7825 results for "canc*"

in 35.07 milliseconds.

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0189_002

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0189_002 for Triple negative breast cancer patient-derived xenograft SA535X8XB03663

  Dataset EGAD00001011229

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0182_002

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0182_002 for Triple negative breast cancer sample SA535X8XB03431

  Dataset EGAD00001011230

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0184_002

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0184_002 for Triple negative breast cancer patient-derived xenograft SA535X8XB03434

  Dataset EGAD00001011231

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0173_002

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0173_002 for Triple negative breast cancer patient-derived xenograft SA535X9XB03617

  Dataset EGAD00001011232

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0173_001

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0173_001 for Triple negative breast cancer patient-derived xenograft SA535X9XB03616

  Dataset EGAD00001011233

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0195_001

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0195_001 for Triple negative breast cancer patient-derived xenograft SA535X8XB03664

  Dataset EGAD00001011234

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0206_002

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0206_002 for Triple negative breast cancer patient-derived xenograft SA535X10XB03696

  Dataset EGAD00001011235

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0206_001

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0206_001 for Triple negative breast cancer sample SA535X10XB03693

  Dataset EGAD00001011236

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0208_002

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0208_002 for Triple negative breast cancer patient-derived xenograft SA535X9XB03776

  Dataset EGAD00001011237

• Sequencing data from a phase II study of nivolumab and ipilimumab in recurrent or refractory cancer of unknown primary (CheCUP trial)

  Sequencing data from a phase II study of nivolumab and ipilimumab in recurrent or refractory cancer of unknown primary (CheCUP trial). Panel sequencing data from baseline FFPE biopsies were used to perform a comprehensive genomic profiling of CUP metastases. Combined targeted next-generation sequencing of patient-specific hotsport mutations and shallow whole genome sequencing of baseline and follow-up liquid biopsy samples were used to analyze ctDNA and to evaluate response to immunei checkpoint inhibitor treatment. In some cases, whole exome sequencing of peripheral blood mononuclear cells was performed to screen for potential CHIP and germline mutations.

  Dataset EGAD00001011130

• RNASeq data from one small cell prostate cancer patient (4 samples from 3 time points)

  RNASeq data from one small cell prostate cancer patient - 4 cancer samples (FFPE) from Patient 1 collected at 3 different time points. mRNA was selected using the Magnetic mRNA Isolation Module (NEB) and sequenced on the Illumina NextSeq 500 as 75bp paired end reads (total read length 150bp).

  Dataset EGAD00001011154

• Total RNA sequencing data from the Triple Negative Trial (TNT)

  BAM files from total RNA sequencing of samples from breast cancer patients in the TNT trial. Data includes 186 primary tumour samples and 13 matched recurrence samples.

  Dataset EGAD00001011141

• Exome sequencing data from two small cell prostate cancer patients

  Exome sequencing data from two small cell prostate cancer patients - 4 cancer samples (FFPE) from Patient 1 collected at 3 different time points and 2 cancer samples (FFPE) from Patient 2 collected at 1 time point. Exonic DNA was enriched using the TruSeq Exome Kit (Illumina) and sequenced on the Illumina NextSeq 500 as 75bp paired end reads (total read length 150bp).

  Dataset EGAD00001011149

• Cell-free DNA sequencing data of healthy control, atrophic gastritis, and gastric cancer patients’ blood

  Sample cohort (n=48) is consisted of healthy, atrophic gastritis and gastric cancer patients. Some of the gastric cancer patients samples are collected at the separate time points: -1 before the operation; -2 after the operation; -3 during the control visit. For the hybridisation capture of the genes unique 15 gastric cancer-related gene panel was developed and very deep sequencing using TruSight Oncology Unique Molecular Identifier (UMI) Reagents (Illumina) was used.

  Dataset EGAD00001011153

• Colorectal cancer organoid-stroma biobank cohort

  In colorectal cancers (CRC) the tumor microenvironment plays a key role for prognosis and therapy efficacy. Patient-derived tumor organoids (PDTOs) show enormous potential for preclinical testing, however, purely epithelial cultures features including the ‘consensus molecular subtypes’ (CMS) are largely eradicated. To better reflect the cell type heterogeneity, we established the CRC organoid-stroma biobank of matched PDTOs and cancer-associated fibroblasts (CAFs) from 30 patients. Whole exome sequencing and transcriptome analysis in various in vitro and in vivo contexts was performed to study the influence of the TME on the CRC phenotype.

