segment-ology A website and blog about segments and autosomal DNA – by Jim Bartlett Share this:TwitterFacebookLike this:Like Loading...
Steve, I have mapped my Chr X. Easy – all overlapping segments form a TG on Mom’s side (no X DNA from Dad). Those TGs have an added feature – the Ancestral line to Chr X TGs can not include any line with two males in a row.
Jim, thank you for the comment. I guess what I am really interested in is the detail of the segment sizes and how many generations back they represent. I am familiar with the usual 22 chromosomes. I have very few matches on the X. One is 49cm a few are around 20cm and the rest are < 10cm. For sure I can work out valid paths, but in real-life experience, how far back did you go to find the MRCA vs cm size ?
The short answer is that I have not tried to determine the generations back to segment sizes on Chr X.
A longer answer may help explain why. A Triangulated Group (TG) “segment” is a specific piece of my DNA – a Chr number, start and end positions, total Mbp, number of SNPs included, and the cMs can be obtained through look-up tables on the internet (I have not done that). A TG segment of my DNA first came from a specific Ancestor. All of my Ancestors who *descended* from the TG Ancestor also had (at least) that segment in their DNA, including the parent who passed it to me. My Ancestors *ancestral* to the TG Ancestor generally had smaller overlapping segments (the original TG segment being formed by the TG Ancestor from DNA from his/her parents). Now to the *shared* DNA segments that are included in a TG group of Matches… Some Matches will be cousins on the TG Ancestor, and may share roughly the same amount of DNA as the TG segment; some may well share smaller segments. Other Matches in the TG group may share smaller segments and be related through a more distant Ancestor of the TG Ancestor. The summary is that the Matches in a TG group can be cousins from many different generations, but all on the same ancestral line. The best estimated guess of relatedness to a TG segment would be a look-up of the cMs and then refer to the Shared cM Project. Generally on Chr X, the relationships may be further back. Jim
Thank you Jim for taking the time to provide me with a comprehensive explanation.
Mapping your X Chromosome – I had a quick search a didn’t find if you’ve mapped out your X-Chromosome. Did you do that ? How did it go for the process and the result ?
Jim, thank you for making all your work available on the net. I really appreciate it. I am following your post ‘Triangulate your Genome – How to example with MyHeritage.
I don’t have any living parents or grandparents. My DNA matches include two siblings and my son.
I don’t feel any of their matching segments can be of any use for grouping as most are the same as mine. Should I simply delete their data from my spreadsheet? If not, how are they of help in creating TGs?
Thank you for your assistance
I have been a follower for some time and user your blog as a reference when working on my family’s DNA matches. I have several family profiles on 23andme, Ancestry, FTDNA and all of them on GEDmatch. I use GEDcom as well.
The many spread sheets is overwhelming. So I started looking for a Microsoft client based software package and found GMP which I loaded almost all of my spreadsheet data. As I worked with the program the next version of the product entered Beta testing which I happily joined hoping I was going to find cross product triangulation support. Not is the product. All of the triangulations depend on the sources system. I started trying to implement Triangulation groups but the product does not easily support such a concept. Your work would be an amazing functional addition to Becky Mason Walkers work. I have suggested this on her Facebook group. Becky is not taking enhancement requests until the program clears Beta testing. It would be an even more amazing tool if you two could come together and add your methodology to her tool. the segementology people could get themselves out of spreadsheet hell.
The ability to “match” shared DNA segments is not as easy as just finding overlapping segments – the SNPS in those segments have to match. Each atDNA test results in a file of 600,000 (give or take) SNP pairs (AA, AC, AG, AT, CC, CG, CT, GG, GT or TT). The companies then compare your 600,000 data file to the data file of each other Match in their system to see if a long enough segment has essentially a match of one value at each SNP in the segment. This takes a lot of computing power. Of course the companies only compare with other Matches in their data base. GEDmatch does compare between companies, but programs you load onto your PC, like GMP, DNAgedcom and others do not – they rely on the results of the big companies, like ICW or Shared Match files. Those are typically compared in Clustering programs, and are only valid within each company’s Matches.
This is another reason why I like Triangulation. Triangulation is based on recombination/crossover points which are fixed on YOUR DNA. No matter where you Triangulate Segments, they should conform to the recombination “map” locked in your own DNA. This is also why we cannot combine the spreadsheets of different people – each recombination “map” is different.
