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.
journal_name
Cancer Resjournal_title
Cancer researchauthors
Solomon DA,Kim JS,Ressom HW,Sibenaller Z,Ryken T,Jean W,Bigner D,Yan H,Waldman Tdoi
10.1158/0008-5472.CAN-09-1055subject
Has Abstractpub_date
2009-07-15 00:00:00pages
5630-3issue
14eissn
0008-5472issn
1538-7445pii
0008-5472.CAN-09-1055journal_volume
69pub_type
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