Oncology collection of the IRA

27.01.2021

The creation of a collection of samples from oncological patients in the International Research Agenda of the 3P Medicine Laboratory of the MUG was initiated in May 2019, after contracts were signed with five hospital units, selected through a tender procedure for the service of collecting biological material. Clinical partners cooperating with IRA are:

• University Clinical Centre in Gdańsk, where the material is collected at the Department of Oncologic Surgery, Department of Urology, Department of General, Endocrine and Transplant Surgery,
• Oncology Centre prof. Franciszek Łukaszczyk Memorial Hospital in Bydgoszcz, where the material is collected at the Clinical Department of Oncological Surgery, Clinical Department of Breast Cancer and Reconstructive Surgery, and Clinical Department of Oncological Urology,
• Maria Sklodowska-Curie National Research Institute of Oncology, Kraków Branch, where we cooperate with the Department of Oncologic Surgery,
• University Hospital in Kraków, where patients are recruited at the Clinical Department of General, Oncological, Gastroenterological and Transplant Surgery, and Clinical Department of Urology and Oncological Urology,
• Specialist Hospital in Kościerzyna, where the material is collected at the Department of General Surgery and Oncological Surgery, as well as at the Department of Urology and Oncological Urology.

In all cooperating hospital units, we have implemented uniform procedures for each cancer diagnosis related to patient qualification and recruitment to the IRA’s program, collecting and securing the material, registering the collected material in a dedicated IT system, as well as shipping biological material along with medical documentation to the IRA’s unit. All procedures were developed as a result of cooperation between the IRA’s biobank group and pathomorphologists and surgeons. The first phase is the qualification and recruitment of the patient to the IRA’s program conducted by oncological surgeons, which occurs only after the patient has given informed consent in writing. For collecting and securing the material responsible are specialists – doctors and pathomorphology technicians, therefore in all partner units, we have established close cooperation with the Chairs, Departments and Laboratories of Pathomorphology. The location and method of collecting individual tissue fragments are precisely described in the collection procedures for individual diagnoses. Furthermore, specialized medical personnel: laboratory diagnosticians and nurses are responsible for the collection and preparation of peripheral blood and plasma. In total, over 70 employees of both medical and administrative staff are involved in the process of obtaining biological material.

At present moment, patients with breast, bladder, pancreatic, prostate, colorectal and rectal cancer, as well as liver metastases are recruited to the oncology collection of IRA. For each diagnosis, 1 or 2 fragments of tumor-derived tissue and 2 to 10 fragments of macroscopically healthy tissue located at different distances from the tumor are obligatorily collected. All collected fragments have matching histopathological examinations, which are evaluated by a pathologist. Whole blood and plasma are collected from each patient as reference material. The biological material is collected into specialized cryotubes with a unique 2D code and is frozen at -80 °C within two hours of collecting from the patient’s body. The registration of the donor’s basic data (without personal data) and the samples collected from the patient is held in an automated manner in a specialized IT system created for this purpose, which regularly communicates with the IRA’s server. This allows to monitor the collection process on an ongoing basis and secure the above-mentioned data. The use of specialized test tubes with 2D codes and a dedicated sample scanning system in the MABData1 system minimizes the risk of mixing biological material samples between donors and within the same donor. Basic medical history is collected for all patients in a form of a questionnaire on chronic illness, family history of cancer and smoking tobacco products, general blood test results, and within 2 to 4 weeks of the procedure, also the histopathological result. Ultimately, it is also planned to complete the data with long-term medical follow-up, especially in the context of cancer relapses and the occurrence of other primary cancers. In the first quarter of 2021, it is planned to implement protocols for another diagnosis – kidney cancer, and in the future for stomach cancer.

All samples are transported quarterly from hospitals to IRA by a delivery company specializing in transporting shipments in dry ice, according to the sample shipping procedure. IRA has an internal dedicated IT system (MABData 2) for the complete management of samples and information about donors and samples, integrated with hospital IT systems. IRA’s low-temperature freezers are connected to 24/7 monitoring, they have CO2 protection in the event of a power failure, and besides, the IRA has an additional empty freezer in the back-up system.

The status of the IRA oncology collection as of January 12, 2021, is as follows:

As part of the existing and constantly expanding oncology collection, IRA can offer scientific and service cooperation consisting in:

1. Providing access to small fragments of tissues for RNA/DNA isolation from oncological samples collected so far,
2. Providing high-quality DNA/RNA aliquots isolated from some of the cancer samples collected so far,
3. Isolation of high-quality DNA/RNA from the collected tissue samples according to the standardized laboratory procedures existing in the IRA,
4. Training people interested in basic molecular biology techniques including DNA/RNA isolation from various types of tissues and cell lines,
5. Preparation of NGS libraries for exome, genome, or transcriptome sequencing from previously obtained oncological samples,
6. Providing available, pseudonymized medical data for selected cancer donors.

photo Paweł Sudara/MUG