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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My Ellis Island Visit: Anger Towards Immigrants is Nothing New!

Sep1

Ellis Island has wonderful displays about immigration to America going back to the land bridge; even though it itself was only used from 1892- 1924. Although it did not close until 1954, in those later years it was only used for exceptional cases, since screening was done at the other end. This came about due to the increased restrictions on immigration (see list at the end of this article), most importantly the National Origins Act of 1924. Click here for the history of Ellis Island and click here for the BBC series of articles “The Open Door policy and immigration to 1928.”

The displays at Ellis Island have photos and letters and recorded voices but what struck me the most was the fact that there were so many anti-immigrant demonstrations back in the 19th century. I learned about them from an exhibit on the 2nd floor and thus learned that that sort of sentiment is not new. First it was the Irish immigrants, then the Chinese, then the Southern Europeans, and so on. There was the No Nothing party and the Nativists in the mid 1800s (click here for an article on the Know Nothings). I don’t remember much of this from my high school American history classes. Was it even covered to the extent shown on those walls?

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A Longevity Gene?

Aug24

While there are probably many genes and lifestyle choices that will affect your longevity, there is one gene, FOX03, that has been identified as a major contributor to having a long life by a number of prominent scientists (click here for the abstract at NIH). I first heard about it when reading (or rather listening to) the book Lifespan by David A Sinclair.

Having at least one C instead of a T in the FOX03 gene at location RS2764264 is associated with longevity. So of course I had to look it up in my DNA and that of my family. This is easy to do if you are tested at 23andme. If you have tested elsewhere you need to download the raw data from your DNA test and search it in a text editor or spreadsheet program.

At 23andme, click on your name or image at the top right of the page to get a menu that includes the words Browse Raw Data. Click that option. The next page has a white box where you can type in the name of a gene or SNP. In this case type RS2764264 and see something like the following:

I have highlighted the C/T for this lucky relative of mine who has one copy of the base pair associated with longevity. Some of my relatives have two Cs, but many others, like poor old me, have two Ts.

To find this SNP in your Ancestry DNA raw data that you have downloaded, you need to open it in a program that can handle a large file. Some text editors can do that, but I prefer to use a spreadsheet program and tell it that the data is tab delimited. This same technique will work for wherever you have tested your DNA, provided this SNP is included in the results. At least one of my cousins did not have this SNP in his Ancestry data, perhaps due to an older version of the test.
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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.