Information on sample and data collection

U-CAN is active in the following diagnosis areas:

• Breast cancer
• Gynecologic cancer
• Brain tumours
• Head and Neck cancer
• Colorectal cancer
• Leukemia
• Liver, Bile duct and Pancreatic cancer
• Liver metastases
• Lung cancer
• Lymphoma
• Kidney cancer
• Gastric and Esophageal cancer
• Neuroendocrine cancer
• Cancer in organ transplant patients
• Prostate cancer
• Testicular cancer
• Cancer and Covid-19 (collection completed)

A brief description of each area is available on the page U-CAN diagnosis areas.

Liquid biopsies

Plasma

Blood samples for plasma preparation use 2x7 ml EDTA tubes (purple cap). Upon arrival at the Clinical chemistry lab the samples are signed in and handled in an automated process and centrifuged at 2400g for 7 minutes (machine: Tecan 100 EVO2/EVO3). The plasma is then transferred into approximately 16 aliquots à circa 220 µl each and then transferred to a 96 well plate which is instantly frozen. Upon arrival at the Biobank the plasma samples are placed in long time storage at -80 °C. The “arm-to-freezer” time should not exceed 4 hours.

Serum

Blood samples for serum preparation use 1x7 ml EDTA tubes with gel (yellow cap). Upon arrival at the Clinical chemistry lab the samples are signed in and handled in an automated process and centrifuged at 2400g for 7 minutes (machine: Tecan 100 EVO2/EVO3). The plasma is then transferred into approximately 8 aliquots à circa 220 µl each and then transferred to a 96 well plate which is instantly frozen. Upon arrival at the Biobank the serum samples are placed in long time storage at -80 °C. The “arm-to-freezer” time should not exceed 4 hours.

Whole blood - DNA

Blood samples for genomic DNA extraction use 1x7 ml EDTA tubes (purple cap). Upon arrival at the Clinical chemistry lab the samples are signed in and instantly frozen. Upon arrival at the Biobank the whole blood samples are placed in long time storage at -80 °C. When later taken for DNA extraction, the tube is thawed and aliquoted into smaller tubes which are subsequently refrozen in order to meet future demands. From of the thawed blood 200 µl is used for DNA extraction in an automated process at Uppsala Biobank (the blood is placed in a 96 well NucleoSpin 96 Blood Core Kit plate and prepared using the Genomic STARlet robot). Extracted DNA is stored at -20 °C.

Saliva - DNA

Saliva samples are collected in OrageneDNA tubes. At the Clinical chemistry lab the samples are signed in and is subsequently stored at 4 °C at Uppsala Biobank before being transported to Karolinska Institutet for DNA extraction (collected saliva samples are sent to KI in batches 1-2 times per year). Extracted DNA is then returned to Uppsala Biobank for long term storage at -20 °C.

Urine

Urine is collected in plastic tubes without any additives. At the Clinical Chemistry lab the samples are signed in and centrifuged manually at 2400g for 7 minutes. Subsequently the urine is transferred into a 7 ml vacuum tube for urine and is immediately frozen. Upon arrival at the Biobank the urine samples are placed in long term time storage at -80 °C.

Tissue samples

Formalin-fixed paraffin embedded tissues

Tissues obtained from surgery or from biopsies are transported to the Clinical Pathology lab on ice or in refrigerated saline solution. The Clinical Pathology lab signs in the tissue sample and a macroscopic evaluation is carried out by a pathologist before representative pieces are selected for fixation and further processing. The tissue is fixed in formalin for approximately 24 hours, dehydrated for approximately 48 hours and is subsequently embedded in paraffin. The tissue is then sectioned and stained to satisfy immediate diagnostic needs. Any remaining tissue and/or tissue blocks may be used for research purposes after the diagnostic needs have been met. However, any current or future diagnostic need always take precedence over the use of tissue samples for research purposes. Hence, the tissue material may never be too severely depleted or be used up completely, which is why a pathologist must evaluate the remaining tissue quantity in each block before any further use or sectioning of the material for research purposes is performed.

Fresh frozen tumor tissue

Tissues obtained from surgery or from biopsies are transported to the Clinical Pathology lab on ice or in refrigerated saline solution. The Clinical Pathology lab signs in the tissue sample and a macroscopic evaluation is carried out by a pathologist. If enough tissue for fresh freezeing is available without compromising the diagnostic need for formalin fixed tissue, a representative piece of the sample is placed in a labelled plastic container and the tissue is covered with OCT freezing medium. The sample is then immediately frozen in Isopentane that has been cooled using dry ice. The frozen tissue sample is placed in a -70 °C freezer for long time storage. The obtained tissue samples is regarded as both diagnostic material and research material, where current or future diagnostic needs always takes precedence over the use for research. Hence, the tissue material may never be too severely depleted or be used up completely, which is why a pathologist must evaluate the remaining tissue quantity in each block before any further use or sectioning of the material for research purposes is performed.

Fresh frozen normal tissue

Tissues obtained from surgery or from biopsies are transported to the Clinical Pathology lab on ice or in refrigerated saline solution. The Clinical Pathology lab signs in the tissue sample and a macroscopic evaluation is carried out by a pathologist. Should the sample contain tumour-adjacent tissue that is macroscopically normal and is not needed for diagnostic purposes, a representative piece of the sample is placed in a labelled plastic container and the tissue is covered with OCT freezing medium. The sample is then immediately frozen in Isopentane that has been cooled using dry ice. The frozen tissue sample is placed in a -70 °C freezer for long time storage. The obtained tissue samples is regarded as both diagnostic material and research material, where current or future diagnostic needs always takes precedence over the use for research. Hence, the tissue material may never be too severely depleted or be used up completely, which is why a pathologist must evaluate the remaining tissue quantity in each block before any further use or sectioning of the material for research purposes is performed.

