This afternoon I watched a Legacy Family Tree webinar (recorded) by Dr Blaine Bettinger, a genetic genealogist, about a DNA technique used to map the segments of DNA that a person does not share with a match. A match, of course, is definable as a string or strings of DNA common to two people. But what about the DNA that they do not share? Can it tell us anything?
Blaine Bettinger showed how, by using DNA information from close relatives such as parents or siblings, we can work out where pieces of DNA came from: how they were inherited. The technique is called deductive mapping, inverse mapping, or inferred mapping.
The key is to recognise that on the chromosome you inherited from your father, your DNA comes either from your paternal grandfather or your paternal grandmother. Similarly, the DNA from your mother comes either from your maternal grandfather or your maternal grandmother.
If you find DNA on the chromosome that you inherited from your father that did not come from your paternal grandfather then it must have come from your paternal grandmother. The principle applies equally to matches on your mother’s side.
I was very keen to put this new technique to the test on my husband Greg’s DNA. Luckily, Greg’s brother Dennis had tested his DNA, and I was able to use his matches in combination with Greg’s. The first match I reviewed was Greg and Dennis’s paternal aunt Betty.
My hypothesis was that for segments of DNA where Dennis shares DNA with Aunt Betty and Greg does not share DNA with Aunt Betty, those segments must have been inherited from Greg and Dennis’s paternal grandmother, Peter’s mother Elizabeth Cross.
All segments on Greg and Dennis’s paternal chromosomes were either inherited from their paternal grandfather Cecil Young or from their paternal grandmother Elizabeth Cross. If Dennis shared a segment with his Aunt Betty, he inherited that segment from Cecil. If Greg did not share that same segment with his Aunt Betty, then he did not inherit that segment from Cecil. He must have inherited the segment from his paternal grandmother Elizabeth Cross.
Using the tools at MyHeritage DNA I was easily able to extract the segment data of the DNA shared by Greg and his Aunt Betty. They share 138.5 centimorgans of DNA across 19 segments. I scrolled down to the chromosome browser on the match screen and clicked on “Advanced Options” on the right side of the screen and then clicked on “Download shared DNA info”.
This gave me a spreadsheet and I was able to copy and paste the data into DNA Painter (I have written about chromosome mapping with DNA Painter at DNA Painter – a new tool). I created a new profile for this exercise as I did the calculations.
I then extracted the segment data for Dennis and Betty.
I then mapped Dennis and Betty’s match at DNA Painter. So I could see Greg and Betty’s match lined up against Dennis and Betty’s, I mapped it as a maternal match. I then looked for the visual clues of segment mismatch. I have highlighted these segment mismatches with green arrows. There were eight segments where Dennis shared DNA with Aunt Betty that Greg did not. (There were also segments that Greg shared and Dennis did not but for the moment we are concentrating on Greg’s chromosome mapping.) Four of these were complete segments and four partial segments.
I took the spreadsheet of Greg and Betty’s shared segments and pasted beside it Dennis and Betty’s shared segments so I could compare them.
I then highlighted the whole segment mismatches in green and the partial segment matches in purple.
I then added the four segments that were inferred to have been inherited by Greg from Elizabeth to the DNA Painter profile. I only needed to add the chromosome number and the start location and end location.
For the purposes of chromosome mapping I did not need the additional data concerning RSID start and end, the number of centimorgans, or SNPs.
When previewing the segments I got a warning from DNA Painter about match segments being overlaid and that I might have already mapped these segments.
When I tried to save the match, DNA Painter told me that there was an overlap with the segments I had already painted of Dennis’s match with Aunt Betty.
The next challenge was to calculate the partial segments where Dennis shared some DNA with Aunt Betty that Greg did not at the beginning or end of a segment. I first did the calculation for Chromosome 5. The segment Dennis shared with Aunt Betty extended beyond the segment Greg shared with Aunt Betty. In the spreadsheet calculations for inferring the DNA Greg inherited from Elizabeth Cross, I copied the end location data for Greg’s segment match with Aunt Betty and the end location data for Dennis’s segment match with Aunt Betty. This created the segment that Dennis shared with Aunt Betty and Greg did not.