I have outlined my Triangulation process, in some amount of detail, in my blog post. It’s “open source” – anyone can use it. Forming the groups is pretty straightforward, and it would be great if someone could automate it. Assigning groups to a side (and thus creating a chromosome map of segments), requires genealogy, and some amount of judgment (much harder to program). I’ve worked with three well-known programmers so far, and none of them have produced a product that I think is accurate enough to endorse. I think the main issue is they want to produce a full “chromosome map” product. I’m looking for the grouping program (to save 120 hours of tedious work). It’s sort of like the Leeds Method which gets you to 4 groups – but then you need to be on your own to figure out which grandparent goes with which group. I want the 300-400 Triangulated Groups – it’s then still a challenge to figure out the ancestral line and Most Distant Common Ancestor for each one.
Hope this helps. Jim
I’m not sure if I’m allowed to ask a newbie question here. Please delete if not
Question – Given I match to someone at a given position on a given Chromosome. Would I expect to match in exactly the same place to one of that persons parents ?
In other words is it possible to match to a person but not to either of their parents ?
The doubt comes because I don’t know if inherited segments can get moved to a different position relative to the parent they were inherited from or whether the inherited segment must align somewhere within the boundaries of the original parental segment.
Best Wishes Steve
Steve, Sorry I missed this question when you sent it. The short answer is No. Parent’s DNA cannot shift around – all of our DNA segments are fixed at the time of conception. Every segment you have must have come from one of your two parents. So I you match someone on a segment, your parent (who has tested at the same company) should also match on the same segments. NB: the opposite is not true – there is a 50/50 chance that your parent passed one of their segments to you – so I they match someone on a segment, you may or may not match on that segment. Possible issues to also consider: small flaws in the testing result; with endogamy you might appear to match on a segment that actually comes from both sides. Jim
I have a question about large segments that triangulate across a pileup region. I’m Ashkenazi Jew and have been trying to figure my complex DNA matches.
How do I handle (real or move on) large 40+ cM segments at CHR 15 20004966 – 33871785 that triangulate in that area plus some 20+ cM that end up in same TGROUP. There is one match with the largest segment and the Total = 42.5 cM
I’ve read your blog a few times and now that I’ve Painted enough segments it’s starting to make sense. Sort of! -Mark
Mark. Triangulation for Ashkenazi is the same as for anyone else. Notwithstanding the fact that AJ may have the same Ancestor in several places in your Tree, from the DNA’s point of view it’s all the same. Each Ancestor block passes down full chromosomes to their children which include large segments from their parents some of which are subdivided at each succeeding generation. Re-read my Top Down and Bottom Up blog posts (which are the same thing from different perspectives). So segment Triangulation is done the same way for everyone.
Now, when you try to assign ancestors to each TG it gets more complicated for AJ. My best advice is to get close cousins tested. Cousins will help sort out which TGs can come from which Ancestral block and which do not. Jim
Thanks, but you didn’t answer my question about large segments across pileup areas. Can they be valid or should I not waste my time.
Large segments that span pile up areas are valid. They are just as valid as any other large segment.
Jim Bartlett – atDNA blog: http://www.segmentology.org
In addition to my response about pile up areas. Your DNA on each chromosome came from a parent and an ancestral line. Many smallish shared segments in a pile up area may be false (and they don’t Triangulate). The smallish ones that do Triangulate are likely to come from very distant ancestors – that’s why they pile up – it’s a common area of DNA that many humans may share. I cull out those smallish shared segments (that stack up by the hundreds), because they are almost certainly beyond my genealogy. However, the larger segments, that happen to include a pileup location, are usually from closer ancestors, so I work with those groups. Jim
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Your description of segments and the relevance to centimorgans helped me to understand how DNA is passed on. Having had several members of my family tested, in particular our grandson with both myself and my wife, here was a chance to see what our daughter did with our DNA when generating the single strand for Charlie’s maternal chromosomes. GEDmatch between Charlie and myself and between Charlie and my wife showed which segments came from which grandparent. It seemed that our daughter had made 41 crossovers within chromosomes and several chromosomes began with the other parent from the one at the end of the previous chromosome. Expecting something around 100cms for the average segment length, it was less than 60.
