Project description:The data in this submission relate to whole exome sequencing from murine ovarian cancer cell line ID8. All sequencing was performed by Beckman Coulter Genomics, Grenoble, France in February 2013.
Project description:This study involves characterization of four head and neck cancer cell lines -- NT8e, OT9, AW13516 and AW8507, established from Indian head and neck cancer patients, using SNP arrays, whole exome and whole transcriptome sequencing.
Project description:Cancer is a disease of the genome. Many genomic abnormalities have been found in a variety of cancer types, which are believed to be attributable to tumorigenesis as well as resistance to treatment and recurrence. Genomic heterogeneity in the same type of cancer or within a tumor reveals the complexity of cancer biology so that intratumor heterogeneity has become an inherent feature of cancer. In this study, we use whole-exome sequencing and array comparative genomic hybridization technology to examine the mutational profiling and copy number changes from multi-region samples within an esophageal cancer in order to understand the genomic phylogeny in the evolution of intratumor heterogeneity in esophageal cancer. Overall design: Four spatially separated tumor samples and a fifth adjacent non-tumor sample were harvested from two patients with esophageal squamous cell carcinomas. An additional, local metastatic sample was obtained from one of the patients. DNAs from these samples were subjected to whole-exome sequencing and array comparative genomic hybridization. Comprehensive bioinformatic analyses were performed.
Project description:Of the multiple anatomical sites represented in oral cancer, squamous cell carcinoma of the tongue (TSCC) shows the highest incidence among younger age group. Chewing betel leaf, areca nut & slaked lime and smoking tobacco are common practises in India which have direct clinical implication in TSCC carcinogenesis. Here, for the first time we define the landscape of genomic alterations in TSCC from the Indian diaspora which would help to identify novel therapeutic targets for clinical intervention and define the genetic basis for TSCC. We performed high throughput sequencing of fifty four tongue samples using whole exome sequencing (n=47, 23 paired normal tumor and 1 unpaired) and transcriptome sequencing (n=17, 10 tumor and 5 normal). Mutation, copy number analysis were carried out using exome sequencing data and transcriptome analysis provided expressed genes and transcript fusions in tongue cancer patients. Further, integrated analysis were performed to identify biologically relevant alterations. Our preliminary analysis revealed presence of most frequently altered mutations in TSCC which includes mutations in TP53, NOTCH1, CDKN2A, USP6, KMT2D etc, consistent with literature. We observed high frequency of CG/T(GC/A) transversions in non-CpG islands, a signature associated with tobacco exposure. Somatic copy number analysis revealed copy number gain in known hallmarks such as CCND1, MYC, ORAOV1 genes along with copy number alteration in novel genes. Significant positive correlation was observed in the genes harbouring copy number gains and showing increased expression.
Project description:Whole exome sequencing of a cell line derived from an Rb1 and Trp53 genetically engineered mouse model (GEMM) to assess the baseline copy number landscape of the cells prior to experimental modification.
Project description:DNA was isolated from Apcmin/+;KrasLSL-G12D/+;VillinCre;Lgr5DTReGFP (AKVL), Apcmin/+;KrasLSL-G12D/+;VillinCre;Lgr5DTReGFP;p53KO (AKVPL) and Apcmin/+;KrasLSL-G12D/+;VillinCre;Lgr5DTReGFP;p53KO,Smad4KO (AKVPSL) organoids as well as the spleen of the AKVL donor animal The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech. Overall design: Whole exome sequencing of murine derived intestinal organoids containing increasing number of CRC driver mutations was performed to identify potential mutations in coding regions that were introduced by off-target binding of the CRISPR-Cas9 complex.