Visual Phasing Part 1 - Setup

Video Transcription

Have you ever wanted to identify a DNA for people who have already passed away and so you can’t get a sample from them? Well, visual phasing might help you out.

Howdy, I’m Andy Lee with Family History Fanatics where we help you understand your DNA, climb your family tree and write the stories of your ancestors along the way. This is a segment of DNA. Be sure to subscribe to our channel and click on that bell if you wanna be notified about upcoming episodes. A visual phasing is an advanced technique that people can use in order to create the DNA of their grandparents. Now, it’s not gonna create all of the DNA of their grandparents, but it can create a lot of that DNA and you can use it to help narrow down your searches for other matches because you’ll be able to tell which grandparent those matches came through. I’ve divided visual phasing up into four parts, and so they’ll have a video for each one of them. Now, this first part is all about setup. We want to get our information set up so that we can start the visual phasing process.

Step one of our setup is that we need three siblings, at least three siblings. If you have more siblings, that’s great, but three siblings is really the minimum to start with. Now, you also want to have all these siblings information uploaded to GEDmatch. If you want to use the graphics from 23 and me, you’ll have limited success in visual phasing. But GEDmatch provides the most detailed information as far as matching segments in order to do visual phasing. If you have siblings that already tested, ask them if they’ll up all that information in GEDmatch. And if you have siblings and they haven’t tested, then talk with them about perhaps taking a DNA test that you can create some of your grandparents DNA. Now through this I’m going to introduce both principles and steps. And these principles are really things to keep in mind as you’re going through.

And this first principle is really important and it can confuse a lot of people, and I’ll talk about it more as we’re visual phasing throughout the four videos. But each chromosome is separate and you have to treat each chromosome separately. And so for visual phasing, one of the things I like to do is I like to visually phase one chromosome at a time before I go on to the next chromosome. So I’ll actually complete this whole process in these four videos with one chromosome. Now, along with this principle, you need to remember that the visual phasing on that chromosome, it’s completely unrelated to all of the other chromosomes. So just because you might have something funky happening on another chromosome, doesn’t mean it’s going to happen on this chromosome. So bear that in mind. Every chromosome is separate. You can’t be looking at these chromosomes together.

You have to be looking at these chromosomes separately. So step two of the setup is you want to go onto GEDMatch and use the one to one tool. And for each one of the siblings, you want to get the graphics of the shared DNA. And so again, this is for a single chromosome. I’m using chromosome number 10, and this is three of my brothers. So I have brother A, brother B, brother C. So I’ve grabbed a comparison between A and B. I’ve grabbed a comparison between A and C, and I’ve grabbed a comparison between B and C. Now, you can use various tools to do this. Some people like to use a spreadsheet, some people like to use PowerPoint. You can even print these out and do it by hand if you want. There is a spreadsheet on a Facebook group by Steven Fox, which helps automate a lot of this process for Excel users.

But that has some limitations if you use a Mac or if you only have Office 365 rather than the full version of Excel. So if you wanna check that out, then check that out. But I’d like to teach people how to do it really manually on a piece of paper without a lot of this automated stuff, just so you understand what’s happening when you start seeing some of this automated information. So again, going back to principle number one, I’m just going to put one chromosome on one sheet of paper. I’m not going to try to clutter it up with everything. I’m just looking at one chromosome that’s shared with all three of these brothers. Now there’s some terminology that just needs to be understood that I’m gonna be using throughout this. And this has to do with the color region. So the first color region is if you have a solid green on the top line and a blue bar underneath that, then that is a full match or an F I R a fully identical region.

So, green on top with blue on bottom means it is a full match, and that’s always going to be the case. The next colored region is if you have yellow on top that has some green or maybe it doesn’t have some green interspersed in it, and you have blue on the bottom when you have the yellow on top with some green interspersed in and blue on the bottom, that is a half match or a half identical region. Now the difference between a full match and a half match is with a full match on both chromosomes. You share the exact same snips with a half match. You only share a snip on one of those two chromosomes. So chromosome 10, you have one from your mother and one from your father. If you had a full match in that area, then you share both of ’em.

If you have a half match in that area, then you just share one. And a third color region is going to be red on the top. Although this is rarely a solid red, it is usually red intermixed with yellow and a black on the bottom. Now what this indicates is this indicates it is not a match. So this is a segment where you don’t match the other person on either one of your chromosomes. Now the reason why I say it is red with some yellow and sometimes even green and dispersed is because we share a lot of DNA, just humans we do. And so just by chance there’s gonna be a lot of what you shared that is in common. And so usually these no match regions are defined by the start or the first red marker and the ending red marker with red markers periodically throughout at various intervals.

