Do Chromosome Segment End Points Matter? | Genetic Genealogy Explained

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Family History Fanatics

Family History Fanatics

Күн бұрын

In some genetic genealogy circles, debates rage over whether the exact start and endpoints of chromosome segments matter between DNA matches.
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Andy compares 23andMe, MyHeritage, and GEDmatch segment start and endpoints to address this question. WARNING: This is an advanced genetic genealogy topic.
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Chapters:
0:00 - Introduction
1:01 - Comparison of Chromosomes: 23andMe, MyHeritage, GEDmatch
1:28 - Analyzing Chromosome Number One
1:59 - Discrepancy in Segment Interpretation
2:22 - MyHeritage's Split Segment Interpretation
2:39 - Segment Counting on GEDmatch
3:12 - Examining Segment Numbers and Variations
3:58 - Position Differences in Chromosome One Segments
4:59 - Identifying Low and High Numbers
5:55 - Highlighting Differences in High Positions
6:51 - Exploring Centimorgan Differences
7:01 - Comparing Segment Centimorgan Values
8:23 - Diverse Number of SNPs Analyzed
9:38 - Dissecting 23andMe, GEDmatch, and MyHeritage
10:15 - Segment Breakdown on MyHeritage
11:04 - Matching Centimorgans on Overlapping Segments
11:34 - Significant Centimorgan Difference
12:07 - Start and End Positions vs. Centimorgans
13:07 - Limited Scope of DNA Testing
13:41 - Matching and Non-Matching SNPs
14:06 - Considerations for Segment Analysis
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Пікірлер: 30
@FamilyHistoryFanatics
@FamilyHistoryFanatics 3 жыл бұрын
If you find the comparison table difficult to read in this video, click on this post to see a larger version. www.familyhistoryfanatics.com/post/dna-segment-end-points
@yahccs1
@yahccs1 7 ай бұрын
Interesting to note the whole chromosome data can end at different numbers from the different companies, so it looks like either My Heritage has defined the chromosome to end further along than Gedmatch did, or the whole data has been shunted along and there might be points on the chromosomes that have different numbers depending which company is counting them. But now you explain about snips perhaps those numbers are the same (for particular places along the chromosome) but they are accounting for more of the snips and measuring more of the chromosome on MyHeritage than they did on Gedmatch. Anyway, I thought this might be about how start and end points might be useful in analysing shared matches. If you have a number of matches whose segments all start or end at the same place is that enough information to assume they all are related to you on the same side and descended from the same ancestor (couple)? I think it's highly likely, but it's possible that there might be maternal and paternal matches that both just happen to line up their shared segments with you at the same place. Unless some might be really related on both sides and some of their segments on one side and some on the other? I've already noticed that a few matches I have on Gedmatch and also on MyHeritage have slightly different numbers on the end points and assumed this was just a difference in the way the different companies define matching segments, as you explained really well here, thanks!
@ejblom11
@ejblom11 3 жыл бұрын
For some chromosomes, the build 36 based segments of FTDNA can be quite off. I had a large segment on FTDNA that didn't or hardly overlapped when I found the same segment on MyHeritage!
@MikePole_the_kiwi
@MikePole_the_kiwi 3 жыл бұрын
Great explanation, thanks. I guess this is the crux of an issue that’s on my mind - how MyTrueAncestry, can report your matches with archaeological DNA, but with implausibly long ‘matches’, but very low SNP counts. I guess that when you are dealing with so few SNPs, the start and end definitions of segments gets very arbitrary?
@MikePole_the_kiwi
@MikePole_the_kiwi 3 жыл бұрын
In other words, if they announce your amazing match with some Viking on a 6.9 cM segment of 60 SNPs, realistically this could be a fudge of several very short cM segments....
@FamilyHistoryFanatics
@FamilyHistoryFanatics 3 жыл бұрын
YEAH. 60 SNPs ain't a lot. To put it in perspective, even GEDmatch would need at least 200 and probably more like 600 SNPs to call that same segment a match.
