Reverse Phase Tool (Borland Genetics)

The 'Reverse Phase Tool in the Borland Genetics toolkit phases a donor's DNA using the DNA of a child (as opposed to a parent).

Until the release of Borland Genetcis v1.5, full phasing of the paternal vs. maternal copies of a donor’s chromosomes could only be accomplished by comparing against raw DNA of one or more parents. However, often, parents are unavailable for testing. This tool accomplishes full paternal vs. maternal phasing of a donor’s chromosomes using a child. However, the process is not fully automatic like traditional phasing, and requires the additional step of visual phasing using DNAPainter. Unlike the “Extract Segments” tool, the DNAPainter profile must be in entered using a specific format:

Output will be in the form of two Mono “grandparent kits” representing parents of the donor, or alternatively stated, the grandparents of the donor’s child. Output may or may not include white noise depending on whether there were gaps between segments as painted.
 * The profile must be set to female.
 * The “paternal” or top chromosome must represent the child’s shared segments with the donor (Parent ∩ Child), with grand-paternal vs. grand-maternal phase assigned.
 * The “maternal” or bottom chromosome must represent the child’s evil twin’s shared segments with the donor (Parent x Child), with grand-paternal vs. grand-maternal phase assigned.
 * Mono kits representing child phased with parent and evil twin phased with parent, or top and bottom files, can be easily prepared in advance using the Ultimate Phaser tool to facilitate/streamline the visual phasing process. Typically, manual visual phasing in preparation for use of the reverse phase tool takes approximately three hours if completed by an expert, although a recent automated spreadsheet created by Diego Quiros has reduced the process to one of approximately half an hour.
 * There should be two entries for each grandparent created in the legend, each named EXACTLY the same. Suggested naming convention would be to use the form Grandpa (child contribution) and Grandma (child contribution), but two copies of each (one for the top chromosome segments and one for the bottom chromosome segments).
 * The screenshot below illustrates an example of a properly formatted DNAPainter profile designed for use with this tool. In this example, Kathy is Kevin’s mother.