11925 results for "cancer rna-seq"

in 26.70 milliseconds.

• WGS of Five Pancreatic Cancer Patients-Tumor and Normal

  We performed whole genome sequence on tumor-derived and normal cell lines from patients who had terminal pancreatic cancer and consented for rapid autopsy upon their death. The 5 samples are from Dr. Christine Iacobuzio-Donahue's rapid autopsy program as reported in Boland et al. (PLOSOne, 2024, In Press, PMID 38352348).

  Study phs003775

• WES to explore mutational landscape of blood and non blood liquids in female patients with metastatic breast cancer.

  Whole Exome Sequencing (WES) to explore mutational landscape of blood and non blood liquids in female patients with metastatic breast cancer. 11 patients. 86 liquid samples, 11 matched normal samples. Median coverage 67X. Illumina paired-end sequencing. Fastq files are provided. WES from Richard et al., Nature Communications, 2025 low-pass Whole Genome Sequencing (lpWGS) to assess the representativeness of seven body liquids from female patients with metastatic breast cancer. 216 liquid samples, 745 solid samples, 20 matched normal samples. 0.5X coverage. lpWGS from Richard et al., Nature Communications, 2025.

  Dataset EGAD50000001852

• Heterogeneity and evolution of DNA mutation rates in microsatellite-stable colorectal cancer

  A mutation accumulation experiment in colorectal cancer (CRC) derived tumoroids, aimed at measuring the spontaneous rates of accumulation of new single-nucleotide sequence variations in seven microsatellite stable CRCs and one microsatellite unstable CRC. Mutations accumulated over six+six months were identified via whole genome sequencing of clonal tumoroids.

  Study EGAS50000000284

• Germline WES-data of pediatric cancer patients with variants in HBOC-related genes

  This study focused on the identification of (likely) pathogenic germline variants (LP/PV) in 25 adult-onset HBOC-related genes in a cohort of 372 pediatric cancer patients. The cohort was sequenced on Illumina platforms. The files uploaded here belong to the 27 individuals with such a LP/PV.

  Study EGAS50000001073

• Intractable Cancer Therapy Development through a New Target Identification by Molecular Profiling

  We collected the cancerous tissues of the primary and recurrence tumors from the same patient with recurrent / metastatic breast cancer, and the purpose of this study is to find the characteristics of recurrent / metastatic breast cancers by carrying out a "molecular profiling", mainly the exome sequence analysis of these tissues.

  Study JGAS000075

• Identification of genetic mutations characteristic for recurrence and metastasis of gastric cancer.

  We collected the cancerous tissues of the primary and recurrence tumors from the same patient with recurrent / metastatic gastric cancer, and the purpose of this study is to find the characteristics of recurrent / metastatic gastric cancers by carrying out a "molecular profiling", mainly the exome sequence analysis of these tissues.

  Study JGAS000086

• Identifying mutations in patient-derived melanoma DCC lines

  To identify mutations that cause resistance, we analyzed two patient-derived cell lines: Mel-DCC-11 (the parental line, sensitive to the BRAF inhibitor) and Mel-DCC-11-R (resistant to the BRAF inhibitor). We employed targeted-panel sequencing to examine the coding sequences of 410 cancer-associated target genes.

  Study EGAS50000001225

• Rare germline variants in patients with personal and family history of colorectal cancer

  A double primary colorectal cancer (CRC) in a familial setting signals a high risk of CRC. In order to find novel high/moderate penetrance CRC susceptibility genes, we performed whole-exome sequencing on germline blood samples of seven familial cases from Poland with a double primary CRC.

  Study EGAS50000000606

• Chordoma_Exome_Sequencing

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from Chordoma cancers and matched normal DNA from the same patients. Three lanes of Illumina GA sequencing will be performed on the resulting exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes.

