12310 results for "cancer rna-seq"

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• WGS and RNA-Seq data from a GBM patient PT-GC1519

  WGS and RNA-Seq data from a GBM patient PT-GC1519

  Dataset EGAD00001004239

• WGS and RNA-Seq data from a GBM patient PT-GJ3716

  WGS and RNA-Seq data from a GBM patient PT-GJ3716

  Dataset EGAD00001004240

• WGS and RNA-Seq data from a GBM patient PT-HO0394

  WGS and RNA-Seq data from a GBM patient PT-HO0394

  Dataset EGAD00001004243

• WGS and RNA-Seq data from a GBM patient PT-VO7089

  WGS and RNA-Seq data from a GBM patient PT-VO7089

  Dataset EGAD00001004263

• WGS and RNA-Seq data from a GBM patient PT-TM5196

  WGS and RNA-Seq data from a GBM patient PT-TM5196

  Dataset EGAD00001004262

• WGS and RNA-Seq data from a GBM patient PT-SK0976

  WGS and RNA-Seq data from a GBM patient PT-SK0976

  Dataset EGAD00001004260

• WGS and RNA-Seq data from a GBM patient PT-RW9277

  WGS and RNA-Seq data from a GBM patient PT-RW9277

  Dataset EGAD00001004259

• CSER: Evaluating Utility and Improving Implementation of Genomic Sequencing for Pediatric Cancer Patients in the Diverse Population and Healthcare Settings of Texas: The KidsCanSeq Study

  Through this Clinical Sequencing Evidence-Generating Research (CSER) with Enhanced Diversity project we are completing a clinical study (The Texas KidsCanSeq Study) comparing the results of targeted cancer panel sequencing versus genome-scale testing in pediatric cancer patients across diverse clinical settings. We will compare the targeted pediatric cancer panel to germline whole exome sequencing (WES) of unselected childhood cancer patients. We will also compare an RNA/DNA targeted pediatric cancer panel versus WES, transcriptome sequencing and copy number array of FFPE tumor samples for the subset of patients with high-risk tumors. Exome sequencing is performed from a blood or saliva sample of the pediatric age (0-18) patient. We are building on our success completing the CSER program BASIC3 exome sequencing trial (which included 60% Hispanic and African-American patients from a single large academic center) in this large multi-institutional study of an even more diverse patient population from six pediatric oncology healthcare settings across Texas. Data from the Texas KidsCanSeq study will be submitted through the CSER Data Coordinating Center for access in NIH-supported databases.

  Study phs002378

• RNA seq of intestinal biopsies and blood cells from patients with celiac disease and controls

  This study presents RNA sequenced from several intestinal phenotypes such as from patients with damaged intestinal mucosa as well as from those without a damaged intestine but still an autoantibody response to tissue transglutaminase (“potential celiac disease”) or those with treated celiac disease. By combining phenotypes in a much larger number of tissue samples from both peripheral blood and mucosal biopsies, we found highly differentially expressed genes, but also identify genes involved in controlling and triggering celiac disease associated changes. This study identifies molecular mechanisms involved in celiac disease and new possible targets for treatment and for identification of individuals at risk.

  Study EGAS50000001104

• 1. Identidication of molecular biological mechanism associated with the development and prognosis of uterine cancer, uterine sarcoma, and endometrial hyperplasia / 2. Identification of molecular biological mechanism associated with the development of endometriosis and malignant transformation, ovarian cancer, fallopian tubal cancer, peritoneal cancer, and other malignant tumors in gynecological organs

  To clarify the biological difference between clear cell carcinoma and other histological subtypes in ovarian carcinomas by comparing copy number variants, and to identify molecular subtypes and carcinogenesis in clear cell ovarian carcinomas by whole-exome sequencing and RNA-sequencing. Then, characterize high-grade serous carcinomas by NGS-based, integrative genomic analyses, with focus on homologous recombination deficiency, molecular subtypes, prognostic factors and effectiveness of PARP inhibitor. Based on the results of whole-exome sequencing, an investigator-initiated, phase 2 clinical trial will be conducted to evaluate the efficacy and safety of the PARP inhibitor olaparib in HRD-positive cases.

