9295 results for "cancer rna-seq"

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• Host pathogen interaction long read transcriptome

  Our incomplete knowledge of the human transcriptome impairs the detection of disease-causing variants, in particular in transcripts only expressed under certain conditions. These transcripts are often lacking from reference transcript sets, such as Ensembl/GENCODE and RefSeq, and could be relevant for establishing genetic diagnoses. We present SUsPECT (Solving Unsolved Patient Exomes/gEnomes using Custom Transcriptomes), a pipeline based on the Ensembl Variant Effect Predictor (VEP) to predict variant impact on custom transcript sets, such as those generated by long-read RNA-sequencing, for downstream prioritization. Our pipeline predicts the functional consequence and likely deleteriousness scores for missense variants in the context of novel open reading frames predicted from any transcriptome. We demonstrate the utility of SUsPECT by uncovering potential mutational mechanisms of pathogenic variants in ClinVar that are predicted to be benign using the reference transcript annotation. In further support of SUsPECT’s utility, we identified an enrichment of immune-related variants predicted to have a more severe molecular consequence when annotating with a newly generated transcriptome from stimulated immune cells instead of the reference transcriptome. Our pipeline outputs crucial information for further prioritization of potentially disease-causing variants for any disease and will become increasingly useful as more long-read RNA sequencing datasets become available.

  Study EGAS00001006779

• The_Genomic_Advances_in_Sepsis__GAinS__RNA_seq

  Sepsis is defined as life-threatening organ dysfunction caused by a dysregulated host response to infection. This cohort comprises a subset of patients enrolled in the Genomic Advances in Sepsis (GAinS) study, an established biobank of adult sepsis patients. Patients with sepsis due to community acquired pneumonia or faecal peritonitis were recruited from 34 hospitals across the UK from 2005-2018, with samples for functional genomics and detailed clinical information collected on the first, third and/or fifth day following ICU admission. RNA was extracted from leukocytes isolated at the bedside using LeukoLOCK kits. We have previously identified sepsis response signatures (SRSs), transcriptomic endotypes that are associated with differential early mortality (Davenport et al, Lancet Respir Med, 2016; Burnham et al, AJRCCM, 2017) and response to treatment in a clinical trial (Antcliffe et al, AJRCCM, 2018). We generated RNA sequencing data on 903 samples, including 134 samples repeated from our previously released microarray data. Libraries were prepared using NEB Ultra II Library Prep kits (Illumina) and sequenced on a NovaSeq 6000. Reads were aligned to the reference genome (GRCh38) using STAR and gene counts quantified using featureCounts (annotation Ensembl v99). Counts were TMM-normalised and log-transformed. Following QC, processed data were available on 864 samples from 667 unique patients.

  Study EGAS00001003772

• Proteogenomic discovery of a novel class of cancer antigens by HLA ligandome analysis of colon cancer tissues

  CD8+ T cells recognize peptides displayed by HLA class I molecules on cell surfaces, monitoring pathological conditions such as cancer. Recent advances in proteogenomic analysis of HLA ligandomes have demonstrated that cells present a subset of cryptic peptides derived from non-coding regions of the genome; however, the roles of cryptic HLA ligands in tumor immunity remain unknown. In the present study, we comprehensively and quantitatively investigated the HLA class I ligandome of a set of human colorectal cancer (CRC) and matched normal tissues, showing that cryptic translation products account for a small fraction of the HLA class I ligandome and serve as antigens for patient T cell surveillance against colon cancer.

  Study JGAS000280

• National Cancer Institute (NCI) Head and Neck Cancer Study

  Head and neck cancers have well-documented associations with tobacco and alcohol exposure, but the disease develops in only a small fraction of users, which implies an important role for genetic susceptibility. Therefore, head and neck cancers are an excellent model for studying genetic susceptibility to environmental carcinogens. The primary goal of this study is to perform a comprehensive two-stage, high-density, genome-wide single-nucleotide polymorphism (SNP) analysis of head and neck cancer cases and corresponding frequency matched controls to identify novel genetic risk factors for head and neck cancer. In the study, we genotyped 2242 head and neck cancer cases and 1198 controls using Illumina HumanOmniExpress-12v1 BeadChip.

  Study phs001173

• Metastatic Breast Cancer Whole Genome

  We propose to definitively characterise the somatic genetics of Metastatic breast cancer through generation of comprehensive catalogues of somatic mutations in Metastatic breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Dataset EGAD00001000899

• GEL_WGS_Comparison

  These samples are to be analysed with the CGP Developed cancer panel and the results will be compared with WGS data from 4 different comercial providers.

