Segment Lab (Borland Genetics)
From ISOGG Wiki
The Segment Lab is the native chromosome map/phase map editor in the Borland Genetics Web Tools suite. Unlike the all-purpose chromosome mapping tool DNA Painter, the Segment Lab is specifically designed to streamline the process of ancestor DNA reconstruction within the Borland Genetics platform. The Segment Lab enables users to manually modify phase maps generated by other Borland Genetics tools, such as the HIR Mapper, to maximize the reconstruction coverage of output ancestor kits.
Contents
Tool Attributes
| Category: | Chromosome Mapping |
|---|---|
| Access: | Subscription |
| Location: | Phase Map Preview screen |
Overview
The Segment Lab is designed to work with chromosome maps, specifically phase maps. Unlike a typical chromosome map, which maps shared segments with cousin matches, a phase map is concerned with blocks of DNA and their parental origin (paternal or maternal) relative to the focus donor. These blocks can be further segmented to represent more distant ancestors on either the paternal or maternal side.
The tool allows users to review the phase of blocks of DNA and make manual adjustments, such as flipping segments between paternal and maternal designations, refining recombination points, and resolving conflicts or unknown segments. This is especially useful in workflows like the Reverse Phase method, where DNA inherited by a subject donor's child and their hypothetical "evil twin" (representing the opposite blocks of DNA) are compared to visualize recombination points.
Functionality
When users open the Segment Lab, they are transported to the first segment of their selected phase map. The screen is divided into multiple sections, providing detailed information about the segment, its matches, and suggestions for phase adjustments:
- **Segment Information**: Displays details about the chromosome, the segment's start and stop positions, the source of the phase map, and the donor and kit involved.
- **Matches**: Lists DNA matches to the segment from the Borland Genetics database. In Reverse Phase maps, both in-phase and evil twin matches are displayed side by side, allowing users to spot discrepancies or phase conflicts.
- **Horizontal Parity**: Indicates whether neighboring segments (to the left and right) are paternal or maternal, if known.
- **Vertical Parity**: In Reverse Phase maps, vertical parity means comparing matches to in-phase segments with matches to their evil twin counterparts to make inferences as to side.
Users can adjust the phase of segments by selecting the appropriate designation (paternal or maternal) and applying the change. Additionally, users can set "trim points" to modify only part of a segment, based on match boundaries.
Use Case: Reverse Phase Workflow
One of the primary use cases of the Segment Lab is in the "Reverse Phase" workflow. In this method, a child’s phased DNA is compared against what their hypothetical "evil twin" (representing the opposite phased segments) would have inherited from the same parent. The resulting phase map features a checkerboard pattern of alternating blue and pink blocks, representing paternal and maternal inheritance, respectively. By analyzing recombination points and segment overlaps, users can visualize how DNA was shuffled between generations.
For instance, if a subject donor's child inherited a segment from the paternal side, their evil twin would have inherited the opposite segment from the maternal side, and vice versa. The Segment Lab allows users to review and adjust these assignments, refining the phase map as needed.
Resolving Conflicts and Making Adjustments
The Segment Lab includes features for resolving conflicts where matches from both the paternal and maternal sides overlap on the same segment (red blocks), or where matches are found but not yet assigned a phase (green blocks). These conflicts may arise from situations like pedigree collapse, endogamy, or missed recombination points. (If it is discovered that a recombination point was missed, this is where the ability to trim a segment into two separate segments comes in especially handy).
Additionally, the Segment Lab calculates the probability that a gap between two known same-phase segments should be assigned the same phase. If the likelihood is greater than 95%, the system recommends flipping the gap to match its neighbors
Users manually apply desired changes to their phase maps and teleport from segment to segment by clicking on an interactive Phase Map Preview at the bottom of the screen.