Tag Archive | Triangulation

When is a DNA segment match a real match? IBD or IBS or IBC?

Oct27

The current technology for personal genome testing cannot tell you which of the two chromosomes, maternal or paternal, in a pair that an allele comes from. It can tell you that there is an AG at a specific position and a CT at the next position but not whether the A came from your mother or your father. This leads to much confusion about DNA segment matching.

ShipleyKittyDancingSmll

Kitty and Shipley; siblings sharing 47% of their DNA

The matches that these testing companies find are for stretches of DNA that are half identical regions (HIRs). This is due to the fact that a relative who shares a DNA segment from a common ancestor with you will match you along the chromosome you got from the parent who is descended from that ancestor. Thus your new relative will match you for half the alleles in those positions. Only a sibling will share fully identical regions of DNA. Click here for a page that has a picture of the DNA I share with my brother Shipley.

For example, if my Dad gave me AAAAAAAAAAA and my Mom gave me CCCCCCCCCCC then I would seem to match absolutely everyone on that segment because every position has both an A and a C. So an ACACCAACCAC or a CCAACCCACA looks like a match, but only those with an  AAAAAAAAAAA or a  CCCCCCCCCC would be real matches. This is simplistic and the segment runs used for matching are much longer than this to try to avoid that sort of false matching. Also note than when your testing company shows an AC it is really an AT and a CG but just one of the known pairing is shown for brevity.

The term for a real match is IBD, which is an abbreviation for Identical By Descent. The term IBS means Identical by State which would apply to any false match. So in our example, the CCAACCCACAA match would be considered IBS.

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New Utilities at GEDmatch: Tier 1 for paid members

Oct20

There are four exciting new utilities at GEDmatch.com which I plan to cover in depth over the next several days. These are only available to for people who have donated  at least $10 (every additional $10 gets you these for another month). A good way for GEDmatch to pay for their extra server costs. The rest of the site will remain free. The utilities are:
Tier1

  1. A Matching Segment Search – Get a list of all your segment matches suitable for cutting and pasting into a spreadsheet
  2. A Relationship Tree projection – calculates probable relationship paths based on Autosomal and X-DNA Genetic Distances. It is experimental, try it and give them feedback
  3. Lazarus – Construct a kit to represent a close ancestor, wow!
  4. Triangulation – takes your top 300 matches and finds which ones match each other with details. The format can be copied to a spreadsheet

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Using GEDmatch to see where you match

Oct3

I think the switch from Ancestry.com DNA test results, where your tree gets searched for you, making using DNA with genealogy easy – to GEDmatch where you have to figure out how to use the data yourself, is quite difficult. So this post is an attempt to help my cousins who have tested at ancestry and uploaded to GEDmatch. It might also help others new to GEDmatch who want to look at where they match a [possible] cousin by walking through that process.

GEDmatch Sample One to One

Sample from the GEDmatch one-to-one comparison

  • First make sure that you understand current DNA basics (click here for my page on that). Genetics have advanced greatly since my high school biology class and perhaps since yours too.
  • Next realize that the raw data from your test is only a small part of your genome, a sampling. It is the SNPs that are currently considered the most interesting. They represent the most likely spots where we are different from each other. If a contiguous sequence of those SNPs is the same in two people for about 10 centimorgans (cMs) or more then they are expected to share a common ancestor. With a match of 7-10 cMs it is likely but not a sure thing. There is a good article in the ISOGG wiki on the likelihood of a match at different segment sizes.
  • In order to see where your DNA matches someone else’s, you need your kit number and his kit number. Then you can use the one-to-one comparison to see on which chromosome(s) you match each other. Your kit number shows on your GEDmatch homepage. You can find the kit numbers of other possible relatives in the one-to-many display or perhaps your new cousin has sent you his kit number.
  • I recommend that you keep a spreadsheet with the information on your matches, sorted by chromosome and start point, so you can see who else a new match might match. I have a number of posts on this blog about using spreadsheets and a template in my downloads area. Many people like to use the genomemate tool to organize their data.

The image above is from a recent new match to my Dad uploaded from ancestry.com. The blue rectangle shows where there is a DNA match. The numbers in the box are what I cut and paste into my master spreadsheet for Dad.

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Mapping an Ancestral Couple: a Backwards Use of my Segment Mapper

Aug29

Sometimes I wonder if the interest in genetic genealogy runs in our DNA. I have found many more new cousins with autosomal testing that are descended from my WOLD line than in any other family. Yes they all had lots of children until recently, but so did the Munsons and the Skjolds.

So I decided to make a picture of the HIR (half identical region) DNA segments that I know come from my great-great-grandparents Jørgen and Anna Wold of Drammen, Norway. To do this I made a CSV file with a list of all the segments that are just from those ancestors. I put the first names of the group of matches in the column that would be the MRCA in the usual style segment map. I have to give credit to my distant DNA cousin (on the AJ side) Israel Pickholtz (he blogs too) for this wonderful idea of making a reverse segment map. Below is my picture of Wold DNA created with my DNA segment mapper tool. Click the image to go to the actual html page which will show the centimorgan values and names when you put your mouse on a colored block.

WoldDNAsmllThe use of two lines is arbitrary; I could have used three or four. The DNA segments shown are not separated into lines for Anna and those for Jorgen. Where that was possible, I had intended to do it with colors, but did not get to it, next version. Knut, OK, Nancy and Aaron are on Anna’s side while Susannah, her mother, and Lester are on Jorgen’s side only.
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IAJGS conference and talking with Greenspan

Jul29

If this were a financial blog you would assume a different Greenspan than Bennett and in fact they may be related, but since Alan won’t do the DNA test, we may never know. Today at the annual IAJGS conference I spent some time chatting with Bennett in the Exhibition Hall.  I asked him if they could implement a triangulation feature where when two people match me on a specific segment I can check if they match each other on that spot. He said yes but gave me no time frame …

Selfie with Bennett Greenspan

Bennett Greenspan and Kitty Cooper

Bennett Greenspan is the founder of Family Tree DNA, one of the big three in personal DNA testing. This came about because a newly retired Bennett wanted to prove that the possible Argentinian relatives he had found were related when there was no paper trail showing this. He had read about Dr. Michael Hammer’s work with DNA and the cohanim Y chromosome marker and wondered why that sort of test could not be used for his case. Dr. Hammer laughed at him and said something like “If you knew how many crazy genealogists have been calling me … someone really ought to start a company.” The rest, as we say, is history.

Tomorrow at 1:45 Elise Freeman is going to speak about  “Understanding Your DNA Results in the Context of Ashkenazi Ancestry.” I can’t wait to hear her.

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