KI Biobank sample handling

Summary

This standard operating procedure describes how incoming samples are to be handled and manually treated at the KI Biobank These instructions regulate sample management of manual and partially automated research studies. The instructions for sample management are based on information in the study integration plan (SIP). Samples for automated sample management that arrive together with samples for manual management should be separated into two groups. Samples for automated sample management are handled according to instruction 0617, Automated Sample Management.

1. Purpose

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

2. Summary

These instructions regulate sample management of manual and partially automated research studies.  The instructions for sample management are based on information in the study integration plan (SIP). 

Samples for automated sample management that arrive together with samples for manual management should be separated into two groups.  Samples for automated sample management are handled according to instruction 0617, Automated Sample Management.

3. Division of Responsibilities

3.1 Responsibilities of the laboratory manager

  • include updating and implementing of the following methods.

3.2 Responsibility of all employees at the KI Biobank

  • all employees at the KI Biobank laboratory that handle samples must follow these methods.

4. Process for sample management

All samples delivered to the KI Biobank must be handled in accordance with the processes described in this document.  Details for sample management are regulated by specific study instructions.  All study instructions are written by the laboratory coordinator and are kept in a binder in the sample reception area of the laboratory.  Complementary instructions regarding different sample types and specific study instructions are included in ‘Instruction 0900, Handling of Different Sample Types. (unpublished)

4.1       Daily routines

The following routines are to be carried out daily prior to sample handling.

  • Start the Tecan aliquoting robot, Bull and run the ‘Fill System’ maintenance script according to the maintenance instructions for the Tecan robot. (Instruction 0567, Tecan Maintenance Instructions.)
  • Refill the cryo (or micro) aliquot tubes in the racks used on ‘Bull’ with empty labelled tubes.

The aliquot tube is predetermined by the study’s volume requirements.  The micro aliquot tubes have a 500 ul capacity.  Cryo tubes are used for volumes >500 ul with a 1800 ul capacity.

  • Check the whiteboard in the sample reception area to see if there are any samples (or shipments) under investigation.

At the end of the day,  control that all arrived samples have the correct status in LIMS. Daily reports used to check this are generated by LIMS under ‘business objects’.  “Summary of studies, sample donors, samples” 

Log in to “Reports” under Business Objects in LIMS and then select “Summary of studies, sample donors, samples” 

Set the ‘from’ date block with the reception date from the previous day and ‘to’ date block with the following day’s date; instead of the current date.  Select the studies (default set to all) or optionally select and then prompt to ‘Show values’.

Select the status to be controlled by clicking ‘Show values’ and select:  Received, Ready and Duplicate.

Select “Run Query”

If samples with status, Received, Ready or Duplicate are found on the query, an investigation as to their whereabouts is required.  If the samples are found, they must be stored properly or discarded in LIMS and their respective status updated.  Discarded samples require a ‘reason for discarding’ to be recorded under deviations for the respective samples.

Note:  In the case of a found duplicate, record the reason for why a duplication was created before the sample is either stored or discarded.

If the sample cannot be found then the status should be changed to ‘Wanted’ and an investigation started in an attempt to find the sample.

5. Delivery of samples to the sample reception

Samples delivered to the KI Biobank may be received by mail, by courier or directly from the study itself depending upon the study agreement.

Sample deliveries can be expected to arrive at MEB’s reception or the KI Biobank reception. The KI Biobank transport cart, the post box or the room outside the entrance to MEB should be checked regularly for samples left there during the day by courier deliveries.

5.1   Mail delivery

Normally, all mail sent to MEB is sorted by the janitor so that sample deliveries are placed in the KI Biobank cart outside of MEB reception.  The samples are later unpacked in accordance with the instructions for unpacking samples.

5.2  Delivery by courier

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

If the courier notifies the KI Biobank that he or she will bring the transport container back to its original source, 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 to be done while the courier is waiting.  The transport container and all of its contents minus the actual biological samples (cool packs, tube containers/sample transport cases, racks, clamps, plastic bags) are then given to the courier to return to the respective study.

If the samples cannot be handled immediately, then the samples are to be placed in a refrigerator (4-10 deg C) and the empty case placed in its specified place in the sample reception area.  Unpacking is performed 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 LIMS within a week.

  • Samples (not frozen) with a referral must be registered and stored according to  “Storage of Samples”

If registration and storage cannot be performed immediately, the samples are placed into the ‘lock freeze’ or “slussen”; awaiting registration and storage.

ELSA-registered samples: Control the number of boxes, samples and sign the delivery form arriving with the samples, which is then placed on the whiteboard in sample reception. (Form 0647  Delivery of Samples to the KI Biobank, ELSA-studier)

Control that the study name, person who signed the delivery, the delivery date and where the samples have been temporarily placed (freezer and shelf number usually in ‘Slussen’) and any other pertinent information are filled in on the form for future reference.  When the samples have been stored, place the delivery note/form in the appropriate binder located in sample reception.