I painted that segment successfully. The black arrow highlights the segment Greg does not share with Betty and can thus be inferred to have been inherited from Elizabeth Cross. Underneath can be seen that Dennis shares that segment with Betty.
I repeated the exercise for chromosome 11. This time Dennis shares DNA with Betty and Greg does not before the segment Greg shares with Betty. So the calculation involved the start location of Dennis being the start location of the inferred segment and the start location of Greg’s match with Betty being the end location of the inferred segment.
I repeated the exercise of inferring segments for the remaining two segments.
I was confident in the logic of the results of this deductive chromosome mapping exercise and added the inferred segments to Greg’s DNA chromosome map. Before this exercise I had mapped 40% of Greg’s DNA with 161 segments being assigned. After adding these 8 segments 41% with 169 segments assigned. I have now mapped 54% of Greg’s paternal chromosome with 94 segments assigned.
I look forward to continuing the exercise and filling in more gaps.
By assigning inferred segments to either the paternal grandfather, paternal grandmother or on the maternal chromosome to either the maternal grandfather or maternal grandmother, I may be able to use the information to deduce how a DNA match links to Greg’s family tree based on the segment shared, even if that match does not have a family tree link to Greg.
A chromosome map is not just a colourful diagram. It’s a useful tool for exploring how DNA matches might be related. Information about the descent of a DNA segment, even if the segment is not directly shared by matches, could help you to calculate their shared ancestry.
Anne's Family History 
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Thank you so much for posting about how you applied Blaine Bettinger’s webinar on Deductive Chromosome Mapping to your own work. Your example helped me make some decisions about how to proceed with my DCM project, but I wonder how far the technique can be expanded. I’d love to see comments from you or your readers about these questions:
1. Can you substitute the DNA of a deceased sibling’s two children to provide at least some of the matches the deceased sibling would have had if he had been tested (if, say, Dennis were deceased and had not been tested but he had two children who had been tested)?
2. Can you use this process with the test results three siblings instead of two (if, say, Greg and Dennis had another sibling who had tested)?
3. Can you use this process with the test results of two siblings and their deceased sibling’s two children or are you limited to comparing only two people in one line of descent (like Greg and Dennis) against a match in another line of descent (like Aunt Betty)? In other words, if Greg and Dennis had a sibling (call him Tom) who was deceased but who had two children who had been tested, could you use the two tested siblings (Greg and Dennis) and Tom’s two children–all four people in one line of descent–to compare against a match in another line of descent (like Aunt Betty)?
4. If #2 and #3 are possible, where/how would you paint them?
5. Does the basic premise of deductive chromosome mapping work just as well for more distantly related matches and for mapping segments from ancestors further back in time, or are there other factors to consider in those cases?
Best wishes and thanks very much!
F.T.C.
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Thank you for visiting and for your kind comments. Yes the process would work equally well for scenarios 1, 2 and 3. You would work through each scenario one at a time, not all together. You could compare the newly identified segments to make sure there were no flaws in your logic or calculations. When you were confident, I would add the newly identified inferred segments to my chromosome map.
In his talk Blaine expressed caution about using more distant matches and I feel likewise. You would need to work carefully through the logic but I think with more distant matches there are more possibilities as to why you did not inherit the shared DNA inherited by somebody else.
Regards
Anne
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Thanks so much for answering my questions! Your input will definitely help me work through the process.
Best wishes,
F.T.C.
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Anne,
Great example and illustration. Your use of screenshots and arrows made it very easy to follow.
Well done,
Paul Baltzer
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Wow you have really mastered the DNA system. I’ve been intimidated to jump in on that. Are these programs free to use?
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MyHeritage charges a small fee now to unlock their DNA tools. DNAPainter is free to use but as a subscriber you get to have more than one chromosome map.
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