Sunday, 6 August 2017

Comparing parent and child matches at AncestryDNA

A number of genetic genealogists have done comparisons of parent and child matches at AncestryDNA to see how many of the smaller matches do not match either parent:

  • Ann Raymont published an article in July 2016 When is a match a false positive? She found that 35.3% of her matches did not match either parent.
  • Blaine Bettinger wrote a blog post on The danger of distant matches back in January this year. He found that 32% of his matches were not shared with either of his parents.
  • Kevin Ireland published his results in an article entitled atDNA case study: two parents and one child. He found that 18.5% of his matches did not match either parent.
  • Karin Lovisa Borgerson has this week published a blog post Baby versus bathwater: distant matches. She found that 17% of her matches were not shared with either parent.
  • I recently tested both of my parents at AncestryDNA and I thought it would be an interesting exercise to do a detailed analysis of my own matches to see how my results compare with the other studies. I used the DNAGedcom Client to download my matches from AncestryDNA. I used the Match-O-Matic tool, which is included with the Client, to analyse my matches. See the methodology section below for details of how the analyses were done.

    My matches at AncestryDNA
    I tested on the AncestryDNA v1 chip in June 2012. I currently have 10,232 matches at AncestryDNA.

    Using the same categories as Blaine Bettinger my matches break down like this:

    Category Number Percentage
    Over 50 cMs 9 0.08%
    25 cMs or more 39 0.38%
    20 cMs or more 71 0.69%
    15 cMs or more 251 2%
    10 cMs or more 1403 14%
    Fewer than 10 cMs 8837 86%
    6-7 cMs 4512 44%

    Two of my matches in the over 50 cMs category are my parents. All the other matches have tested independently at AncestryDNA.

    Sharing with my parents at AncestryDNA
    My parents were tested on the AncestryDNA v2 chip in June 2017

    My dad has 8350 matches at AncestryDNA.

    My mum has 11285 matches at AncestryDNA.

    Here are my findings after comparing my matches with my mum and dad:
    • 3299 (32%) of my 10232 matches are shared with my dad
    • 3276 (32%) of my 10232 matches are shared with mum
    • 20 (0.2%) of my matches appear on the match lists of both my mum and my dad.
    • 3671 (36%) of my matches do not appear on the match lists of either of my parents.
    • Of the 3671 matches which do not match either of my parents 3559 (97%) shared a single DNA segment and 112 (3%) shared 2 segments. Ninety-six (86%) of the two segment matches shared less than 10 cMs, and 16 (14%) shared between 10 and 16 cMs.
    I divided the matches into "bins" to see what the match rate was for different levels of sharing. The results are shown in the table below.

    cM bins Total
    matches
    Total matching
    a parent
    % matching
     a parent
    Total matching
     neither parent
    % matching
     neither parent
    50 cMs + 9 9 100% 0 0%
    40-50 cMs 1 1 100% 0 0%
    30-40 cMs 10 10 100% 0 0%
    20-30 cMs 51 51 100% 0 0%
    19-20 cMs 25 25 100% 0 0%
    18-19 cMs 18 17 94% 1 6%
    17-18 cMs 30 30 100% 0 0%
    16-17 cMs 46 45 98% 1 2%
    15-16 cMs 61 58 95% 3 5%
    14-15 cMs 96 86 90% 10 10%
    13-14 cMs 148 134 91% 14 9%
    12-13 cMs 180 161 89% 19 11%
    11-12 cMs 291 274 94% 17 6%
    10-11 cMs 437 386 88% 51 12%
    9-10 cMs 799 679 85% 120 15%
    8-9 cMs 1275 1001 79% 274 21%
    7-8 cMs 2241 1534 68% 707 32%
    6-7 cMs 4512 2058 46% 2454 54%

    Double matches
    I also took a look at the 20 matches that my parents shared with each other. My parents do not appear as matches to each other and do not have any identifiable common genealogical ancestors. I also checked to see if these shared matches appeared on my match list. Here is the breakdown:

