RNA sequencing (RNA-Seq) of the NCI-60

本研究将产生多种形式的数据。这些将包括：a)存在的变体总数，b)它们在1000基因组计划或ESP5400非癌基因组中的存在或不存在，c)它们在COSMIC数据库中的存在或不存在，d)它们的SIFT评分，e)它们的POLYPHEN评分，f)它们的染色体位置，g)每个变体的类型（错义、移码、无义等），h)每个基因的总体转录水平，i)每个等位基因的表达比例（异质时），以及剪接状态。将比较发育治疗计划（DTP） 20,602种公共化合物和药物的变体和化合物活性。这种分析的版本既可以是单基因变异，也可以是基因变异的组合。将考虑这些变异中的哪些会对蛋白质产生有害影响（由SIFT或POLYPHEN评分决定，或由移码、过早停止或读透变异的存在决定）。将确定在本研究中获得的哪些变异也在癌症基因组图谱（TCGA）知识库http://tcga-data.nci.nih.gov/tcga/的临床癌症样本中发现。鉴定将由基因融合和易位进行。

Multiple forms of data will be generated from this study. These will include: a) the total number of variants present, b) their presence or absence in the 1000 Genomes Project or ESP5400 non-cancerous genomes, c) their presence or absence in the COSMIC database, d) their SIFT score, e) their POLYPHEN score, f) their chromosomal location, g) the type of each variant (missense, frameshift, nonsense, etc.), h) the overall transcript level for each gene, i) the proportion of expression of each allele (when heterogeneous), and the splicing status. Comparison will be made between the presence of variants and compound activity for the Developmental Therapeutics Program (DTP) 20,602 public compounds and drugs. Versions of this analysis for both single gene variants, as well as combinatorials of variants from a gene will be done. Consideration will be given to which of these variants are projected to have deleterious affects on the protein (as determined by either SIFT or POLYPHEN scores, or the presence of frameshift, premature stop, or read-through variants). A determination will be made as to which variants obtained in this study are also found in clinical cancer samples from The Cancer Genome Atlas (TCGA) repository at http://tcga-data.nci.nih.gov/tcga/. Identification will be made of gene fusions and translocations.