0236 Sample management

Summary

This document detail the standard operating procedures for how samples are to be handled and manually treated at the KI Biobank.

1.      Purpose

To describe how incoming samples are to be handled and manually treated at the KI Biobank.

2.      Coverage

This instruction regulates management of manual and partially automated research studies. The instruction for sample management is based on information in the study integration plan (SIP), contact between researchers and KI Biobank as well as specific study instructions.

Samples for automated sample management sent in together with samples for manual management should be sorted out and handled according to instruction 0617 Automated sample management.

3.      Division of responsibilities

3.1       Responsibility of lab manager

  • Responsible for updating and implementing these methods.

3.2       Responsibility of all employees at KI Biobank

  • All employees at KI Biobank lab that handle samples must follow these methods.

4.      Process for sample management

All samples delivered to KI Biobank must be handled in accordance with the process described in this document. Details for sample management are regulated by specific study instructions. The study instructions are written by the laboratory coordinator and are kept in a binder at the Sample reception. In support of specific study instructions there is also Instruktion 0900 Hantering för olika provtyper (not yet published online)

4.1       Daily routines

The following routines are to be carried out daily before samples are being handled:

  • Start Bull (aliquotation robot) and run ”Fill system” according to the maintenance instructions of the Tecan robot.
  • Refill the cryo tube rack in Bull with empty and labelled cryo tubes.
  • Check the whiteboard in the sample reception to see if there are any samples under investigation.

At the end of day, control that all incoming samples got the right status in the LIMS. Daily reports are to be extracted from Business Objects:

  1. Log in to “Reports” in Business Objects LIMS and select Summary studies, sample providers and samples.
  2. Set the reception date and select the studies (usually all) that are to be controlled by selecting ”Show values”.
  3. Select the status to be controlled by clicking ”Show values” and  select Received, Ready and Duplicate.
  4. Select ”Run Query”.
  5. If samples with status Received, Ready or Duplicate aren’t stored, investigate why:
    • If the samples are found, then they must be either stored properly or discarded. Update their status in the LIMS, if samples are thrown away, record the reason under “Deviations” on the sample entry. NOTE: in case of a Duplicate, record the reason for why it is a duplicate before it is either stored or discarded.
    • If the sample cannot be found. Then the status should be changed to Wanted and an investigation be started in order to find the sample.

5.      Delivery of samples to the sample reception

Samples delivered to KI Biobank can be sent through mail, by courier or by the study itself depending on agreements. Delivery can be done to MEBs reception, the KI Biobank reception, the KI Biobank cart, the post box or the room outside the entrance to MEB. The cart, the post box in the mail room and the entrance in front of the MEB reception are to be checked regularily as misdelivered samples can be placed there under the day or courier deliveries may occur without notification from the courier.

5.1       Mail delivery

Normally all post to MEB is sorted by the janitor so that sample deliveries are placed in the KI Biobank cart outside the MEB reception.

Mail is gathered outside the MEB reception circa 9:15 AM and is placed at the unpacking station at the Sample reception. The samples are unpacked in accordance with the instructions for Unpacking samples.

5.2       Delivery by courier

Courier delivery can be done in the following ways:

  • A box may be placed in the KI Biobank cart outside the MEB reception.
  • A box may be placed in the specified spot between the entrance doors at the main entrance to MEB.
  • The box may be retrieved immediately at the reception after a phone call from the courier service to KI Biobank.
  • The courier comes up to KI Biobank after being let in by the receptionist in the MEB reception.

If the courier notifies the KI biobank that he or she will bring the transport case back with them. Then the samples should be immediately unpacked from the transport case and placed in a sample tube rack together with any associated documentation. This is done while the courier is waiting. The case as well as any coolers is handed back to the courier.

If the samples cannot be handled immediately, then the samples are to be placed in a fridge and the empty case placed in the specified place at the Sample reception. Unpacking is done according to the instructions for Unpacking samples

5.3       Delivery of study samples

Frozen samples are delivered with a referral or are pre-registered in ELSA. The samples must be registered in the LIMS within a week.

  • Samples (not frozen) with a referral must be registered and stored according to Storage of samples. If registration and storage isn’t done immediately, place the samples in the “locker freeze” before this is done.

ELSA-registered samples: Control the number of boxes, samples and sign the delivery note (form 0647 Leverans av prov till KI Biobank [ELSA-studier], not available online) which is then placed at the whiteboard at the Sample reception. Control that the study name, person who signed the delivery, delivery date and what freezer the samples have been placed in is recorded. Sign the delivery note when the samples have been stored and place the delivery note in the appropriate binder in the Sample reception – in general, store the samples with the oldest delivery date first.

