HIR Mapper (Borland Genetics)
From ISOGG Wiki
The HIR Mapper is a chromosome mapping tool within the Borland Genetics Web Tools and Database designed to streamline the mapping stages of DNA reconstruction workflows. The tool identifies segments of DNA shared by the focus donor and each of that donor's DNA matches within the Borland Genetics database, and uses that information to generate a chromosome map that illustrates recombination events that occurred in the most recent generation of inheritance. The HIR Mapper fits into a precise and systematic approach to DNA reconstruction.
| Category: | Chromosome Mapping |
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| Access: | Subscription |
| Location: | Kit Toolbox (located on Kit Laboratory screen) for all mono kits |
| Stages: |
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Contents
Multi-Stage Workflow
The HIR Mapper is designed to guide users through a multi-stage process to map DNA segments and visualize the most recent recombination events. Below is a breakdown of each stage in the workflow:
1. Textual List of Matching Segments
In the first stage, the HIR Mapper compiles a list of DNA segments shared between the focus donor and their matches. The segments are listed in order based on their location on the chromosomes of the focus donor. This screen also allows the user to incorporate output from GEDmatch's Segment Search tool as additional data for the subsequent analysis.
2. Close Relatives Review
The second stage provides the user with a list of close relatives of the focus donor, using the logic from the site's Relationship Manager tool, which attempts to exclude false matches resulting from endogamy. For each close relative, the user is prompted to classify the relationship to the focus donor based on how they are related:
- Paternal Only: The relative is related only on the paternal side.
- Maternal Only: The relative is related only on the maternal side.
- Unknown: The relationship is not yet determined; this relative will be included in the analysis but will not be used to assign parental phase.
- Related on Both Sides: The relative is related both paternally and maternally (e.g., full sibling or double cousin); these relatives are excluded from the analysis to avoid phasing conflicts.
- Exclude: The relative is manually excluded from the analysis.
The parental phase designations for some relatives may be pre-selected if the user has placed the matches in their family tree or if the HIR Mapper was launched from a Smart Project containing a Relationship Manager widget. In these cases, the user simply reviews the chart for completeness and accuracy.
Additionally, at this stage, the tool provides two match grouping modes. The radio button for this option should already have the correct mode selected based on how the user arrived at the tool, but it allows for a manual override for advanced users. The user can choose between:
- Group by Segment: This method is recommended for most scenarios, where matches are grouped based on shared DNA segments.
- Group by Block: This option is not recommended except for specific use cases such as the Phased Pseudo-Sibling method of visual phasing.
3. Results Screen
The final stage of the workflow presents a graphical Phase Map Preview, and provides the user the following navigation and action buttons:
- Launch Segment Lab: Allows users to edit individual segment attributes in a more detailed interface.
- View Phase Map Locker: Returns the user to the locker to view and manage their stored maps.
- Download Phase Map: Allows users to download the phase map for external use, such as importing it into DNA Painter or other tools.
- Delete: Removes the phase map from the Phase Map Locker, if desired.
Output Chromosome Map (Phase Map)
The output chromosome map generated by the HIR Mapper is a special type of chromosome map called a phase map. Instead of mapping DNA matches directly, the phase map indicates whether each segment of a phased kit is inherited from the paternal or maternal side of the donor's family tree.
For example, if you phased your DNA into paternal and maternal kits and ran the HIR Mapper on the paternally phased kit (which would be linked to the profile for your father, and your father would be considered the focus donor since the paternally phased kit is essentially a 50% reconstruction of him), the blue segments in the resulting map would represent the segments your father passed to you from his father (your paternal grandfather), while the pink segments would represent the segments he passed to you from his mother (your paternal grandmother).
The boundaries between the blue and pink segments mark recombination points, indicating where recombination events occurred during meiosis, when DNA from both parents is shuffled and passed on to the next generation.
The phase map color-codes the segments as follows:
- Blue: Indicates paternal segments relative to the focus donor.
- Pink: Indicates maternal segments relative to the focus donor.
- Green: Indicates matches found but not assigned a side in the previous step. These segments may require further review in the Segment Lab, as sometimes the user will recognize distant relatives, but they often represent pile-ups or endogamy.
- Black: Indicates spans where no matches were found in the Borland Genetics database for that segment.
- Red: Indicates a conflict, where overlapping matches from both sides of the family tree are observed for the same segment.
Importantly, any black, red, or green sections, as well as suspected errors in phasing, can be manually modified using the Segment Lab tool, which is specifically designed to handle phase maps and make corrections where needed.