  Dataset EGAD00001011173

• Intra-prostatic tumour evolution, steps in metastatic spread and histogenomic associations revealed by integration of multi-region whole genome sequencing with histopathological features

  We performed whole genome sequencing on 42 prostate cancer samples from the prostate, seminal vesicles and regional lymph nodes of five treatment-naive patients with locally advanced disease who underwent radical prostatectomy. Whole genome sequencing was performed as 150bp paired end reads on the Illumina NovaSeq 6000 platform.

  Dataset EGAD00001011174

• cfDNA methylation profiling in Metastatic Cancer and Cancer of Unknown Primary

  This study contains methyl-binding domain sequencing and shallow whole genome sequencing from circulating cell-free DNA (cfDNA) for 143 patients with metastatic cancer of known type, 41 patients with Cancer of Unknown Primary (CUP) and 27 non-cancer controls.

  Dataset EGAD00001011178

• Cancer treatment re-shapes the somatic mutational landscape of normal esophagus - wgs

  Ageing epithelial tissues, including the esophagus, are progressively colonized by somatic mutant clones, some carrying mutations linked to cancer. However, whether normal epithelial mutational landscapes that evolve over decades can be altered by short term interventions such as cancer treatment is not known. Here we sequenced normal esophageal epithelium removed from patients after 5-8 weeks of therapy for esophageal cancer. Some patients had no prior treatment (NT), while others had 8 weeks of 5 Fluorouracil (5-FU) containing chemotherapy (FLOT) or 4 weeks of chemotherapy and radiation directed at the tumor (CROSS). Despite the brief duration of therapy, we observed treatment specific differences in the selection of mutant clones. The median size of mutant TP53 and PPM1D clones in the CROSS group was double that in the other groups. Mutants of the tumor suppressor SPOP were selected in CROSS but not FLOT or NT patients. In FLOT patients we found positive selection of activating MTOR mutations, consistent with the hypothesis that these mutants confer 5-FU resistance. Sequencing densely mutated normal epithelia after cancer reveals treatment specific selection of mutations with potential therapeutic impact.

  Dataset EGAD00001011181

• Cancer treatment re-shapes the somatic mutational landscape of normal esophagus - 0.25mm punches targeted

  Ageing epithelial tissues, including the esophagus, are progressively colonized by somatic mutant clones, some carrying mutations linked to cancer. However, whether normal epithelial mutational landscapes that evolve over decades can be altered by short term interventions such as cancer treatment is not known. Here we sequenced normal esophageal epithelium removed from patients after 5-8 weeks of therapy for esophageal cancer. Some patients had no prior treatment (NT), while others had 8 weeks of 5 Fluorouracil (5-FU) containing chemotherapy (FLOT) or 4 weeks of chemotherapy and radiation directed at the tumor (CROSS). Despite the brief duration of therapy, we observed treatment specific differences in the selection of mutant clones. The median size of mutant TP53 and PPM1D clones in the CROSS group was double that in the other groups. Mutants of the tumor suppressor SPOP were selected in CROSS but not FLOT or NT patients. In FLOT patients we found positive selection of activating MTOR mutations, consistent with the hypothesis that these mutants confer 5-FU resistance. Sequencing densely mutated normal epithelia after cancer reveals treatment specific selection of mutations with potential therapeutic impact.

  Dataset EGAD00001011182

• Cancer treatment re-shapes the somatic mutational landscape of normal esophagus - nanoseq

  Ageing epithelial tissues, including the esophagus, are progressively colonized by somatic mutant clones, some carrying mutations linked to cancer. However, whether normal epithelial mutational landscapes that evolve over decades can be altered by short term interventions such as cancer treatment is not known. Here we sequenced normal esophageal epithelium removed from patients after 5-8 weeks of therapy for esophageal cancer. Some patients had no prior treatment (NT), while others had 8 weeks of 5 Fluorouracil (5-FU) containing chemotherapy (FLOT) or 4 weeks of chemotherapy and radiation directed at the tumor (CROSS). Despite the brief duration of therapy, we observed treatment specific differences in the selection of mutant clones. The median size of mutant TP53 and PPM1D clones in the CROSS group was double that in the other groups. Mutants of the tumor suppressor SPOP were selected in CROSS but not FLOT or NT patients. In FLOT patients we found positive selection of activating MTOR mutations, consistent with the hypothesis that these mutants confer 5-FU resistance. Sequencing densely mutated normal epithelia after cancer reveals treatment specific selection of mutations with potential therapeutic impact.

