Biobank technologies provides services for high quality and capacity preparation and profiling of biobank samples, covering the needs of modern clinical and life science research. The services include digital microscopy scanning, advanced tissue preparation and profiling, as well as artificial intelligence-based analysis of various sample types for medical biobanking projects, pre-clinical studies and biomarker research. The platform provides know-how and equipment for best phenotypic and quality characterization of biobanked samples and for automated assessment of tissue sample stainings, high-throughput nucleic acid, cell and extracellular vesicle sample preparation services. The services enable a seamless route of the biobank sample to analytics through 1) integration of tissue whole-slide imaging, routine tissue staining, singleplexed and multiplexed immunohistochemistry, computational tools for image analysis and biomarker discovery, as well as linking of results to clinical data and patient outcomes, and 2) nucleic acid, cell or extracellular vesicle isolation, quality control and normalization with delivery to down-stream analysis, e.g. omics. Thus, true to its name, Biobank Technologies serves to facilitate the most efficient use of various biobank samples for high-quality and high-impact research.


Nodes


Node/Host UniversityNode PI
Digital Microscopy and Molecular Pathology unit at FIMM, UH (FIMM-DP)
Johan Lundin, UH
johan.lundin@helsinki.fi
High-end sample preparation and analytics core at FIMM, UH (HiPREP)
Maija Puhka, UH
maija.puhka@helsinki.fi
Liquid biopsy sampling, processing and analysis of circulating cells and NAs (LIQUID) – services, UEF

New service, website under construction
Arto Mannermaa, UEF
arto.mannermaa@uef.fi

UEF: University of Eastern Finland; UH: University of Helsinki; UO: University
of Oulu; UTU: University of Turku; TAU: Tampere University



Contact details


Chair
Johan Lundin, UH, johan.lundin@helsinki.fi
Digital Microscopy and Molecular Pathology unit at FIMM, UH (FIMM-DP)



Services


FIMM-DP


Digital Microscopy and Molecular Pathology unit at FIMM (FIMM-DP), UH provides high throughput whole-slide scanning services and has top-level expertise in digital microscopy and image-based diagnostics.
Services:
  • Pathology laboratory techniques, such as tissue processing and sectioning of paraffin and cryo blocks
  • Routine stainings such as HE and MGG
  • Chromogenic and fluorescent IHC on paraffin sections, in-house developed protocol for Multiplexed fluorescent IHC
  • Preparation of tissue microarray blocks, both manual and automated punching by a Minicore automated TMA puncher is possible
  • High throughput whole-slide scanning services, both fluorescence and brightfield
  • Image analysis with conventional and AI-based methods

Please contact us at fimm-scanning@helsinki.fi for more information.


FIMM HiPREP


HiPREP Core at FIMM (FIMM HiPREP), UH, provides services for high-throughput and high-quality nucleic acid, cell and extracellular vesicle sample preparations and quality analytics.
 
Services:
  • Nucleic acid isolations by magnetic bead or silica-membrane -based methods.
    • Including pre-treatment steps such as pre-clearing, sample concentration, or enzymatic treatments
    • Dual extractions – RNA and DNA starting from the same sample
  • Nucleic acid sample concentration, buffer exchange or clean-up from contaminants
    • e.g. DNA removal from RNA samples
  • Nucleic acid normalization or aliquoting to target concentration and volume
    • Normalization is required for e.g. sequencing and genotyping applications
  • Nucleic acid integrity, fragment length profile, purity and concentration measurements
    • We measure parameters needed to ensure proper quality in downstream analytics e.g. concentrations, DNA/RNA-% or RNA/DNA-%, RIN, DIN, cfDNA-%, DV200, A260/A280, A260/A230
  • Extracellular vesicle services including isolations and electron microscopy
  • Coming 2025: Tissue dissociation service for single cell analytics
Sample types:
  • Fresh or frozen tissue (fresh frozen or in RNAlater), including biopsies and tissue sections, Formalin-fixed paraffin-embedded (FFPE) samples
  • Blood, serum, plasma, urine, saliva and other body fluids
  • PBMC (Peripheral blood mononuclear cells), PaxGene Blood tubes, Tempus Blood tubes
  • Cultured cells, laser capture microdissected cells and extracellular vesicles (EV)
  • Nucleic acids: Total RNA, smallRNA, gDNA, cfDNA, cfRNA, EV-RNA
Please contact maija.puhka@helsinki.fi for more information.

LIQUID


Liquid biopsy sampling, processing and analysis of circulating cells and nucleic acids (LIQUID) – services, UEF, focus on precision sampling from patient material through routine biobank processes.
 
Services:
Professor Mannermaa’s team has successfully created a process where minimal amounts of circulating nucleic acids can be collected and characterized. The node is currently extending the liquid biopsy analysis (services) to catching live circulating cells, cell enrichment and characterization. This node offers service starting from selection of customized patient cohort in collaboration with the Biobank of Eastern Finland at Kuopio University Hospital, liquid biopsy sampling of nucleic acids and live cells, and characterization of nucleic acids and cells. The new cell catchment service will be set up by the end of 2024.
 
Please contact arto.mannermaa@uef.fi for more information.

Instrument, personnel and further service descriptions can be found in FIMM-DP and FIMM HiPREP.

Recent user publications


Pellinen T, Paavolainen L, Martín-Bernabé A, Papatella Araujo R, Strell C, Mezheyeuski A, Backman M, La Fleur L, Brück O, Sjölund J, Holmberg E, Välimäki K, Brunnström H, Botling J, Moreno-Ruiz P, Kallioniemi O, Micke P, Östman A. Fibroblast subsets in non-small cell lung cancer: Associations with survival, mutations, and immune features. J Natl Cancer Inst. 2023;115(1):71-82. doi: 10.1093/jnci/djac178.

Bychkov D, Joensuu H, Nordling S, Tiulpin A, Kücükel H, Lundin M, Sihto H, Isola J, Lehtimäki T, Kellokumpu-Lehtinen PL, von Smitten K, Lundin J, Linder N. Outcome and Biomarker Supervised Deep Learning for Survival Prediction in Two Multicenter Breast Cancer Series. J Pathol Inform. 2022;13:9. doi: 10.4103/jpi.jpi_29_21.

Ollila H, Mäyränpää MI, Paavolainen L, Paajanen J, Välimäki K, Sutinen E, Wolff H, Räsänen J, Kallioniemi O, Myllärniemi M, Ilonen I, Pellinen T. Prognostic Role of Tumor Immune Microenvironment in Pleural Epithelioid Mesothelioma. Front Oncol. 2022;12:870352. doi: 10.3389/fonc.2022.870352.

Karvinen S, Korhonen TM, Sievänen T, Karppinen JE, Juppi HK, Jakoaho V, Kujala UM, Laukkanen JA, Lehti M, Laakkonen EK. Extracellular vesicles and high-density lipoproteins: Exercise and oestrogen-responsive small RNA carriers. J Extracell Vesicles. 2023;12(2):e12308. doi: 10.1002/jev2.12308.

Holmström O, Linder N, Kaingu H, Mbuuko N, Mbete J, Kinyua F, Törnquist S, Muinde M, Krogerus L, Lundin M, Diwan V, Lundin J. Point-of-Care Digital Cytology With Artificial Intelligence for Cervical Cancer Screening in a Resource-Limited Setting. JAMA Netw Open. 2021;4(3):e211740. doi: 10.1001/jamanetworkopen.2021.1740.


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