6.      Unpacking of incoming samples

Unpacking of all samples take place at the Sample reception at the station labelled ”Unpacking”. How samples are managed after unpacking is regulated by the specific study instructions.
 

  • Sort the envelopes by their studies. Open one envelope at a time, remove the referral, consent and sample from the transport case. Empty one envelope at the time, throw the envelope in the garbage bin and the transport case in a plastic recycling bag.
  • Deliveries in package may contain a temp.logg. This must be turned off when the package is unpacked. This is done by pushing the Start/stop-button until the light has flashed 6 times. Control the temp.log ID, compare it with the accompanying form and thereafter sign it. The turned off temp.logg is placed in accordance with the specific study instruction.
     
  • Boxes are packaged and returned with an equal number of PVT-racks as were delivered to the biobank. All cooling packs and bags are returned in the appropriate bag.
     
  • Place samples in racks according to the study and sample donor. If a referral exists, control that the sample label contain the same information as the referral.

 

  • Check if samples should be sorted for arrival registration according to:

Figure 1, sample registration. Samples are delivered (box 1), unpacked (text box 2) and then either loaded onto the sorter for registration (if centrifuged already) or immediately centrifuged before being loaded onto the sorter for registration.

  • Referrals and consent documents are put underneath the rack of each study. In some studies the referrals are scanned, this is done by the reception according to the instructions for scanning referrals. When the samples are done, place the referrals and consent documents in the post box of each study.
  • Samples to be loaded onto the sorter are unpacked and placed in a PVT rack that is the placed in the fridge, instrument ID 199, in the freezer room. Other samples are handled according to the respective study instruction and fall within two categories:
    • Receive and store immediately (“receive and store”).
    • Register for further handling (”receive”).

7.      Registration of incoming samples

For samples received to be registered (”receive”) in LIMS, the workflow below is to be used. For deviations in the process, see Instruction 0902, avvikelser på prov (not published online).

Log into the LIMS and select ”Main” and ”Receive samples”. Follow the instructions on the screen. Register the bar code on the sample and select “cancel” to stop adding more samples (this process depend on the LIMS system being used).

8.      Centrifugation

Samples for aliquotation are centrifuged at the sample reception in a calibrated and approved centrifuge at the sample reception. Centrifuged tubes are aliquoted immediately after centrifugation. If this is not doable, place the samples in a fridge in wait for centrifugation.

Samples are centrifuged according to table in Instruktion 0900 Hantering för olika provtyper (Instruction 0900 Handling for different sample types) if nothing else is specified in the study instruction.

Centrifugation is performed at room temperature if nothing else is specified. The same procedure applies for samples in the sorter.

9.      Aliquotation of samples

Samples must be registered in the LIMS and centrifuged before aliquotation. Samples. Chose the typ of aliquotation according to the study instruction. Issues or discrepancies are to be according to Instruktion 0902 Avvikelser på prov (Instruction 0902 Sample discrepancies, not published online).

9.1       Automated aliquotation of samples

  1. Centrifuge the samples according to point 8 (remember that the robot can only pipette 32 samples at a time).
  2. Log in to Evoware on the Bull-computer and start the maintenance script – Fill system (see Instruktion 0567 Underhåll Tecan).
  3. Control if the samples are hemolytic or not. In case of hemolysis, note a deviation according to Instruktion 0902 Avvikelser på prov (instruction 0902 sample discrepancies).
  4. Remove the lid of the samples after centrifugation and place them in robot racks. Run the samples according to Instruktion 0570 Tecan robotscript (Instruktion 0570 Tecan robotskript).
  5. When the robot is done, remove the robot racks with cryo tubes and put lids on pipetted samples. Check the first empty cryo tube in each row in the LIMS under ”View sample” to see if it is created or not. If an entry exist, change the status to “Discarded” and write the reason under “Deviation” on the sample.
  6. Retrieve the robot rack with mother tubes and replace the lid. NOTE: Aliquots must always be stored in first followed by the mother tubes. To avoid issues with ”receiving” [what does this mean?], place the mother tubes with the ”child tubes” (aliquots). Discarded tubes should be thrown into the biological waste disposal. Sort out mother samples for storage and store these together with all aliquots according to storage of samples.

