5731 results for "canc*"

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• Genentech gastric cell line sequencing

  RNAseq and exome sequencing data of gastric cancer cell lines.

  Dataset EGAD00001001013

• PLCRC study

  Genomic libraries (500 bps) will be generated from total genomic DNA derived from Colorectal cancer patients and subjected to short paired end sequencing on the llumina platform. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.

  Dataset EGAD00001000947

• Subclonal diversification of primary breast cancer

  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.

  Dataset EGAD00001000965

• Cancer-Normal chronic myeloid leukaemia sequencing data for "A comparative analysis of algorithms for somatic SNV detection in cancer", Bioinformatics 29 (2013) 2223

  This dataset contains the fastq sequencing data collected from bone marrow DNA of a chronic myeloid leukaemia patient at time of diagnosis.

  Dataset EGAD00001000967

• Distinct evolutionary trajectories of primary high grade serous ovarian cancers revealed through spatial mutational profiling

  High-grade serous ovarian cancer (HGSC) is characterized by poor outcome, often attributed to emergence of treatment-resistant sub-clones. We sought to measure the degree of genomic diversity within primary, untreated HGSC to examine the natural state of tumor evolution prior to therapy. We performed exome sequencing, copy number analysis, targeted amplicon deep sequencing and gene expression profiling on thirty-one spatially and temporally separated HGSC tumor specimens (six patients) including ovarian masses, distant metastases, and fallopian tube lesions. We found widespread intra-tumoral variation in mutation, copy number, and gene expression profiles, with key driver alterations in genes present in only a subset of samples (e.g. PIK3CA, CTNNB1, NF1). On average, only 51.5% of mutations were present in every sample of a given case (range: 10.2% to 91.4%), with TP53 as the only somatic mutation consistently present in all samples. Complex segmental aneuploidies, such as whole genome doubling, were present in a subset of samples from the same individual, with divergent copy number changes segregating independently of point mutation acquisition. Reconstruction of evolutionary histories showed one patient with mixed HGSC and endometrioid histology with common etiologic origin in the fallopian tube and subsequent selection of different driver mutations in the histologically distinct samples. In this patient, we observed mixed cell populations in the early fallopian tube lesion, indicating diversity arises at early stages of tumorigenesis. Our results reveal that HGSC exhibit highly individual evolutionary trajectories and diverse genomic tapestries prior to therapy, exposing an essential biological characteristic to inform future design of personalized therapeutic solutions and investigation of drug resistance mechanisms.

  Dataset EGAD00001000974

• Harnessing transposons for drug resistance gene discovery in cancer

  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.

  Dataset EGAD00001000980

• 65 prostate cancer cases wgs sequencing

  65 prostate cancer cases wgs sequencing

  Dataset EGAD00001000983

• Metastatic Prostate Follow Up

  Validation/deeper sequencing for metastatic prostate cancer samples

  Dataset EGAD00001000988

• Metastatic Prostate Follow Up 2

  Validation/deeper sequencing for metastatic prostate cancer samples

  Dataset EGAD00001000989

• 65 prostate cancer cases wgs sequencing

  65 prostate cancer cases wgs sequencing

  Dataset EGAD00001001004

• Exome sequencing

  Exome sequencing of peripheral blood from 4 individuals of a family with familial colorectal cancer type X

  Dataset EGAD00001001009

• Somatic cancer gene mutation screening

  Sequencing of colorectal tumors and normal tissue using Ion AmpliSeq Cancer Hotspot Panel V2

  Dataset EGAD00001001010

• Lung Multi-site Targeted Sequence Capture

  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.

  Dataset EGAD00001001017

• Metastatic breast cancer targeted gene screen (2014-09-24)

  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

  Dataset EGAD00001001018

• OncoCis: Annotation of cis-regulatory mutations in cancer

  RNA-seq dataset used for the validation of CDK6 cis-regulatory mutation annotated by OncoCis. NB bam files for manuscript A_Proteomic_Chronology_of_Gene_Expression_through_the_Cell_Cycle_in_Human_Myeloid_Leukemia_Cells are now available at the following link:http://www.ebi.ac.uk/ena/data/view/ERP008483

  Dataset EGAD00001001019

• Bladder cancer sequencing data

  Dataset EGAD00001001036

• Cancer Cell Line Exome Sequencing

  Genomic characterisation of a large series of cancer cell lines.

  Dataset EGAD00001001039

• Multifocal Breast Project

  Comparison of genomic rearrangements and DNA methylation patterns between different foci of multiple synchronous (multifocal and multicentric) invasive breast cancers.

