15077 results for "cancer studies using rna-seq"

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• Genomic Characterization of Patient-Derived Xenograft Models to Improve Targeted Therapy for HER2+ Breast Cancer Brain Metastases Treatments

  We have developed orthotopic patient-derived xenograft models of HER2 positive breast cancer metastasized into the brain of patients to test novel therapeutic strategies. In this study, we identified a novel combinatorial therapeutic strategy that has resulted in a durable remission and markedly increased overall survival in majority of patient-derived xenograft (PDX) models tested. We performed whole exome sequencing analysis of these PDX tumors and their matched blood and patient samples to investigate drug sensitive and resistance mechanisms. Our sequencing data revealed an interesting association of genotyping and phenotyping with tumors responses to drug treatment.

  Study phs001063

• Multiregion Sequencing of Localized Prostate Cancer

  Ten patients with treatment-naïve, locally advanced or localized prostate cancer underwent radical prostatectomy. Pathological stage ranged from T2aN0 to T3bN1, and Gleason scores from 3+4 to 4+5. Tumor foci were mapped, and DNA was extracted from multiple (5-9) regions from a single, contiguous index focus. Whole exome sequencing was performed to identify single nucleotide variants and indels, and low coverage whole genome sequencing was performed to estimate copy number variation. Phylogenetic relationships between foci was determined, and alterations associated with advanced disease or response to targeted therapy were identified.

  Study phs001465

• Combined Targeting of CDK4/6 and HER2 Signaling in Orthotopic Patient-Derived Xenografts of HER2-Positive Breast Cancer Brain Metastases

  Patients with metastatic HER2-positive (HER2+) breast cancer will frequently develop brain metastases (BCBMs). Here, we report that p16INK4A, a tumor suppressor, is deficient in the majority of HER2+ BCBMs. Furthermore, p16INK4A deficiency, as measured by protein immunohistochemistry, can be a predictive marker associated with response to combined treatment with tucatinib and abemaciclib in our orthotopic patient-derived xenografts (PDXs) models of HER2+ BCBMs. Our findings provide the rationale for a biomarker-driven clinical trial of combined treatment with CDK4/6- and HER2-targeted agents for patients with HER2+ BCBM.  

  Study phs002482

• Tumor Infiltrating Lymphocytes (TIL) Recognize Unique Somatic Mutations and Mediate Objective Clinical Responses in Metastatic Breast Cancer

  The purpose of this study is to investigate the immunogenicity of tumor mutations in patients with metastatic cancer. Harvest and analysis of progressing metastatic lesions are used for generation of tumor infiltrating lymphocyte (TIL) cultures and the detections of somatic mutations. In vitro T cell activation assays are used to examine the immune recognition of tumor mutations by autologous TIL. Once a candidate is determined to have a cell product that meets the requirements of one of the Surgery Branch clinical trials, the candidate is evaluated for enrollment in a prospective adoptive cell therapy trial.

  Study phs002735

• ERBB2/HER2 alterations in ctDNA and metachronous tissues of patients with metastatic urothelial cancer - WGS

  Whole genome sequencing data related to the publication "ERBB2/HER2 alterations in ctDNA and metachronous tissues of patients with metastatic urothelial cancer." ERBB2 alterations, usually amplifications or activating mutations, are seen in up to 20% of urothelial carcinoma and can be targeted by monoclonal antibodies, small molecule inhibitors, and most recently, antibody-drug conjugates. Here, we perform targeted and whole-genome sequencing of cell-free DNA and archival FFPE of mUC with and without ERBB2 alterations to identify unique genomic and clinical features of ERBB2-altered cancers, accompanied by IHC, FISH, and detailed clinical outcomes.

  Study EGAS50000001082

• WES analysis of paired tumor and non-tumoral DNA of 4 patients with non-muscle-invasive bladder cancer

  We performed WES of tumor DNA and non-tumoral DNA (extracted from PBMC) of 4 patients with non-muscle invasive bladder cancer, who after the tumor resection went on to receive BCG treatment as they had high-risk disease. In order to identify tumor-specific mutations that could give rise to patient-specific neo-epitopes, we performed paired WES of tumor and non-tumoral DNA for each patient. For patient UC2, 3 different tumors were resected at the same time and DNA from these 3 tumors were sent separately for WES.

  Study EGAS50000001382

• Whole transcriptome sequencing of chemotherapy-resistant muscle-invasive urothelial bladder cancer

  All mRNA sequencing data were acquired from single patients (BC159T) at a different time (BC159-T#1, BC159-T#2, and BC159-T#3). The first transurethral resection of bladder tumor (TUR-BT) (BC159-T#1) was diagnosed with non-MIUBC (muscle-invasive urothelial bladder cancer). Despite of intravesical bacillus Calmette-Guerin (BCG), the patient progressed into MIUBC at the second TUR-BT (BC159-T#2). After undergoing multiple neoadjuvant chemotherapy regimens (gemcitabine/paclitaxel and sequential paclitaxel), the patient developed local recurrence and multiple lung metastases and removed following palliative partial cystectomy (BC159-T#3).

