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ALERT – Bug in the GEDmatch “Are Your Parents Related Tool”

Dec12

UPDATE: 13-Dec-2020: FIXED! The code had not changed but the environment had, so an initialization was different. Thus my analysis that it was always the first few chromosomes helped the programmer solve the issue.

 

The “Are Your Parents Related Tool” (AYPR) has been an enormous aid to those adoptees who discover that they were a result of an in-family relationship. Thus it is very distressing to have gotten a report from a reader that the tool is suddenly showing less cM that are ROH than it used to.

My investigation has shown that the first few chromosomes have segments that are not marked as ROH when they should be and were in previous versions. The programmer who can fix this told me that this bug goes back perhaps as far as this past summer He does have a working copy from July, but is in the middle of a major new project. Thus he may not be able to attend to this until later this coming week,

In the meantime, here is an example of how this looks so you can try to make your own estimate. The results for a child of first cousins was shown in my blog post about this tool (click here for that post).

ROH for child of first cousins,  buggy version on left, previous correct version on right (click for larger version)

To the left is how that looks now, while on the right is how it looked last year. Notice that the first three chromosomes on the left have not been included in the ROH listing. Also, the previous total was 215.3 which, when multiplied by 4, fit the first cousin scenario, now confirmed. The total without those first few chromosomes today is 126.8.

The cases from closer relations are even further off. A child of siblings had 744cM ROH last year but now gets only 465.6. A child from a father daughter pairing was was 750.4 and is now 547.9. In both cases the problem was the first four or five chromosomes were not having their ROH segments counted any more.

I will post an update on this blog post once the issue is fixed.

Monday Presentation: MyHeritage’s Theory of Family Relativity

Nov22

MyHeritage has been producing a wonderful series of live presentations via their FaceBook page. At 11 a.m. Monday (tomorrow) California time I will be giving a talk on how to use the Theory of Family Relativity. If you come to this free lecture you might win a free DNA kit plus you can ask me DNA questions live.

Otherwise you can view it later by clicking on the videos tab on their page. I am amazed that my last video for them about finding cousins using DNA at MyHeritage had over 20K views!

One of the slides in my talk, slides are at https://slides.com/kittycooper/myheritagetofr

In other news from MyHeritage, this year they finally have the ability to give a gift membership in time for the holidays and they have already started their Black Friday sale.

UPDATE 23-Nov-2020: The video of my talk is now available on the MyHeritage FaceBook page here:https://www.facebook.com/6572227821/videos/150034700143856 and the image above is linked to the slides. Plus here is the Black Friday sales link: this limited-time offer ends November 27, and the price is $39, plus free shipping on 2+ kits if ordering from this link.

New DNA Tools and Blog from a Scientist at Cornell

Nov5

Much of the work to build tools and write articles to help testers with their DNA results has been done by citizen scientists, bloggers, computer programmers, and scientists from other fields like Andrew Millard (behind the WATO math). In an exciting development, Amy Williams, a computational biologist at Cornell University, has built a few DNA tools, with more to come, and started a blog at https://hapi-dna.org/blog/

Her blog article titled “How often do two relatives share DNA” is particularly interesting. It includes the beautiful chart shown below which is created from simulations. Click it to go to the actual page where you can mouse over the columns to get the detailed numeric breakdowns.

Chart of How Often 2 Relatives Share DNA from https://hapi-dna.org/2020/11/how-often-do-two-relatives-share-dna-2/

The other article on her blog has a detailed explanation of what a centiMorgan is, the measurement used for DNA segment sizes (click here). I usually recommend not worrying about the exact definition since it is a measure of the frequency of recombination rather than a physical length. It is important just to know that there is not a one-to-one relationship between the cM and the sizes shown in the chromosome browsers. On the those charts, the same cM amount looks smaller at the ends of chromosomes than it does in the middle because recombination is more active on the ends.

The final statement of that article is: “In an upcoming post, we’ll talk more about cM lengths of DNA and how recombination leads more distant relatives to share fewer segments that are also on average smaller than those that close relatives share.” Something to look forward to!

Now to take a look at the tools that are available there so far.

Of particular interest to adoptees is the maternal versus paternal predictor for half siblings or grandparents. I tried it out on a number of half sibling pairs who I have helped in the past.

Here is the prediction created for a brother and sister who share the same father but have different mothers, using the comparison of their segment data from 23andme:

However I discovered  number of minor usage issues when trying to use data from the different DNA testing sites.
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Please Help Collect Sibling DNA Statistics

Oct25

I need more data from full and three quarter siblings that are either tested at 23andme or have uploaded to GEDmatch. Ever since I published my article on why full siblings don’t share more DNA, I have been getting inquiries from people who are concerned that they are only ¾ siblings, so I would like more cases in order to help them figure that out.

My article (click here for it) included the insight that if you sum the FIRs (fully identical regions) and HIRs (half identical regions) of full siblings you get a result of about 3600 cM. This is roughly the same amount shared with a parent, thus a true half of the inherited DNA. My article also discussed the expected numbers for ¾ siblings.

Here is the form to help me collect this information, Please do not include the X if you are using 23andme. Below are some more instructions if you need them.

If you are using GEDmatch, the instructions for collecting this data are in my previous article, click here. For the 23andme instructions click the read more below.
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Comparing Ethnicity Estimates Across Companies

Oct12

Both Ancestry and FamilyTreeDNA have recently updated their ethnicity results. As much fun as it is to look at your ancestry composition, those estimates do not really reflect the populations of today’s countries, but rather human migrations hundreds of years in the past. Therefore the big picture is more accurate than the smaller areas. Examples that I have found to be realistic are North versus South Europe or East versus West versus South Asia.

To the left is a simple pie chart showing the known ancestry for my brother and myself for the last 300 years or so. Our father was Norwegian American, documented back to the 1600s, and our mother was born in Munich to a Jewish father and German (Bavarian) mother. In 2016 I wrote a blog post showing how my brother’s ethnicity appeared at a number of DNA companies and third party sites (click here for that post). This post will look again at the ethnicity predictions for each of us from the main testing companies.

One thing I always find interesting is that they all show my brother Shipley with less DNA from our Jewish grandfather than I have. The variations between full siblings can be quite large.

Let’s look at the new Family Tree DNA results first:

My Origins at Family Tree DNA for my brother and myself

Nice and simple but not very accurate. We have no British ancestors in the last 500 years that we know of. However there is no such thing as German DNA because that area was a crossroads. It usually shows up as French, Scandinavian, British, or even Eastern European. Jewish DNA is quite distinct due to centuries of endogamy. Interestingly, our Jewish never comes out at the expected 25%. All the companies show me with more than that and my brother with less. Although you inherit half of your DNA from each parent, they do not have to pass you an equal amount from each of their parents.

Here are our results at MyHeritage:

Our ethnicity predictions at MyHeritage

MyHeritage is an excellent site for working with your DNA since it includes a chromosome browser that shows triangulations and it also looks through user trees to try and figure out your relationships to your DNA cousins. However, although their ethnicity estimates have improved over time, like Family Tree DNA, they incorrecty find lots of British Isles DNA for us. They call it Irish, Scottish, and Welsh. The Jewish component is only few percentage points different from Family Tree DNA.

Frankly I find the estimates at 23andme and Ancestry more accurate.

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