TECHNOLOGIES We are using and developing a range of technologies on extracting genomic and proteomic data from patient derived archival material. We perform our genomic analyses including single cell and bulk RNA sequencing for gene expression profiling and DNA exome- & shallow-sequencing for mutation calling and assessment of DNA copy number alterations. These are followed by validation of the data with in situ hybridization or immunohistochemistry on tissue microarrays. We are also developing computational pathology approaches for extracting morphological, spatial and geometrical data from patient derived archival material. By integration of clinical, pathology, genomic and proteomic data we aim to discover new diagnostic and prognostic markers in breast and ovarian cancer, to identify potential therapeutic targets. Read more about the techniques on extracting genomic, proteomic and morphological data on clicking the individual links below: Bulk RNA sequencing Single cell RNA sequencing DNA whole genome and exome sequencing DNA shallow sequencing Tissue micro arrays (TMA) Multiplex Immunohistochemistry VECTRA multi-spectral imaging Multiplexed Ion Beam Imaging (MIBI) Digital Spatial Profiling (Nanostring Tissue Cytof (Fluidigm) Computational Pathology approaches Tools / applications Redcap: electronic CRF application OpenSpecimen: open source biobanking informatics platform. Slidescore: for viewing & scoring pathology slides and TMA Qupath: open source software for Quantitative Pathology CBIOPORTAL: integration and analysing Cancer Genomics Cytosplore: visual analysis of mass cytometry (CyTOF) data BRCA1/2: classifier for Breast and Ovarian Cancer Software Archive SIRAC code for analysis of aCGH data PROTOCOLS Handling of Biospecimens (Tissue, DNA, RNA, Blood, Stool) Collect Store Process Analyse Report Ad 1. Collecting of biospecimens and related information Clinical (DWH, WA, HIX, Trial desk)Tool = Castor Imaging (DWH, PAX)àTool = NXPACT Pathology (DWH, Poema, LMS)Tool = Castor Molecular Diagnostics (MD database, Hartwig)Tool = cbioportal Blood (Glims, AKL)àTool = Castor Ad 2. Storage of Biospecimens Tissue, blood, stool (OpenSpecimen) Ad 3. Processing of Biospecimens Histology Hematoxylin and Eosin Stain for Parraffin sections Construction of Tissue Micro Array Single Immunostaining Laser capture microdissection Molecular DNA and RNA isolation from Frozen Material DNA and RNA extraction from FFPE material RNA / DNA Library construction for sequencing Fluorescent In Situ Hybridization (FISH) RNAscope Sequencing RNA sequencing Nano-string encounter RNA sequencing DNA Sequencing ATAC sequencing Multiplex visualisation of labeled Antibodies in paraffin Section Multiplex Immunostaining (DAB) Fluorescent labeling (Vectra) Tissue Cytof (UMC Utrecht) MIBI (NolanLab) Codex (NolanLab) DSP Nanostring Ad 4. Analysing of processed data RNA seq data nCounter Nanostring data Shallow sequencing data (Copy number altertations) Whole exome sequencing data (Variant calling) Mutational signatures Mutational Tumor Burden Ad 5. Reporting and Distribution of bio-specimens and data Material and Transfer agreement DataTransfer Agreement Packaging instructions of Tissue, DNA, RNA and Blood samples