  Dataset EGAD00001011183

• Cancer treatment re-shapes the somatic mutational landscape of normal esophagus - 2mm targeted

  Ageing epithelial tissues, including the esophagus, are progressively colonized by somatic mutant clones, some carrying mutations linked to cancer. However, whether normal epithelial mutational landscapes that evolve over decades can be altered by short term interventions such as cancer treatment is not known. Here we sequenced normal esophageal epithelium removed from patients after 5-8 weeks of therapy for esophageal cancer. Some patients had no prior treatment (NT), while others had 8 weeks of 5 Fluorouracil (5-FU) containing chemotherapy (FLOT) or 4 weeks of chemotherapy and radiation directed at the tumor (CROSS). Despite the brief duration of therapy, we observed treatment specific differences in the selection of mutant clones. The median size of mutant TP53 and PPM1D clones in the CROSS group was double that in the other groups. Mutants of the tumor suppressor SPOP were selected in CROSS but not FLOT or NT patients. In FLOT patients we found positive selection of activating MTOR mutations, consistent with the hypothesis that these mutants confer 5-FU resistance. Sequencing densely mutated normal epithelia after cancer reveals treatment specific selection of mutations with potential therapeutic impact.

  Dataset EGAD00001011184

• HiSeq Colorectal Cancer Dataset

  Set of 19 patients afflicted with colorectal cancer with matching preoperative and postoperative blood plasma, PBMC, and tumor biopsy sequencing data. Originally referenced by Genome-wide cell-free DNA mutational integration enables ultra-sensitive cancer monitoring. Nat Med. 2020, Zviran et. al.

  Dataset EGAD00001011186

• Genome and transcriptome sequence data from a metastatic melanoma patient

  Genome and transcriptome sequence data from a metastatic melanoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001011018

• Genome and transcriptome sequence data from a metastatic pancreatic neuroendocrine tumour patient

  Genome and transcriptome sequence data from a metastatic pancreatic neuroendocrine tumour patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001011019

• Genome and transcriptome sequence data from a metastatic carcinoma of unknown primary patient

  Genome and transcriptome sequence data from a metastatic carcinoma of unknown primary patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001011020

• Genome and transcriptome sequence data from a metastatic breast ductal carcinoma patient

  Genome and transcriptome sequence data from a metastatic breast ductal carcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001011021

• Genome and transcriptome sequence data from a melanoma patient

  Genome and transcriptome sequence data from a melanoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001011022

• Genome and transcriptome sequence data from a follicular lymphoma patient

  Genome and transcriptome sequence data from a follicular lymphoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001011023

• Genome and transcriptome sequence data from a neuroendocrine tumor patient

  Genome and transcriptome sequence data from a neuroendocrine tumor patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001011024

• Genome and transcriptome sequence data from a metastatic thymic carcinoma patient

  Genome and transcriptome sequence data from a metastatic thymic carcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001011025

• Genome and transcriptome sequence data from a small cell lung carcinoma patient

  Genome and transcriptome sequence data from a small cell lung carcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001011026

• Genome and transcriptome sequence data from a pancreatic cancer patient

  Genome and transcriptome sequence data from a pancreatic cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001011027

• Genome and transcriptome sequence data from a nasopharyngeal carcinoma patient

  Genome and transcriptome sequence data from a nasopharyngeal carcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001011028

• Genome and transcriptome sequence data from a colorectal carcinoma patient

  Genome and transcriptome sequence data from a colorectal carcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001011029

• Genome and transcriptome sequence data from a pancreatic adenocarcinoma patient

  Genome and transcriptome sequence data from a pancreatic adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001011030

• Genome and transcriptome sequence data from a urachal adenocarcinoma patient

  Genome and transcriptome sequence data from a urachal adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001011031

• Genome and transcriptome sequence data from a liposarcoma patient

  Genome and transcriptome sequence data from a liposarcoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001011032

• Genome and transcriptome sequence data from a gastrointestinal stromal tumor patient