The segment lengths on Charlie’s paternal chromosomes were much longer with Charlie’s father making only 22 within-chromosome crossovers. Is it normal for more crossovers to be made by the mother creating the ovum than when the father creates the sperm?
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Geoff, Yes, I believe the actual observed averages are 27 for males and 41 for females (average 34) in one generation. These tend to dampen out and move to the average of 34 when you look at the it in more distant generations. So for a living individual, looking at the grandparents – use 27 on the paternal chromosome and 41 on the maternal chromosome. At the great grandparent level and beyond, it tend toward the average.
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I am new to all of this. I just learned using My Heritage DNA matching and one to one comparisons that I found two people who have triangulated segments, one has 7 and the other 4. The program advises if you have triangulated segments you have a common ancestor. Apparently,(reading here) the segment that are triangulated need to be 7cm long? My real question is how many triangulated segments are meant to be an indicator of a common ancestor?
Richard – You and a Match have a Shared DNA Segment – which segment comes from a Common Ancestor. This is true for each of your Matches – no Triangulation involved. When two of your Matches share the same DNA segment, the three of you have the same Common Ancestor. This is the power of Triangulation – all of the Matches who Triangulate in one Group will share the same ancestry. On your DNA Matches page – on the right side – see the link that says Advanced Options – click on that and then open Export shared DNA segment info… you’ll get a spreadsheet with all your Matches and shared segments – I think every Match will have a segment over 8cM, and they may have additional segments down to 6cM. The short answer to your questiion is three. Any that show up with the Triangulation Icon circling the segments, will have the same Common Ancestor for the overlapped portion. Jim
sorry about the formatting Jim. I have a document which maps it out better now. but it won’t let me use it inside the blog. The rate above expected (Eur) field spans two columns , the first is Germline and the second is ISCA if that makes anything clearer to you. cheers Steve
Steve, see my comments on your other comment.
Hi Jim , I got a reply off a wikitree G2G which whilst I don’t understand the ‘rate above expected(Eur) field thought I would pass on. The matches in most cases are pretty large. I do have an overlap in two positions from an overlap set of segments from two Lazarus files of maternal and paternal family lines. My understanding is that these positions do not change very frequently so will pull an above average set of matches in these specific positions which may then be considered regional matches rather than IBD . The answer below suggests the list will vary with genetic geography.
Reply starts below.
High Risk Segment list
Your question on WikiTree G2G has been answered by Davidson-8450:
These are the segments I have found from links in ISOGG. I hope the formatting works, because they are in wiki table format, but the edit window is too smart for that. My guess as to why they removed percentage values is that some seem to be very sensitive to which population sample were used to test them.
I have a suspicion that Ancestry.com have a further set of data that they use to reject other segments.
chr start pos stop pos cM rate above expected (Eur) notes
1 118 153.4 9.95 19 47 Li 2014
2 85.3 99.6 6.53 21 2 Li 2014
2 132.7 141.4 9.16 7 4 Li 2014
2 192.4 198.1 5.04 4 4 Li 2014
5 153.2 158.8 0.6 Albrechtson 2010
6 29.8 33.1 HLA
6 29.3 31.5 2.2 Albrechtson 2010
8 8.4 10.5 2.1 Albrechtson 2010
8 10.4 13.5 7.96 38 10 Li 2014
9 38.3 72.6 8.15 39 2 Li 2014
10 44.6 53.2 7.58 22 2 Li 2014
11 49.3 51.1 1.8 Albrechtson 2010
15 20.1 25.5 10.46 15 42 Li 2014
15 27.1 30.3 9.29 9 3 Li 2014
16 19.4 24 6.18 6 5 Li 2014
17 59.5 65 6.23 9 4 Li 2014
17 77.2 78.4 5.66 11 0.1 Li 2014
21 16.3 19.4 6.91 22 2 Li 2014
22 16.05 25.1 20.8 22 3 Li 2014
Steve, I think what you have here is what we call “pile-up” areas. These segments may have pieces of DNA that are valuable, and many folks have them. I’ve written several posts about “pile-ups”. One fundamental thought is that each of these areas are part of your DNA. Actually twice – on both chromosomes. So you got each of these areas from your parents, who got them from their parents, etc. etc. An AncestryDNA TIMBER algorithm may delete many Matches who share these segments, but they cannot delete the DNA in your body. I keep shared segments identified at GEDmatch which Triangulate, even if they over lap these areas. So I tend to get a lot more Matches over some of these Triangulated Groups – so what? I recognize that many of those segments may have come from very distant ancestors. But I also know there is a distribution curve, and some of these segments are with closer cousins. Those are the ones I’m looking for. Jim
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I am running into trouble in my mapping project because both maternal and paternal families seem connected on some segments. This may be true but I also signed up for the genesis project on GEDMATCH and heard there were high risk segments which didn’t change very often and consequently got a very high set of match kits in the specific regions. Has anyone to your knowledge mapped this high risk segments ?
