16823 results for "sec+and+unspecified+malignant+neoplasm"

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• Analysis of genomic alterations in dedifferentiated liposarcoma

  Multiomics analysis of rare cancers to identify genetic alterations related with pathogenesis and prognosis. To identification of genetics alterations of Dedifferentiated liposarcoma, DNAs and RNAs were extracted from dedifferentiated liposarcoma and paired non-cancer (normal) tissues. NGS libaraies were prepared by using Agilent SureSelect XT Human All Exon V5 + IncRNA kit for whole exome sequencing (WES) and TruSeq Stranded mRNA Prep kit or TruSeq RNA Access Library Prep kit (RNA seq). Sequencing was perfomred by Illumina HiSeq 2500.

  Study JGAS000182

• Personalized analysis of ctDNA for detection of molecular residual disease and recurrence in a cohort of surgically treated patients with head and neck squamous cell carcinoma

  Despite advances in multimodal treatment, survival for patients with advanced head and neck squamous cell carcinoma (HNSCC) has improved only modestly. The recent advent of tumor-informed assays capable of detecting circulating cell-free tumor DNA (ctDNA) has enabled early detection of molecular residual disease (MRD) and recurrence following curative therapy. We assessed ctDNA in plasma from 76 and saliva from 54 HNSCC patients, respectively, who received primary curative-intent surgery.

  Study EGAS50000001018

• Insights into Adult Gut Microbiota Composition Using the Estonian Cohort

  This study explores the gut microbiota of 1,826 adult individuals, predominantly from the Estonian population. The cohort includes 16S rRNA gene V4 region amplicon sequencing data along with metadata, such as age, sex, health status, anthropometric parameters, and stool consistency. The research aims to characterise the microbial community structure, identify distinct enterotypes, and examine their associations with host characteristics. The dataset provides a valuable reference for understanding gut microbiota composition and supports research in personalised nutrition and lifestyle-related health strategies.

  Study EGAS50000001611

• IMMUcan SCCHN1 cohort

  The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes patients with confirmed locally recurrent and/or metastatic squamous cell carcinoma of the head and neck (SCCHN) who receive first-line treatment with immune checkpoint inhibitors (ICI) or ICI combined with chemotherapy. Comprehensive profiling data are integrated with longitudinally collected clinical information. Cellular profiling of the same tumor samples was performed using multiplex immunofluorescence imaging, imaging mass cytometry, and H&E staining.

  Study EGAS50000001533

• Molecular biomarkers in progression from refractory celiac disease to the lethal cancer variety enteropathy associated T cell lymphoma (EATL)

  Enteropathy associated T cell lymphoma (EATL) is frequently preceded by a state of refractoriness to the gluten-free diet, called “refractory celiac disease” or RCD. We aim to study which mutations and copy number aberrations are already manifest in RCD and to identify differences between RCD patients that do, and do not, develop EATL. We have applied whole exome sequencing to detect mutations and copy number aberration predictive for progression from RCD to EATL.

  Study EGAS00001006669

• Emirati Phased Diploid Trio-Assemblies

  This study, conducted under the Emirati Genome Project, aims to build a foundational pangenome reference to enable precision medicine in the United Arab Emirates. We generated phased diploid genome assemblies for 27 Emirati nationals using deep PacBio HiFi sequencing and a trio-based assembly procedure. In total, this produced 54 haplotype-resolved assemblies representing maternal and paternal genomes for each participant. The resulting high-quality reference captures population-specific genetic diversity and will accelerate translational research, variant interpretation, and genome-informed healthcare in the region.

  Study EGAS50000001234

• RNA sequencing from patient-derived intestinal organoids

  RNA from the duodenal organoids was isolated using an RNeasy Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. RNA purity and concentration were measured using a NanoDrop One spectrophotometer (NanoDrop Technologies, Wilmington, Delaware, USA). Preparation of the RNA library and transcriptome sequencing was conducted by Novogene Co., LTD (Cambridge, UK). Messenger RNA was purified from total RNA using polyA selection and subjected to library construction. Sequencing was performed on an Illumina platform, and 150 bp paired-end reads were generated.

  Study EGAS50000000338

• A first step towards clinical routine long-read sequencing in Sweden, a national pilot study on chromosomal rearrangements

  Here, the Genomic Medicine Sweden Rare Diseases (GMS-RD) consortium validated HiFi Revio long-read whole genome sequencing (lrGS) for clinical digital karyotyping of SVs nationwide. The first 16 samples included in this study were collected from all health care regions in Sweden. We established a national pipeline and a shared variant database for variant calling and filtering. The included validation samples cover a spectrum of simple and complex SVs including inversions, translocations and copy number variants.

  Study EGAS50000000468

• Human dorsal root ganglia after plexus injury - RNA-fragment sequencing from histological slices

  Human dorsal root ganglia from patients with brachial plexus injury and from subjects from forensic autopsy were extracted and fixed with paraformaldehyde. The cellular composition of these DRG was analysed in histopathological slices. From some of the slices, total RNA was extracted and total RNAseq was performed. The RNA sequencing data represent DRG with neuronal preservation (n=6) or neuronal loss (n=2) versus control (n=6). Details can be found in the corresponding publication and supplement to this publication.

  Study EGAS50000000682

• Calprotectin in vitro effects on human early hematopoiesis

  Dataset content : Raw data from sequencing (fastq) 184 samples from 4 experiments : - Bulk mRNA seq - 24h and 48h, CTRL, CAL, IL6 and combination treatment - single-cell RNAseq - 7days CTRL, CAL, IL6 and combination treatment - ATACseq - 7days CTRL, CAL, IL6 and combination treatment To explore the effects of calprotectin (CAL) on early hematopoiesis, we incubated CD34+ cells from four healthy donors for 7 days in the presence of stem cell factor (SCF), FLT3-ligand and thrombopoietin (TPO) without and with CAL, interleukin-6 (IL6) and the IL6_CAL combination before collecting cells. We performed the same experiment with CD34+ cells collected from three patients with JAK2-V617F-mediated myelofibrosis (MF). A total of 135,545 cells from healthy donors and 111,725 cells from myelofibrosis patients were analyzed by single-cell RNA sequencing (scRNA-seq) using the 10X Chromium droplet-based platform.

  Dataset EGAD50000000659