Search Results - EGA European Genome-Phenome Archive

Nanopore low-pass WGS of human brain tumors

Nanopore low-pass WGS of human brain tumors for evaluation of DNA methylation-based classification of cancer

Dataset EGAD00001009663

Randomized Phase II 2 x 2 Factorial Trial of the Addition of Carboplatin +/- Bevacizumab to Neoadjuvant Weekly Paclitaxel Followed by Dose-Dense AC in Hormone Receptor-Poor/HER2-Negative Resectable Breast Cancer

This randomized phase II trial studies how well paclitaxel with or without carboplatin and/or bevacizumab followed by doxorubicin and cyclophosphamide works in treating patients with breast cancer that can be removed by surgery. Drugs used in chemotherapy, such as paclitaxel, carboplatin, doxorubicin, and cyclophosphamide, work in different ways to stop the growth of tumor cells, either by killing the cells or by stopping them from dividing. Bevacizumab may stop the growth of tumor cells by blocking blood flow to the tumor. Giving chemotherapy together with bevacizumab before surgery may make the tumor smaller and reduce the amount of normal tissue that needs to be removed. All participants in this study were female.

Study phs001863

CIDR Estrogen Receptor Negative Breast Cancer in African American Women: DNA Methylation, Reproductive Events, and Mammary Epithelial Cell Populations

We conducted methylation profiling of breast tumor DNA from Formalin-Fixed Paraffin-Embedded (FFPE) samples for 1,550 cases from a cohort of Black women from the Black Women’s Health Study (BWHS), the Women’s Circle of Health Study (WCHS), and from the Pathways Study using the Illumina MethylationEPIC array. We will examine differentially methylated loci (DML) between ER+ and ER- tumors, and by age at onset of breast cancer. Combining these data with previously analyzed samples (n=385), we will consider associations between reproductive risk factors and top DML by age at diagnosis and ER status, examining the complex relationships between methylation, tumor and patient characteristics, and reproductive risk factors using structural equation modeling.

Study phs002688

Translating Gene-Calcium Interactions to Precision Medicine for Colorectal Cancer

Identify functional and rare SNPs and their interactions with Ca intake levels in relation to risk of incident adenoma using whole-exome resequencing of 2468 colorectal adenoma cases and controls from PLCO. We will genotype promising rare and functional SNPs associated with incident adenoma in 570 incident cancer cases, 1,710 healthy controls, 710 adenoma recurrence cases and 966 recurrent adenoma controls from the intervention arm of PLCO to both confirm the associations with adenoma, and to identify when, in the natural history of CRC, chemoprevention by Ca-gene interactions occurs. We hypothesize that Ca-gene interactions prevent early-stage (incident adenoma) and mid-stage (adenoma recurrence) carcinogenesis as well as span the entire CRC carcinogenesis spectrum (i.e. incident CRC).

Study phs002164

Integrative analysis of small cell lung cancer

Small-cell lung cancer (SCLC) is an aggressive lung tumor subtype. We conducted integrated analysis of genome sequencing, transcriptome, and copy number analysis and found an extremely high mutation rate of 7.4±1 protein-changing mutations per million basepairs. Evidence for inactivation of TP53 and RB1 was found in all sequenced cases. Furthermore, we identified recurrent mutations in CREBBP, EP300, and MLL, observed mutations in PTEN, in SLIT2, and EPHA7, as well as focal amplifications of the FGFR1 locus. As a major feature of SCLC we found mutation in histone modifying genes, observed genome alterations that are therapeutically tractable, and provide a framework for identifying biologically relevant genes in the context of a high mutation rate. Peifer et al., 2012, Nature Genetics.

Study EGAS00001000299

TGS___Comprehensive_Molecular_Characterization_of_Colorectal_Cancer_Metastases__MOSAIC_

Systematic next generation sequencing efforts are beginning to define the genomic landscape across a range of primary tumours, but we know very little of the mutational evolution that contributes to disease progression.We therefore propose to obtain a comprehensive description of genomic, transcriptomic and epigenomic changes in a cohort of matched primary and metastatic colorectal cancers, and additionally to explore the extent to which those mutations identified as recurrent in the metastatic setting are able to subvert normal biological processes using both genetically engineered mouse models and established cancer cell lines. This study will enable us to define to what extent primary tumour profiling can capture the biological processes operative in matched metastases as well as the significance of intratumoural heterogeneity.

Study EGAS00001000958

Comparison of sequencing assays for sensitive detection of circulating tumour DNA in stage IA-IV breast cancer

This study compared different assays for the detection of circulating tumour DNA (ctDNA) in serial plasma from stage IA-IV breast cancer patients, targeting structural variants (SVs), single nucleotide variants (SNVs) and/or somatic copy-number aberrations (SCNAs). SV-multiplex PCR, SNV-/SV-hybrid capture, and different depths of whole-genome sequencing (WGS) were used to evaluate ctDNA levels, demonstrating concordant results. SNV-hybrid capture targeting 1,347-7,491 mutations was the most sensitive assay, detecting 67% (36/54) of samples down to an allele fraction (AF) of 0.00024%. SV-multiplex PCR, targeting 21-47 mutations, detected 63% (34/54) of samples down to 0.00047% AF and has potential as a clinical assay.

Study EGAS00001006040

Clonal dominance defines metastatic dissemination in pancreatic cancer

Using patient-derived cells from a pancreatic ductal adenocarcinoma, we created orthotopic clonal replica tumors to trace in an unbiased fashion clonal lineage dynamics of unperturbed tumor expansion and dissemination over time. The model revealed the complex multifaced nature of tumor clonal expansion and uncovered brisk changes in fitness that lead to a continuous reshuffling of tumor clonal architecture and alternating clonal dominance as a distinct feature of cancer growth. Paired analysis of clonal lineages in primary and secondary sites revealed fitness in the primary tumor as a major contributor to dissemination, although other clonal intrinsic and extrinsic factors may contribute to metastatic process. Molecular characterization of lineages with differential metastatic potential identified actionable strategy to suppress dissemination at the subclonal level.

Study EGAS00001006358

12216 results for "cancer rna-seq"

in 36.60 milliseconds.

Nanopore low-pass WGS of human brain tumors

Randomized Phase II 2 x 2 Factorial Trial of the Addition of Carboplatin +/- Bevacizumab to Neoadjuvant Weekly Paclitaxel Followed by Dose-Dense AC in Hormone Receptor-Poor/HER2-Negative Resectable Breast Cancer

CIDR Estrogen Receptor Negative Breast Cancer in African American Women: DNA Methylation, Reproductive Events, and Mammary Epithelial Cell Populations

Translating Gene-Calcium Interactions to Precision Medicine for Colorectal Cancer

Integrative analysis of small cell lung cancer

TGS___Comprehensive_Molecular_Characterization_of_Colorectal_Cancer_Metastases__MOSAIC_

Comparison of sequencing assays for sensitive detection of circulating tumour DNA in stage IA-IV breast cancer

Clonal dominance defines metastatic dissemination in pancreatic cancer

Genome and transcriptome sequence data from a metastatic pancreatic cancer patient

Genome and transcriptome sequence data from a prostate cancer patient

Genome and transcriptome sequence data from a serous ovarian cancer patient

Genome and transcriptome sequence data from a low-grade serous ovarian cancer patient

Genome and transcriptome sequence data from a metastatic lung cancer patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from an ovarian cancer patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a presumed metastatic lung cancer patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a metastatic colorectal cancer patient