0350 Sample withdrawal from KI Biobank by customers

Summary

The instruction describes the process when withdrawing samples from KI Biobank. Withdrawal of samples from KI Biobank should be performed and initiated upon request from a customer.

1.      Purpose

The instruction describes the process when withdrawing samples from KI Biobank. Withdrawal of samples from KI Biobank should be performed and initiated upon request from a customer. By customer is intended the responsible researcher or the person assigned by the responsible researcher.

The purpose of the process is to make sure that:

  • The customer receives the samples as ordered.
  • The delivery is done within a reasonable time after ordering.
  • Documentation is provided that enables traceability.

2.      Scope

The instruction includes all handling, from the request of the customer to the delivery of the samples and sending the invoice.

3.      Responsibility

The person responsible for withdrawal (the Withdrawal Coordinator) is responsible for dealing with the request, controlling before delivery, and closure according to instruction. The staff at the lab is responsible for performing the withdrawal according to the instruction. 

4.      Reference document

0360 Withdrawal Order

0743 Material Transfer Agreement(MTA)

0281 Checklista för uttag (Checklist for withdrawal)

0400 Customs Invoice/USDA Statements

0231 LIMS Användarmanual (LIMS user guide)

0567 Underhåll Tecan - Instruktion (Maintenance tecan – Instruction)

0570 Tecan robotskript

0316 Prover till MAF för SNP genotypning (samples to MAF for SNP genotyping)   

0359 Sample Delivery from KI biobank

5.      Abbreviations

UK: Uttagskoordinator (withdrawal coordinator)

LIMS: Laboratory Information Management System

WDO: Withdrawal order

PL:  plocklist (pick list)

CDK: Customer Donor Key

MTA: Material Transfer Agreement

6.      Process

6.1 Handling

6.1.1 initiating withdrawal

No

Activity

Responsible

1

Receiving request from customer (responsible researcher or representative) via e-mail, telephone, personal contact, or signed 0360 Withdrawal Order. The information is documented in the 0281 Checklist for withdrawal, under Handläggning (handling). The checklist follows the process until the samples are delivered.

UK

2

The withdrawal is registered in the queue list under P:\Biobank\Labb\Scheman\Uttag and documented in the time plan in 0281 Checklist.

UK

3

Discussion, if any, with the receiving lab about the format of the withdrawal, type of plates, DNA concentration, volume, and empty wells, etc.

UK

4

Notify the customer about the time plan.

UK

5

If needed, the document Withdrawal Order is sent to the customer via e-mail. If the withdrawal is to be sent outside KI/SLL, a basis for MTA is also sent to the customer. Document in 0281 Checklist for withdrawal under Handläggning. It the customer requests it, send a study report and concentration report from the LIMS via e-mail.

Customer

6

The customer fills in the 0360 Withdrawal Order and the PI signs it. The document is returned by regular mail and the file with the CDK is sent to KI Biobank via e-mail.

Customer

 

6.1.2       Control of Sample Withdrawal Order and file

No

Activity

Responsible

7

The Withdrawal Order and a file are registered upon arrival with the date under Handläggning in the 0281 Checklist for withdrawal. The file is saved in a new folder under P:\Biobank\Kunder\Biobanksstudier\Studiens namn\Uttag\ År\Fil with customer as receiver, lab, month, sample type, number of samples.

UK

8

Check that the Withdrawal Order contains all the information needed (see table 1) and that it has been signed by the customer/responsible researcher. The approved order is documented in the 0281 Checklist for withdrawal.

UK

9

Check that the file with the CDK contains the right information and that no duplicates, strange characters, empty lines, etc exist. The approved file is documented in the 0281 Checklist for withdrawal.

UK

10

If needed, the 0360 Withdrawal Order and the file with the CDK can be discussed via phone, e-mail, or in a personal meeting. Document in the 0281 Checklist for withdrawal.