And that has to do with the thresholds. And I’ve done videos on that, but you’re rarely going to see a solid red. What you’re usually seeing as you can see here with a couple of examples, is some red bars with some yellow and maybe even some green interspersed in them, but it’s going to be black on the bottom, and that indicates it is a no match. Now the second principle that we can learn from this is that the color ranges changes represent recombination points. Now recombination happens when the cells are dividing before they’re being passed on, and these are the egg and the sperm cells. And as part of that, the two chromosomes swap different places. So that what’s passed on is actually a recombination of that chromosome. It is a combination of the two parental chromosomes. Now, sometimes this doesn’t happen at all and you receive a full chromosome.

Other times it might happen a lot and you receive a really jumbled up chromosome from your mother or your father. When we’re looking at these three graphs here, every time we go from a color region one to a color, region two, that’s a recombination point or vice versa. Now the next principle, and I know it’s looking like we really haven’t gotten very far because I haven’t drawn anything on here at all I have is these graphs up here. But these other principles are important to understand before you start drawing so you can start to keep things straight. And principle number three is a really important one because it tells us that a full match cannot be adjacent to a no match. That would be a color region. One cannot be adjacent to a color region three, or you can’t have a solid green followed by a bunch of red.

There has to be some yellow in between those two. There has to be a transition point. Now you can start a chromosome with either red or full green, or it can start with a yellow and you can end a chromosome with a red or a full green or even with a yellow. But inside you can’t go from green to red. You always have to go to yellow in between those colors. So now we’re ready to actually start drawing our recombination point lines. And so remember our recombination points are where we have a color change, and I’m gonna go through and draw these out. So if we’re looking at this, there might actually be a green right here at the beginning. And so I’m gonna draw a line right here on down. And then I can see this next point here. There’s this solid green right here.

And then there’s some more solid green right here. It looks like there’s a little bit right here and another point right here. And so you can see I’m changing from green to yellow to green to yellow to green, back to yellow. And then I have this big long stretch of just the yellow on the top and then the green from BC and then it changes. And I go from a yellow to a red. So I didn’t go from a green to a red. I went from a yellow to a red, which is perfectly fine. And then it’s very shortly thereafter, it goes from red to yellow and we can see, hey, this is where that principle three comes in, because I had this big long stretch of green and then it had to go to yellow just for a little tiny bit. Then it goes to this big red region.

So, I had to have this yellow region in there. And then here there is another one where it goes back from red to yellow. Now it doesn’t go to solid green because it was red right there, but that is my recombination points. And so once you’ve done that, you have completed step number three. Let me clean this up just a bit for you. So that leads us now to step number four is we want to assign the recombination points to a certain person. Now, how do we assign those recombination points? Well, what we need to look at is we need to look at where they are happening. And so a recombination point is going to affect one person at a time, but because we’re comparing that person with another person, it’s going to affect at least two lines at the same time. So what we’re looking is which lines are changing and what’s the common person between those?

So if we look at this first recombination point right here, okay, we can see that we go from green to yellow. So there’s a change. So a B is that, and then it goes from green to yellow, a C, well, that is a common A. And so we can assign that first line to a person A. Now we go to the second one and we see that it’s going from yellow to green. So that’s an A, B, and it doesn’t change on AC right here, but down on BC it goes from green to yellow. So what’s common between AB and bc, that’s gonna be B. So this next one is gonna be B. Same thing as we go through all of these. This next one, one is going to be an A, cuz it has those two in common. This one is gonna be a B because it has those two in common. This next one is an A. We are going with an A, B, a, B, a. Now if you start to think that, hey, there’s a pattern, and guess what the next one is, don’t think that this pattern is going to happen. This is purely by chance right now that we have this pattern. This next one could be anything. It just so happens it’s B, but the next one is also A B. And this last one, well that looks like that’s a C.

So, what we’ve done is we’ve gone through each one of these recombination points and we have made a assignment as to which person that recombination point belongs to. And with this our setup is complete. We have gathered the data that we need in order to get started with visual phasing. We’ve identified our recombination points and we’ve assigned those recombination points. So if you’ve been able to get this far on just one chromosome, then congratulations, you are ready to go on to the next step. If you want to try this out yourself, then make sure you have at least three siblings go to GEDmatch and download that data. Then you can set up your visual phasing. So I hope this introduction to visual phasing has been helpful. If you have any questions about how to get your visual phasing set up, then put it in the comments below and I’ll try to answer it for you. And if you like this video, then give it a thumbs up and share it with all your friends.