    Match cMs shared
     with Dad 
    cMs shared
     with Mum
    Match to Debbie
    Match 1 8.7576 7.9563 Yes
    Match 2 9.2653 6.984 Yes
    Match 3 9.3549 7.363 No
    Match 4 6.082 7.5295 Yes
    Match 5 6.4811 8.0814 No
    Match 6 9.3519 7.4345 Yes
    Match 7 27.0902 8.1206 No
    Match 8 10.009 14.0302 Yes
    Match 9 6.5761 9.6979 Yes
    Match 10 6.262 7.8819 No
    Match 11 6.4201 7.5106 No
    Match 12 7.9815 6.1787 Yes
    Match 13 9.2775 6.3962 No
    Match 14 11.4808 6.3302 Yes
    Match 15 7.26 6.1234 Yes
    Match 16 6.8033 7.0212 Yes
    Match 17 8.8658 6.2839 Yes
    Match 18 7.1988 6.0201 Yes
    Match 19 6.5682 8.9985 Yes
    Match 20 10.7345 14.5475 Yes

    Discussion
    Although 36% of my matches did not match either of my parents, the headline figure is not as gloomy as it might at first appear. The vast majority of these non-matches were on small segments under 10 cMs, and the lion's share of non-matches were on the very tiny segments under 7 cMs.

    All matches sharing 19 cMs or more were shared with one of my parents so this can be considered my personal safe zone where matches are guaranteed to be valid.

    There were just four out of my 155 matches sharing between 15 and 19 cMs which did not match one of my parents. The largest non-shared match was 18.2 cMs. This means that 87.5% of my matches in this range were valid.

    Below 10 cMs the chance of not sharing a match begins to increase exponentially. With the very smallest matches sharing just 6-7 cMs only 46% matched one of my parents.

    Matches that do not match my parents are either false positives, which means the matches are not real matches, or false negatives, which means that the match is not showing up in the match list of my parent for one reason or another. However, without further investigation it is not possible for me to determine whether these matches are false positives or false negatives. This can only be done by careful chromosome mapping and by testing multiple close family members.

    AncestryDNA use a phased matching technique. Phasing is the process of assigning individual alleles to the maternal and paternal chromosomes. A lack of phasing results in many false matches. These are sometimes known as pseudosegments. For a discussion of the reasons for these false matches see the ISOGG Wiki article on identical by descent. Because AncestryDNA use phasing they are able to deliver matches on smaller segments than the other companies. While phasing provides more accurate matches, the process is not without its problems. One of the limitations is that we are not tested on our whole genome but rather a sampling of markers scattered across our genome. If matching were to be done on the whole genome we would no doubt find that many of our matches are not valid after all. A second problem is that the phasing algorithms are not perfect. Sometimes they break up a longer match into smaller segments. There is also a problem of what are known as phase switch errors, when the phase accidentally switches from the maternal to the paternal chromosome or vice versa.

    I am fortunate that I've been able to test both my parents which allows me to do a sanity check on my matches. However, if you are not able to test your parents you will have no way of knowing which of the small segment matches are likely to be valid. It was also interesting to note that some of my matches were shared by both my parents. If I hadn't tested both my parents or if I'd only tested one of my parents I could easily have been led astray with these matches.

    Matches at Family Tree DNA and 23andMe are not phased so the false match rate is going to be even higher there.

    Even if these small segments are real, the odds are still stacked against the match falling within a genealogical timeframe. We know from computer simulations that over 60% of 10 cM segments are likely to trace back beyond ten generations. This does of course also mean that 40% of 10 cM matches are likely to fall within the last ten generations, but computer simulations have the advantage of working in an idealised world where every segment can be reliably attributed. In real life it is much more complicated and with the current matching algorithms there is an additional risk that these segments will not be accurately identified.

    The genetic genealogy community has known for a long time the problem of using small segments in genealogical research, and my findings simply add to the existing evidence base. I already have 1773 matches at AncestryDNA that share 10 cMs or more. I can still only find genealogical connections with a handful of those matches. There is really no reason to get down in the weeds with these small segments under 10 cMs.

    Methodology
    I am using version 1.5.1.3 of the DNAGedcom Client with a PC running Windows 7. The DNAGedcom Client is a subscription service costing $5 a month. The Match-O-Matic tool is included in the subscription. Match-O-Matic was designed for a Mac but converted to a Windows format by Rob Warthen for use in the DNAGedcom Client. For details of the DNAGedcom Client and Match-O-Matic see the user guide

    I downloaded my match lists into Excel spreadsheets using the DNAGedcom client on 4th and 5th August.

    I used the Match-O-Matic tool provided with the DNAGedcom client to analyse my matches.

    To see how many matches I shared with my parents I used the report labelled Matches in common (matches in both files) [ICW] to combine the match lists for my mum and dad..

    To see how many matches did not appear in either of my matches lists I then used the report labelled Combine files (all matches without duplicates) [ALL]. In order to get the program to work correctly I renamed the output file with the prefix m_.