The genesis project’s focus seems to be to illuminate these potential mismatches but they removed a useful risk assessment measure from the match table. Before they did I saw large matches , some 18cM classified as high risk.
By the way, I am finding the approach you espouse has completely transformed my ability to ‘read’ the segment map on each chromosome, especially on the smaller chromosomes with a low number of crossovers…….. I can now see some segments and make a ‘good guess’ at probable family line at the grandparent level and follow through on the more interesting segments to map out the great grandparent marker segments.
Steve – You need to Triangulate shared segments from all over your DNA to form a chromosome map. Finding the Common Ancestors for each TG is a separate evolution. Jim
Hi Jim, I am on the case. I am helping a friend and have a single Lazarus file for his collective paternal grandparents using 2 female first paternal cousins, and a niece. We have also been able to create a maternal grandmother lazarus kit. Our goal is to identify the parents of his paternal great grandfather who died in the whaling fleet in the southern Ocean in 1840. Its a real challenge, he was born in Jamaica but absolutely no records can be found. DNA will now be the only way to establish a connection and Segmentology techniques look ideal to map the target families DNA across the whole family. It was a surprise when we found the two grandparent Lazarus kits were ‘related’. We have scrubbed the inputs carefully and, after initially discounting the ‘pile up’ segments, it still shows a relatively strong connection, possibly second cousin relationship between grandparents. We now believe there is a real connection at that level between both sides of the family. I have the tier 1 segmentation files for all the cousins and the two Lazarus kits and have begun mapping the segments and identifying first and second generation crossovers. I have also used the flow of the X chromosome DNA into the Lazarus process to identify his maternal grandparent’s family. Only her X chromosome DNA is common between the female cousins and the niece so any overlap with the Paternal Grandparent lazarus on X must be from that side. We are using these markers to help with the mapping process. cheers Steve
Steve, Looks like you have a good plan and the energy to carry it out. Good luck.
Love the site, it is helping me create the database bridge to the various testing sites. No one site has all the tools that people need to match up with their matches.
Dennis; Thanks! I hope you’ll report on any new tools here.
Thanks, Doug – it’s truly a journey!
I started with the DNA portion of my Ancestry work 2 years ago and have collected a large amount of data. I am now on the Triangulation band wagon. Your blog is extremely helpful and appreciate your sharing your education with the rest of us. So much to learn!
Jim, love your blog. Full of valuable ideas and examples.I intend to read every post and digest as much as possible. Thank you for sharing – I hope to put it to good use.
Joel, Thanks for the kind words, and encouragement. Let me know of any additional topics I might address.
Hi Jim, I’ve appreciated your blogs as they have been very helpful. I noticed that your latest blog was on Feb 2016 and have not seen one since.Have you posted more recent blogs that I may missed?
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Life got in the way. I’m working on more articles now.
Hi Jim, Find your site most informative. Are you planning on adding more topics on the site….I noticed that the last post was in June?
Jean, Thanks for the kind words. Yes, there are several in draft. It’s been a busy summer: beach weeks with different family groups, extended Africa trip (12,000 pictures; and they turn the generators and hot water off from 10pm to 5am); back for another beach week with grandkids – two weddings coming up soon…. I’m supposed to be retired!
On deck are: Genetic Ancestors – the Porcupine Chart (shows “sticky segments” visually), and Do Cousin Ancestors Double your DNA or Matches? Stay tuned….
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