11756 results for "cancer rna-seq"

in 20.17 milliseconds.

• Subclonal variation in patients with pediatric T-lymphoblastic leukemia (T-ALL)

  Variations in TP53 and KRAS genes indicate a particularly poor prognosis in relapsed pediatric T-ALL. We hypothesized that these variations might be subclonally present at disease onset and contribute to relapse risk. To test this, we examined 386 children diagnosed with T-ALL, including more than 100 patients who relapsed as well as matched non-relapsing controls.

  Study EGAS50000000794

• Genotyping microarray data of molecular tumorboard patients in the context of the HRD-manuscript published in IJC

  Intensity files (.idat) derived from the Infinium CytoSNP-850K BeadChip microarray (Illumina) were used to analzye a possible Homologous-Recombination-Repair Deficiency (Molecular Rationale for a PARP-Inhibitor therapy) of n= 39 tumor patients (each n= 39 .idat files of the green and red chanel respectively) presented in the Molecular Tumorboard at the University Hospital Erlangen. Using these files a Genomic Instability Score was bioinformatically deducted (R-based scripts, e.g. ASCAT, scarHRD) based upon the presence of three parameteres "Loss of Heterozygosity, LOH", "Large Scale Transitions, LST" and "Telomeric Allelic Imbalances, TAIs". The associated manuscript is published in International Journal of Cancer, IJC.

  Dataset EGAD00010002736

• Clonal hematopoiesis in rheumatoid arthritis

  To evaluate the clinical impact of CHIP on RA phenotypes and outcomes, we collected DNA samples from four distinct RA patient cohorts of newly diagnosed, previously untreated, RA patients without hematologic malignancies. A total of 573 RA patients and 163 healthy controls underwent targeted NGS sequencing using a sequencing panel consisting of 65 genes recurrently mutated in myeloid malignancies.

  Study EGAS50000000890

• Labcorp® Plasma Detect™ assay: whole genome sequencing analyses of plasma cfDNA, white blood cells and FFPE tumor tissue

  The dataset "Labcorp® Plasma Detect™ assay: whole genome sequencing analyses of plasma cfDNA, white blood cells and FFPE tumor tissue" includes CRAM and CRAI files derived from WGS of 555x plasma cfDNA, 209x white blood cells (normal DNA) and 209x FFPE tumor tissue (tumor DNA) samples for 209 stage III colorectal cancer patients. WGS (150bp PE) was performed on a NovaSeq 6000 with a target depth of coverage of 80x for tumor DNA, 40x for normal DNA and 30x for cfDNA. Reads were aligned to GRCh37 (plasma cfDNA) or GRCh38 (tumor/normal DNA).

  Dataset EGAD50000001180

• TSO500 sequencing of ovarian tumour samples

  This dataset consists of 8 ovarian cancer DNA sample libraries prepared using the Illumina TruSight Oncology 500 Kit (Illumina, cat no. 20076480) following the manufacturer's protocol. Library quality and quantity were assessed with High Sensitivity/D5000 Screentape Assay (Agilent Technologies, cat no. 5067-5592) on 4150/4200 Tapestation Quant-IT/Qubit dsDNA HS (Qiagen, cat no. Q32851) assay according to the supplier’s recommendations. Libraries were then pooled together in equal ratios and sequenced using PE-150bp mode on NovaSeq S1 flow cell 300 cycles kit (Illumina, 20028317) or S4 flow cell 300 cycles kit (Illumina, 20028312) aiming for 100 million reads per sample. The dataset contains sequence reads in fastq file format.

  Dataset EGAD50000001451

• Melanoma_multi_site_metastases

  Despite multiple large-scale sequencing studies offering substantial insight into the genomic landscape of cutaneous melanoma, the molecular events surrounding disease progression and the resulting molecular heterogeneity between metastases have not been fully elucidated. We have been applying whole genome and transcriptome sequencing across metastases collected during post mortem as well as to multi-site metastases during treatment

  Study EGAS00001001348

• Somatic Inactivation of Breast Cancer Predisposition Genes in Tumours Associated with Pathogenic Germline Variants

  Breast cancers (BC) from susceptibility gene carriers, including BRCA1/2, PALB2 and RAD51C, have been shown to have bi-allelic loss in the respective genes and be associated with triple-negative (TN) BC and distinctive somatic mutational signatures. Tumour sequencing thus presents an orthogonal approach to assess the role of candidate genes in BC development.

  Study EGAS00001006532

• WGS___Mutant_clone_mapping_in_normal_oesohagus_and_skin

  We will use whole genome sequencing to examine normal appearing oesophageal epithelium and skin to determine the mutational burden. DNA will be extracted from epithelia of a defined size and we will overlay positional information from the epithelial pieces to give clone maps over a wide area. This will be done in both oesophageal epithelium and skin

  Study EGAS00001002416

• Multiple_Myeloma_Diagnosis_to_Relapse_study_samples

  The study will investigate serial samples from the same patient taken at the time of MGUS or SMM diagnosis, and later at the time of evolution towards MM. Samples will be sequenced by whole genome along with a matched normal to obtain the highest possible amount of information toinvestigate genomic changes at disease evolution.

  Study EGAS00001001299

• Single-cell transcriptome sequencing of regulatory and conventional T cells in breast cancer patients and healthy individuals.

  Identification of tumor-specific effects on gene expression profile of regulatory T cells and conventional T cells in humans, investigation of the clonal origin of regulatory T cells and impact analysis of tumor-specific conversion of conventional T cells into induced regulatory T cells on the peripheral regulatory T cell repertoire in humans.

  Study EGAS00001002933