Vital frozen cells from blood and bonemarrow

Mononuclear leukocytes are separated through gradient centrifugation with Ficoll-Paque Premium 1.077 g/l. Blood- or bone marrow samples are layered on the Ficoll solution and centrifuged at 400g for 30 minutes during careful deceleration. The centrifugation process produce layers in the gradient containing different cell types. The cell layer containing mononuclear cells is harvested and washed by transferring to a new tube with PBS which is centrifuged at 400g for 10 minutes, after which the supernatant is then decanted. The resulting cell pellet is resuspended in new PBS and the number of viable cells are counted in a Bürker chamber. Depending on the number of viable cells available the cells will be allocated either to a number of vials for vital freezing or to tubes allocated for DNA extraction.

To generate pellets for DNA extraction, part of the cell suspension is transferred to a new tube filled with PBS which is centrifuged at 350g for 10 minutes. The supernatant is removed and 1 ml freezer medium with DMSO is added prior to freezing the tubes and placing them in cryo containers (Nalgene) containing room tempered isopropanol. The cryo container is frozen as decribed below.

Vitally frozen cells are generated by taking the remaining volume of the of above mentioned cell suspension, diluting it in new PBS and centrifuging at 400g for 10 minutes. The supernatant is removed, the cells are resuspended and 1 ml freezeing medium with DMSO is added per vial before the tubes are placed in cryo containers (Nalgene) containing room tempered isopropanol.

The cryo container is placed in a -70 °C freezer in order to slowly freeze the cells at the speed of approximately -1 °C per minute before the vials are transferred to liquid nitrogen tanks for long time storage.

Patients participating in U-CAN are asked to answer a U-CAN questionnaire. A revised and more comprehensive version of the U-CAN questionnaire with in total 70 question areas was launched in 2019 (available as a PDF:s on the page "For health care staff", OBS! page only in Swedish). Question areas present in the questionnaire version predating 2019 are marked by an asterisk in the list below (*).

• Height/weight *
• Genetic/geographical origin
• Civil status *
• Type of living *
• Number of residents in household
• Social situation
• Financial situation
• Education *
• Occupations *
• Percieved capacity and energy level
• Alcohol habits *
• Smoking habits *
• General health condition
• Previous cancers *
• Diabetes *
• Hypertension *
• High cholesterol *
• Heart problems *
• Hypothyroidism *
• Liver and bile diseases *
• Renal diseases *
• Pulmonary diseases *
• Inflammatory bowel diseases *
• Stroke *
• Organ transplants
• Previous surgeries *
• Mental health disorders *
• Other chronic conditions *
• Cancer investigation in the family *
• Parents with cancer *
• First degree relatives with cancer (e.g. your siblings or children) *
• Second degree relatives which cancer (e.g. your grandparents, aunts, uncles...) *
• Third degree relatives with cancer (e.g. your cousins) *
• Questions about menstruation *
• Use of hormonal contraceptives *
• Use of oestrogen supplements *
• Fertility treatments
• Gynecological surgeries
• Ovarian cysts
• Endometriosis
• Pregnancies/breast feeding *

The overall response rate is around 70% across all diagnostic areas in Uppsala. Filled out questionnaires are sent for scanning and automatic data extraction once yearly. Following scanning, extracted data are then manually curated with respect to correcting reading errors and reviewing information from free text fields before the curated data is imported into the questionnaire database.

Clinical data is primarily gathered from the patient journal and is subsequently manually registered into U-CANs own database "Octopus". The clinical data collected from the patient journal and stored in Octopus by U-CAN is relatively limited and is mainly focused on clinical events related to the sampling of the patients (see list below). Octopus was launched as late as 2019 which entails that a large amount of historical data from the years 2010-2019 is still left to register in the database (a continuous work in progress).

Please note that the list below only show the key variables registered in Octopus and leaves out for instance comment sections, variables used for statistics, information on special or extended samplings beyond normal routines and, where such exists, diagnosis-specific variables.

Overall parameters

• Social registration number
• Sex
• Year of inclusion in U-CAN
• Hospital of inclusion
• County of residence
• Date of informed consent
• Version of informed Consent
• Comment on informed consent
• Vital status
• Date of death, if occurred

Diagnostic data

• Diagnosis
• Date of diagnosis
• Comment(s) on diagnosis
• Stage
• T-stage
• N-stage
• M-stage

Surgery/Biopsies

• Date of surgery or biopsy
• Type of procedure (surgery, biopsy, other)

Relapse/progressive disease

• Date of relapse or progressive disease
• Type of relapse: local or distant metastases
• Verification method of relapse or progressive disease
• Anantomical site of relapse

Treatments

• Type of treatment
• Treatment indication
• Start date of treatment
• End date of treatment
• Comment(s) on treatment

Pathology

• Pathological Anatomical Diagnosis (PAD) number
• PAD year
• FFPE tissue collected, yes or no?
• Fresh frozen tumour tissue collected, yes or no?
• Fresh frozen normal tissue collected, yes or no?

Fluid based samples

• Date of sampling
• Reason for sampling (e.g. end of treatment, relapse, etc)
• Number of remaining vials in the Biobank of:
  • Saliva
  • Whole blood
  • Urine
  • DNA
  • Plasma
  • Serum

Researchers can apply to use relevant data from the U-CAN database for their study, provided that it is necessary for the scope of the study and that such permission is granted by the study's ethical permit. For other and more comprehensive clinical data researchers are advised to extract research data from the Swedish national cancer quality registers, or to themselves review the patients’ journal and records.

Researchers also have the possibility to apply for images from radiological examinations or for images from histological stainings.