Archives

When GEDmatch says your Parents are Related but they are not …

Sep18

GEDmatch.com has a wonderful free tool called Are Your Parents Related which I have previously blogged about (click here). This function looks at your raw DNA results for long stretches where you have the exact same DNA on each side of a paired chromosome, known as Runs Of Homozygosity (ROH). In other words where you got the exact same DNA from each parent. I always check this for unknown parentage cases.

When you have ROH segments, it is expected that your parents are related. However there is one other way this can happen: in very rare cases, you can get a whole or partial chromosome from only one parent. This is known as uniparental disomy (UPD).

An example of UPD on chromosome 6  from the Are Your Parents Related (AYPR) tool.

How can you tell that this is the case? Likely it is UPD when you have only one ROH segment and it is for the whole chromosome like the image above or for one arm of a chromosome (from or up to the centromere). In the less than one hundred cases I have looked at, I have seen UPD only twice. Once a whole chromosome as shown above and once the long arm of chromosome 14.

UPD can result in some dangerous medical conditions as per Science Direct (click here). Please see a professional genetic councilor if you suspect you have this.
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Ancestry Breaks Down Your Ethnicity by Parent

Jul27

Recently Ancestry came up with a tool to show your bio-ancestry by parent without even having a parent tested! Now they have taken it a step further and added a chromosome painting which shows you which segments of your chromosomes have what origins. Not everyone has this yet and for those whose parents are primarily one ethnicity, it is not very useful. However the more mixed your heritage, the more interesting it is.

The Sideview circles for an Australian woman with a half chinese Dad  (click here for that blog post)

This feature is part of your DNA story so go there from your DNA menu at Ancestry. Once on that page, scroll down until you see a box on the right side titled Ethnicity Inheritance like the one in the image on the left here. Click anywhere in that box to get to the page that breaks it down by parent.

The Sideview technology, previously released and shown above, has two circles next to each other, where the left one shows the expected ancestry of each parent and the right circle shows your own.

For those of us whose parents are from different parts of the world, it is easy to tell which parent is Parent1 and which is Parent2. Plus Ancestry gives you the option to label them Maternal or Paternal. To do that, scroll down past the circles to the section titled Detailed Comparison, then click on the pencil next to the words Edit Parents as shown below (red arrow added by me). Next you get a little window which shows you half your inheritance and lets you designate which parent it is from. As my Dad is 100% Norwegian-American and my mother a Bavarian and Jewish mix, this was easy for me to do.

 

Since my father is tested at 23andme, I decided to compare that result to the prediction from Ancestry. Both Ancestry and 23andme predict a little bit of Finnish in addition to the 98% Norwegian. Only Ancestry finds a bit of Irish which is likely backwards; those Irish matches more likely have some Norwegian. No sliver of Irish is found in my brothers’ results. Remember, as improved as these results are at Ancestry, unlike close relationship predictions, they are still not accurate science.

My circles of Ancestry Composition, note that I have designated which parent is which

If you have elected to Beta test new features (under Extras > Ancestry Lab), then you will also have the chromosome browser painting of the ethnicity. Although this feature looks to be slowly rolled out to everyone.

There is a tab at the top of the Ethnicities Inheritance page that lets you click over to the Chromosome Painter or you can click on those words from the initial box on the DNA story page.
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My talk about GEDmatch and more about GEDCOMs

Jun6

Finally! The video of the GEDmatch basics talk I did on May 26 for Verogen is now available. Best to view it full screen at youtube in order to see the images well.

Click here for the slides for that talk

GEDmatch, a DNA tools site, was originally created to compare GEDCOMs, a function you can still use it for. A GEDCOM is a plain text file of your family tree formatted so that any genealogy program can understand it. Click here for the wikipedia entry explaining this in more detail.

In my talk I emphasized that it is best to upload a privatized GEDCOM with no more than 10 generations of ancestors then connect it to the DNA test for that person. This will help you use the relative matching tools. I promised in the presentation to explain how to create a GEDCOM. So here are a few of the many ways.

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My Recent Talk on BioAncestry

Feb2

The interpretation of the origins of your ancestors from your DNA is called different things by different companies: ancestry composition, admixture, or, incorrectly, ethnicity. The latter term is borrowed from anthropology and refers to a shared cultural heritage and does not necessarily include shared DNA although it often will. Click here for the definition of ethnicity online. Ann Turner and Debbie Kennett, two genetic genealogists I admire, both like the word bioancestry instead of ethnicity, so that is the word I will attempt to use from now on.

I did a recent talk for the Southern California Genealogy Society’s (SCGS) webinar series on why the predictions vary so much from company to company and whether they are at all accurate. The slides are here and the webinar, free to SCGS members, is archived here (log in to view it). Click here for the schedule of SCGS webinars.

I explained that each company has different reference populations and they were originally focused on Europeans. I suggested reading the article at the ISOGG wiki (click here). I discussed that our ancestors moved around more than you might realize so that bioancestry predictions are not accurate at a country level. Your admix can mainly be determined on a macro scale: the North, South, East, and West of each continent. Some populations were isolated and inbred and thus are easier to predict from the DNA.

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My new puppy’s DNA says she is mainly Heeler

Jan23

Did you know that your dog has 39 pairs of chromosomes? Many more than us humans. The pet DNA testing companies now have features similar to the people testing sites, relative matching, messaging, raw data download, health results, and even a chromosome browser and painting.

Rockie at about 6 weeks (photo by my friend Rochelle)

Last fall I was given a puppy, found by the side of the road near Shiprock, NM by friends of mine. Of course I had to test her DNA. This time I decided to use Embark (this link should give you a discount*). Last time I used Wisdom (click here for that post) which now claims similar features to Embark. The Embark test shows only 38 chromosomes, thus not the sex chromosome, the XY or XX pair. The test is an easy cheek swab and the results came back within a few weeks.

It is important to understand that we humans deliberately created dog breeds, originally to help us hunt or herd, but also for protection or lap pets. The Victorians developed most of the more recent breeds we know today. Wikipedia has a good article on dog breeds (click here) which says “In 2004, a study looked at the microsatellites of 414 purebred dogs representing 85 breeds. The study found that dog breeds were so genetically distinct that 99% of individual dogs could be correctly assigned to their breed based on their genotype…” That sounds like these tests are likely to be accurate as to breeds.

Embark Home Page for Rockie showiin one message (red arrow added by me)

When I logged into Embark after her results came in, I saw the image above.  I was surprised that she had no border collie. because that is how her black and white markings looked to me, but apparently the white is from her Great White Pyrenees ancestor. On that home page there are many areas to explore. First I checked her health results, of course, and there was nothing bad there, phew.

Next I looked at the Breeds page which had the same image as above plus a chromosome painting by breed of her DNA. I can see that she has heeler (australian cattle dog) on both sides but Pyrenees only on one side. Both are herding breeds that might have been useful in the South West for cattle ranchers and sheepherders.

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