  Genome and transcriptome sequence data from a gastrointestinal stromal tumor patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001011033

• Genome and transcriptome sequence data from a granulosa cell ovarian tumor patient

  Genome and transcriptome sequence data from a granulosa cell ovarian tumor patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001011034

• Genome and transcriptome sequence data from a pancreatic adenocarcinoma patient

  Genome and transcriptome sequence data from a pancreatic adenocarcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001011035

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001011036

• Genome and transcriptome sequence data from a metastatic triple negative breast cancer patient

  Genome and transcriptome sequence data from a metastatic triple negative breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001011037

• Genome and transcriptome sequence data from a papillary thyroid carcinoma patient

  Genome and transcriptome sequence data from a papillary thyroid carcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001011038

• Genome and transcriptome sequence data from a thymoma patient

  Genome and transcriptome sequence data from a thymoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001011039

• Genome and transcriptome sequence data from a rectal adenocarcinoma patient

  Genome and transcriptome sequence data from a rectal adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001011040

• Pediatric Patient-Derived-Xenograft development in MAPPYACTS – international pediatric cancer precision medicine trial in relapsed and refractory tumors

  Pediatric patients with recurrent and refractory cancers are in most need for new treatments. This study developed patient-derived-xenograft (PDX) models within the European MAPPYACTS cancer precision medicine trial (NCT02613962). To date, 131 PDX models were established following heterotopical and/or orthotopical implantation in immunocompromised mice: 76 sarcomas, 25 other solid tumors, 12 central nervous system tumors, 15 acute leukemias, and 3 lymphomas. PDX establishment rate was 43%. Histology, whole exome and RNA sequencing revealed a high concordance with the primary patient’s tumor profile, human leukocyte-antigen characteristics and specific metabolic pathway signatures. A detailed patient molecular characterization, including specific mutations prioritized in the clinical molecular tumor boards are provided. Ninety models were shared with the IMI2 ITCC Paediatric Preclinical Proof-of-concept Platform (IMI2 ITCC-P4) for further exploitation. This new PDX biobank of unique recurrent childhood cancers provides an essential support for basic and translational research and new treatments development in advanced pediatric malignancies.

  Dataset EGAD00001011048

• Bone marrow single cell genomics from blood cancer samples

  Four different types of transcriptomic single-cell sequencing of blood from childhood B acute lymphoblastic leukemia.

  Dataset EGAD00001011055

• Spatially resolved antigen receptor and gene expression data from breast cancer patients

  The dataset includes spatially-resolved and single-cell antigen receptor, as well as gene expression, data from two different HER2+ breast cancer patients. The tumor piece obtained during surgery from each patient was divided into several regions and tissue sections were used for spatial transcriptomics (Visium, 10x genomics). As indicated, some tissue sections were analyzed by a new method (Spatial VDJ) to spatially resolve antigen receptor sequences (target capture), which was developed in our publication. In parallel, tissue pieces from the same tumor were dissociated for single-cell gene expression analysis (10x genomics GEX, VDJ, and feature barcoding/Hash Tag Oligonucleotide). The deposited data is in the form of fastq files. All processed data, metadata, micrographs of the tissue sections (of those used for spatial transcriptomics), and scripts used for the analysis are publicly available at Zenodo (DOI: 10.5281/zenodo.7961605). Final libraries were sequenced on NextSeq2000 (Illumina) or NovaSeq6000 (Illumina) and analyzed with Cell Ranger, Seurat, Space Ranger, and STutility pipelines.

  Dataset EGAD00001011061

• 47 urothelial cancer patients WES and 38 RNAseq

  We performed a global mutational landscape analysis using tumor samples from the 47 urothelial cancer patients included in MATCH-R or MOSCATO studies, with advanced metastatic disease and WES available (RNAseq is included for 38 patient samples).

  Dataset EGAD00001011063

• Whole genome sequencing of breast cancer and related clones

  Paired WGA (whole-genome amplificated) samples from 65 single cell-derived organoids and six fresh single cell-derived organoid samples both of which were established from normal mammary epithelial cells, 84 FFPE LCM (laser-capture microdissection) samples of breast cancer and related clones, 79 fresh-frozen LCM samples of non-cancer lobules of breast cancer patients, and 36 matched germline controls were subjected to whole genome sequencing using NovaSeq 6000 system (Illumina) or DNBSEQ-G400RS (MGI Tech).

