Search Results - EGA European Genome-Phenome Archive

Detection of cancer cell transcriptomes

Single cell transcriptomes, generated using chromium 10X 3' sequencing, for two tumour types (AT/RT, and Ewing's sarcoma). For each individual, tumour and normal whole genome sequencing was also obtained using Illumina short read sequencing to an average depth of 30X. These data were used to validate the accuracy of a method for identifying cancer cell transcriptomes based on the allelic shift produced by copy number changes.

Dataset EGAD00001009005

WES and RNAseq of Simultaneous Bilateral Breast Cancer

This dataset includes NGS profiling of 13 women with simultaneous bilateral breast cancer. Seven women have WES of untreated surgical resections and matched healthy tissue. The six other women have WES of healthy tissue, WES+RNAseq of pre-neoadjuvant tumor biopsies, and when residual disease was present (6 tumors in 4 patients), WES+RNAseq of residual disease from post-neoadjuvant therapy surgery. One patient from the WES+RNAseq cohort had multifocal bilateral disease at diagnosis so there are 2 pre-neoadjuvant biopsy samples from each breast.

Dataset EGAD00001009987

Single Cell Genome Variation Induced by Mutational Processes in Cancer - HGSOC Trios Study

Mutational signatures derived from whole genome sequencing have potential prognostic significance. Identification of high grade serous ovarian cancer patients with deficiency in homologous recombination repair pathways could identify a subset of patients that would benefit from homologous recombination deficiency-specific treatments independent of identification of a pathological BRCA1/2 gene mutation. Clinical protocols rely on a pathologist's assessment of formalin-fixed paraffin-embedded (FFPE) tissues, and thus FFPE tissue samples are readily available. However, the bulk of mutational signature analyses have been performed on fresh frozen tissues. In this study, we aimed to assess the reliability of whole genome sequencing, variant calling, and mutational signature analysis from FFPE tissue samples.

Study phs003036

Sequence Analysis of Mutations and Translocations Across Breast Cancer Subtypes

This study combined whole exome (103 samples) and whole genome (22 samples) sequencing over a total of 108 breast tumors and matched normal DNA to identify novel mutations and translocations. Samples were subjected to paired-end Illumina sequencing with goal of 30x coverage of tumor/normal for whole genomes and 100x tumor/normal coverage for whole exomes. From these sequences, we used various computational techniques to identify somatic point mutations, insertion/deletions and structural rearrangements in these tumors. From these data, we identified new insights into the rates of background mutations in these cancers, novel recurrent mutated genes, and multiple gene rearrangements. One of these rearrangements appears to be a recurrent event in breast cancer.

Study phs000369

Improved Detection and Identification of Microsatellite Instability Features in Colorectal Cancer

In this study, we analyzed a series of colorectal cancers using a new sequencing technology that sequences more than 200 microsatellite regions in parallel. With this technology, we evaluated mono-, di- , tri- and tetranucleotide repeats to provide a broad spectrum of microsatellite instability (MSI) events. This deep sequencing technology provides greater than 2000X coverage and eliminates the need for PCR amplification. Because every read corresponds to a single DNA molecule, we eliminated artifacts introduced by PCR that obscured true MSI events. Also included in our analysis is a new method for detection of somatic copy number changes in 83 cancer genes, with which we can infer chromosomal instability (CIN) status.

Study phs001914

Biomarker Research for Anti EGFR Monoclonal Antibodies by Comprehensive Cancer Genomics

The purpose of this study is to explore new biomarkers for predicting the effectiveness of an anti-epidermal growth factor receptor (anti-EGFR) antibody in patients with advanced colorectal cancer. The investigation involves analyzing the entire exome, conducting a genome-wide association study (GWAS), and analyzing copy number variations (CNVs) using single nucleotide polymorphism (SNP) arrays. Genetic material from both cancerous and non-cancerous tissues, as well as blood samples from patients who received the antibody treatment, will be used. The goal is to identify genetic mutations and SNPs associated with treatment efficacy and adverse events, and to assess the correlation between their presence and treatment effectiveness using statistical methods.

Study JGAS000779

Insights into BRCA1 and TP53 associated breast cancer development from integrated whole genome analysis of mouse model mammary tumors

Germline mutations in BRCA1 are a leading cause of hereditary breast cancer. We generated Brca1;Trp53 double conditional knockout (CKO) and Trp53 single CKO mouse models, both with either one or two copies of Trp53 deleted by Cre. We used whole-genome sequencing and optical genome mapping to interrogate the genomes of the resulting mammary tumors. Our comprehensive genomic analyses show that the Brca1;Trp53-CKO tumors recapitulate major genomic features of the human BRCA1 breast samples indicative of conserved fundamental mutational processes. This study also provides new insights into the genetic mechanisms of tumor development with potential implications for the treatment of BRCA1 cancers.

Study EGAS50000001402

A Combined Omics and Tissue Biobank for Paediatric Cancers

The Swedish Childhood Tumour Biobank (BTB) is a nonprofit national infrastructure for samples and genomic data collection from pediatric patients diagnosed with central nervous system and other solid tumours in Sweden. Fresh frozen tumour tissue and patient’s matched blood are collected from affected patients and genomic data is continuously generated and made available for approved medical research projects. We expect that the accessibility of biological samples and/or data to the research community will contribute to further advances in the understanding of tumour biology, which in turn will impact many aspects of clinical care of children with cancer, by refining diagnosis and/or identifying oncogenic drivers and therapeutic targets.

Study EGAS50000000209

12312 results for "cancer rna-seq"

in 30.01 milliseconds.

Detection of cancer cell transcriptomes

WES and RNAseq of Simultaneous Bilateral Breast Cancer

Single Cell Genome Variation Induced by Mutational Processes in Cancer - HGSOC Trios Study

Sequence Analysis of Mutations and Translocations Across Breast Cancer Subtypes

Improved Detection and Identification of Microsatellite Instability Features in Colorectal Cancer

Biomarker Research for Anti EGFR Monoclonal Antibodies by Comprehensive Cancer Genomics

Insights into BRCA1 and TP53 associated breast cancer development from integrated whole genome analysis of mouse model mammary tumors

A Combined Omics and Tissue Biobank for Paediatric Cancers

Genome and transcriptome sequence data from a non-small cell lung cancer patient

Genome and transcriptome sequence data from a metastatic prostate cancer patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a metastatic rectal cancer patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a metastatic gastric cancer patient

Genome and transcriptome sequence data from a metastatic gallbladder cancer patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a metastatic serous ovarian cancer patient

Genome and transcriptome sequence data from a metastatic cecal cancer patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a metastatic pancreatic cancer patient

Genome and transcriptome sequence data from a non-small cell lung cancer patient

Genome and transcriptome sequence data from a metastatic colorectal 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