancer Res 2009;69(14):5630-3] 10.1158/0008-5472.CAN-09-1055}, author = {Solomon, David A. and Kim, Jung-Sik and Ressom, Habtom W. and Sibenaller, Zita and Ryken, Timothy and Jean, Walter and Bigner, Darell and Yan, Hai and Waldman, Todd}, citeulike-article-id = {5156559}, citeulike-linkout-0 = {http://dx.doi.org/10.1158/0008-5472.CAN-09-1055}, citeulike-linkout-1 = {http://cancerres.aacrjournals.org/cgi/content/abstract/69/14/5630}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19567670}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19567670}, day = {15}, doi = {10.1158/0008-5472.CAN-09-1055}, journal = {Cancer Res}, keywords = {bias, biobank, circ\_dna, genetics, specimen, target\_dna}, month = {July}, number = {14}, pages = {5630--5633}, posted-at = {2009-07-15 09:08:16}, priority = {2}, title = {Sample Type Bias in the Analysis of Cancer Genomes}, url = {http://dx.doi.org/10.1158/0008-5472.CAN-09-1055}, volume = {69}, year = {2009} }

TY - JOUR ID - citeulike:5156559 L3 - citeulike-article-id:5156559 N2 - There is widespread agreement that cancer gene discovery requires high-quality tumor samples. However, whether primary tumors or cultured samples are superior for cancer genomics has been a longstanding subject of debate. This debate has recently become more important because federally funded cancer genomics has been centralized under The Cancer Genome Atlas, which has chosen to focus exclusively on primary tumors. Here, we provide a data-driven "perspective" on the effect of sample type selection on cancer genomics research. We show that, in the case of glioblastoma multiforme, primary tumors and xenografts are best for the identification of amplifications, whereas xenografts and cell lines are superior for the identification of homozygous deletions. We also note that many of the most important oncogenes and tumor suppressor genes have been discovered through the use of cell lines and xenografts, and highlight the lack of published evidence supporting the dogma that ex vivo culture generates artifactual genetic lesions. Based on this analysis, we suggest that cancer genomics projects such as The Cancer Genome Atlas should include a variety of sample types such as xenografts and cell lines in their integrated genomic analysis of cancer. [Cancer Res 2009;69(14):5630-3] 10.1158/0008-5472.CAN-09-1055 IS - 14 JF - Cancer Res EP - 5633 TI - Sample Type Bias in the Analysis of Cancer Genomes VL - 69 SP - 5630 KW - bias KW - biobank KW - circ_dna KW - genetics KW - specimen KW - target_dna AU - Solomon, David AU - Kim, Jung-Sik AU - Ressom, Habtom AU - Sibenaller, Zita AU - Ryken, Timothy AU - Jean, Walter AU - Bigner, Darell AU - Yan, Hai AU - Waldman, Todd PY - 2009/07/15/ UR - http://dx.doi.org/10.1158/0008-5472.CAN-09-1055 ER -