  Study EGAS00001004232

• MutWP5__CRUK_Mutographs_of_Cancer__Lung__PD37920__Targeted_

  Sequencing of LCM-derived microbiopsies from explanted lung from COPD patient. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Deep sampling throughout multiple regions of the lung will determine whether there are differences in smoking-related mutation burden in different portions of the lung. Targeted sequencing will be conducted on samples to identify drivers of interest and clonality of the samples, well-performing samples will be sent for subsequent whole-genome sequencing. Results from this portion of the study will be compared to other individuals with smoking-related diseases (COPD, pulmonary fibrosis, lung cancer), and normal, non-smoking lungs.

  Study EGAS00001003321

• Breast Cancer - Subtype defined by an amplification of the HER2 gene

  Clinically positive HER2 (cHER2+) breast cancers (BC) are defined by the amplification and overexpression of the human epidermal growth factor receptor (HER2/ERBB2) gene on chromosome region 17q12 and represent 15% of all BCs. Although anti-HER2 targeted therapies have improved BC’s natural history, the magnitude of their benefit varies widely between patients and deciphering the genomic heterogeneity of cHER2+ BC may provide a basis to better understand patients’ outcome. As part of the ICGC Breast Cancer Working Group effort, we combined whole genome sequencing and transcriptomic analyses of 64 cHER2+ primary invasive carcinomas.

  Study EGAS00001001431

• Spatial and temporal intra-tumoural heterogeneity in advanced High-Grade Serous Ovarian Cancer: implications for surgical and clinical outcomes

  Limited evidence exists on the extent and impact of spatial and temporal heterogeneity of high grade serous ovarian cancer (HGSOC) on tumour evolution and patients surgical and clinical outcome. We investigated this through systematic mapping of multi-site tumours at initial presentation and matched relapse from 49 chemo-naïve HGSOC patients with high tumour load, operated upfront. Our data provides a unique insight into the tumour evolution and metastatic pathways of HGSOC across time and space, how this complexity relates to surgical and clinical outcome and its consequences on clinical decision-making.

  Study EGAS00001007164

• Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects.

  CRISPR-Cas9 genome editing is widely used to study gene function, from basic biology to biomedical research. Structural rearrangements are a ubiquitous feature of cancer cells and their impact on the functional consequences of CRISPR-Cas9 gene-editing has not yet been assessed. Utilizing CRISPR-Cas9 knockout screens for 250 cancer cell lines, we demonstrate that targeting structurally rearranged regions, in particular tandem or interspersed amplifications, is highly detrimental to cellular fitness in a gene independent manner. In contrast, amplifications caused by whole chromosomal duplications have little to no impact on fitness. This effect is cell line specific and dependent on the ploidy status. We devise a copy-number ratio metric that substantially improves the detection of gene-independent cell fitness effects in CRISPR-Cas9 screens. Furthermore, we develop a computational tool, called Crispy, to account for these effects on a single sample basis and provide corrected gene fitness effects. Our analysis demonstrates the importance of structural rearrangements in mediating the effect of CRISPR-Cas9-induced DNA damage, with implications for the use of CRISPR-Cas9 gene-editing in cancer cells.

  Dataset EGAD00001004124

• EGAD00010000266

  Metabric breast cancer samples (Genotype raw data)

  Dataset EGAD00010000266

• ICGC Prostate Cancer Whole Genome Sequencing

  A small subsample of EGAD00001000689. Please do not use.

  Dataset EGAD00001000263

• Whole exome sequencing of bulk primary tumor (and one lymph node metastasis) and matched blood of six non-metastatic breast cancer patients

  Dataset EGAD00001002746

• methylation_ec

  Raw methylation data from cervical samples in individuals with endometrial cancer.

  Dataset EGAD00010002084

• methylation_oc

  Raw methylation data from cervical samples in individuals with ovarian cancer.

  Dataset EGAD00010002086

• VCF dataset of Colorectal Cancer Synthetic genomes

  This dataset contains genomic variants data from VCF files of four patients synthetically generated in the EOSC4Cancer project

  Dataset EGAD50000000314

• germline pathogenic variants found in African patients of prostate cancer

  70 new blood samples added in this project

  Study EGAS50000001132

• Wilms_Tumour_organoid_sequencing_WGS

  This study investigates the genomic and transcriptomic characteristics of Wilm's tumour organoids

  Study EGAS00001002692

• The_mutational_landscape_of_recurrent_Glioblastome_multiforme

  Targeted gene screen of approx 120 patients with primary GBM and recurrent samples.

  Study EGAS00001001764