  Dataset EGAD00001010833

• RNAseq

  RNAseq of pancreatic cancer organoids.

  Dataset EGAD00001010834

• WGS

  Whole-genome sequencing of pancreatic cancer organoids and matched germline controls.

  Dataset EGAD00001010835

• pilot

  Pilot study for genome-wide sequencing of cell-free DNA from nipple aspirate fluid and plasma of breast cancer patient

  Dataset EGAD00001010836

• Transcriptomic analyses of a large cohort of adult B cell acute lyphoblastic leukemia

  Total mononuclear cells (MNC) were isolated from peripheral blood (PB) or bone marrow (BM) samples of 105 Ph-/-/- (B-cell acute lymphoblastic leukemia [B-ALL] triple negative) and 31 Ph+ B-ALL adult patients using Lymphosep (Biowest, Nuaillé, France). A total of 15 samples from healthy subjects were processed including hematopoietic stem-progenitor cells (CD34+) from bone marrow specimens (n = 3), and bone marrow mononuclear cell samples (n = 3) from STEMCELL Technologies (Vancouver, Canada). PB MNC samples (n=5) and cord blood samples (n = 4). CD34+ cells were enriched from cord blood samples by immunomagnetic separation (CD34 MicroBead Kit, Miltenyi Biotec, Bergisch Gladbach, Germany).Libraries were prepared using the TruSight RNA Pan-Cancer Panel Kit (Illumina, San Diego, California, USA), following the manufacturer’s protocol. Sequencing was performed using the Illumina MiSeq instrument.

  Dataset EGAD00001010837

• Digital tEchnology For Lung Cancer Treatment

  DEFLeCT metadata: 1) A table containing the mutational profile for all human genes across the cohort of the 81 PROMOLE lung cancer samples. 2) A table containing the expression levels for all human genes across the cohort of the 81 PROMOLE lung cancer samples. 3) A table containing the clinical, histology data and follow-ups of the cohort of 81 PROMOLE lung cancer patients.

  Dataset EGAD00001010838

• Genome and transcriptome sequence data from a tongue mass patient

  Genome and transcriptome sequence data from a tongue mass patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016080

• Genome and transcriptome sequence data from a high-grade urothelial cancer patient

  Genome and transcriptome sequence data from a high-grade urothelial cancer patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016081

• Genome and transcriptome sequence data from a metastatic endometrioid endometrial cancer patient

  Genome and transcriptome sequence data from a metastatic endometrioid endometrial cancer patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016082

• Genome and transcriptome sequence data from a peritoneal mesothelioma patient

  Genome and transcriptome sequence data from a peritoneal mesothelioma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016083

• Genome and transcriptome sequence data from a metastatic lung adenocarcinoma patient

  Genome and transcriptome sequence data from a metastatic lung adenocarcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016084

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

  Genome and transcriptome sequence data from a non-small cell lung cancer patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016085

• Genome and transcriptome sequence data from a primary unknown patient

  Genome and transcriptome sequence data from a primary unknown patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016086

• Genome and transcriptome sequence data from a acral lentiginous melanoma patient

  Genome and transcriptome sequence data from a acral lentiginous melanoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016087

• Genome and transcriptome sequence data from a triple negative breast cancer patient

  Genome and transcriptome sequence data from a triple negative breast cancer patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016088

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016089

• Genome and transcriptome sequence data from a lung cancer patient

  Genome and transcriptome sequence data from a lung cancer patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016091

• Genome and transcriptome sequence data from a poorly differentiated adenocarcinoma more consistent with metastatic melanoma patient

  Genome and transcriptome sequence data from a poorly differentiated adenocarcinoma more consistent with metastatic melanoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016092

• Genome and transcriptome sequence data from a lung adenocarcinoma patient

  Genome and transcriptome sequence data from a lung adenocarcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016093

• Genome and transcriptome sequence data from a clear cell ovarian cancer patient

  Genome and transcriptome sequence data from a clear cell ovarian cancer patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016094

• Genome and transcriptome sequence data from a metastatic cervical cancer patient

  Genome and transcriptome sequence data from a metastatic cervical cancer patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016095