  Study JGAS000789

• Single-Cell Genomic Analysis of Gastrointestinal Cancer

  Our study aimed to define the heterogeneity of gastrointestinal cancers at a single-cell resolution. We subjected single-cell suspensions derived from surgical resections of gastrointestinal cancer tissue, paired normal tissue, peripheral blood mononuclear cells (PBMCs) or their ex vivo cultures to high-throughput microfluidics based single-cell RNA and DNA sequencing. We analyzed the features of the tumor microenvironment including fibroblasts, endothelial cells, macrophages and lymphocytes to determine their contribution to tumor growth and progression. We also characterized the mechanisms of immunosuppression in these tumors. This analysis led to novel insights into the biology of the microenvironment and also enabled the identification of new treatment targets.

  Study phs001818

• Personalised Mapping of Tumour Development in Synchronous Colorectal Cancer Patients

  We performed an in-depth characterisation of 12 tumours from 3 syCRC patients by analysing histopathological, whole genome sequencing and RNA-sequencing data. We assessed the extent of genetic overlap between synchronous tumours and examined associations between clinicopathological information and the molecular, microbial and immune features of each tumour genome.

  Study EGAS00001004413

• Comparison of fresh and slow-frozen cancer samples for different applications

  Surplus tissues from multiple solid human cancers directly slow-frozen after resection can subsequently be used for different types of methods including the establishment of 2D, 3D, and ex vivo cultures as well as single cell RNA sequencing (scRNAseq) with similar results when compared to freshly analyzed material.

  Study EGAS00001005891

• SU2C-MARK Lung Cancer Consortium - Checkpoint Blockade Response Project

  Immune checkpoint inhibitors have become a critical part of the armamentarium against advanced Non-Small Cell Lung Cancer (NSCLC). While early studies have identified Tumor Mutation Burden (TMB) and PD-L1 staining as important biomarkers of response, they remain imperfect predictors. Here we describe a multi-institutional effort as part of the SU2C-MARK Lung Cancer Consortium in which Whole Exome Sequencing (WES) - and in select cases, RNA sequencing – was performed on a large collection of NSCLC samples prior to immune checkpoint blockade therapy, along with matched clinical response data following therapy. (Profiling of a small number of on- or post-treatment samples was also performed.) We anticipate this dataset to be of high value for the development of a deep understanding of the molecular determinants of immune checkpoint blockade response as well as the discovery of novel biomarkers.

  Study phs002822

• Long-Read Sequencing to Identify Inherited Mutations Predisposing to Breast Cancer

  We aimed to detect deeply intronic mutations within genes linked to breast/ovarian cancer that are potentially under-reported in clinical testing due to technical limitations. Current DNA and RNA tests typically exclude these regions, which harbor many variants within complex repetitive sequences that short-read sequencing cannot align. By employing targeted long read sequencing together with recent in silico prediction tools, we assessed the implications of rare deep intronic variants in severely affected patients with breast, ovarian, and/or metastatic prostate cancer, who had previously tested negative using standard genomic or cDNA methods. Through this approach, we identified participants who carried deep intronic mutations in tumor suppressor genes, resulting in abnormal transcripts causing premature truncations and loss of gene function. This study underscores the potential of long read DNA and cDNA sequencing in enhancing mutation discovery efforts.

  Study phs003638

• RNA sequencing and Illumina 2.5M SNP array data collected from 675 commonly used human cancer cell lines.

  Tumor-derived cell lines have served as vital models to advance our understanding of oncogene function and therapeutic response1. Although substantial effort has been directed to defining the genomic constitution of cancer cell line panels2–4, the transcriptome – which represents the active program of a cell – remains understudied. Here, we describe RNA sequencing and SNP array analysis of 675 commonly used human cancer cell lines. We explore numerous transcriptome features including coding and non-coding gene expression, transcribed mutations, gene fusion and expression of non-human sequences. Aside from many known aberrations we find new surprising characteristics, including more than 2200 unique fusion gene pairs representing a vast, testable repertoire of oncogenic fusions, many of which have analogs found in primary human tumors. We show that a combination of multiple genome and transcriptome features in a novel pathway-based approach enhances prediction of response to various targeted therapeutics. Our results provide valuable new insights into these critical pre-clinical models and provide added context for interpreting the numerous studies that employ these widely used cell lines.

