Precision Medicine Sample Central
Precision Medicine Sample Central (PMSC) is a joint cancer sample and data infrastructure at the Pathology department at Medical Diagnostics Karolinska University Hospital, Oncology-Pathology at Karolinska Institutet and Data Center at SciLifeLab.
Email: foi.pmsc.karolinska@regionstockholm.se
What do we do?
- The sample: Consent & enrolmentThe patient agrees to take part in a study.The record: Study identityClinical details, held apart from the person’s name.
- The sample: Sample collectedSurgery, biopsy, blood or bone marrow, at the hospital.The record: Unique sample IDA web address that names this one sample, worldwide.
- The sample: Expert preparationFresh tissue and living cells, prepared at PM Sample Central.The record: Handling recordProtocols, reagents, storage, and any deviations.
- The sample: Advanced analysisGenes, proteins, single cells and drug response.The record: Results & qualityWhat was measured, and how reliable it is.
Both tracks lead to the Dashboard and knowledge graph
Samples, analyses and clinical facts linked to one another, findable and reusable by other researchers, without revealing who the patient is.
The sample
Sample preparation for multimodal data generation
We have established a physical laboratory and a team of specialists, currently located at Cancer Centrum Karolinska next to the hospital’s pathology department. Their job is to receive fresh material such as tissue, cells and blood and prepare it for multimodal analyses. These procedures are intended to outlive the specific projects and become part of the hospital practices once deemed mature enough and when clinical need arises.
A hospital, a university and a national research infrastructure each have their own rules, budgets and legal obligations. PMSC works through them by mapping where samples get stuck today, agreeing who pays for what, and establishing when medical-device or data protection regulation applies to the tools being built. This is the least visible part but often the step that decides whether procedures become useful in the long term.
Services provided
PMSC provides practical support for researchers and clinical projects requiring standardised sample handling, preparation and tracking for precision medicine applications. Our services are designed to ensure high-quality sample processing and reproducible workflows across projects.
Current services include:
- Reception and handling of fresh tissue, blood and cellular samples
- Cryogenic tissue preparation (CryoPrep)
- DNA, RNA and protein extraction (AllPrep)
- DNA and RNA extraction (QIAamp DNA mini kit and RNeasy mini kit)
- DNA and RNA quality control and concentration measurements (Qubit)
- Ficoll-based separation of peripheral blood samples
- Formalin-fixed paraffin-embedded (FFPE) tissue sectioning
- Protein extraction from fresh frozen and FFPE tissue according to validated standard operating procedures (SOPs)
- SP3-based protein preparation workflows
- Protein concentration measurements
- Sample tracking, documentation and metadata collection
- Support for multimodal molecular profiling workflows
PMSC continuously expands its service portfolio based on the needs of researchers, clinical partners and precision medicine initiatives.
Tailored support and method development
In addition to the services listed above, we work closely with project teams to develop and implement new sample preparation workflows when needed. If a project requires a procedure that is not yet part of our standard service offering, we can evaluate the request, develop new SOPs and establish fit-for-purpose sample handling workflows whenever feasible. Our goal is to provide flexible support and help enable innovative research and emerging diagnostic applications.
The record
Sample data and structure
We also focus on building tools that give every sample a unique identity that can be followed across organisations and define what information must be recorded at each step, and in which standard format, so that data from different laboratories can later be combined instead of sitting in incompatible silos.
A unique identity for every sample
Each sample, and each piece cut from it, is given an identifier in the form of a web address, so it can be named unambiguously anywhere in the world. Today, a sample’s number usually only means something inside the hospital system that issued it, which makes tracking a sample between organisations unreliable.
A common way of describing samples and patient data
The standardisation of clinical data recorded in a project is supported by directly linking to the international OMOP Common Data Model, whereas laboratory data is harmonised using a common way of describing samples and patient data. Clinical data are collected in a structured format that supports future integration with international standards such as the OMOP Common Data Model. Sample and laboratory metadata are captured through standardised REDCap templates developed within PMSC, enabling harmonised data collection across projects and facilitating future data integration and reuse. A template built for both in REDCap, a research data tool already familiar to Swedish study teams, gives projects a ready-made place to enter this information and to connect both clinical and sample data in one place.
Dashboard and knowledge graph
The collected information regarding patient samples is displayed in a knowledge graph, a visual network of connections that make patterns visible, and lets researchers find their sample data. The dashboard also gives the study team the shape of their study at a glance: how many samples of which type, from how many patients, which analyses are finished and which are yet to be done. The aim is for the dashboard to become a live view, showing the study in real time.