• Genome and transcriptome sequence data from a metastatic hepatocellular carcinoma patient

  Genome and transcriptome sequence data from a metastatic hepatocellular carcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016096

• Genome and transcriptome sequence data from a metastatic cholangiocarcinoma patient

  Genome and transcriptome sequence data from a metastatic cholangiocarcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016097

• Genome and transcriptome sequence data from a endometrial carcinosarcoma patient

  Genome and transcriptome sequence data from a endometrial carcinosarcoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016098

• Genome and transcriptome sequence data from a mucosal melanoma patient

  Genome and transcriptome sequence data from a mucosal melanoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016099

• Genome and transcriptome sequence data from a metastatic undifferentiated pleomorphic sarcoma patient

  Genome and transcriptome sequence data from a metastatic undifferentiated pleomorphic sarcoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016100

• Genome and transcriptome sequence data from a recurrent peritoneal mesothelioma patient

  Genome and transcriptome sequence data from a recurrent peritoneal mesothelioma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016101

• Genome and transcriptome sequence data from a right buccal mucosa squamous cell cancer patient

  Genome and transcriptome sequence data from a right buccal mucosa squamous cell cancer patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016102

• Genome and transcriptome sequence data from a nras mutated metastatic melanoma patient

  Genome and transcriptome sequence data from a nras mutated metastatic melanoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016103

• Genome and transcriptome sequence data from a squamous cell lung carcinoma patient

  Genome and transcriptome sequence data from a squamous cell lung carcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016104

• Genome and transcriptome sequence data from a lung adenocarcinoma patient

  Genome and transcriptome sequence data from a lung adenocarcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016105

• Genome and transcriptome sequence data from a squamous cell carcinoma of the right oro/hypopharynx patient

  Genome and transcriptome sequence data from a squamous cell carcinoma of the right oro/hypopharynx patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016106

• Genome and transcriptome sequence data from a primary unknown - suspected metastatic scc of lung vs thymus patient

  Genome and transcriptome sequence data from a primary unknown - suspected metastatic scc of lung vs thymus patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016107

• Genome and transcriptome sequence data from a gallbladder adenocarcinoma, nos patient

  Genome and transcriptome sequence data from a gallbladder adenocarcinoma, nos patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016108

• Genome and transcriptome sequence data from a uroepithelial carcinoma patient

  Genome and transcriptome sequence data from a uroepithelial carcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016109

• Genome and transcriptome sequence data from a metastatic intrahepatic cholangiocarcinoma patient

  Genome and transcriptome sequence data from a metastatic intrahepatic cholangiocarcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016110

• Genome and transcriptome sequence data from a metastatic adenocarcinoma (endometrioid vs. clear cell) patient

  Genome and transcriptome sequence data from a metastatic adenocarcinoma (endometrioid vs. clear cell) patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016111

• Genome and transcriptome sequence data from a urothelial carcinoma patient

  Genome and transcriptome sequence data from a urothelial carcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016112

• Genome and transcriptome sequence data from a metastatic triple negative breast cancer patient

  Genome and transcriptome sequence data from a metastatic triple negative breast cancer patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016113

• Genome and transcriptome sequence data from a adenocarcinoma of the lung patient

  Genome and transcriptome sequence data from a adenocarcinoma of the lung patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016114

• Genome and transcriptome sequence data from a metastatic melanoma patient

  Genome and transcriptome sequence data from a metastatic melanoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016115

• Extensive and differential platinum chemotherapy mutagenesis in livers of children - RNA

  Bulk RNA sequencing of normal liver and liver tumours from children. Five of the children had liver cancer and samples was taken at surgery. Two children had non-liver type of cancer and liver samples were obtained postmortem.

  Dataset EGAD00001016117

• Extensive and differential platinum chemotherapy mutagenesis in livers of children - Targeted NanoSeq

  Targeted NanoSeq using a bait set consisting of 285 genes, comprising mostly cancer genes, of a Validation cohort that includes platinum-exposed (n=195) and platinum naïve (n=60) samples from 26 individuals (children and foetal tissues). The samples are mainly liver samples (normal and cancer tissues) and obtained from children with liver cancer.

