Search Results - EGA European Genome-Phenome Archive

RNAseq data of polyA+ RNA from Leukocytes from 624 individuals of the ProgeNIA cohort.

We sequenced the polyA+ fraction of the RNA of the leukocytes from 624 sardinian individuals with RNAseq. Prior to library preparation we added either ERCC ExFold RNA Spike-In. An average of 60M reads per samples with 51 bp paired-end reads were generated on a HiSeq 2000 (Illumina). Sequencing reads were then aligned using STAR-2.2.0c2 to the h37d5 reference genome supplemented with the ERCC spike-ins sequences. We further provided an exon-exon junction database that we generated from the GENCODE v14 annotation. In order to remove a contamination from a parallel experiment, we discarded any reads that mapped to the genomic regions of CBLB (chr3:105370773-105592330) and BCL11A (chr2:60672555-60784156). Filtered aligned reads (bam format) are shared.

Dataset EGAD00001003102

DNA and RNA sequencing data from Ovarian Carcinosarcoma patients from the Glasgow Cohort.

In this study, we analysed DNA and RNA sequencing data from Ovarian Carcinosarcoma patients, from isolated carcinoma and sarcoma components and investigated DNA variants as well as gene expression. Genomic analyses from this data and further investigation from preclinical models of ovarian carcinosarcoma support the conversion theory for disease development and indicate that microtubule inhibitors could be used to suppress EMT and stimulate anti-tumour immunity.

Study EGAS00001006605

Single Cell RNA sequencing of Organoids from TSC2+/- patient IPSCs in H- and L-medium

This dataset contains single cell RNA sequencing data from Organoids grown in high nutrient (H) and low nutrient (L) medium. Organoids were grown for 110 days. Organoids were grown from a patient IPS cell line with a heterozygous mutation in TSC2 (Patient 1 TSC2+/- iPSCs) and an isogenic control cell line (TSC2+/+).

Dataset EGAD00001006332

Dataset on keratinocytic gene expression pattern in Hidradenitis suppurativa

Human skin samples were obtained from HS patients after informed consent (Ethical vote, University of Würzburg; No. 306/12). Lesional and perilesional were taken and epidermis and dermis separated. Isolated epidermal keratinocytes were further processed for RNA isolation. mRNA was extracted from five pairwise-matched lesional and perilesional epidermal HS pellets and RNA sequencing was performed.

Dataset EGAD00001008005

RNA-sequencing data of post-mortem brain tissue taken from individuals with SCA3 and controls

Spinocerebellar ataxia type 3 (SCA3) is the most common autosomal dominant inherited ataxia worldwide, caused by a CAG repeat expansion in the Ataxin-3 gene resulting in a polyglutamine (polyQ)-expansion in the corresponding protein. Here we have RNA-sequencing data from the cerebellum of individuals with SCA3 and matched controls.

Dataset EGAD00001009317

Total NF1 sequence in the patients with neurofaibromatosis type1

<html>We analyzed whole <i>NF1</i> gene region at DNA (including whole exon and intron sequences) and RNA (full length cDNA of leukocyte) level for 20 patients with neurofibromatosis type 1.</html>

Study JGAS000288

The study on genomic profiling using clinical specimens (tissue, blood, etc.) form patients with lung and thymic tumors

The objective is to generate a comprehensive immunogenomic profiling in thymoma using RNA sequencing and TCR repertoire analysis and to evaluate the potential of immunotherapy in thymoma from multiple perspectives.

Study JGAS000552

Rapid Idiosyncratic Mechanisms of Clinical Resistance to KRAS G12C Inhibition

Using deep RNA and whole exome sequencing of pre- and post-treatment autopsy samples, we reveal diverse clonal populations that occurred through altered cell intrinsic, tumor microenvironment and immunologic remodeling mechanisms of resistance.

Study phs002734

Longitudinal evaluation of serum microRNAs as biomarkers for neuroblastoma burden and therapeutic p53 reactivation

Accurate assessment of treatment response and residual disease is indispensable for the evaluation of cancer treatment efficacy. However, performing tissue biopsies for longitudinal follow-up poses a major challenge in the management of solid tumours like neuroblastoma. In the present study, we evaluated whether circulating miRNAs are suitable to monitor neuroblastoma tumour burden and whether treatment-induced changes of miRNA abundance in the tumour are detectable in serum. We performed small RNA sequencing on longitudinally collected serum samples from mice carrying orthotopic neuroblastoma xenografts that were exposed to treatment with idasanutlin or temsirolimus. We identified 57 serum miRNAs to be differentially expressed upon xenograft tumour manifestation, out of which 21 were also found specifically expressed in the serum of human high-risk neuroblastoma patients. The murine serum levels of these 57 miRNAs correlated with tumour tissue expression and tumour volume, suggesting potential utility for monitoring tumour burden. In addition, we describe serum miRNAs that dynamically respond to p53 activation following treatment of engrafted mice with idasanutlin. We identified idasanutlin-induced serum miRNA expression changes upon one day and 11 days of treatment. By limiting to miRNAs with a tumour-related induction, we put forward hsa-miR-34a-5p as a potential pharmacodynamic biomarker of p53 activation in serum.

Study EGAS00001006678

The PEMDAC phase 2 study of pembrolizumab and entinostat in patients with metastatic uveal melanoma

Patients with metastatic uveal melanoma (UM) have an abysmal prognosis. Preclinical studies have suggested that epigenetic therapy could enhance immunogenicity of cancer cells. Here we test if epigenetic therapy would enhance PD-1 immunotherapy in patients with metastatic UM. We report the results of the PEMDAC phase 2 clinical trial (n=29; NCT02697630) where the HDAC inhibitor entinostat was combined with the PD-1 inhibitor pembrolizumab in patients with metastatic UM. The primary endpoint was objective response rate (ORR), and was met with an ORR of 14%. The clinical benefit rate at 18 weeks was 28%, median progression free survival was 2.1 months and the median overall survival was 13.4 months. Toxicities were manageable, and there were no treatment-related deaths. Extensive genomics studies were performed using DNA/RNA and single cell sequencing and flow cytometry. Objective responses and prolonged survival were seen in three patients with BAP1 wildtype tumors, and in one patient with an iris melanoma that exhibited a UV signature. Longer survival also correlated with low baseline ctDNA levels or LDH. In conclusion, HDAC inhibition and anti-PD1 immunotherapy results in durable responses in a subset of patients with metastatic UM. Further exploration of combined immunotherapy and epigenetic therapy in metastatic UM is warranted.

Study EGAS00001005478

9296 results for "cancer rna-seq"

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