Double Visual Phasing

Many articles have been written lately about visual phasing. This is a method developed by Kathy Johnston. I would like to write about double visual phasing. Previously, I had tested my father in law and his two sisters and tried visually phasing them. Here is the result of my attempt to visually phase their Chromosome 15:

I can tell that I did this a while ago as it was done in MS Word which I don’t use now for visual phasing. L is Lorraine, R is Richard and V is Virginia.

What is Double Visual Phasing?

This is a term I made up. I’m guessing that others have tried this, but I have not seen any Blogs on the subject. Richard has a second cousin named Fred. He is related on the Pouliot side (in orange above). Fred has had his sister Sleuth tested and his brother Don. If I phase Fred and his two siblings who are related to Richard and his two siblings, I’ll have double phasing. As they both share a Pouliot grandparent, it will be interesting to compare the results.

A Brief Genealogy

For the purposes of this Double Visual Phasing, here are the people involved:

Let’s Visually Phase Fred and His Two Siblings on Chromosome 15

The first step is to compare the three siblings to each other at Gedmatch.com using the Chromosome Browser:

I used MS Excel for this and I adjust the columns to the segment changes. Note that all the segments don’t line up perfectly, but I’ll say they are close enough. Next I add locations in millions:

I also put in darker vertical markers. I’m hoping that the places where the segments don’t align perfectly do not indicate additional crossovers.

Next I need to show who the crossovers belong to:

From this, it looks like Fred has four crossovers, Sleuth has two and Don has only one. Fred’s first crossover is at position 22M.

Next, I can assign colors based on Fully Identical Regions (FIRs). In these regions, there will be a match on both one maternal and one paternal grandparent. These grandparents will be represented by two of the same colors in that region extending to the person’s next crossover.

Where there is no match, I can assign two different colors and extend those to each persons’ crossover.

I make sure that the boundaries for each person line up with their crossovers. So on Fred’s map his first FIR with Don is short as it is within Fred’s two crossovers.

Mapping Half Identical Regions (HIRs)

Here I get one chance to map an HIR. My inclination is to map the HIR on the right between Sleuth and Don. My reasoning is that Sleuth is already at her last crossover at that point, so I’ll extend her segments all the way to the right. I already know from my previous map for my father in law’s family that Fred has some matches with my father in law and his two sisters on the left side of Chromosome 15 shown in Orange. So that information may help me map the left side of Chromosome 15:

Here is Fred and family’s partially completed Chromosome 15 with the HIR added for Sleuth:

However, there are blanks. Also we haven’t figured out which side is maternal and which side is paternal.

Two other testers

There are also two other testers: Patricia and Joe. They are my father in law’s first cousins. They are related like this:

The next thing I do is to compare all these eight people in gedmatch.com to each other. I download the results into a spreadsheet. Here are the matches on Chromosome 15:

I have the matches between siblings filtered out so they don’t show. I have Fred, Don, and Sleuth in the first column and the others in the second column. Every match represents DNA from Joseph Pouliot (or his wife Josephine Fortin – let’s not forget her). The way I have it mapped right now, the most important match is Joseph to Don and Sleuth. The only place that match could be is on the blue portion:

This is good news, because this sets the paternal and maternal sides for Fred, Sleuth and Don. It also sets where their paternal grandparents are. Here are Fred’s grandparents:

That means that blue is Pouliot and pink is Ford. Like my father in law’s family, Fred has a French Canadian side and an Irish side.

Next, we should be able to fill in the left side of the puzzle using the other matches:

A few observations:

• The same match that Fred had with my father in law’s family helped finish my father in law’s visual phasing and Fred’s visual phasing.
• All four of Fred’s grandparents DNA is represented between the three siblings. The one exception is a small portion of green from 22 – 27 M on the maternal side
• The purple segment that Fred has from 22 – 27 seems quite small. It is a little unusual to have a small internal segment like that. By internal, I mean a segment that is not right on either end of the chromosome
• Without the match between Joe, Sleuth and Don, I don’t know if I would have been able to complete this Chromosome
• I don’t know about Fred’s maternal [Irish] side. He may already have matches that would identify the Halloran and Drennan DNA.

Comparison of the Double Visual Phasing

• Unlike Fred’s results, my father in law’s family does not have good Pouliot coverage (in orange) between the three siblings.
• This explains why Richard’s family matches Fred’s family in the beginning of the Chromosome and not the end. Pouliot DNA is missing between 60 and 95M.
• It appears that Sleuth and Richard could have matched between 95 and 100, but I didn’t find a match over 3cM. Could this be because one received DNA from Joseph Pouliot and one received DNA from his wife, Josephine Fortin? Perhaps this is also an explanation of why the match between Don and Viginia (V) stops at position 38M.

Summary

• Double visual phasing has benefits in that there are at least six people to compare matching DNA results with each other.
• Double visual phasing should result in a crosscheck for the visual phasing of each family and better Chromosome maps of contributing grandparent DNA.
• There are benefits in noting which group has the better coverage of DNA of a shared ancestor.
• Comparison of results appear to indicate deeper crossovers between ancestors

Next Up

There are matches between Fred and his two siblings and the other five tested people on every chromosome except for 18, 19 and 22. That should make mapping the chromosomes with matches relatively easy.

I would like to try double visual phasing between two sets of siblings where the siblings are from different generations. However, it may take a while to get the additional samples done.