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Visual Phasing usually involves three siblings, their DNA, and comparing it to each other to identify which segments came from which grandparent. Many people have asked, can you do Visual Phasing with two siblings instead of three siblings?
The answer is yes. It's a little bit different process, but you can do it.
What is the Visual Phasing of DNA matches?
First, let's remember the goal of Visual Phasing. The whole purpose of Visual Phasing is to divide each chromosome into which segments came from our four grandparents.
Typically, Visual Phasing requires the Autosomal DNA of at least three siblings. The DNA of a parent or a grandparent is not needed.
Not every family had three or more siblings to do traditional visual phasing. Such is the case with my wife. Additionally, not every family with three or more siblings will take a DNA test. As such, I have developed an alternative strategy of phasing the DNA with only two siblings.
How are Three Sibling and Two Sibling Visual Phasing Different?
There are some differences with Visual Phasing with two siblings as opposed to three siblings. It mainly has to do with assigning Recombination Points. Plus, you need to have identified some of your DNA matches and how they relate to you. This knowledge will help you figure out which segments belong to which grandparent's line.
If you need to understand how DNA recombines, watch the video: Watch how DNA disappears - Understanding DNA Inheritance.
If you don't know how some of your matches are related to those two siblings, you can't do Two Sibling Visual Phasing.
While this blog post will highlight the principles and steps necessary to do this process, you should watch the video to view how to do Visual Phasing with Two Siblings.
Visual Phasing Principles to Keep In Mind
While phasing your chromosomes, several principles will help you with the process.
1. Each chromosome is separate and unrelated to others.
You can't use the data from one chromosome pair to fill in data for another chromosome. Think of visual phasing as 22 individual projects for your 22 autosomal chromosome pairs.
2. Recombination Points happen where color regions change.
As you recognize the Color Coding regions described below, you'll notice when color segments change from a half, full, or no match to another. Mark where the color changes with a line to indicate a Recombination Point.
A switch from a solid green section to a red with some yellow or green indicates a Recombination Point. Additionally, a segment will continue until it reaches the next recombination.
During Two Sibling Visual Phasing, each chromosome pair (1-22) will have four chromosomes to analyze:
Sibling A Maternal Chromosome
Sibling A Paternal Chromosome
Sibling B Maternal Chromosome
Sibling B Paternal Chromosome
(Note: The term chromosome is confusing. It can mean a single chromosome that is part of chromosome 1-23, or the chromosome pair numbered 1-23. If only scientists thought of different terms to make everything simpler. )
3. A Fully Matched Region cannot be adjacent to a No-Match Region.
Visually this means that the solid green sections can not touch a red segment with black beneath. A Half-Match Region will always appear between a Fully Matched Region and a No-Match Region.
4. Every chromosome pair has a maternal and a paternal chromosome.
You receive one chromosome from your mother and one from your father. Recombination Points usually don't happen at the exact same place on those two chromosomes. By chance, they may happen close together, but they don't occur in the same place.
We will attempt to identify which segments represent the paternal or the maternal chromosomes during phasing.
5. Each chromosome contains grandmother and grandfather segments.
Segments from your maternal grandfather and grandmother make up your maternal chromosome. Segments from your paternal grandfather's and grandmother's DNA make up your paternal chromosome.
You can't have a chromosome that is partially a maternal grandmother and a paternal grandmother. But each chromosome will have segments from the same familial line, unless, of course, it is all from a grandfather or all from a grandmother.
6. Segments only switch colors at a Recombination Point for that person.
Recombination Points are distinct. They rarely happen in more than one chromosome at a time. As we go through each step, whenever we identify where a recombination occurs on a particular chromosome, we know that none of the other chromosomes have that Recombination Point.
Understand the Colors of One-to-One Comparisons
The One-to-one Comparison Tool on GEDmatch will return colored bar lines for each person. You will see a top line with yellow, green, and red sections on the top. The bottom bar will have blue or black segments. What do the colored regions mean?
Solid Green Areas with Blue Sections Below
Suppose you have a solid green area with a blue section underneath it. This colored area indicates a Fully Matched Region - a Fully Identical Region (FIR). Both siblings receive the same DNA segment from both of their parents.
Yellow with Green Areas with Blue Below
When you notice yellow regions with little green lines interspersed and then blue underneath, these regions are a Half Matched Region or Half Identical Region (HIR). In other words, each match received the same DNA from one of their parents in these locations.