UK

 

Table 1. Type of information needed in the Withdrawal Order with the most common withdrawal types. (There might be variations to these using other types of withdrawals).

Withdrawal of tubes

Withdrawal of DNA for pipetting to plate

Withdrawal of DNA for normalization

 

Sample type

 

Amount of DNA

 

Normalization concentration

No of tubes

If withdrawal of last aliquot possible

No of samples

Layout of plate

Delivery address

Normalization volume

Max volume that can be taken from the sample (stock)

2D-rack or deep well plate

Delivery address

Invoice address

Invoice address

Signature of PI

No of samples

Delivery address

Signature of PI

 

Invoice address

 

 

Signature of PI

 

 

 

 

 

6.1.3       Create Withdrawal Order (WDO) in the LIMS

No

Activity

Responsible

11

When both the Withdrawal Order and the file are OK, a ”Withdrawal Order” (WDO) can be created.

UK

12

Open the file from the researcher and remove headlines and other text, if any, so that only the CDK remains. Save the file as *.csv in the WDO-folder. Note the file name in 0281 Checklist for withdrawal. Check that no strange characters have been created in the saved file. The file is saved in a new folder under :\Biobank\Kunder\Biobanksstudier\Studiens namn\Uttag\ År\Fil till LIMS.

UK

13

Log in to the LIMS and create a WDO under Withdrawal with the saved csv-file from step 12 and the information from the withdrawal order. See the instruction 0231 LIMS User guide on how to create a WDO.

UK

14

Document in the 0281 Checklist for withdrawal the date when the WDO was created and the WDO: ID. If an error message appears, it must be checked and fixed.

UK

 

6.1.4       Control of samples

No

Activity

Responsible

15

Open the correct WDO in the LIMS. Go to SD samples. Select and copy the information to an empty Excel-document. Save the Excel-file in a new folder called Arbetsfiler (working files). Check the status, volume, concentration of the samples, etc. If normalization is performed, check that the samples have a high enough concentration; higher than or equal to the normalization concentration. The ratio of the samples should also be checked. If the ratio is lower than 1,7, the samples should not be normalized. If there are deviations of the samples which mean they cannot be part of the withdrawal, the customer should be notified. Document in the 0281 under Handläggning – WDO.

UK

 

6.1.5       Create a pick list and check the WDO

No

Activity

Responsible

16

When the withdrawal is started, a pick list should be created for the current WDO in the LIMS, see 0231 LIMS User Guide on how to create a pick list. The WDO can be divided into several different pick lists if needed. From one WDO there can only be one active pick list at the time. Print the pick list.

UK (in some cases delegated to the lab)

17

Review the WDO in the LIMS using WDO Statistics. The samples should have the status Sample Assigned. If they do not, this should be checked and fixed. Document in the 0281 Checklist for withdrawal.

UK

18

The customer should be informed about information and deviations of samples that cannot be included. Document in the 0281 Checklist for withdrawal.

UK

19

Place the 0281 Checklist for withdrawal together with the printed pick list in a folder in the lab next to the robot Bill. (Other documentation can be found in the binder Pågående Uttag (current withdrawals) at the Withdrawal Coordinator.

UK

 

6.2       Withdrawal process

No

Activity

Responsible

20

Pick the samples from the freezer according to the pick list and the 0563 Utplock av kryorör från plocklista (withdrawal of cryo tubes from pick list). Also see the 0231 LIMS 0563-1 Utplock av kryrorör från plocklista and the 0250-2 BioMicrolab, Sorteringsrobot (sorting robot).

Lab

21

If the samples are to be pipetted: Process the samples according to the instruction in 0281 Checklist for withdrawal and the associated Tecan-instruction, see 0567 Maintenance Tecan and 0570 Tecan robot script.

Lab

22

Hand over the basis for withdrawal to the withdrawal coordinator to be checked.

Lab

 

6.3       Delivery

When samples are to be sent outside KI, no samples can be delivered without the withdrawal coordinator having a correctly filled in and signed withdrawal form and a signed MTA. Also see the 0290 Uppdragshantering gällande MTA (Assignment handling regarding the MTA).

