Contents -

Sample Management

Before ABI sequence files (i.e. *.ab1 files) can be analyzed by SBTengine, a sample and locus name must be defined to each ABI sequence file. This can be done in the Sample Management window in two ways:
  • Automatic Name/Locus Assignment (recommended)
  • Manual Name/Locus Assignment

    Operating procedure

    General
    The user is requested to properly document each sequencing run within the operating software of the automatic DNA-sequencer as supplied by the manufacturer. To facilitate the analysis procedure we advise you to name each sequence file according to an uniform format. For example, start with the sample name (e.g. DNA1), use an underscore ( _ ) as a separator, followed by the locus name (e.g. HLA-C), another underscore and end with the exon and strand that is sequenced (e.g. exon 5 forward strand). This would result in the following file name: DNA1_HLA-C_Ex5F

    We advise you to store the sequencing data in a dedicated SBTengine analysis folder (e.g. SBTdata). If your computers are connected through a network we recommend to store the sequence data on a file server that is accessible from each workstation where SBTengine is installed.
    If the computers are not part of a network and hence are stand-alone computers we recommend to use one computer for SBT analysis with SBTengine. You can generate a dedicated 'SBTdata' folder on the hard drive. Please make sure that you regularly make backups form this computer to prevent accidental loss of data.
    Whether you use a networked environment or not, in this manual we will refer to the folder containing the sequencing files as the 'SBTdata' folder.



    The SBTdata folder contains all run folders from the sequencer. SBTengine needs to know the location of the SBTdata folder. You only need to make this setting once per installation of SBTengine.

    Instructions
    1. When the sequencing run is completed you need to copy the complete run folder to the SBTdata folder.
    2. Start SBTengine, go to the Sample Management window and select the SBTdata folder in the left pane.
    3. Click the 'Hide Tree' button if you want to zoom in on all sequences in the specified SBTdata folder and hide the folder tree. This is particularly useful to prevent accidental deselection of your SBTdata folder.

    All sequence files in the run folders that were copied to the SBTdata folder will appear in the middle pane. SBTengine registers all sequence files in the SBTdata folder and all sub folders. Sequence files located in a deeper level of the SBTdata folder are not detected.

    An overview of the sequence files is given in the right pane: the number of ABI sequence files per HLA locus is shown for each sample name. Below the right pane you can click the 'Refresh' button to refresh the Sample Management. This is particularly useful when new run folders were added while SBTengine was running. The list is automatically refreshed with each start up of SBTengine. Using the "Advanced File Management" button you may access the sequence files in the Windows Explorer. By clicking the "Delete Sequence" button you delete the selected sequence files shown in the middle pane. This can be useful to remove sequence files of empty (water containing) wells in your sequencer plates.

    Follow one of the two procedures below to assign a sample and locus name to each sequence file:
  • Automatic Name/Locus Assignment (recommended)
  • Manual Name/Locus Assignment

    Once the sample name and locus are assigned, the sequence files can be analyzed in the Sequence Overview window. You rarely need to access the Sample Management window once you defined the appropriate settings for your situation. When a sample is analyzed and approved all sequence files from this sample will be moved into the 'Archive' folder. 


    How to use the "show options"?
    The options at the middle bottom of the Sample Management window allow you to view a selection of the ABI sequence files. This is very useful when manually defining sample or locus names.


  • The "All" option shows all files in the selected folder.
  • The "Unnamed" option shows all files in the selected folder without a sample name.
  • The "Unknown" option shows all files in the selected folder without a locus name.
  • Checking the "Masked box" allows you to view a specific selection of the ABI sequence files based on the search string you enter.
    Example: entering "Utrecht" in the field before the Masked box and pressing the "Enter key" shows you all ABI sequence files that contain the word "Utrecht" in any of the columns displayed in the middle window.
  • The "Archive" option shows all files that have been analyzed, approved and were (automatically) moved to the appropriate location within the Archive folder.


    How to add an additional sequencing file to an already analyzed and approved sample?
    When new sequencing information of a sample becomes available (e.g. after sequencing GSSPs) this will be analyzed automatically together with earlier approved data. When a sample is selected within SBTengineŽ it will automatically look within the Archive map to detect if there is already data present. If so, these data will be opened again. The newly added data may change the final allele assignment, mostly by eliminating genotype or allele ambiguities. When the analysis is completed it should be approved again. Newly added files will be moved to the archive map and the XML file will be exported. SBTengineŽ assumes that the latter allele assignment will be superior above the earlier one. Therefore the old XML file will be overwritten, without prior notice.