  Study EGAS00001000188

• Breast_Cancer_Sequential_Sampling_Targeted_Capture

  This study aims to target capture sequence regions of interest from DNA derived from breast cancer patients who received neo-adjuvant chemotherapy. All patients had multiple biopsies performed before chemotherapy. Patients who had residual disease after the course of treatment underwent a further biopsy. We aim to characterise the mutations involved.

  Study EGAS00001000596

• The_life_history_of_colorectal_cancer_metastases_study_WGS_X10

  Whole genome sequencing of a series of metastasis collected from 2 patients at autopsy will be used to construct a life history of the cancer, including phylogenetic relationship between the different metastases an also whether there is evidence of convergence towards common biological processes that underpin the metastatic process but though different mutational events

  Study EGAS00001000864

• Meningioma_Exome

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from Meningioma tumour samples and matched normal DNA from the same patients. Three lanes of Illumina GA sequencing will be performed on the resulting exome libraries and mapped build 37 of the human reference genome to facilitate the identification of novel cancer genes.

  Study EGAS00001000177

• sWGS on cfDNA and matching tumor DNA in pediatric cancer

  This dataset contains shallow whole genome sequencing data from paired cfDNA - tumor DNA samples of various pediatric cancer entities. Files are provided in fastq format. Samples were sequenced on an Ion Proton sequencer (Thermo Fisher Scientific) or a Hiseq3000 (Illumina). Data analysis is available at https://github.com/rmvpaeme/sWGS_pediatric_cancer.

  Study EGAS00001005198

• X10_sequencing_of_Oesophageal_Adenocarcinoma_Organoids

  X10 Sequencing of 5 patient derived organoid cell models. Each model was derived from a piece of patient tumour taken following surgical resection of the tumour. All model derivations took place with the CGaP facility in Sanger. This PacBio data will be combined with other sequencing data in order to generate accurate reference cancer genomes.

  Study EGAS00001003264

• Genomic and transcriptomic landscape of aggressive thyroid cancer

  Molecular characteristics of anaplastic thyroid cancer (ATC) and advanced differentiated thyroid cancers (DTCs) have not been fully elucidated. In this study, we applied various types of massively-parallel sequencing technology to 113 advanced TCs, including 27 ATCs and 86 advanced DTCs, to reveal their genomic and transcriptomic characteristics.

  Study EGAS00001003540

• MicroRNA profiling by next-generation sequencing for colorectal cancer screening

  The study was conducted as the marker discovery phase to identify potential microRNA (miRNA) candidates for colorectal cancer (CRC) screening. Genome-wide profiling with next-generation sequencing (NGS) was performed using plasma samples from 20 newly diagnosed CRC cases and 20 controls free of colorectal neoplasms matched by age and sex.

  Study EGAS00001005030

• Oesophageal_Adenocarcinoma_Organoid_10x

  10x Sequencing of 6 patient derived organoid cell models. Each model was derived from a piece of patient tumour taken following surgical rescetion of the tumour. All model derivations took place with the CGaP facility in Sanger. This 10x data will be combined with other sequencing data in order to generate accurate reference cancer genomes.

  Study EGAS00001003191

• Oesophageal_Adenocarcinoma_Organoid_PacBio

  PacBio Sequencing of 6 patient derived organoid cell models. Each model was derived from a piece of patient tumour taken following surgical resection of the tumour. All model derivations took place with the CGaP facility in Sanger. This PacBio data will be combined with other sequencing data in order to generate accurate reference cancer genomes.

  Study EGAS00001007163

• TRACERx Reduced-representation bisulfite sequencing (RRBS)

  RRBS data from TRACERx non-small cell lung cancer (NSCLC) tumours and matched normal adjacent tissue. TRACERx (TRAcking Cancer Evolution through therapy (Rx)) is a prospective cohort study designed to investigate intratumor heterogeneity (ITH) in relation to clinical outcome, and to determine the clonal nature of driver events and evolutionary processes in early stage non-small cell lung cancer (NSCLC).

