This DAC controls 225 datasets:

Dataset Accessionsort descending Technology Samples Description
EGAD00001000948 Illumina HiSeq 2000; 6 A comparison of the somatic variation present in a primary colorectal tumour and three different liver metastases from the same patient.
EGAD00001000965 Illumina HiSeq 2000; 331 Cancers are ecosystems of genetically related clones, competing across space and time for limited resources. To understand the clonal structure of primary breast cancer, we applied genome and targeted sequencing to 295 samples from 49 patients’ tumors. The extent of subclonal diversification varied considerably among patients and encompassed many spatial patterns, including local growth, intraductal dissemination and clonal intermixture. Landmarks of disease progression, such as acquiring invasive or metastatic potential, arose within detectable subclones of antecedent lesions, suggesting that subclonal mutations could be relevant if actionable. No defined temporal order of mutation was evident, with the commonest genes, including PIK3CA, TP53, BRCA2, PTEN and MYC, mutated early in some, late in others, often exhibiting parallel evolution across subclones. Signatures of homologous recombination deficiency correlated with response to neoadjuvant chemotherapy. Thus, the interplay of mutation, growth and competition drives clonal structures of breast cancer that are complex, variable across patients and clinically relevant.
EGAD00001000980 Illumina MiSeq; 144 This study involves a forward genetic screen to identify common insertion sites in drug resistant clones. We will be utilising piggybac transposon systems in order to generate multiple drug resistant clones in a range of human cancer cell lines.
EGAD00001000990 Illumina HiSeq 2000; 11 mRNA-Seq on total RNA from primary osteoblastomas and phosphaturic mesenchymal tumours, focussing on fusion transcript expression
EGAD00001000998 Illumina HiSeq 2000; 24 Targeted capture of exonic and intronic regions of interest for the study of genomic alterations in multiple myeloma.
EGAD00001001014 Illumina HiSeq 2000; 2597
EGAD00001001015 Illumina HiSeq 2000; 76
EGAD00001001017 Illumina HiSeq 2000; 31 DNA extracted from multiple biopsies taken from different areas of primary lung tumours will be subjected to targeted re-sequencing and analysed in order to assess intra-tumour heterogeneity with respect to mutations in a selection of cancer related genes.
EGAD00001001018 Illumina HiSeq 2000; 374 The samples will be sequenced for a targeted panel of cancer relevant genes (n ~ 370) and analysed for somatic mutations. This dataset contains all the data available for this study on 2014-09-24
EGAD00001001028 Illumina MiSeq; 18 DNA belonging to 16 tumour/normal samples were treated with bisulfite, then up to 5 different bisulfite PCRs were performed in each one of the samples. Amplicons form the same sample were pooled and submitted to sequencing on a MiSeq platform.
EGAD00001001039 Illumina HiSeq 2000; 1072 Genomic characterisation of a large series of cancer cell lines.
EGAD00001001041 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 305 Comparison of genomic rearrangements and DNA methylation patterns between different foci of multiple synchronous (multifocal and multicentric) invasive breast cancers.
EGAD00001001046 Illumina HiSeq 2000; 33 We propose to biopsy 20 consented BRAF mutant melanoma patients at Addenbrooke's Hospital pre-treatment with vemurafenib and also upon the development of resistant disease, with the aim of using exome sequence and SNP6 data to identify novel sequence variants and copy number alterations that can be used to validate observed resistance mechanisms in our cell line models and also to use these models to inform as to likely candidate small molecule inhibitors to overcome resistance and that could be tested in the clinical trial setting.
EGAD00001001050 Illumina HiSeq 2000; 8 We propose to biopsy 20 consented BRAF mutant melanoma patients at Addenbrooke's Hospital pre-treatment with vemurafenib and also upon the development of resistant disease, with the aim of using exome sequence and SNP6 data to identify novel sequence variants and copy number alterations that can be used to validate observed resistance mechanisms in our cell line models and also to use these models to inform as to likely candidate small molecule inhibitors to overcome resistance and that could be tested in the clinical trial setting.
EGAD00001001061 Illumina MiSeq; 4 This experiment is to inform us of the validity of using pre-made library material to perform a bespoke pulldown experiment to validate the mutations found between the whole genome sequencing of the DNA from the same individuals cancer and normal material. This is to identify the valid and informative mutations in cancer genomes.

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