9.2       Manual aliquotation

There are two ways to aliquot samples depending on if the mother sample should be stored or not:

  • Mother sample discarded: Use the flow Aliquote sample – aliquotation.
  • Mother sample saved: Use flow Blood fractioning - fractioning.
  1. For samples that prior to aliquotation/fractionation is to be decanted/pipetted to a new tube (see study instruction or Instruktion 0900 Hantering för olika provtyper): Log in to the LIMS and select ”Copy barcode” under ”Main”. Follow the instructions on screen and print a new bar code label by reading one bar code label. Select “Cancel” to end the flow in the LIMS. Label the decantation tube with the printed labels.
  2. If necessary, centrifuge according to the above instructions in Centrifugation.
  3. Control the samples if they are in hemolysis or not. Record hemolysis as a deviation in the sample management system.
  4. Decant/pipett of the samplet to the respective decantation tube. Verify that the mother tube got the same bar code as the decantation tube. See the tube type in Instruktion 0900 Hantering för olika provtyper if the sample should be decanted or pipetted.
  5. Pipette the predetermined volume to the labelled kryo tubes (see the respective study instruction for volume) from the decantation tube. Put any remaining sample in the last sample tube if there is less than 500 µl, otherwise make a new aliquot/fraction.
  6. Log in to the LIMS and select “Main and Aliquote sample” or “Bloodfractioning – Check the respective study instruction regarding what information to store.
  7. Follow the instructions on screen and register the aliquotes/fractions to the mother sample by reading the bar code on the samples. Select “Cancel” to stop the flow in the LIMS.
  8. Gel tubes or decantation tubes should be thrown into hazardous waste disposal. Tubes without gels are sometimes saved for exraction – Check the individual study protocol.
  9. Change the volume in the LIMS if the last aliquote contain less than 1 ml.

10.  Storage of samples

Storage in LIMS is done after sample reception (”store”) or at the time of reception (”receive and store”) in accordance with the below instructions. For deviations see Instruktion 0902 Avvikelser på prov.

10.1   Storage of samples already registered as recieved

  1. Log into the LIMS, select ”Storage” and ”Store Sample”. Follow the instructions on the screen and store the sample by reading the bar code on the box and the sample. Place the sample on the designate place in the box. Repeat for one sample at the time.
  2. If the box is filled during the storage procedure, stop the flow with ”Cancel” and create a new box in accordance with the LIMS instructions. Thereafter continue filling the new box according to the above instructions. Select “Cancel” to stop the flow when all samples are stored.
  3. Put any non-filled boxes into the work freezer and handle filled boxes according to instructions for Storage of boxes.

10.2   Storage of samples not yet registered as recieved

  1. Samples that do not require further processing at KI Biobank can be stored by selecting ”Recieve and Store” in the LIMS under ”Main”. Follow the instructions on screen and store the samples by reading the bar code on the box and on the sample. Place the samples in the specified location of the box. Repeat for one sample at the time.
  2. If the box is filled while storing samples, cancel the flow with ”Cancel” and create a new box according to the LIMS instructions. Thereafter continue storing samples in the new box according to the instructions above. Select “Cancel” to finish the flow when all samples have been processed.
  3. Put any non-filled boxes into the work freezer and handle filled boxes according to instructions for Storage of boxes.

11.  Storage of boxes

Full boxes are to be stored as freezer racks in the LIMS under ”Storage” and ”Storage container to rack”. Follow the instruction on the screen and store the full box by reading the bar code on the box. Repeat with one at a time and press “Cancel” when all boxes are stored. Follow the instructions on the white board at the sample reception to see what freezer rack each box should be stored in.

A list of storage locations is printed and the box placed according to it on the specified spot in the specified freezer.

12.  Storage

All samples sent to KI Biobank and handled manually must be placed in a study specific storage box. Stored according to specific study instructions or if an instruction is missing according to Instruktion 0900 Hantering för olika provtyper. See the LIMS user manual for specific instructions on storage of boxes. Always control the position of samples in the box. If the positions are wrong, immediately correct the placement of samples. When a storage box is full it must be immediately moved to storage in a low temperature freezer. See the LIMS instructions on how to store samples in the system.

13.  Downtime

In case of downtime the following sample management procedures must be followed.

13.1   Network down

  • Immediately contact the IT-support at KI Biobank.
  • Put samples I a fridge while waiting for the network to come back online. Samples that can be frozen should be put in a freezer.
  • No new work may be initiated on the robots. If pipetting have already started, let the project to continue and inform the IT-support at KI Biobank.
  • Write a disruption report of the event in Centuri.

13.2   Power outage

  • Put samples in a fridge while waiting for power to return. Samples than can be frozen should be put in a freezer instead.
  • No robots may be used.
  • -80°C freezers will switch to reserve power until the power supply is restored.
  • Avoid opening any fridges or freezers more than necessary in order to preserve the cold.
  • Write a disruption report of the event in Centuri.

14.  Reference documents

Instruktion 0567 Underhåll Tecan

Instruktion 0570 Tecan robotskript

Instruktion 0231 LIMS Användarmanual

Instruktion 0900 Hantering för olika provtyper

Instruktion 0902 Avvikelser på prov

                     

 

Citation

SOP collection, KI Biobank. 0236 Sample management. The Molecular Methods Database. 2016/01/26

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