  Dataset EGAD00001009707

• Genome and transcriptome sequence data from a colorectal adenocarcinoma patient (Response to Angiotensin Blockade with Irbesartan in a Patient with Metastatic Colorectal Cancer)

  Genome and transcriptome sequence data from a colorectal adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study. These data are included in the manuscript entitled, "Response to Angiotensin Blockade with Irbesartan in a Patient with Metastatic Colorectal Cancer".

  Dataset EGAD00001001876

• Advancing Precision Oncology in a Humanized, Fully Autologous Mouse Model

  Progress in the early detection and treatment of cancer requires accurate model systems to further evaluate new, promising discoveries. Small animal and, in particular, mouse model systems are attractive to researchers for numerous reasons, including their ease of use and well-described platforms. The ability to grow human tumors in immune-deficient mice (so-called patient-derived xenografts, or PDXs) allows researchers to work directly with human cancer tissue in a controlled setting. However, PDX models are limited by their lack of an intact immune system. Immunotherapy has revolutionized clinical oncology, but lacks pre-clinical models of the human immune system and human cancer to investigate new modalities and limitations/toxicities of treatment regimens. The broad objective of this study is to validate an in vivo model to evaluate human tumors in the context of a complete and intact human immune system in a completely personalized and autologous fashion to study cancer immunotherapy. Herein, we will: (1) validate the ability of our humanized system to serve as a model for cancer immunotherapy treatment response and toxicity in patients with melanoma, including immunotherapy checkpoint blockade and vaccine strategies, and (2) extend our current work in melanoma by validating the ability to establish humanized mice and evaluate tumor growth and leukocyte development in autologous human pancreatic and colorectal tumors established in humanized mice. In each of these areas, we will leverage our multi-institutional team's individual expertise along with our institutional infrastructure to maximize the success of the experimental aims. The results from this project will be widely available to the general research community for future, hypothesis-driven research. Taken together, our study will meet multiple goals and address several unmet needs in cancer immunotherapy, thus significantly enhancing the applicability of a fully autologous and immunocompetent precision model system for use in translational oncology research.

  Study phs003090

• Multi-omics bulk and single-cell profiling of epithelioid sarcoma

  Epithelioid sarcoma (EpS) is an aggressive sarcoma, characterized by the loss of SMARCB1 expression. EpS is traditionally classified as distal or proximal according to clinicopathological features, but its molecular characteristics remain largely unknown. To establish an EpS molecular classification and uncover determinants of inter- and intra-patient heterogeneity in EpS, we used multi-omics profiling and integrated the genomic, transcriptional and methylome landscapes with single-cell RNA sequencing on fresh samples as well as spatial transcriptomics. We identified two molecular subtypes of EpS: “distal-like” and “proximal-like”, which were distinct from the histological subtypes. Distal-like tumors include all morphological distal subtypes and a subset of proximal and hybrid EpS. They express a specific molecular single-cell derived epithelial-to-mesenchymal transition signature, which associates with improved patient survival and includes Desmoglein 2 (DSG2), which we identify as a potential routine immunohistochemical biomarker to improve diagnosis. Distal-like EpS also display increased peri-tumoral CD8+ T cell infiltrates and specific tumor-immune cell interactions. Conversely, proximal-like EpS harbor a higher inter-tumoral molecular heterogeneity with some cases resembling other SMARCB1-deficient tumors by DNA methylation profiling, and increased intra-tumoral pro-tumoral macrophage infiltrates. Our study introduces a novel molecular classification of EpS with prognostic value, associated diagnostic biomarkers and distinct tumor immune microenvironments, which extends beyond traditional clinicopathological classification. This paves the way for precision medicine-based therapeutic strategies for patients with EpS.