Red with Yellow Areas with Black Below
Finally, wherever you red sections with yellow mixed and black underneath, this section indicates the area is Not A Match. In other words, the matches receive different DNA from both of their parents. That's why they're not matching in that area. (Sometimes, a stripe of green will be in the predominately red region. You would still call this a No-Match Region.)
If you are finding this blog post confusing, perhaps you would do better to discover the order in which to use GEDmatch tools before tackling phasing.
Ten Steps to Do Visual Phasing With Two Siblings
There are ten basic steps to phase a chromosome pair using DNA from two siblings.
1. Upload Data to GEDmatch
You need DNA test results from two siblings uploaded to GEDmatch.
By so doing, you can view both the Half Identical Regions and the Fully Identical Regions on your chromosomes. If you haven't uploaded your sibling data to GEDmatch, do that now.
2. Screen Capture the One-to-One Comparison Graphics for Each Chromosome
After you have uploaded everything to GEDmatch, use the One-to-One Comparison to obtain the graphics necessary for Visual Phasing. Since you only have two people, you will screen capture one illustration for each one chromosome.
This single graphic capture is a big difference between Three Sibling Phasing and Two. With the DNA of three siblings, we captured three different graphics to make all the relevant comparisons. With Two Sibling Visual Phasing, you don't have that luxury, so you use one illustration for each chromosome.
What do you do with the screen captures?
You can insert the graphics into an MS Word file or a spreadsheet. Some researchers use a presentation program like Google Docs or PowerPoint. Devon would use Photoshop Elements. (She uses that program for everything graphically related.)
The point is to use a program that allows you to insert image files. Plus, you need the ability to add text boxes or overlays, draw lines, and colorize additional boxes.
3. Draw Recombination Lines
Wherever you notice color regions change, draw lines across the one-to-one graphic into your visual phasing workspace. Do not label these lines at this time. That happens in Step 8.
4. Create Two "Chromosomes" for Each Person
As mentioned in step three, you need a workspace. Create two bar lines or rectangular boxes that will represent the two chromosomes for each person. Sibling A will have two bar lines that touch. Sibling B will have two similar bar lines.
Be sure to visually layer the "chromosomes" below the Recombination Lines.
You may see how the Recombination Points separate the bars into potential segments. I say possible regions because each of these four chromosomes does not have all of these recombination points.
5. Color the Largest No-Match or FIR Region
When doing Two Sibling Visual Phasing, begin with the largest No-Match or Fully Identical Region (FIR) because these regions provide us information for both siblings.
When phasing three siblings, we do not start with a No-Match or FIR. In Two Sibling Phasing, we have to skip many 'traditional' steps because we're working with much less information.
Choose four distinct colors to represent your four grandparents. In this example, I used the following colors:
Parent A - maroon and orange
Parent B - teal and purple
While we can not know which color belongs to which grandparent, we understand that maroon and orange will represent either the paternal grandparents or the maternal grandparents.
In the video's example, the largest region was a No-match region. I can color each area between the recombination lines on both chromosomes for Sibling A and Sibling B. I can fill the top section for Sibling A with maroon and Sibling B's top section with orange.
I also colored the bottom section teal for this No-Match region of Sibling A. I colored Sibling B's matching No-Match bottom segment with purple.
6. Compare Siblings with Known DNA Match Relationships to Identify Each Segment
The goal for this step is to capture two graphics for a DNA Match that both siblings match. These graphics also come from the One-to-One Comparision Tool.
To complete this step, you should have identified how a DNA match to the siblings is related. This DNA Match could be a 1st cousin, 1st cousin once removed, or a 2nd cousin. The key is the DNA match has to match through a specific grandparent line.
Devon has four grandparent surnames: Hankinson, Brown, Geiszler, and Zumstein. Knowing a match is a "Hankinson Match" and not from the other lines, I can proceed through this step.
Run the One-to-One Comparison Tool for Sibling A compared to the DNA match. Screen capture the graphic for the chromosome number you are phasing. Place image under the chromosome bars representing Sibling A. Repeat this process for Sibling B and the same DNA match. Now you can analyze Sibling A and Sibling B compared to a previously determined DNA match through a specific grandparent line.
Look for sections between the match and Sibling A that overlap the first identified region. In the image above, you'll notice I highlight the Sibling A chromosome colored region (with maroon and teal) that is above the Hankinson match region that has yellow on top and blue below.
The Yellow / Blue Sections represent a Half-Matched Region which means we can choose either the maroon or the teal to represent the Hankinson DNA.
