Project description:In this study, we conducted a histopathological-based analysis of 10x Genomics Visium spatial transcriptomics data on a human kidney sample corresponding as closely as possible to the reality of the interpretation of a kidney biopsy in a healthcare or research context.
Project description:This clinical trial studies the effectiveness of a web-based cancer education tool called Helping Oncology Patients Explore Genomics (HOPE-Genomics) in improving patient knowledge of personal genomic testing results and cancer and genomics in general. HOPE-Genomics is a web-based education tool that teaches cancer/leukemia patients, and patients who may be at high-risk for developing cancer, about genomic testing and provide patients with information about their own genomic test results. The HOPE-Genomics tool may improve patient’s genomic knowledge and quality of patient-centered care. In addition, it may also improve education and care quality for future patients.
Project description:To enable the implementation of precise genomics in a local healthcare system, we devised a pipeline for filtering and reporting of relevant genetic information to healthy individuals based on exome or genome data. In our analytical pipeline, the first tier of filtering is variant-centric, and it is based on the selection of annotated pathogenic, protective, risk factor, and drug response variants, and their one-by-one detailed evaluation. This is followed by a second-tier gene-centric deconstruction and filtering of virtual gene lists associated with diseases, and VUS-centric filtering according to ACMG pathogenicity criteria and pre-defined deleteriousness criteria. By applying this filtering protocol, we were able to provide valuable insights regarding the carrier status, pharmacogenetic profile, actionable cardiovascular and cancer predispositions, and potentially pathogenic variants of unknown significance to our patients. Our experience demonstrates that genomic profiling can be implemented into routine healthcare and provide information of medical significance.
Project description:The data provided here is related to the publication “Peptidomic and proteomic analysis of precision-cut lung slice supernatants”. In this study, we sought out to develop a method that could incorporate a peptidomic and proteomic endpoint within the same workflow. The developed workflow was adapted from single-pot, solid-phase-enhanced sample preparation (SP3) for examining the proteome and peptidome of precision-cut lung slice supernatants in one experimental procedure to save sample material. A part of the study compared potential differences when utilizing different organic solvents for binding peptides and proteins to magnetic beads for biological replicates of PCLS supernatant. In connection, the workflow robustness was also characterized by investigating technical replicates of the same biological PCLS supernatant sample.
