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How can I anonymise MLPA data before sending it to MRC Holland?

in Raw Data Interpretation & Troubleshooting

It may sometimes be necessary or useful to share raw MLPA data files from capillary electrophoresis devices with MRC Holland, e.g. for troubleshooting or as part of a test or validation phase. Such data should be free from personal information such as patient names.

Note
At MRC Holland, we take the privacy of our customers very seriously. If you accidentally send us data with privacy-sensitive information, we will anonymise the data and destroy the original copies. For more information on how we handle your data, see our privacy policy.

For some systems it is sufficient to rename the data files. However, FSA files produced by capillary electrophoresis devices from Thermo Fisher Scientific/Applied Biosystems (ABI) contain the original sample name in the file. Simply renaming the files is not enough to anonymise them. There are two methods to completely anonymise FSA files.

For efficient troubleshooting, we recommend retaining information about replicates or reactions on DNA derived from the same patient in the sample name, e.g. by renaming the reactions to 'Patient 1' and 'Patient 1 repeat'. You can also specify this information in your message to us.

Method 1: Re-extract the data

The first option is to re-extract the data from the ABI. This is only possible if the plate is still visible in the Plate Manager. These instructions are based on the Foundation Data Collection software (v3.0) that is used for our ABI system. The details for your setup may vary, but the idea should be similar.

  1. Check if the plate is still in the Plate Manager. If not, the data has been deleted from the device, and the procedure will not work.
  2. Go to Run History, and click Find All.
  3. Go to Reextraction and find the appropriate run in the drop-down box.
  4. Edit the sample names where necessary.
  5. Click the Extract button.
  6. The data will be stored in the same location as usual.

Method 2: Use the MLPA Sample Anonymiser Support Tool

You can also use MRC Holland's free MLPA Sample Anonymiser Support Tool to anonymise your FSA files. This is particularly useful if the previous method is not available to you because the original data is no longer available, or because you do not have easy access to the ABI system.

Step-by-step instructions on how to anonymise your FSA files with the tool can be found in the User Manual. You can also view the video below.

Warning
A file called MLPA Sample Anonymiser Support Tool - Summary.txt is saved next to the new FSA files. This file contains a tab-separated list of all old filenames and sample names and their corresponding new names. Keep this file as a record to ensure that the renamed samples can be matched to the original files if required. Do not send this file to MRC Holland.

The tool does not require installation, but does require Microsoft .NET Framework v4.5. The tool can automatically check for updates to ensure that you have the latest version, provided that you have an internet connection (see the User Manual for more details).

In case you are unable to view the video on YouTube you can also download it here.

Note
The MLPA Sample Anonymiser Support Tool is provided free of charge as a service to our customers, and is solely intended to remove personal information from sample names in, and filenames of, FSA files with MLPA data before you share these with MRC Holland. MRC Holland is not responsible or liable for any damages that may result from the misuse of this program.

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Disclaimer

The information provided in this material is correct for the majority of our products. However, for certain applications, the instructions for use may differ. In the event of conflicting information, the relevant instructions for use take precedence.