Generally, samples from the oldest delivery date are stored first.

6.Unpacking of incoming samples

Unpacking of samples takes place at sample reception.  How samples are managed after unpacking is regulated by the specific study instructions.

  • Sort the envelopes by their studies.   Opening one envelope at a time, remove the referral, consent and the samples from the transport cases.  The empty envelopes are thrown in the garbage bin and the transport cases in a plastic recycling bag.

Deliveries in packages may contain a temperature log.  This must be turned off when the package is unpacked.  This done by pushing the start/stop button until the light has flashed 6 times.  Control the temperature log ID; comparing it with the accompanying form and thereafter sign it.  The de-activated temperature log is placed in storage in the laboratory or in accordance with specific study instructions.

  • Boxes are packaged and returned with an equal number of PVT-racks as were previously delivered to the Biobank.  All cooling packs and bags are returned in the appropriate shipment container.
  • While unpacking, place samples in separate racks according to the study; keep each set of donor samples separate in a group.  If a referral exists, control that the sample labels contain the same information indicated on the accompanying referral.
  • Separate the samples according to the type of arrival registration;  that is, whether it will be performed by using the sorting robots in ‘large scale’ sample reception (automated reception) or by manual sample reception.

  • Referrals and consent documents are put underneath the rack of each study.  In some studies, the referrals are scanned and this is performed at Ki Biobank reception according to the instructions for scanning referrals.  When the sample processing is completed, place the referrals and consent documents in the post box designated for each separate study.
  • Samples to be loaded/received by the automated sorter are unpacked and placed into PVT racks that are then placed in the refrigerator (4-10 deg C, instrument ID 199 located in the freezer room)  Other samples are handled according to the respective study instructions and within two categories:
  • Receive and store immediately
  • Register for further handling

 

7. Registration of incoming samples

For samples received to be registered in LIMS the workflow below is to be used.  For deviations in the process, see Instruction 0902, Deviations on samples.

Log into 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 depends upon the LIMS system that is being used.)

8. Centrifugation

Samples for aliquoting 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 possible place the samples in a refrigerator awaiting centrifugation.

Samples are centrifuged according to the table in Instruction 0900, Handling of Different Sample Types; if nothing contrary is specified in the study instructions.

Centrifugation is also performed at room temperature unless otherwise specified by the study.  The same procedure applies to samples routed through the automated sorter.

9. Aliquotation of samples

Samples must be registered in LIMS and centrifuged before aliquoting.  Samples are to be aliquoted according to the study’s instructions.  Issues or discrepancies are to be noted as deviations and recorded for each affected sample.  (Instruction 0902 Sample deviations)

9.1  Automated aliquoting  of samples

1.                Centrifuge the samples according to point 8 (Remember that the Tecan robot can only pipette a maximum of 32 samples during one script run)

       2.                 Log in to Evoware on the ‘Tecan robot, Bull’-computer and start the maintenance script, “Fill   System”  (Instruction 0567, Maintenance Tecan)

       3.    Check the samples for hemolysis and if present, note the hemolysis as a deviation on the sample in LIMS.  (Instruction 0902 Sample Deviations)

       4.                 Remove the caps from the samples after centrifugation and place them in the robot racks designated for the specific size vacutainer blood collection tubes.

Run the samples according to Instruction 0570, Tecan robot scripts.

After aliquoting has been performed remove the robot racks and cryo tubes keeping them in the same order as during the aliquoting process.  Cap all sample tubes and aliquot tubes. 

Check the first empty cryo tube in each row in LIMS under “View sample” to see whether it has been created or not.  If an entry exists, change the status to ‘Discarded” and write the reason under deviations for the sample.

 

     6.    Retrieve the robot rack with mother tubes and cap them with the caps intended for 10 ml. vacutainer tubes and cap each 1,8 ml cryotube with the smaller screw caps intended for that purpose.

 NOTE:  Aliquots must always be stored first followed by the mother tubes.  The aliquots are pipetted in series from the original/mother sample tube in the same row and thus serves as a quick reference to both the study in which the sample belongs to and its sample type when retrieving freezer boxes and storing the aliquoted samples.  Thereafter, the original/mother samples are stored, (if required by the study).  In most cases, the aliquoted remaining contents of the 10 ml mother tube is saved in the box designated as stored ‘extraction’ samples with another full tube stored in a ‘back-up’ box.

The plasma removed is well above the ‘buffy coat’ or ‘cell phase’ of the sample.

Mother tubes that have no further purpose should be disposed of properly in biological waste containers.

9.2     Manual aliquotation

There are flow methods for aliquoting samples depending upon whether the lower blood fractioned portion of the mother sample will be saved and stored after aliquoting or not. 

  • Mother sample is discarded:  Use the flow ‘aliquot sample’
  • Mother sample saved:  Previously referred to as ‘blood fractioning’ but, recently changed to  ‘cell fractionation’.
  1. For samples that prior to aliquotation/fractionation are to be decanted/pipetted to a new tube (see study instruction or instruction 0900, Handling of different sample types.)