  Dataset EGAD00001001041

• MDS 5q- exome reads

  Cancer exome reads consisting of FASTQ paired end reads from bone marrow samples

  Dataset EGAD00001001058

• Whole exome sequence of biliary tract cancer

  Fastq files of 239 samples of biliary tract cancer

  Dataset EGAD00001001076

• Targeted Pulldown Validation of mutations found in whole genome sequencing

  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.

  Dataset EGAD00001001061

• Angiosarcoma targeted pulldown cancer gene panel

  Extension of angiosarcoma whole genome sequencing study

  Dataset EGAD00001001064

• Dynamics of genomic clones in breast cancer patient xenografts at single cell resolution

  Dynamics of genomic clones in breast cancer patient xenografts at single cell resolution

  Dataset EGAD00001001066

• Chordoma Extension (known cancer genes)

  Extension analysis to pursue candidate genes of interest in chordoma

  Dataset EGAD00001001239

• Use of Deep Sequencing to Dectect Clonal Mutations In Sun Exposed Skin Epidermis

  This study aims to define the landscape of somatic mutations in sun exposed human skin by deep sequencing, analyse their frequency and use the data to infer the effect of mutations on proliferating cell behaviour. The frequency of each mutation will reflect the size of the clone of cells in the tissue sample. By analyzing small samples, clones with as few as 100 cells will be detectable. Allele frequency distributions for each mutation will be used to infer cell fate using published methods (Klein et al. 2010). This study will shed unprecedented light on the early clonal events that lead to the emergence of cancer.

  Dataset EGAD00001001090

• Cancer-associated genome-wide hypomethylation and copy number aberrations

  Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing

  Dataset EGAD00001001093

• WGS and WES of 78 pairs Chinese gastric cancer

  Gastric Cancer (GC) is a highly heterogeneous disease. To identify potential clinically actionable therapeutic targets that may inform individualized treatment strategies, we performed whole-exome sequencing on 78 GCs of differing histologies and anatomic locations, as well as whole-genome sequencing on two GC cases, each with 3 primary tumours and 2 matching lymph node metastases. The data showed two distinct GC subtypes with either high-clonality (HiC) or low-clonality (LoC).

  Dataset EGAD00001001118

• FFPE Normal Panel V3 Cancer Panel

  FFPE normal panel generation for use with V3 cancer panel 0618521

  Dataset EGAD00001001122

• WGS of Asian lung cancers

  VCF files of somatic variants from tumor-normal pairs of Asian lung cancer patients

  Dataset EGAD00001001240

• Validation for human early embryonic substitutions (2017-05-11)

  PCR and MiSeq validation for early embryonic substitution candidates from 400 Breast cancer patients This dataset contains all the data available for this study on 2017-05-11.

  Dataset EGAD00001003332

• ICR96 exon CNV validation series

  A resource for assessment of exon CNV calling methods in targeted NGS data, we here present the ICR96 exon CNV validation series. The dataset includes high-quality sequencing data from a targeted NGS assay (the TruSight Cancer Panel) together with Multiplex Ligation-dependent Probe Amplification (MLPA) results for 96 independent samples. 66 samples contain at least one validated exon CNV and 30 samples have validated negative results for exon CNVs in 26 genes. The dataset includes 46 exon CNVs in BRCA1, BRCA2, TP53, MLH1, MSH2, MSH6, PMS2, EPCAM and PTEN, giving excellent representation of the cancer predisposition genes most frequently tested in clinical practice. Moreover, the validated exon CNVs include 25 single exon CNVs the most difficult exon CNV to detect.

  Dataset EGAD00001003335

• RNA-seq and WGS data of MB-0152

  Identification of fusion transcripts by RNA-sequencing and Whole genome sequencing of a breast cancer patient sample (METABRIC ID MB-0152)

  Dataset EGAD00001003342

• Recalibrated whole-exome sequencing alignment files of Saudi papillary thyroid cancer

  The dataset consists of samples from papillary thyroid cancer patients. A total of 181 DNA samples from blood/normal and cancer tissue are subjected to whole exome sequencing using Illumina. The fastq files generated were aligned with reference genome ‘hg19’, duplicates were marked, realignment around indels and quality recalibration were performed to produce good quality variants. The recalibrated “.bam” files are included with this dataset.

