14977 results for "cancer studies using rna-seq"

in 18.13 milliseconds.

• Spatially resolved antigen receptor and gene expression data from human tonsil tissue

  The dataset includes spatially-resolved gene expression and antigen receptor data from two Tonsil samples (1 and 2). Tissue sections from the tonsil samples were used for spatial transcriptomics (Visium, 10x genomics). Tonsil 2 tissue sections were analyzed by a new method (Spatial VDJ) to spatially resolve antigen receptor sequences (target capture), which was developed in our publication. Nearby or adjacent tissue sections (from Tonsil2) were also analyzed by a bulk antigen receptor sequencing approach (amplicon sequencing), by a method also newly developed by us in the same publication (Bulk SS3 VDJ). For Visium, the data were anonymized (all SNPs removed) using Bamboozle (Ziegenhain and Sandberg, Nature Communications 2021). The deposited data is in the form of fastq files. All remaining data, metadata, micrographs of the tissue sections (of those used for spatial transcriptomics), and scripts used for the analysis are available at Zenodo (DOI: 10.5281/zenodo.7961605). Final libraries were sequenced on NextSeq2000 (Illumina) or NovaSeq6000 (Illumina) and analyzed with Seurat, Space Ranger, and STutility pipelines.

  Dataset EGAD00001011062

• Human Cancer-Targeted Immunity via Transgenic Hematopoietic Stem Cell Progeny

  Analysis of a patient biopsy from the clinical trial (NCT03240861), a first-in-human study of transgenic NY-ESO-1 TCR- T cells and NY-ESO-1 TCR+ sr39tk autologous hematopoietic stem cells tandem therapy for solid tumors after myeloablative conditioning chemotherapy with busulfan and fludarabine. Single-cell RNAseq and single-cell ATACseq analysis from peripheral blood mononuclear cells obtained from subject NYSCT-03.

  Study phs003898

• Mutational signatures in normal tissues of patients treated with clinical stage G-quadruplex binder CX5461

  Drug induced photoreactions following exposure to UVA have been documented for several therapeutic compound classes, including psoralens and fluoroquinolones. We used deep (~80X) whole genome sequencing to examine the mutagenic spectrum of CX5461, quinolone-derived small molecule, in normal tissues of cancer patients undergoing treatment. We compared the distribution of somatic base substitutions and short indels from skin biopsies taken from non-sun exposed areas pre and post CX5461 exposure of patients. To further characterize the mutational pattern of CX5461 photoreactivity, we compared mutational profiles of human retinal pigment epithelial cells exposed to UVA, CX5461, or a combination of both UV and CX5461.

  Dataset EGAD50000001640

• Excised DNA Circles from V(D)J Recombination Promote Relapsed Leukaemia

  In this study, we show that ESCs replicate and persist through many cell generations. High ESC copies at diagnosis of BCP-ALL strongly correlate with subsequent relapse. These data provide the first demonstration that the V(D)J recombination by-product, when replicated to elevated levels, potently associates with the V(D)J recombinase to cause adverse disease outcomes.

  Study EGAS50000000407

• Bevacizumab plus erlotinib in advanced solid cancers with Krebs cycle gene mutations: A multicenter phase II study

  Targeting aberrant metabolism in tumors with alterations in genes encoding Krebs cycle enzymes, a central component of glucose metabolism, is a promising therapeutic strategy. These tumors rely on aerobic glycolysis and promote VEGF-dependent angiogenesis; furthermore, EGFR signaling enhances aerobic glycolysis. This phase 2 trial evaluated bevacizumab and erlotinib in patients with solid tumors harboring Krebs cycle gene mutations.

  Study EGAS50000001243

• Whole-genome sequencing on hepatocellular carcinoma with nodule-in-nodule appearance reveals stepwise cancer evolution

  We examined five cases with hypovascular early HCC with hypervascular foci, so-called nodule-in-nodule HCC. Multiregional sampling was performed from both the inner hypervascular region and outer hypovascular region, together with noncancerous liver tissue and lymphocytes as controls. Comprehensive analysis of genomic aberrations, such as single nucleotide variants (SNVs) and structural variations (STVs), was performed by whole-genome sequencing.

  Study JGAS000190

• Whole genome sequencing informs treatment decision of end-stage metastatic cutaneous angiosarcoma in a patient with Xeroderma Pigmentosum

  Whole genome sequencing (WGS) detects all mutations in a cancer. “Mutational signatures” are patterns of mutations that report the DNA damage and subsequent DNA repair processes that have occurred in cancers. We present a patient with Xeroderma Pigmentosum that developed metastatic angiosarcoma, unresponsive to all lines of sarcoma therapy. Primary tumour WGS revealed a hypermutated tumour, including clonal ultraviolet light-induced mutational patterns (Signature 7) and subclonal signatures of activating mutations of DNA Polymerase-epsilon (POLE)(Signature 10). These signatures are associated with response to immune-checkpoint blockade. Immunohistochemistry confirmed high PD-L1 expression in metastatic deposits. The patient was commenced on anti-PD-L1 therapy and has responded.

  Dataset EGAD00001004786

• Cylindromas_sun_protected_and_exposed

  The project aims to look at mutational signatures in a rare inherited skin tumour syndrome called CYLD cutaneous syndrome. These patients develop multiple skin tumours that are seen at sun exposed and sun protected sites. We plan to carry out WGS on carefully curated tumours from such patients. We then plan to analyse this data for mutational signatures, comparing this between sun exposed and sun protected sites.

  Study EGAS00001002521

• Clonal architecture and genomic features of smoking versus non-smoking oncogene-driven East-Asian non-small cell lung cancer

  Unlike smoking-related non-small cell lung cancers (NSCLC), oncogene-driven tumors are characterized by low mutational burdens and complex genomic landscapes. However, the clonal architecture and genomic landscape of the oncogene-driven tumors in smokers remains unknown. Here, we investigate the impact of tobacco smoking on the genomic and transcriptomic alterations in the context of oncogene-driven NSCLC.

  Study EGAS00001006942

• Transcriptomic Analysis of Pluripotent Stem Cell-Based Model of Human Amniogenesis

  The amniotic epithelium is the innermost layer of the amniochorionic membrane that physically divides the maternal and fetal environments. Amniogenesis is initiated during implantation in humans. In implanting blastocysts, the pluripotent epiblast cells undergo apical-basal polarization to form a cyst with a central lumen, the future amniotic cavity. This event is followed by the fate transition of pluripotent epiblast cells at the uterine-proximal pole of the cyst to squamous amniotic ectoderm, forming a sharp boundary between amnion and pluripotent epiblast portions of the cyst. To enable mechanistic investigations into amnion fate progression, several in vitro models based on human pluripotent stem cells were recently developed. In this study, transcriptomic features of human pluripotent stem cell-derived amniogenesis models were examined.

  Study phs002184