  Study EGAS00001000649

• Osteosarcoma_RNAseq

  We propose to definitively characterise the somatic genetics of Osteosarcoma cancer through generation of comprehensive catalogues of somatic mutations by high coverage genome and transcriptome sequencing.

  Study EGAS00001000615

• Lung_Cancer_Whole_Genomes

  We propose to definitively characterise the somatic genetics of Lung cancer through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing.

  Study EGAS00001000148

• 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

• HKU Gastric Cancer Genomics study - WGS, DNA genotyping array, expression and methylation profiling

  HKU Gastric Cancer Genomics study - Whole Genome Sequencing, DNA genotyping array, Expression profiling and Methylation profiling

  Study EGAS00001000597

• Microdissected Pancreatic Cancer Whole Exome Sequencing

  109 micro-dissected pancreatic cancer cases and normal control tissue were subjected to whole-exome sequencing. Microdissection enriches tumor cellularity and enhances mutation calling.

  Study phs000953

• Mutational Landscape Determines Sensitivity to PD-1 Blockade in Non-Small Cell Lung Cancer

  Patients with non-small cell lung cancer were treated with pembrolizumab. Their tumors and matched normal blood were sequenced.

  Study phs000980

• Tam-seq of tumor samples for HGSOC copy-number signatures study

  This dataset contains targeted amplicon sequencing of DNA extracted from 300 samples of 142 patients (158 methanol-fixed relapse biopsies and 142 FFPE archival diagnostic tissues). Samples were sequenced on Illumina HiSeq 2500 and were aligned to human genome assembly GRCh37 (hg19)to produce 600 bam files (2 technical replicates per sample).

  Dataset EGAD00001004173

• Paired-end Whole Exome-seq analysis of the 3D evolution of glioma cell populations. Part 1.

  Dataset contains Exome sequencing data (aligned and base quality score recalibrated BAM files) for 236 tumor samples + matched normal from blood, collected from 21 patients with adult diffuse glioma. The majority of these samples were spatially-mapped during sample collection, enabling the genomic information derived from them to be mapped in 3D space.

  Dataset EGAD00001005221

• A spatiotemporal organ-wide gene expression and cell atlas of the developing human heart

  Dataset includes 2 scRNA-seq samples from a 6.5-7 post-conception weeks human embryonic heart and 19 samples from 4.5-9 post-conception weeks human embryonic hearts analyzed with the Spatial Transcriptomics method. H&E stains can be sent if requested.

  Dataset EGAD00001005468

• McGill Sperm Methylome Capture Sequencing Data

  The study includes methylC-capture sequencing (MCC-Seq) on 94 sperm DNA samples derived from both fertile and infertile individuals who were recruited from the Men’s Health Clinic at the Royal Victoria Hospital, Montreal, Quebec. All the data were generated with 100bp paired-end reads using the Illumina NovaSeq 6000 systems.

  Dataset EGAD00001005795

• Multiple Myeloma ChipSeq data on six histone modifications

  The data contained in this dataset is ChipSeq BAM files aligned to reference genome hg38. The ChipSeq was based on a combination of six histone modifications as follows: H3K4me1, H3K4me3, H3K9me3, H3K27me3, H3K27Ac and H3K36me3. The samples are patient-derived xenografts generated by passaging primary patient CD138+ selected cells through the SCID-rab myeloma mouse model.

  Dataset EGAD00001008353

• Mixture of 2 (closer mtDNA)

  Mixture of 2 unrelated individuals (of close mtDNA haplogroup) sequenced by 10x as a scRNA-seq. The dataset was then processed by Cell Ranger and deconvoluted to yield each individuals genetic profile. The clustering of SNPs is submitted as the processed file. The Sequencing fastqs are submitted as unprocessed files.

  Dataset EGAD00001008727

• scRNA-seq of first and second trimester human gonads - HUGODECA dataset

  Comprehensive map of first- and second-trimester gonadal development in humans using a combination of single-cell and spatial transcriptomics, chromatin accessibility assays, and imaging. ArrayExpress Accession: E-MTAB-10551

  Dataset EGAD00001009386

• Triple Negative Breast Cancer sequencing

  Triple Negative Breast Cancer sequencing

  Dataset EGAD00001000063

• HER2 positive Breast Cancer

  HER2 positive Breast Cancer

  Dataset EGAD00001000126

• OICR PANCREATIC CANCER DATASET 2

  OICR PANCREATIC CANCER DATASET 2

  Dataset EGAD00001000276

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

  Study EGAS00001007308

• Concurrent germline and somatic pathogenic BAP1 variants in a patient with metastatic bladder cancer

  Study EGAS00001004055

• Expression profiles and genetic makeup of metastases of a cancer of unknown primary.

  Study EGAS00001004059