  Dataset EGAD00001003358

• EPO2_Illumina_RNA_XEN

  RNAseq on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from colorectal cancer primary tumor sample (EPO2_cohort)

  Dataset EGAD00001003362

• EPO2_Illumina_WXS_XEN

  Whole-exome sequencing on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from colorectal cancer primary tumor sample (EPO2_cohort)

  Dataset EGAD00001003363

• OT2_Illumina_RNA_MET

  RNAseq on Illumina HiSeq2000/2500 of colorectal cancer metastasis sample (OT2_cohort)

  Dataset EGAD00001003364

• OT2_Illumina_RNA_MET_CELL

  RNAseq on Illumina HiSeq2000/2500 of PDO culture derived from colorectal cancer metastasis sample (OT2_cohort)

  Dataset EGAD00001003365

• OT2_Illumina_RNA_MET_XEN

  RNAseq on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from colorectal cancer metastasis sample (OT2_cohort)

  Dataset EGAD00001003366

• OT2_Illumina_RNA_T

  RNAseq on Illumina HiSeq2000/2500 of colorectal cancer primary tumor sample (OT2_cohort)

  Dataset EGAD00001003367

• OT2_Illumina_RNA_T_CELL

  RNAseq on Illumina HiSeq2000/2500 of PDO culture derived from colorectal cancer primary tumor sample (OT2_cohort)

  Dataset EGAD00001003368

• OT2_Illumina_RNA_T_XEN

  RNAseq on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from colorectal cancer primary tumor sample (OT2_cohort)

  Dataset EGAD00001003369

• OT2_Illumina_WGS_MET

  Whole-genome sequencing on Illumina HiSeq2000/2500 of colorectal cancer metastasis sample (OT2_cohort)

  Dataset EGAD00001003372

• OT2_Illumina_WGS_MET_CELL

  Whole-genome sequencing on Illumina HiSeq2000/2500 of PDO culture derived from colorectal cancer metastasis sample (OT2_cohort)

  Dataset EGAD00001003373

• OT2_Illumina_WGS_MET_XEN

  Whole-genome sequencing on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from colorectal cancer metastasis sample (OT2_cohort)

  Dataset EGAD00001003374

• OT2_Illumina_WGS_T

  Whole-genome sequencing on Illumina HiSeq2000/2500 of colorectal cancer primary tumor sample (OT2_cohort)

  Dataset EGAD00001003375

• OT2_Illumina_WGS_T_XEN

  Whole-genome sequencing on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from colorectal cancer primary tumor sample (OT2_cohort)

  Dataset EGAD00001003376

• OT2_Illumina_WXS_MET

  Whole-exome sequencing on Illumina HiSeq2000/2500 of colorectal cancer metastasis sample (OT2_cohort)

  Dataset EGAD00001003379

• OT2_Illumina_WXS_MET_CELL

  Whole-exome sequencing on Illumina HiSeq2000/2500 of PDO culture derived from colorectal cancer metastasis sample (OT2_cohort)

  Dataset EGAD00001003380

• OT2_Illumina_WXS_MET_XEN

  Whole-exome sequencing on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from colorectal cancer metastasis sample (OT2_cohort)

  Dataset EGAD00001003381

• Spatial heterogeneity of follicular lymphoma

  Follicular lymphoma (FL) is an incurable B cell malignancy characterized by advanced stage disease and a heterogeneous clinical course. Recent genomic studies have focused on profiling “single” FL biopsies over several time-points, however, multi-site sampling in solid cancers has demonstrated profound spatial intra-tumor heterogeneity (ITH) with implications for precision medicine based initiatives. This study examined the extent of spatial heterogeneity in FL by whole exome sequencing 22 synchronously removed spatially separated biopsies from 9 patients. We observed significant differences in the extent of ITH across cases, with two distinct patterns of high and low spatial heterogeneity emerging. Site-specific alterations in genes with biological, prognostic or therapeutic relevance included, TNFRSF14, PIK3CD, TNFAIP3, PTEN, EP300 and XBP1. In depth characterization of these variants using deep-sequencing techniques confirmed their discordant nature, suggesting on-going genetic diversification driving evolution after widespread tumor dissemination. There was evidence of tumors comprising multiple competing subclones, with distinct clusters of mutations demonstrating differential expansions within spatially-separated sites. For cases where spatial tumors were examined at two time-points (FL and transformation to diffuse large B cell lymphoma (DLBCL)), the degree of heterogeneity increased with transformation. Collectively, our results demonstrate that spatial ITH is prevalent in FL. The existence of site-specific aberrations suggests that a single biopsy may not be sufficient in all patients to capture the full genomic complexity present and these spatial variations need to be considered in biomarker-led clinical studies.

  Dataset EGAD00001003553