Developed and tested on real clinical studies
The tools are being developed alongside ongoing cancer studies that act as pilots to maintain relevance of the tools: anything that does not survive contact with a real clinic does not belong in the infrastructure. We support workflows in the following studies:
PreDDLung
- Cancer
- Lung cancer
- Partners
- Karolinska Institutet
- Karolinska Hospital
PreDDLung is a feasibility study testing whether multimodal profiling can guide the use of immune checkpoint inhibitors in non-small-cell lung cancer. It brings together healthcare, clinical laboratories and researchers to improve how lung cancer samples are collected, processed and profiled. The project has helped bring clinical proteomics into healthcare. It now supports pre-implementation of further precision medicine diagnostics, showing in practice how new molecular technologies can move from research into the clinic.
Sarcoma
A workflow covering both diagnostics and research. For diagnostic cases, DNA and RNA are extracted from tumour samples and sent for genomic profiling and methylation-based classification. Results go back into the clinical workflow to support diagnosis and treatment planning. In parallel, protein extracts are prepared for proteomics, adding molecular data for research and future clinical use. The long-term aim is to make these multimodal data available through the MTB Portal for Molecular Tumour Board discussions.
MAATEO
- Cancer
- Acute myeloid leukaemia (AML)
- Partners
- Karolinska Institutet and international partners?
A functional precision medicine workflow using drug sensitivity assays (DSA). Mononuclear cells are isolated from patient blood and bone marrow by Ficoll density gradient separation, then exposed to drugs. Viability is measured with CellTiter-Glo, and the results are analysed and reported as functional drug response data. We are also building a REDCap setup for standardised sample registration, freezing, tracking and data management.
BioBladder
- Cancer
- Bladder cancer
- Partners
- Karolinska Institutet
- KTH
A functional precision medicine workflow built on fresh tumour samples. Primary cancer cells are prepared for 3D culture and tested against single drugs and combinations. Drug response is then measured by imaging and analysis. FFPE blocks are collected, tracked and sectioned for complementary analyses. The long-term aim is to use these data to pick the most effective treatment for each patient.
Why is it needed?
Patients with what looks like the same cancer can respond quite differently to the same treatments, and much of the time we cannot yet say why. One of the goals of precision medicine is telling them apart on the molecular level, matching each patient to the treatment most likely to help, at the time it will help.
To achieve this level of precision, samples from a single patient need to be examined on the molecular level in many ways at once. This means that samples must consistently be prepared to a high standard and their corresponding records kept complete and described in the same way, so that results from different laboratories can later be brought together. The PM Sample Central is being built to make this possible.
Reading a tumour’s genome is now routine, but recent studies show that genome data alone points to a treatment for only about half of cancer patients. Answering the question for the other half means looking at a sample from several angles at once: its genes, its proteins, its individual cells, how its tissue is organised, and how living cancer cells respond to drugs. This is what researchers call multimodal profiling.
Multimodal analyses are demanding: many of them need fresh, living material, handled, prepared and transported quickly and correctly. Today that work is largely left to each research group or department to arrange project by project leading to sample information being scattered across spreadsheets and separate systems. At best, this means samples yield less knowledge than they could but at worst, something goes wrong along the way, and, with no complete record, it goes unnoticed and cannot be traced afterwards.
PM Sample Central tackles this problem on two fronts: the physical handling of the sample and the trail of information that has to travel with it.
Submit your project request
Researchers, clinical teams and collaborative projects interested in using PMSC services are encouraged to contact us early in the planning phase of their study or initiative. Early engagement allows us to optimise sample workflows, logistics and data management solutions from the start.
Project requests can be submitted through:
Email: foi.pmsc.karolinska@regionstockholm.se
Following an initial review, the PMSC team will contact you to discuss project requirements, sample types, expected volumes, timelines and service needs.
Follow your project
PMSC is developing digital tools that enable study teams to follow the progress of their samples and associated workflows throughout the project lifecycle.
Through the PMSC dashboard, users will be able to access information such as:
- Sample collection and processing status
- Available sample inventories
- Completed and ongoing analyses
- Project-specific metadata and study progress
- Traceability of samples across workflows
The long-term goal is to provide a real-time overview of project activities and sample status, improving transparency, coordination and communication between healthcare, research and analytical platforms.