segment-ology

A website and blog about segments and autosomal DNA – by Jim Bartlett

18 thoughts on “segment-ology

  1. 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?
    Hopefully, Jean

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    • 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….
      Sincerely, Jim

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  2. 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?
    Jean Thornton

    Liked by 1 person

  3. Jim
    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!
    Doug

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  4. 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.

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  5. Jim,
    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.
    cheers Steve

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      • 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

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  6. 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

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    • 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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  7. 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

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