@Darigar
@Darigar 3 жыл бұрын
Maybe MH show's more because of the imputation they do (I heard that)
@FamilyHistoryFanatics
@FamilyHistoryFanatics 2 жыл бұрын
Yes, this is a possible explanation.
@GeneaVlogger
@GeneaVlogger 3 жыл бұрын
I wonder if the different companies use different Q-scores and that causes the major difference in the number of SNPS. Having dealt with so many degraded DNA samples in IGG, I have begun researching how Phred Quality might be used to mitigate issues of degradation and this video plays into some of what I have been researching (although not so much in the comparison of companies and more degraded DNA vs non-degraded).
@FamilyHistoryFanatics
@FamilyHistoryFanatics 3 жыл бұрын
The companies would have to tell us what they are using to make their determinations. There is not enough data available otherwise to suss it out.
@martnal
@martnal 3 жыл бұрын
Question 2: Andy, Could you say more about the section of DNA which has a gap in it? I have two or three examples of segment matches where the middle third is missing. What does that gap indicate, and, also, what is indicated if somebody else matches with that missing gap i.e. having a normal match rather than having a gap.
@FamilyHistoryFanatics
@FamilyHistoryFanatics 2 жыл бұрын
That gap doesn't have any tested SNPs (probably because there are few if any in that region). As such, different companies may indicate that you have two segments (separated by a non-tested region) or they may assume that the non tested region belongs with the two segments. Since there are no SNPs in that region, there is no way to tell whether a recombination or two happened in that region.
@suelane3628
@suelane3628 3 жыл бұрын
Again, I am a bit confused as I thought that different companies varied as to which SNPs they choose to test, and how many.(250,000 for 23 and Me, and 500,000 on Ancestry?) I assumed the same testing methods were used. However different companies do have enough SNPs tested in common, so that results can be compared on GedMatch. Hopefully one day there will be full genome testing for family historians. Then how are recent, and even somatic mutations computed?
@FamilyHistoryFanatics
@FamilyHistoryFanatics 2 жыл бұрын
Full genome testing is available already. However, there is no platform to do any kind of matching for it. The amount of computing power (assuming you are just looking at the 3 million SNPs) would be 5-20 times what is currently used for any of the companies matching algorithms. The result would only be moderately more accurate, so a large cost for not much improvement.
@whychromosomesmusic5766
@whychromosomesmusic5766 3 жыл бұрын
This is a really good question and I've never really thought about it. I just presumed that the different companies had different ways of testing and left it at that. I did notice differences in the levels of the same matches in Ancestry DNA vs. Family Tree DNA and did just put it down to different testing methods. Although I think that can affect the perception of how close a match really is. No matter what the "numbers" say I usually just contact people and exchange information with them.
@FamilyHistoryFanatics
@FamilyHistoryFanatics 3 жыл бұрын
No one should haggle over the end points. It makes little difference for the vast majority of matches.
@whychromosomesmusic5766
@whychromosomesmusic5766 3 жыл бұрын
@@FamilyHistoryFanatics So, does the number of centiMorgans indicate the level of the match? And is there a kind of formula for that? Like I said I usually just go by the personal contact (if I get one) and the exchange of information and/or subsequent research (particularly in reference to source documents). I don't really pay that much attention to the "numbers" and I pay practically NO attention to the ethnicity part of it. I am fascinated by history and well aware of the numerous migrations and refugee populations, conquered territory or even mixing of noble lineages that make nailing down somebody's "ethnicity" really practically impossible to verify with any degree of accuracy. However, all of these things concern my mother and when she sees her matches and the numbers and ethnicity associated with them she gets very confused and asks me for some kind of explanation. The last time she asked me I did compare her match with the same person on FTDNA and Ancestry DNA and why did she match at a closer cousin level on one than the other and I did look at the numbers and they were different and the formulas that created them were different and I told her that was probably the reason. This is a person whom my mother has NO clue how they are related, BUT, there seems to be a fairly close (second or third cousin) relationship which we SHOULD be able to find some common ancestor, but, there seems to be none that I can confirm (based on the pedigree the other person has provided at FTDNA). And all attempts to contact the person in question have had no response. What is more interesting is that this person contacted my mother first and all excited about the "closeness" of their match. So incidents like that WILL induce me to check out the "numbers" to try to figure something out to explain it to my mother. I did just think of this. Maybe I could revisit that pedigree and do a little more sleuthing on who those families are and who they are related to and maybe another shared match's pedigree might make it clearer where a possible common ancestor may be. Just another item on the growing list of genealogy projects. Oh well, it's like I keep saying, at least I'm NEVER bored! lol My new Yamaha keyboard gives me something to fall back on when I need to take a breather. ;-)
@mariacapaldi5062
@mariacapaldi5062 3 жыл бұрын
🧬thanks Andy!