For the first DNA match, we haven't assigned any labels to any of the colors. Choose whichever one you want to Hankinson. However, we must label the box reflecting how the DNA is related to the Sibling, either paternal or maternal. In the graphic above, the Hankinson match is a maternal relative of Sibling A. So the Teal chromosome section is labeled Hankinson for Sibling A (maternal grandfather).
Notice in the graphic above that Sibling B does not match the Hankinson Match in that same segment. Sibling A and Sibling B do not match in this region. Thus, the two siblings received DNA from separate grandparent lines. Since the Hankinson Match matches Sibling A in this section, we know that we can label the purple region the maternal grandmother. In this case, that would be Brown.
7. Extend the Segments and add any new sections as needed.
Once we identify how the first DNA match for the siblings relates in the first labeled segment, we can extend the phased areas.
Look at the graphics again.
Extend sections of the DNA until you reach a recombination point.
If you notice new matching areas, fill in that segment and label it with the appropriate grandparent lines.
In the graphic below, notice how I extended the phased grandmother sections based on the Hankinson Match.
I see a No-Match Region for Sibling A and Sibling B on the left end of the chromosome. As such, I can color this section for Sibling A and B with opposite colors. The maternal grandmother match (Hankinson) shares DNA with Sibling B and not Sibling A. We can color and label Sibling A to match the paternal grandmother and Sibling B as a maternal grandmother segment.
8. Identify Recombination Points
While in Step 3, we drew recombination lines, we now have data to specify recombination. Look for where the colors change. Use letters or symbols to name the recombination points for each sibling. I use "A" for Sibling A's recombination points. I use "B" for Sibling B.
In the graphic below, I found a color change on Sibling A near the end of the chromosome. I labeled that line with the letter A. I found another color change for Sibling B, so I named that recombination point B.
9. Extend Segments Across Recombination Points
Once we have labeled these recombination points, we extend the colored segments across the lines.
Recombination points relate to one chromosome of the chromosome pair. Whenever you identify that a color changes on a chromosome, the opposite chromosome can not change colors at that point.
In this example, I noticed that the maternal chromosome changed colors, which means the paternal chromosome can not change colors at that point. So now, I can extend the paternal colored regions across those segments.
We still have not identified which colors belong to each paternal grandparent. Because of the visual phasing rules, we can color code longer segments for use when we compare the siblings to a known paternal DNA match.
10.. Repeat Steps Six - Nine with Other Known DNA Matches
After comparing your first DNA match to the siblings, chose a different genetic relative. I recommend using a relative from the opposite line. If we used a maternal one for steps 6-9, now use a paternal match.
Sometimes you will have a DNA match that only matches only one Sibling. You might think this DNA won't work. However, you can still identify genetic segments using this scenario.
In this example, a paternal grandfather match had a Half-Match Region that overlaps into the previously identified region (represented by maroon). This match to Sibling A also shares DNA across two recombination lines to the left of the colored area. Since DNA can only switch colors at recombination lines, then we can color the entire Fully Matched Region (indicated by the green segment break) as the same color.
Since we know that Sibling A shares DNA with the relative on the paternal grandfather's line, we can label the paternal colored section with that surname. In this case, the surname is Geiszler.
For Sibling B, we can not extend the colored region based on the person they do not match. However, we can identify the paternal colored region as the other grandfather. In this case, the orange segment on Sibling B receives the Zumstein surname.
When we extend colored regions across recombination lines for one sibling, that sibling will not recombine at that point. That means the other sibling will have a recombination point. Label the line to represent the sibling that changes.
In the video linked above, I repeat steps 6-9 for a known maternal grandmother DNA match. Be sure to watch it to see how to continue identifying segments of DNA.
You Can Do Visual Phasing With Two Siblings
In the video, we looked at three matches for one chromosome that two siblings share. We still need to repeat this process for all 22 chromosome pairs.
Here's the amazing thing! We've identified four of the seven recombination points on this chromosome pair. That's more than half of them!
Additionally, we've assigned 65% of all the segments to a grandparent, which is pretty great.
If we repeat the steps using known paternal grandmother relatives and other matches for the three lines used already, we may completely phase each chromosome.
Visual Phasing with just two siblings is possible. It is different from Three Sibling Visual Phasing because we rely on our known matches to identify and assign those segments. But with a handful of genetic relatives, you can actually phase most of the 22 chromosomes.
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