  Study EGAS00001000610

• RNAseq of GEPARSIXTO

  294 formalin-fixed paraffin-embedded (FFPE) tissue samples were sent to the UNC Lineberger Comprehensive Cancer Center Translational Genomics Lab (TGL) for RNA isolation using the Maxwell 16 MDx Instrument (Promega AS3000) and the Maxwell 16 LEV RNA FFPE Kit (Promega AS1260) following the manufacturer’s protocol (Promega 9FB167). 279 total RNA sequencing libraries were prepared at TGL using a Bravo Automated Liquid-Handling Platform (Agilent G5562A) and the TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina 20020599) following the manufacturer’s protocol (Illumina 1000000040499). RNAseq library quality and quantity were measured using a TapeStation 4200 (Agilent G2991AA) and Qubit 3.0 fluorometer (Life Technologies Q33216), pooled at equal molar ratios, and denatured following the manufacturer’s protocol (Illumina 1000000106351). 271 total RNA sequencing libraries were sequenced at TGL on NovaSeq 6000 (Illumina 20012850) S4 flow cells (Illumina 20028313) following the manufacturer’s protocol (Illumina 1000000019358) using a 2x50 bp paired-end configuration and pool sizes of 91 libraries to target a read depth of 110 million clusters per library on average.

  Dataset EGAD00001010201

• Hofer et al., A specific subpopulation of cancer-associated fibroblasts promotes resistance to chemotherapy in triple-negative breast cancer by upregulating G0S2 protein

  Chemotherapy is the standard of care for patients with triple-negative breast cancer (TNBC), but the mechanisms of chemoresistance remain poorly understood. Here, we investigated the role of cancer associated fibroblasts (CAFs) in the chemotherapy response of TNBC, by combining in vivo analyses of TNBC patients with ex vivo cancer modeling, using tumor-on-chip (ToC) technology. Transcriptomic analysis revealed that the proportion of a specific CAF population, the extracellular matrix-producing myofibroblasts (ECM-myCAFs), is reduced after chemotherapy in chemo-sensitive, but not in chemo-resistant TNBC patients. In ToC devices, primary ECM-myCAFs promoted TNBC cell survival under Doxorubicin and Paclitaxel treatment. The mechanism of chemoresistance was elucidated by using single-cell RNA sequencing, advanced cell imaging and functional assays: ECM-myCAFs upregulate the G0/G1 switch 2 (G0S2) protein in TNBC cells, via activation of SRC family kinases. Altogether, our work identifies G0S2 as a new player in CAF mediated chemotherapy resistance in TNBC.

  Study EGAS50000000886

• Examination of Engineered LINE-1 Integration Events in HeLa Cells

  Long Interspsesed Element-1 (LINE1 or L1) encodes two proteins (ORF1p and ORF2p) required for its mobilization (i.e. retrotransposition) in the human genome. Human ORF2p, a 150kDa protein, has endonuclease (EN) and reverse transcriptase (RT) activities. L1 EN is classified as apurinic/apyrimidin-like endonuclease (APE) and is responsible for initiating target-site primer reverse transcription (TPRT) during the L1 retrotransposition cycle. During canonical TPRT, the L1 EN activity makes a single-strand endonucleolytic nick at a double-strand DNA target sequence in genomic DNA. The endonucleolytic nick is typically made at an L1 EN degnerate consensus cleavage sequence (5'-TTTT/A-3') exposing a free 3' hydroxy group that can be used as a primer by the ORF2p L1 RT activity to reverse transcribe the associated L1 RNA. Here, we characterized over 21,000 de novo engineered L1 retrotransposition events in HeLa cells to determine if L1 exhibits overt integration preferences in the human genome. Bru-seq of HeLa cells to determine actively transcribed regions of the genome was also performed. This Bru-seq data was used to determine if engineered L1 integration events preferentially integrate into transcribed regions of the genome, and to determine which strand during transcription may present itself as preferential during L1 retrotransposition.

