Masking personal health information (PHI) for a subject
 | You can specify which personal health information to mask for a subject only before carrying out the corresponding mtDNA alignment project. |
When carrying out a forensic analysis, a lab technician must remain aware of the potential of exposing personal health information (PHI) about a subject that is not relevant to the investigation. For example, the alignment results could reveal that a subject is a carrier for a an inherited disease such as Leigh’s syndrome. To prevent this, you can hide regions from the alignment that could reveal PHI. You can elect to load default hidden regions, which hides the PHI regions that MITOMAP has identified, and/or hide the PHI regions that you explicitly define in a BED file.
 | For detailed information about the format for a BED file, see BED file. |
For a default or custom hidden region, the following is applicable:
• Nucleotides that are in the region are not displayed in the Pile-Up pane in the GeneMarkerHTS Viewer.
• The CIGAR string is hidden in the tooltip for a read in the Pile-Up pane.
• You cannot copy sequences for reads that cross the region.
• Allele counts are hidden from all reports.
• No variants are called within the region.
1. On the New Project dialog box, click PHI Settings.
The PHI Settings dialog box opens.
2. Do one or both of the following:
Option | Description |
|---|---|
Hide the PHI regions that MITOMAP has identified | Click Load Default Regions. Note: For a list of the MITOMAP locations that are the built in to PHI, see the following: |
Hide the PHI regions that you have identified | Click Load BED File to open the Open BED File dialog box, and then browse to and select the appropriate BED file. |
3. Optionally, after you have loaded the default and/or custom regions that are to be hidden, do any or all of the following as needed:
Option | Description |
|---|---|
Manually add a region Note: You can manually add as many regions as needed. You can add only a single region at a time. | Click Add. A new region is added. As you add a new region, it is numbered sequentially. By default, the chromosome is set to M, and the Start and End positions are both set to “1,” but you can edit any or all of these values as needed. |
Remove one region at a time | Select the region, and then click Remove. After you remove a region, the remaining regions are automatically re-numbered. Warning: No confirmation message is displayed before you remove a region, so be cautious when doing so. |
Remove all regions in a single step | Click Remove All. |
4. Click OK.
The PHI Settings dialog box closes. The New Project dialog box remains open. The selected regions will be hidden from alignment.
5. Continue with setting up the new project.