  Study EGAS50000000973

• Identification_of_synthetic_lethal_genes_by_CRISPR_Cas9_library

  Sequencing is performed on PCR products from the amplification of gRNA segments introduced into cell lines (some are commercial, some are derived by collaborators, as described in HMDMC 13/076). Cellular DNA or RNA are not sequenced. This data is defined as "Other Biological/Biochemical Assay Data" under the WTSI datasharing guidelines and consequently will be released at the time of publication and/or through faculty websites. SEQUENCING DETAILS: in October 2016 3 DNA samples will be submitted for PCR amplification and purification through CGP pipeline using Thompson's custom primer set and PCR settings and sequencing with Hiseq using a custom protocol (with 3 forward reads to read sgRNA1, sgRNA2 and the index, optimized with Illumina Bespoke Sanger team); read length 50bp. The following set of samples will be submitted in later 2016 and ealry 2017 as cell pellet to be processed through CGP Cas9 pipeline (Thompson's oligos and protocols) and sequences on Hiseq (same custom sequencing protocol described above) We are utilizing a custom CRISPR/Cas9 library to identify synthetic lethal gene pairs. Cells will be transduced with LV expressing Cas9, then infected with LV expressign the library of 42'000 sgRNA pairs. Cell pellet will be collected from the cell population at different timepoints. The samples will be processed by CGP pipeline customized for the specific protocol and then sequenced to identify the 19bp of the sgRNA and quantify their representation.

  Study EGAS00001002117

• Drug-perturbation-based stratification of blood cancer

  As new generations of targeted therapies emerge and tumor genome sequencing discovers increasingly comprehensive mutation repertoires, the functional relationships of mutations to tumor phenotypes remain largely unknown. Here, we measured ex vivo sensitivity of 246 blood cancers to 63 drugs alongside genome, transcriptome, and DNA methylome analysis to understand determinants of drug response. We assembled a primary blood cancer cell encyclopedia data set that revealed disease-specific sensitivities for each cancer. Within chronic lymphocytic leukemia (CLL), responses to 62% of drugs were associated with 2 or more mutations, and linked the B cell receptor (BCR) pathway to trisomy 12, an important driver of CLL. Based on drug responses, the disease could be organized into phenotypic subgroups characterized by exploitable dependencies on BCR, mTOR, or MEK signaling and associated with mutations, gene expression, and DNA methylation. Fourteen percent of CLLs were driven by mTOR signaling in a non–BCR-dependent manner. Multivariate modeling revealed immunoglobulin heavy chain variable gene (IGHV) mutation status and trisomy 12 as the most important modulators of response to kinase inhibitors in CLL. Ex vivo drug responses were associated with outcome. This study overcomes the perception that most mutations do not influence drug response of cancer, and points to an updated approach to understanding tumor biology, with implications for biomarker discovery and cancer care.

  Study EGAS00001001746

• Detection of mutational patterns in cell free DNA (cfDNA) of colorectal cancer by custom amplicon sequencing

  Monitoring the mutational patterns of solid tumors during cancer therapy is a major challenge in oncology. Analysis of mutations in cell free (cf) DNA offers a non-invasive approach to detect mutations that may be prognostic for disease survival or predictive for primary or secondary drug resistance. A main challenge for the application of cfDNA as a diagnostic tool is the diverse mutational landscape of cancer. Here, we developed a flexible end-to-end experimental and bioinformatics workflow to analyze mutations in cfDNA using custom amplicon sequencing. Our approach relies on open software tools to select primers suitable for multiplex PCR using minimal cfDNA as input. In addition, we developed a robust linear model to identify specific genetic alterations from sequencing data of cfDNA. We used our method to design a custom amplicon panel suitable for detection of hotspot mutations relevant for colorectal cancer and analyzed mutations in serial cfDNA samples from 34 patients with advanced colorectal cancer. Our data demonstrates that recurrent and patient-specific mutational patterns can be reliably detected for the majority of patients. Furthermore, we show that the allele frequency of mutations in cfDNA correlates well with disease progression. Finally, we demonstrate that monitoring of cfDNA can outperform the predictive power of currently used tumor markers and reveal mechanisms of resistance to anti-EGFR antibody treatment.

  Study EGAS00001003382