  Study phs001669

• Single-cell level characterization of B cell depletion and repopulation following rituximab in systemic lupus erythematosus

  Rituximab, a CD20+ B cell depletion therapy, is frequently used in the treatment of systemic lupus erythematosus (SLE). However, variability in patient response highlights the need for a deeper understanding of the underlying immune cell dynamics of B cell depletion and repopulation. In this study, we conducted longitudinal single-cell profiling of nine SLE patients treated with rituximab from pretreatment to up to 15 months post-treatment. These were compared to eight healthy controls. We profiled PBMCs via 10X Genomics single-cell RNA, surface protein (CITE-seq), B cell receptor (BCR), and T cell receptor (TCR) sequencing and sequenced bulk BCR repertoires in parallel. For single cell sequencing, 10 pools were created with an equal number of cells from 4 samples each. Samples collected at different timepoints from the same patient were distributed across different pools to allow demultiplexing of individuals using genotypes captured from the scRNA-seq data. Libraries were pooled using a ratio of GEX:CITE:TCR:BCR=9:2:1:1 and were sequenced across two lanes of the NovaSeq 6000. For bulk BCR sequencing, individual samples were demultiplexed using primer barcodes and paired-end BCR amplicon reads were merged prior to submission; data are provided as unmapped single-end reads.

  Study EGAS00001006798

• IBD-dysplasia

  This data set concerns DNA copy number alterations and mutation data from 30 IBD-associated dysplastic lesions and 13 IBD-associated cancers. DNA was isolated from formalin-fixed, paraffin-embedded material. Whole-genome shallow seq and Truseq amplicon cancer panel (Illumina) were used for detection of DNA copy number alterations and gene mutations, respectively.

  Dataset EGAD00001005196

• Shallow whole genome sequencing from plasma DNA of BC, CRC and NSCLC patients

  This is the raw data obtained from shallow whole-genome sequencing of plasma DNA (plasma-Seq) for calling of somatic copy number alterations as well as focal amplifications and deletions from patients with breast, colorectal and non-small cell lung cancer.

  Dataset EGAD00001006288

• PsychENCODE Consortium: Epigenetic and Transcriptional Dysregulation in Autism Spectrum

  Our current understanding of autism spectrum disorders (ASD) delineates a highly heritable, yet etiologically heterogeneous disease. Forward genetic approaches to find disease associated mutations or common variation have been successful and continue to offer considerable power. Yet, given the accumulating evidence for very significant heterogeneity and environmental influences, complementary approaches to classic forward genetics become necessary. Genetic polymorphism and mutation data to date have identified dozens of causal or contributory variants, yet our preliminary data from autism brain suggest that common molecular pathways are involved in a significant subset of cases. This convergence at the tissue level suggests that other mechanisms, specifically epigenetic changes, combined with genetic background, are contributing to such final common pathways. We further tested this hypothesis by taking a comprehensive and integrative genome-wide approach to assessing brain gene-expression, miRNA levels and the related, causal epigenetic mechanisms in ASD etiology. We performed RNA-seq analyses of four cerebral cortical regions and cerebellum from ASD cases and controls, to assess mRNA, miRNA, and splicing isoform regulation. In parallel, we identified key differences in chromatin state and DNA methylation across multiple brain regions in the same ASD and control individuals used in the expression analyses using ChIP-Seq and MeDIP. We assessed the mechanisms by which changes in DNA methylation, histone modification, and DNA sequence contribute to the observed differences in gene expression. This work, which represents an unprecedented effort to unify these often disparate data (usually produced without integration in mind), delineates potential shared molecular pathways in ASD and the underlying mechanism of these differences at the level of miRNA, the chromatin regulatory apparatus, and DNA methylation. The following substudies are part of the PsychENCODE release at dbGaP and offer additional molecular data: PsychENCODE: RNA-Sequencing - SRRM4 Splicing Study phs000872 PsychENCODE: Global Changes in Patterning, Splicing and lncRNAs phs001061 PsychENCODE: Chromatin Contact Map in Fetal Cortical Laminae phs001190 PsychENCODE: Epigenetic Dysregulation in Autism Spectrum Disorder phs001220

