1 / 18

Infrastructures for Personalised Medicine Janna Saarela

Infrastructures for Personalised Medicine Janna Saarela. International research institute Member of Nordic EMBL Partnership for Molecular Medicine Located in the largest hospital campus in Finland. FIMM accomplishes translational research & molecular precision medicine.

pwells
Download Presentation

Infrastructures for Personalised Medicine Janna Saarela

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Infrastructures for Personalised Medicine Janna Saarela

  2. International researchinstitute Member of Nordic EMBL Partnership for Molecular Medicine Located in thelargesthospital campus in Finland

  3. FIMM accomplishes translational research & molecular precision medicine • BIOBANK INFRASTRUCTURE • National population biobanks • Disease biobank projects (FHRB, HUB, Helsinki biobank) • TECHNOLOGY INFRASTRUCTURES • Genomics & NGS • Bioinformatics • High throughput biomed • Metabolomics • Imaging & clinical informatics • Biomarkers and molecular pathology • MOLECULAR MEDICINE RESEARCH • Grand challenges: • Human genomics and preventive healthcare • Digital molecularpathology • Systems medicine and precision oncology

  4. Biobank infrastructure FIMM Technology Centre and Biobank infrastructure Genomics/NGS National research infrastructure 50 technology experts 1. Method development and research services 2. state-of –the-art infrastructure 2. Translation of the novel technologies to clinical practice Bioinformatics & data management Metabolomics High-throughput Biomedicine Imaging & clinical informatics IT & Scientific Programing

  5. Personalised medicine

  6. Results of the first 63 pediatric patients Mutation in a known gene • GATA2 • STAT1 • LIG4 • NLRP3 • RECQL4 • WAS • PIK3CD • LIPA • RTEL1 • CUBN • HIBCH • CYBB • TERT • IFNGR1 • CECR1/ADA2 • DOCK2 • ALOXE3 • DOK7 • JAK3 • FAS 36% No conclusion 36% 7% 20% Previously known mutation confirmed, no additional findings Potential novel or known gene identified, but requires further research

  7. FIMM grand challenges: Personalized leukemia research and therapy FIMM TC & BBI FIMM Research Groups

  8. Drug Sensitivity and Resistace Testing (DSRT) 1. Pre-plated 306 Oncology actionable drugs (1,10,100,1000 and 10 000 nM) 2. Dispensing of cells, 25 ml (500-10 000 cells/well) 3. Incubation 72 h (-7 days) In vivo Ex vivo 4. End-point measurements (Plate-readers, Protein Lysate Microarrays, High-Content Imaging) 5. Quality control (Z’-factor, SSMD, plate heat map, well-scatter plots, dose-response curves, IC/EC50) In vitro 1 2 3 4 5 R-scripts and Breeze web-interface 6. Data analysis (normalization, dose-response curves, IC/EC50) 7. Hit selection (DSS, Rank Product) Group Wennerberg & HTB

  9. Parallel clinical processes in Genomics & HTB Sample processing • Exome, genome, RNA • & amplicon sequencing • Mutation analysis • germline mutations • somatic mutations • fusion transcripts • QC & Validation • Reporting • DSRT screen • Cancer vs normal • Cell viability • Cell death • QC • Reporting Saarela, EATRIS FInland Research

  10. FIMM Metabolomics Work Flow UPLC/3Q ACN HILIC Samples Automated sample extraction, separation MS analysis Multiple Reaction Monitoring Extracted Metabolites + ISTDs Calibration curves PLSDA/PCA Hierarchical clustering Retention time Daughter ions chromatogram Metabolite quantification Chemometrics/statistical analyses Extracted sample AE/AI Mechanistic understanding New research hypothesis Biological insights Biomarker identification - Integration with other Omics data - Metabolic Pathway analysis - Biological interpretation Concentration 10

  11. FIMM Biobank Infrastructure 1. Pioneering clinical biobanking 2. Modern biobank infrastructure 3. iPS cells and living biobanks 4. National BBMRI.fi network 5. Participating in the Biobank act (2013) follow up group THL Population cohorts 200 000 DNAs/40 year follow-up Patient cohorts (e.g. HUB & FHRB) high quality samples through a professional logistical chain IT Infrastructure for big data Automated storage at -180/-20C Long-term storage at -180C

  12. Founder population

  13. Finns are a founder population Population history: fewer founder alleles, population bottlenecks, isolation • fewer variable sites overall • more low-frequency loss-of-function variants and complete gene knockouts • enrichment certain loss-of-function variants, lack of others

  14. http://sisuproject.fimm.fi/

  15. High quality biobank collections Active research Common Nordic databases Genome and molecular profiling

  16. FIMM TC & BBI is >50 technology experts High-throughput Biomedicine Digital Pathology Genomics Bioinformatics Metabolomics IT Biobank

  17. Research focus: Translational research and adoption of personalized medicine in health care Main research areas • Human Genomics and Preventive Health Care • Systems Medicine and Precision Therapeutics 3 national grand challenge research programmes • Finnish genomes empowering personalized and predictive health • Individualized systems medicine (ISM) in cancer, AML and beyond • Digital pathology & medicine

More Related