No

Activity

Responsible

23

If the samples are to be sent outside KI, check that the MTA has been correctly filled in and signed.

UK

24

Samples stored in delivery boxes: Take out a report on all boxes via Business Objects and BoxesPosition. Save the report as an excel file in a new folder under P:\Biobank\Kunder\Biobanksstudier\Studiens namn\Uttag\ År\Filer_till_kund

UK (in some cases delegated to the lab)

25

Samples on plates: Take out a report on all plates via the LIMS under Reports and Delivery Plate Info. The report is created on Plate Reports on arthur (M:) Plates. Save the report under Filer till kund (files to customer).

UK

26

Open the report in Excel. If there are several reports, they should be put together as one file. Create an empty document in Excel. In column A, paste the CDKs, which the WDOs are based on, found in the files to customer for the withdrawal. In column B, paste the column with CDKs found in the report created in step 23 and 24. Sort each column in numerical order separately. In column C, cell C1, enter =A1=B1 and press Enter. The value SANT (true) should then be shown. Copy this formula to the whole column C, and check that only SANT is shown. If FALSKT (false) shows, check and fix. Also check against the excel file in the folder Förberedelse i uttagsmappen (=SD samples in LIMS-WDO). Make a note in 0281 Checklist for withdrawal. Save the file under Arbetsfiler (working files) as a control.

UK

27

Files to MAF: Take out a report for all plates via LIMS under MAF files.  The report is created on N: Save the report under Filer_till_kund (files to customer). See 0316-3 sample to MAF for SNP genotyping.

 Broad Institute and Tomas Axelsson in Uppsala and other labs with their own file format:

First, all plate files are created as in step 24 above. The withdrawal is checked and additions, if any, are made. Then, the specific files are created to Broad.

 

UK

28

When the withdrawal has been finally checked, the preparations for delivery can be made. Print the 0359 Sample delivery from KI Biobank and fill in two copies.

UK

29

Notify the customer that the samples are ready for pick-up.

UK

30

Go into the LIMS and choose Deliver WDO Sample. The status of the samples is then updated to Delivered and a report is generated.

UK (in some cases delegated to the lab)

31

When picking up the samples, the customer should sign the 0359 Sample Delivery from KI Biobank. One copy is given to the customer and Ki Biobank stores one for documentation. Document the delivery in 0281 Checklist for withdrawal.

 

Customer/ UK (in some cases delegated to the lab)

32

When the samples are to be sent, transport is ordered from World Courier. Contact the customer to get a confirmation that someone can receive the samples before ordering the transport. Notify the World Courier to bring a transport box with dry ice. If transporting outside the EU, special custom invoices are required, (see 0400 Customs Invoice/USDA Statements). The custom invoices are filled in, signed, and sent by fax to World Courier. Demand that the receiver sends an e-mail when the samples have been delivered. The 0359 Sample Delivery from KI Biobank is filled in and signed by the person sending the samples. One copy is sent with the samples and one is saved for documentation.

UK (in some cases delegated to the lab)

33

The signed 0359 Delivery from KI Biobank and the delivery note from World Courier, if any, is saved together with the other documentation about the withdrawal.  

UK

34

Send reports from step 25 via e-mail to the customer and the responsible researcher.

UK

35

Information on the samples not included in the withdrawal should also be sent to the person who ordered the withdrawal.

UK

36

The WDO is finished in the LIMS. Sign the 0281 Checklist for withdrawal. 

UK

37

The Withdrawal Coordinator prepares the basis for the invoice concerning the withdrawal.

UK

38

All the documentation about the withdrawal is saved in the binder for withdrawals (uttag).

UK

 

 

Citation

SOP collection, KI Biobank. 0350 Sample withdrawal from KI Biobank by customers. The Molecular Methods Database. 2016/01/20

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