Biobank for Translational Medicine: Standard Operating Procedures for Optimal Sample Management

Biobanks are essential resources for basic translational and clinical research, but they also act as key players linking academic research and the pharma-biotech industry. This protocol presents the standard operating procedures of the biobank at the IAO, a fully certified biobank working in compliance with the newest standard for biotechnology, biobanking, and general requirements for biobanks. The availability of high-quality biospecimens from cancer patients is critical for the development of next-generation diagnostic tools and therapists tailor it to individual patients.

Biobanking of biological material from cancer patient requires specialized personnel and numerous certification. The personnel must be constantly trained and updated. This protocol must, therefore, be the starting point for those wishing to establish a biobank.

To begin, broadcast an educational cartoon video in waiting rooms to inform the patients about the importance of the impact of RPA. Provide gadget bookmarks to all the patients. Use LIMS software to track all biological samples.

Identify patients using codes. Assign a unique code to each individual which matches the medical record number. Verify whether the patient is enrolled in a clinical trial or a specified approved research project by correctly completing the study project field in each patient profile.

Inform technicians if the risk of infection is unknown. Discard specimens with positive results or unknown risks. For fresh samples, register the blood samples in the biobank software.

Label the vacutainers with the biobank ID code and deliver them to the authorized users. For frozen samples stored in the biobank, prepare two cryobank 2D coated tubes each of 900 microliters of blood. Register the aliquots in the biobank software.

Place them on a specified barcode plate and store them at minus 80 degrees Celsius to ensure a constant temperature. Pour the blood from the EDTA collection tubes into the empty sterile 50 milliliter conical tube and dilute it using sterile 1X PBS. Use the PBS to rinse the blood tube.

Centrifuge the tubes at 400 RCF for 30 minutes at 20 degrees Celsius and process the tubes under a biohazard hood. Recover the middle white layer containing PBMCs using a Pasteur pipette and place it in a new sterile 50 milliliter conical tube. Add up to 45 milliliters of PBS to wash the PBMCs.

Mix and centrifuge at 400 RCF for 10 minutes at four degrees Celsius. Recover the pellet and resuspend it in PBS. Then count the cells using disposable Burker chambers.

Repeat the PBS wash for PBMCs as described in the text manuscript. Dilute the PBMCs in the freezer medium and prepare cryobank 2D coated tubes by transferring one milliliter of resuspended cells into each cryo tube. Place the samples in a specific cryo box and store them at minus 80 degrees Celsius as soon as possible.

Centrifuge the vacutainer containing the whole blood samples at 2, 000 G for 10 minutes at four degrees Celsius. Remove the upper layer of the plasma using a three milliliter Pasteur pipette and transfer it to a sterile 15 milliliter conical tube. Then centrifuge at 16, 000 RCF for 10 minutes at four degrees Celsius to eliminate contaminating blood cells.

Transfer the plasma into one milliliter cryobank 2D coated tubes. Register the aliquots in the biobank software. Place them on a specific barcode plate and store them at minus 80 degrees to ensure a constant temperature.

Have tissue samples examined by a pathologist to determine whether the material that is not necessary for diagnostic procedures is sufficient for research purposes. Whenever possible, collect even the non-pathological counterpart of the pathological tissue. Place the samples in sterile cell culture Petri dishes labeled as P and NP.Keep the tissue on the ice at four degrees Celsius and divide it into three parts each.

A, B, and C if enough material is available. For fresh tissue samples labeled as A, place the fresh aliquots of P and NP tissue in tubes with the appropriate culture medium defined in each specific protocol and send them to external research units. For OCT tissue samples labeled as B, fill them with OCT resin and immediately place them in a flash freeze apparatus at minus 80 degrees Celsius.

For tissue samples labeled as C, place the remaining tissue samples in cryobank 2D coated tubes in the flash freeze apparatus. Store the plates at minus 80 degrees Celsius. A total of 38, 446 annotated biological liquid biopsies and 10, 205 tissue samples were collected from April 2012 to December 2021.

The number of collected samples, especially tissues from 2020 to 2021, decreased due to the COVID-19 pandemic and the related reduction in oncologic procedures. The collected samples obtained from the divisions of urology, gynecology, sonology, and the divisions of head and neck, abdominal, pelvic, and thoracic surgery were analyzed in detail. The highest number of tissue samples were collected from breast tumors.

The collection of other biological specimens, such as urine, stool, and buccal swabs, has significantly increased following the demand over the years. This option provide a fundamental platform for the storage of biological sample and improve the reproducibility of cancer research programs. These samples can be used for different research applications such as next-generation sequencing or mass spectrometry.

Our platform is able to implement new artificial intelligence algorithms into translational research with the potential to change the way cancer patients are treated.