  Study phs001022

• Ex vivo RNA-seq in moderate COVID-19 monocytes

  This dataset was used to compare gene expression profiles of ex vivo isolated classical CD14+ monocytes from patients with moderate COVID-19 to those of healthy individuals. Blood samples were taken from patients with moderate COVID-19 admitted to hospitals in London (Hammersmith Hospital, Charing Cross Hospital, Saint Mary’s Hospital) 3-14 days after disease onset and 0-2 days after hospitalization and positive PCR, and before study treatment initiation. Moderate patients displayed mild or moderate COVID-19 pneumonia, defined as grade 3 or 4 WHO severity. Samples were collected from March 2020 to February 2021. Healthy donors were Imperial College staff with no prior diagnosis of or recent symptoms consistent with COVID-19, and where possible, were matched in age and sex distribution with COVID-19 patients. None of the participants of this study were COVID-19 vaccinated. Peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll Hypaque (GE Healthcare) gradient centrifugation <4 hours after blood collection. CD14+ monocytes were isolated using a positive selection magnetic sorting kit (StemCell Technologies, UK) from total PBMC and stimulated with vehicle, UV-inactivated SARS-CoV-2 (CoV-2). RNA was isolated using the RNeasy Micro Plus Kit (QIAGEN) following the manufacturer’s guidelines. RNA-sequencing was performed by the Oxford Genomics Centre. PolyA-enriched strand- specific libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kits (Illumina). All samples were pooled together and 150bp PE reads were sequenced on a Novaseq 6000 system.

  Dataset EGAD00001009800

• FASTQ files of total RNA-Seq data from the POPS SGA (Small for Gestational Age) samples

  All the samples were obtained from the Pregnancy Outcome Prediction–a prospective cohort study of nulliparous women attending the Rosie Hospital, Cambridge (UK) for their dating ultrasound scan between January 14, 2008, and July 31, 2012. Ethical approval for the study was given by the Cambridgeshire 2 Research Ethics Committee (reference number 07/H0308/163) and all participants provided written informed consent. Cases of preeclampsia (PET) were defined on the basis of the 2013 ACOG criteria and cases of small for gestational age (SGA)infants were confined to severe SGA, i.e. a customized birth weight <5th percentile. Chorionic villi from the corresponding placentas (free from decidua, visible infarction, calcification, hematoma, or damage) were collected and processed within 30 minutes of separation from the uterus. After repeated washes in chilled phosphate buffered saline, the samples were placed in RNA later (Applied Biosystems) and stored at -80°C. Total placental RNA was extracted using mirVana Isolation Kit (Ambion). For each placenta, approximately 5 mg of tissue were homogenized in the Lysis/Binding solution for 20 sec at 6 m/s using a bead beater (FastPrep24) and Lysing Matrix D Tubes (MP Biomedicals). The samples were then spun at 13,000 rpm for 5 min at 4°C and the supernatants recovered. Afterwards, the manufacturer's instructions were followed. Immediately after the RNA extraction, placental RNA samples were DNase-treated using DNA-free DNA Removal Kit (Ambion), aliquoted, and stored in -80°C. Quantity and quality of the RNA samples were assessed using the Agilent 2100 Bioanalyzer, the Agilent RNA 6000 Nano Kit (Agilent Technologies), and Qubit fluorometer. Libraries were prepared starting with 300-500 ng of good quality total RNA (RIN ≥7.5) using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat (Illumina), according to the manufacturer's instructions. The kit contains 96 uniquely indexed adapter combinations in order to allow pooling of multiple samples prior to sequencing. After determining their size (with the Agilent 2100 Bioanalyzer and the Agilent High Sensitivity DNA Kit by Agilent Technologies) and concentration (by qPCR with the KAPA Illumina ABI Prism Library Quantification Kit, Kapa Biosystems), libraries have been pooled and sequenced (single-end, 125 bp) using a Single End V4 Cluster Kit and an Illumina HiSeq2500 or HiSeq4000 instrument.

  Dataset EGAD00001003507