@FamilyHistoryFanatics
@FamilyHistoryFanatics 3 жыл бұрын
You bet!
@chriskeller272
@chriskeller272 Жыл бұрын
Did you ever figure out why my heritage saw so many more SNPs? I would guess it's because you and your brother tested on different chips. Also I'm guessing My heritage probably had knowledge of 23andme's algorithm and just copied it. Good white board explanation of start and end points. Are the red lines the "hard breaks" they are talking about at gedmatch?
@AlexandraNMorgan
@AlexandraNMorgan Жыл бұрын
I really wish you could do Ancestry's Chromosome painter because I'm still confused on how to read it.
@FamilyHistoryFanatics
@FamilyHistoryFanatics Жыл бұрын
I'm back from a summer break. I am discussing this during my upcoming video. kzfaq.info/get/bejne/bNxjirCktMq-XZs.html
@jmanwarren
@jmanwarren 2 жыл бұрын
Hi Andy, great video! Can you explain how you got that diagram of chromosones with segments on it? You show it first on the video at 1:13 when you are showing the chromosones that you share with your brother. It's yellow lines with segment markers on it. I believe you said it was from Gedmatch. How can I see my chromosones like that on Gedmatch?
@jmanwarren
@jmanwarren 2 жыл бұрын
Never mind, I found it! It is when I am comparing my kit to another in the One-to-One Autosomal DNA comparison option. I'll leave my comment here in case anyone else wondered how to view that same feature.
@FamilyHistoryFanatics
@FamilyHistoryFanatics 2 жыл бұрын
I'm glad you figured it out.
@martnal
@martnal 3 жыл бұрын
Question 1: Andy, This is slightly off topic for this presentation but related, can you explain why the total number of segment matches that I have on each chromosome isn't in proportion to the length of each chromosome? For example I have just over 1,000 segment matches on each of chromosomes 1, 10, 12, 17 and 20 even though they are of very different lengths. On comparatively long chromosomes like 4, 5 and 7, I only have about 500 different matching segments. Why aren't they in proportion ROUGHLY to the length of each chromosome?
@FamilyHistoryFanatics
@FamilyHistoryFanatics 2 жыл бұрын
Because DNA is random. Also, because some chromosomes have pile up regions and others don't. Also, because it is not a random sample but a representation of those people who have tested (for instance, if there was a family that had 8 kids and they all matched you on Chromosome 20, it might look like you have more matches on that Chromosome than on a single person matching you on Chromosome 1). More about pile-up regions kzfaq.info/get/bejne/iZanp61qnMi2aaM.html
@martnal
@martnal 3 жыл бұрын
Question 3: Andy, I have a 76cM match on chromosome 3 from 7,017,919 to 71,828,420. We both also have smaller matches, 10-30cM, starting at exactly the same point. There are also a few matches that start a few (200,000) base pairs later and I have always wondered what I can infer from this. Does what you have said mean that they are effectively the same? And that we still share a common ancestor?
@FamilyHistoryFanatics
@FamilyHistoryFanatics 2 жыл бұрын
That is a good assumption to start with. Matching trees can help show whether you have a common ancestor that can be identified. Check out this playlist kzfaq.info/sun/PLcVx-GSCjcdmsw25mbI-wJin_9_9QQUzI
@earlscottchambers4280
@earlscottchambers4280 8 ай бұрын
How about giving us more display of the data and you can be transparent so we can keep our lunch from leaving us? We don’t need to see you! We would like to see your data displayed more. Just saying!
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