    I used the report labelled Matches in A that are not in b [ANB] to extract a list of matches that were in my match list but were not in the combined match list of my parents.

    Acknowledgements
    Thank you to Rob Warthen for developing the DNAGedcom Client. Thank you to Don Worth for developing the Match-O-Matic. Thank you to Richard Weiss for advice on using Match-O-Matic.

    Update
    Since publishing my blog post Alex Coles has also done an analysis of her parent and child matches at AncestryDNA. Alex and her parents all tested on the v1 chip. Alex found that 31% of her matches did not match either parent. All the non-matches were below 17 cMs apart from one intriguing outlier. Read Alex's article Imprecise science. Part 1 AncestryDNA on her Winging It blog

    Related blog posts

    8 comments:

    Jackson said...

    Really thorough discussion --thanks!

    Alex Coles said...

    As Jackson said, this is a very thorough discussion, thanks for sharing your results. I was inspired to run a similar process over my own matches, and ended up with fairly similar results - see http://wing-ops.blogspot.co.nz/2017/08/imprecise-science-part-1-ancestrydna.html.

    Debbie Kennett said...

    Thank you Alex for doing this analysis. I've added a link to your article in my blog post in a section at the end on updates. I hope that other people will also rise to the challenge. I still don't have any sense of the false positive versus false negative rate in these non-matches. I suspect that more of them are false negatives. However, this exercise has highlighted the need for caution when working with small segment matches and we need to factor in the uncertainty when drawing conclusions about genealogical relationships.

    KerrieAnne Christian said...

    thanks for referring me to this article - very interesting and informative

    Robert Julian Braxton said...

    A reader who seemed mildly annoyed with me pointed me to this excellent post which I greatly appreciate. Personally I view my exploration less as "conclusions" and more as "process" and so do not, up front, exclude contacting anyone by trying to ferret out the false negative / false positive. I am 73 years old and got FT-DNA family finder results 13 months ago July 15 after testing early April, 2016. I have not unlocked a major "knot" on paternal (who is father of my grandmother Flossie Emma) and maternal (who is father of my 3rd highest "half-aunt" surprise match or, conversely, who is father to my own mother - if not the one I have always known as grand-daddy). As much as I can, I let the DNA lead where it may rather than denying a connection. My saying "DNA doesn't lie - except when it does" - reflects that especially in the "small potatoes" DNA is not totally exact science; however, based on the excitement of those who were adopted when they find family (biological), it seems light years better than paper trail only of the past before DNA discovered.

    Debbie Kennett said...

    Robert, I think most people tend to regard the research as an ongoing process. However, I do sometimes see people writing blog posts claiming that they have proven a particular connection based on small segments. In every case they have failed to consider any alternative hypotheses.

    DNA is great for providing clues and with close relations it doesn't lie. However, the interpretation of DNA evidence is not always so straightforward especially once you get beyond the second cousin level. It is easy for people to jump to false conclusions if they don't consider all the possibilities. Now that the databases are so big, most people should have at least a few high-quality matches that they can work with.

    Robert Julian Braxton said...

    Less than 14 months ago we began quest to find potential (half-) sister who appears as infant "ward" in 1940 census. My parents had eight (one has died,I am firstborn) and this would potentially be a half-sister - we have not yet found. What I am finding: my paternal grandmother reared as surname WRIGHT has a half-sister Rachel PERRY. My DNA matches a male PERRY Jr. at 2nd to 4th cousins; but for myself it is about relationship, not simply proof - so I am dependent upon the kind of reponse (or not) in reaching out. Also what I was not looking for, surprise on my maternal line - even closer match: my 3rd highest, female who grew up in Iowa (I grew up in NC) - the only higher matches are my one full brother and a brother of my mother. This DNA match is at the level of half-aunt. I follow the DNA hints as well as high match while also using the full range of FT-DNA suggested matches as clues. To me it would be a mistake to decide in advance which ones NOT to pursue. When I chose to test DNA, I made the choice to be flexible and to be open - since if what I already knew was not shakeable there would have been no best reason to have tested DNA to begin with, in my view.

    Debbie Kennett said...

    Robert, It's great that you've made so much progress with your research. I find the best strategy is to focus on people who share the surnames and who have ancestry from the same locations. I only have two shaky leaf hints at Ancestry and no DNA Circles so I have to work with what I've got. All clues are worth following up, but we just need to exercise caution with the matches on smaller segments and recognise that many of them might not be legitimate matches.