Log in to LIMS and select “Copy barcode” under “Main”.  Follow the instructions on screen and print a new barcode label by reading one barcode label.  Select “Cancel” to end the flow in LIMS.  Label the decantation tube with the printed label (s).

 

  1. If necessary, centrifuge according to the previous instructions under ‘Centrifugation’. 
  2. Check the samples for visible hemolysis and if present make a note of its presence as a deviation in LIMS.
  3. Decant/pipet the sample to the respective decantation tube.  Verify that the mother tube has the same barcode as the decantation tube.  Note whether the sample should be decanted or pipetted.  (Instruction 0900, Handling of different sample types)
  4. Pipette the predetermined volume established by the study from the decantation tube to the labelled cryotubes.  Put any remaining sample in the last cryotube if there is less than the specified amount and change its volume in LIMS.  Otherwise, make a new aliquot/fraction.

An example:  Some samples received can, in fact, be whole EDTA blood; yet, designated as ‘plasma’ for its sample type according to the study remiss and in LIMS.  The samples though whole blood, are received in LIMS as ‘plasma’.  The plasma portion after centrifugation is to follow the ‘aliquot sample’ flow as opposed to the ‘blood fractioning/cell fractionation’ flow and the bottom cell portion/fraction is discarded afterward.

  1. Log in to LIMS and select ‘Main and ‘Aliquot sample’ or ‘Cell Fractionation’.  See the study instructions as to whether the mother tube should be saved or not.
  2. Follow the instructions on screen and register the aliquots/fractions to the mother sample by reading/scanning the barcodes on the samples.  Select “Cancel” afterward to stop the flow in LIMS.
  3. Gel tubes or decantation tubes should be disposed in a hazardous waste container.  Once again, tubes without gels are sometimes saved for DNA extraction.  Insure whether this is the case or not by checking individual study protocols.
  4. Change the aliquoted volume in LIMS if the last aliquot contained 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 instructions below.

10.1 Storage of samples already registered as received.

  1.   Log into the LIMS, select “Storage” and “Store Sample”.  Follow the instructions on the screen and store the sample by reading the barcode on the box and then, the sample.  Place the sample in the designated place in the box; repeating the same process in sequence for each sample.
  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 have been stored.
  3. Put any non-filled boxes into the ‘work freezer’ and handle filled boxes, according to the instructions for ‘Storage of boxes’.

10.2 Storage of samples not yet registered as received

  1. Samples that do not require further processing at KI Biobank can be stored by selecting ‘Receive and Store’ in LIMS under ‘Main’.  Follow the onscreen instructions and store the samples by reading the barcode on the box and then the sample.  Place the samples in the specified location of the box.  Repeat for each sample.
  2. If the box is filled while storing samples, cancel the flow with ‘Cancel’ and create a new box according to 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 in the working freezer and handle filled boxes according to the instructions for Storage of Boxes.  Boxes contained in the working freezer are not stored in racks in LIMS but, are store in boxes.  Boxes in the working freezer are therefore partially filled and awaiting to be stored in racks after filling.

11. Storage of Boxes

Follow the instructions on the white-board in sample reception observing which freezer rack that each study and box type should be stored.

Full boxes are stored in freezer racks in LIMS under ‘Storage’ and ‘Store Container to Rack’.  Follow the instructions on screen and store the full box by reading the barcode on the box.   Repeat the process for each box and then, press ‘Cancel’ when all boxes are stored. 

After the box location is stored in LIMS a list of box storage locations is created in LIMS for printing and using as a reference during the actual storage in the racks; in the freezers.

12. Storage

All samples sent to KI Biobank and handled manually must be placed in a study specific storage boxs;  stored according to specific study instructions.  If an instruction is missing, samples are to be stored according to ‘Instruction 0900, Handling of different sample types’.  See the LIMS user manual for specific instructions regarding storage of sample boxes.

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

 

13.1Network down

  • Immediately contact the IT-support at the KI Biobank
  • Place the samples in a refrigerator (4-10 deg C) while awaiting for the network to come back online. Samples that can be frozen should be placed in a freezer, instead.
  • No new tasks may be initiated on the robots.  If, for example, pipetting has already begun, let the process continue and inform IT-support at the KI Biobank after the process has completed.
  • Write a deviation in Centuri.

   

13.2 Power outage

  • Put the samples in a refrigerator (4-10 deg C) while awaiting for the power to return.   Samples that can be frozen should be put in a freezer.  The -80 deg C freezer will switch to reserve power until the power supply is restored.
  • Avoid opening any refrigerator or freezer during a power outage in order to preserve the cold temperature within the units.
  • Write a deviation report of the event in Centuri.

Citation

SOP collection, KI Biobank. KI Biobank sample handling. The Molecular Methods Database. 2015/05/19

Group content visibility

Use group defaults

Groups

Procedures and protocols from Karolinska instutet Biobank