  Dataset EGAD00001016120

• GBM-Space: Transcriptomic Profiling of Patient-Derived Glioblastoma Cell Lines (Parse Biosciences - Evercode WT)

  Cancer cells display heterogeneous and dynamic states in glioblastoma, but how these malignant states arise and whether they follow a tractable cellular trajectory across tumours is poorly understood. Here, we generate a deep single cell and spatial multi-region atlas of 12 isocitrate dehydrogenase wild-type (IDH-wt) primary glioblastomas that integrates transcriptomic, epigenomic and genomic analysis to comprehensively characterise their tumour heterogeneity. This dataset comprises sequencing data from single-cell transcriptomic profiles of patient-derived glioblastoma cell lines (Parse Biosciences Evercode WT v3), towards experimentally validating the malignant cell trajectory from developmental-like to gliosis-hypoxia states.

  Dataset EGAD00001016126

• Extensive and differential platinum chemotherapy mutagenesis in livers of children - Whole genome NanoSeq

  Whole genome NanoSeq of a cohort predominantly consisting of paired blood, normal liver and liver tumour from children with liver cancer. The cohort includes platinum-exposed and platinum naïve samples.

  Dataset EGAD00001016142

• Genome and transcriptome sequence data from a metastatic breast carcinoma (ductal) patient

  Genome and transcriptome sequence data from a metastatic breast carcinoma (ductal) patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001015570

• Genome and transcriptome sequence data from a squamous cell carcinoma left base tongue patient

  Genome and transcriptome sequence data from a squamous cell carcinoma left base tongue patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001015576

• Genome and transcriptome sequence data from a malignant peripheral nerve sheath tumor patient

  Genome and transcriptome sequence data from a malignant peripheral nerve sheath tumor patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001015583

• Genome and transcriptome sequence data from a pancreatic neuroendocrine tumour patient

  Genome and transcriptome sequence data from a pancreatic neuroendocrine tumour patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001015588

• Sperm sequencing reveals extensive positive selection in the human germline -NanoSeq

  Mutations that occur during human ageing in the cell lineages of sperm or eggs have the potential to be transmitted to offspring. In males, positive selection of driver mutations during spermatogenesis is known to increase the birth prevalence of certain developmental disorders and cancer predisposition syndromes. However, direct observation of the scope of this selection in sperm has been limited by the error rates of sequencing technologies. Using the duplex sequencing method known as NanoSeq, we sequenced bulk sperm samples from individuals aged 24 to 75 years. Our findings revealed a linear accumulation mutations per year and mutational signatures consistent with pedigree studies. Deep targeted and deep exome NanoSeq of sperm samples identified genes subject to significant positive selection in the male germline, which are linked to diverse cellular pathways including RAS/MAPK and BMP signaling. Strikingly, nearly all positively selected genes are associated with developmental or cancer predisposition disorders in children. We find that this effect drives an elevated risk of known likely disease-causing mutations in sperm across a wide age range. This implies that the disorders attributed to these genes likely exhibit elevated birth prevalence in human populations, particularly among older fathers. These findings shed light on the dynamics of germline mutations and highlight an increased disease risk for children born to fathers of advanced age.

  Dataset EGAD00001015590

• Sperm sequencing reveals extensive positive selection in the human germline -TargetedNanoSeq

  Mutations that occur during human ageing in the cell lineages of sperm or eggs have the potential to be transmitted to offspring. In males, positive selection of driver mutations during spermatogenesis is known to increase the birth prevalence of certain developmental disorders and cancer predisposition syndromes. However, direct observation of the scope of this selection in sperm has been limited by the error rates of sequencing technologies. Using the duplex sequencing method known as NanoSeq, we sequenced bulk sperm samples from individuals aged 24 to 75 years. Our findings revealed a linear accumulation mutations per year and mutational signatures consistent with pedigree studies. Deep targeted and deep exome NanoSeq of sperm samples identified genes subject to significant positive selection in the male germline, which are linked to diverse cellular pathways including RAS/MAPK and BMP signaling. Strikingly, nearly all positively selected genes are associated with developmental or cancer predisposition disorders in children. We find that this effect drives an elevated risk of known likely disease-causing mutations in sperm across a wide age range. This implies that the disorders attributed to these genes likely exhibit elevated birth prevalence in human populations, particularly among older fathers. These findings shed light on the dynamics of germline mutations and highlight an increased disease risk for children born to fathers of advanced age.

  Dataset EGAD00001015591