14676 results for "PLOS+ONE+Pennsylvania+German+ACS+language+code+pdc+open+access+study"

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• Genetic Evaluation of Autoinflammatory Diseases

  Many pediatric patients with early-onset autoinflammatory disease (AID) phenotypes are mutation-negative for genetically known AIDs. Recent data suggest a role for Type-I interferon (IFN) dysregulation in causing AID phenotypes with clinical features that are distinct from those found in patients with IL-1 mediated AIDs. We screened patients for the presence of an IFN-response gene signature (IRS) to characterize their clinical phenotypes, IFN-related biomarkers, and genetic causes.

  Study phs001946

• Platinum-based chemotherapy induces opposing effects on immunotherapy response-related spatial and stromal biomarkers in the bladder cancer microenvironment

  The goal of the current project was to investigate the modulation of the tumor-immune microenvironment (TME) by neo-adjuvant platinum-based chemotherapy in muscle-invasive bladder cancer. Furthermore, we aimed to focus on how this modulation affects biomarkers of response to immune checkpoint inhibitors. Additionally, we aimed to explore the differences between MVAC and gemcitabine-containing platinum-based regimens regarding their effects on the bladder TME.

  Study EGAS50000000309

• Panel sequencing of endocrine-resistant breast cancer

  Patients with endocrine-resistant breast cancer in Stockholm Sweden. DNA obtained from patients primary and relapse tumors, and tumor-free lymph nodes used as germline control. DNA was extracted from formalin-fixed paraffin-embedded tissue and sequenced by 370-gene panel-based sequencing with Kapa HyperPlus library preparation and Twist Bioscience hybrid capture. Custom bait sets (panels) from Twist Bioscience. Paired end 2x150 bp using NovaSeq X. The data is presented as fastq-files.

  Study EGAS50000000236

• LCM-isolated buccal epithelial cell sequencing

  Single buccal epithelial cells were dissected and collected on an adhesive cap with laser capture microdissection (LCM) with approximately 13-60 cells per cap. Each adhesive cap containing 13-60 cells was independently processed with QIAamp DNA micro kit (Qiagen) for DNA extraction. The NEBNext ultra II FS DNA library kit was used to prepare DNA libraries with low starting material. Paired-end whole genome sequencing reads were obtained with the NovaSeq.

  Study EGAS50000000098

• DNA methylation database for gynecological cancer detection, classification and assay development

  DNA methylation changes are associated with cancer the best predictor of the presence of cancer. In order to detect and classify gynecological cancer, we performed MeD-seq to generate DNA methylation profiles of vulvar, cervical, endometrial, fallopian tube and ovarian cancers and their associated healthy tissues. DNA methylation profiles were used to find general cancer, regional cancer and specific cancer biomarkers that can be used for cancer detection, classification and treatment monitoring.

  Study EGAS50000000417

• Cergentis FFPE-TLC sequencing of colorectal carcinoma

  In this study, formalin-fixed paraffin-embedded targeted locus capture (FFPE-TLC) sequencing is used as a novel technology for targeted detection of tumor-specific genomic structural variants (SVs) in the primary tumor of 29 colorectal cancer patients with metastatic disease. The tumor region was macrodissected and sequenced for 29 patients, and the "normal" region of the same slide was macrodissected and sequenced for 8 of these patients. SVs were found in the common fragile site (CFS)-associated genes MACROD2, PRKN, FHIT and WWOX as well as SVs caused by three LINE transposable elements. Tumor-specificity of selected SVs was independently verified by droplet digital PCR of tumor tissue DNA and their applicability as plasma circulating tumor DNA biomarkers was demonstrated. This dataset contains the hg19 reference alignment of the FFPE-TLC sequences for all 29 colorectal cancers and 8 adjacent normals.

  Dataset EGAD50000000618

• Whole genome and transcriptome sequencing of cancer of unknown primary tumours

  Whole genome and transcriptome sequencing of cancer of unknown primary tumours was used to determine yield of clinical biomarkers for a molecular guided trial or for resolving cancer type of origin. This study includes profiling of germline DNA and tumour DNA and RNA by whole genome and transcriptome sequencing. All samples are in BAM format aligned with GRCh38 reference genome. This dataset includes: 1. Whole genome sequencing (WGS) of 78 cancer of unknown primary tumour samples and 73 matched germline DNA. 2. Whole transcriptome sequencing (WTS) of 69 cancer of unknown primary tumour samples (matched to WGS cases) 3. Whole genome sequencing of 22 cell-free DNA samples from cancer of unknown primary patients and matched Germaine DNA(8 samples matched to tumour WGS)

  Dataset EGAD50000000656

• Characterisation of Cyr61-enriched myeloid angiogenic cells

  We previously demonstrated the enrichment of an angiogenic precursor cell population from peripheral blood mononuclear cells by CYR61, a protein of the CCN family. In vivo, CYR61 mediates the binding of leukocytes and particular monocyte populations at sites of vascular inflammation. Here, we present an in vitro enrichment system mimicking (patho)physiology and at the same time representing an effective tool for enrichment of the CYR61-binding blood cells and analyzed this cell population in depth.

  Study EGAS50000000533

• Genomic Profile of Multiple Localised Spiradenoma and Spiradenocarcinoma

  Multiple spiradenomas and spiradenocarcinoma from a single donor were subjected to exome sequencing. Tumor samples were microdissected from formalin-fixed, paraffin-embedded tissue, and genomic DNA was extracted. The DNA samples were subjected to library generation using the xGen ssDNA & Low-Input DNA Library Preparation Kit, followed by exome capture using the xGen Exome Research Panel v2. The libraries were sequenced on DNBSEQ G400RS. Reads were aligned to GRCh37 with BWA.

  Study EGAS50000000554

• Transcriptome Sequencing PPGL (2)

  RNA-Seq data (n=81) library preparation was performed as previously reported by Calsina et al 2023 using QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, 015). The prepared libraries were subsequently sequenced on NovaSeq™ system (Illumina). To combine the new CNIO samples (n=81) with the CNIO+TCGA dataset generated in Calsina et al., 2023, RNA data were processed using ComBat-seq as described in that same article.

  Study EGAS50000000013