Search Results - EGA European Genome-Phenome Archive

Metatranscriptomic Sequencing of Pulmonary Fluid in Immunocompromised Children

Despite improved diagnostics, pulmonary pathogens in immunocompromised children frequently evade detection, leading to significant mortality. In version 1.0 of this study, we performed RNA-based next generation sequencing (mNGS) on 41 lower respiratory samples collected from 34 children. We identified a rich cross-domain pulmonary microbiome containing bacteria, fungi, RNA viruses, and DNA viruses in each patient. Potentially pathogenic bacteria were ubiquitous among samples but could be distinguished as possible causes of disease by parsing for outlier organisms. Potential pathogens were detected in half of samples previously negative by clinical diagnostics. In version 2.0, we included an addition 278 samples from 229 pediatric stem cell transplant patients with pulmonary disease.

Study phs001684

Genetics of diffuse large B-cell lymphoma in Japan

Diffuse large B-cell lymphoma (DLBCL) is a common hematological malignancy. Treatment with standard chemotherapy results in long-term remission in approximately 60% of patients. Whole-exome sequencing studies of large DLBCL cohorts revealed the biological diversity of tumors and facilitated the identification of genetic subtypes based on genetic alterations. Despite the progress facilitated by NGS, genetic classification is difficult to apply in clinical practice because of the complexity of the clustering algorithm. Furthermore, only a few reports included large Asian cohorts. Thus, a genetic overview of Japanese patients with DLBCL is still needed. Thus, in this study, we aimed to establish the clinical application of our simplified genetic classification algorithm in Japanese DLBCL.

Study JGAS000307

bulk RNAseq analysis of tumor from 3 non-muscle-invasive bladder cancer patients

We performed screenings of patient-specific neo-epitopes by tumor-infiltrating CD8+ T lymphocytes of 4 non-muscle invasive bladder cancer patients. After the tumor resection, these patients went on to receive BCG treatment as they had high-risk disease. In order to select the neo-epitopes, we performed bulk RNAseq of the bladder tumor to select the mutated genes that were expressed in the tumor (TPM >1). For patient UC2, 3 different tumors were resected at the same time and RNA from these 3 tumors were sent separately for RNAseq. For patient UC4, no RNA was available, so this patient is not included in this study.

Study EGAS50000001383

Metagenomic characterization of tracheal aspirates from non-pulmonary sepsis patients

Our previous studies in mechanically ventilated Intensive Care Unit (ICU) patients with extrapulmonary sepsis revealed that pulmonary dysbiosis within 8 h from sepsis diagnosis was associated with ICU mortality. These observations offer promising options that could be technologically adapted to rapidly identify those patients at higher risk of death. However, they relied on 16S rRNA sequencing experiments which impedes deep characterization of the bacterial communities that could help to further substantiate the association. To further discern this association, here we assessed the pulmonary bacterial communities in these patients by leveraging metagenomics and evaluated if the presence of antibiotic resistance genes could explain the higher mortality of the patients.

Study EGAS50000000384

16758 results for "sec+and+unspecified+malignant+neoplasm"

in 29.61 milliseconds.

Metatranscriptomic Sequencing of Pulmonary Fluid in Immunocompromised Children

Genetics of diffuse large B-cell lymphoma in Japan

bulk RNAseq analysis of tumor from 3 non-muscle-invasive bladder cancer patients

Metagenomic characterization of tracheal aspirates from non-pulmonary sepsis patients

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a mucinous colloid carcinoma of the pancreas patient

Genome and transcriptome sequence data from a metastatic melanoma patient

Genome and transcriptome sequence data from a non-small cell adenocarcinoma patient

Genome and transcriptome sequence data from a metastatic leiomyosarcoma patient

Genome and transcriptome sequence data from a metastatic synovial sarcoma patient

Genome and transcriptome sequence data from a osteosarcoma patient

Genome and transcriptome sequence data from a metastatic adenocarcinoma of the rectosigmoid patient

Genome and transcriptome sequence data from a metastatic non-small cell lung cancer patient

Genome and transcriptome sequence data from a metastatic gastric cancer patient

Genome and transcriptome sequence data from a double-hit lymphoma patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a metastatic rectosigmoid cancer patient

Genome and transcriptome sequence data from a metastatic non-small cell lung cancer patient

Genome and transcriptome sequence data from a metastatic adenocarcinoma of the stomach patient

Genome and transcriptome sequence data from a metastatic mmmt of the endometrium patient

Genome and transcriptome sequence data from a anorectal gastrointestinal stromal tumor patient

Genome and transcriptome sequence data from a ganglioglioma of the left temporal lobe patient

Genome and transcriptome sequence data from a metastatic follicular thyroid carcinoma patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a metastatic pancreatic adenocarcinoma patient