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Going Gluten Free: What Does Your DNA Say?

Celiac disease (CD) is an autoimmune system response to gluten which can damage the small intestine. Gluten is a protein found in wheat, barley, and rye. Added gluten is often used by commercial bakers to make breads rise faster.

So why are so many people claiming major benefits from going gluten free? I am usually dubious of the latest diet craze but …

I discovered that my usual morning congestion vanished after the first two weeks of a weight loss diet which had eliminated bread. It occurred to me that I had inadvertently been gluten free. So I asked a cousin who had given up gluten about her experience and she explained that her perpetual debilitating sinus infections were gone now. Still dubious, I added bread slowly back into my diet. One ear infection and much congestion later, I started to think that gluten might actually be a problem for me.

I wondered if there was anything reported on this in my DNA. I opened my latest 23andme Genetic Health Risk report (under the top menu item Health)


(red arrow added by me) and saw that I have an increased risk for celiac disease:

When I clicked the Slightly increased risk to get the report I saw this:

It is important to understand that having a genetic variant associated with a disease does not mean you will get it, just that you are more at risk. There are usually many other factors that are needed to cause the condition. Science is still at the very early stages of figuring out the roles our genes play in various diseases.

My initial research suggests that people with celiac disease (CD) just about always have one or both of these variants, however having them does not guarantee that you will have gluten issues.

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Finally, Ancestry’s New Ethnicity Estimates

Today we all got an email from Ancestry announcing new ethnicity reports for everyone. Adding five times the reference populations plus a better algorithm that can often indicate the modern countries. This time I really do have the new ancestry composition estimates!
Updates Available box
Naturally I immediately went and looked. Then I messaged and emailed all my tested cousins to accept the new update. When you log in to Ancestry and click on DNA in the top menu you get a page with three panels. Click on the panel to the left called “DNA story” to go to a page with a world map and the Updates Available box on the upper right.

Click the green button that says View your Updated Estimate in that box. Next you have to answer a few questions about your expectations and your thoughts on the previous ethnicity. I am afraid I did not understand that below each was a slider which I could move to indicate the level of accuracy, so until the last one that I answered, I left it alone. I wonder how many others will make that error.

The first time on your new ethnicity page, you will see a panel on the right showing how your estimates have changed. Here is mine. I was sad to say goodbye to that unlikely 1% Polynesian!

My father was Norwegian American with one fourth grandad (2% of his DNA?) who was German. My mother was born in Munich to a Jewish father and Bavarian Catholic mother. So how does that play out in these new estimates? Could the Swedish be a remnant from the 30 years war where Swedish soldiers rampaged through Bavaria? Actually I think my Norwegian dad had a fifth grandparent who was Swedish but that would hardly show either.

Here is my brother’s  page showing the new estimates with the changes:

I am still 29% Jewish but my brother is down to 20% from 22%. Our maternal grandad was Jewish and I randomly got more of his DNA than my grandmother’s. When a 2nd cousin on our maternal grandmother’s side tested, my brother did indeed share a third again as much DNA with her as I did (Click here for that post)

By the way you can get back to the page showing the changes together with the new estimates by clicking on the small blue Updates at the top of your ethnicity estimate then the View Previous Estimate at the bottom of the Ethnicity box followed by Compare these results to your most recent AncestryDNA estimate on the next page.

Now to look at some more interesting ethnic makeups from my cousins and people I have helped.
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Ancestry’s Updated Ethnicity Reports

UPDATE 3-SEP-2018: My apologies, my account and my cousins do NOT have the latest updates. Since they are more recent and prettier than the last time I looked, I had made that false assumption. Thanks to the members of the Ancestry DNA Matching Facebook group for showing me what the real update looks like.

To see what your version is click on the “up to date” or the “i” in a circle on top of your ethnicity results. Then it will show you a box that tells you what version you have. If you only have 3000 reference samples, then, like me, you do not have the very latest.

I look forward to writing a new post whenever I finally get those changed reports! Meanwhile this post may still be of some interest…

 

Original post was:

Over the summer Ancestry DNA has been rolling out their new ethnicity estimates and they have finally arrived in my account.

My brother’s ethnicity has not changed, it just has more features.

These changes have been made for two reasons. First of all, Ancestry has lots more data; they have added 13,000 new samples to an original group of 3,000 reference populations.* Secondly they have changed their algorithm to look at runs of DNA rather than just single points (23andme uses this technique as well). You can read their full explanation here: https://www.ancestry.co.uk/cs/dna-help/ethnicity/faq

The predictions for my brother, as shown above, have not changed (click here for my previous article on his ethnicity). He is still 62% Scandinavian (our Dad is Norwegian American) and 22% Jewish (Mom’s dad was German Jewish). While the Bavarian from Mom’s mother is still showing as Scandinavian, Europe South (this was Italy/Greece), and West European. The English comes from Dad according to various other sites where he was tested. This is discussed in my article Norwegian or English? where I suggest that it is the English who have some Norwegian.

The new presentation is prettier and it has some very accurate subcategories. Yes all our Norwegian ancestors are from the circled areas, Western and Southern Norway.

and my ancestors ended up in the city of Brooklyn, NY

One thing I find very enjoyable are the descriptions of the subgroups and migration groups. Also of interest is the story they tell you when you click on one of your groups and a date like 1875 as above.

 

My ancestry is different from my brother’s but not wildly so. I have more Jewish (German Jewish so within the predicted subgroup), less Scandinavian, and a few interesting bits of noise like Polynesian. I remember one ethnicity estimate somewhere which claimed I had 1% Amerind. I like to think there is a sprinkling of Sami that creates that blip.

I have examples from a wide variety of people thanks to the many adoptees and relatives that I have helped. By the way, my perfect cousin (who I often blog about) is still 100% Scandinavian with the expected subpopulations of South and East Norway.

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Eliminating the DNA Matches from One Side

Unless you get lucky with a first cousin or closer match, searching for an unknown parent or grandparent involves building lots of trees for your DNA relatives and looking for common ancestors among them. Then you build down from those ancestors looking for someone in the right place at the right time. It is best to have two pairs of common ancestors because then you are looking for where their descendants meet in a marriage.

Sample ancestor list from GWorks – linked to slide in my GWorks presentation – using-dna-for-adoption-searches

It is wonderful to have automation to compare trees for you. The GWorks tool suite from DNAgedcom.com does just that and, no surprise, I have written many blog posts about how to use those tools. They can collect all your Ancestry matches and then all the ancestors in their DNA connected trees and give you a list of the most frequently seen ancestors. You can also upload GEDcoms collected elsewhere or created by your own research to use in the comparison.

There are many times I would like to automatically exclude half the ancestors collected from Ancestry. For example when I am helping a person who knows only one parent but has a half sibling or the known parent tested. Specifically when they look at the results from a GWorks run, how do they eliminate the matches from the other side?

View Trees with an example for deleting

One way is to go to the “View Trees” on the GWorks menu at DNAgedcom and delete all the trees from the known side by clicking the red X to the far right of each tree. Then rerun the “Match GEDcom files” in the Manage Tree Files function. This could take forever in a half sibling case.

However, it is very useful to delete trees when one person has tested multiple family members and they are all in the same tree. In that case I keep the tree for the person who is further up the line. Very conveniently you can click on the tree name to go to that match at Ancestry, as long as you are logged in there, so you can easily figure out which one to keep. But again, this is too lengthy a process for a half sibling case.

DNAgedcom client home window

I have long used the Match-O-Matic (M-O-M) feature in the DNAgedcom client (DGC) to get the lists of matches for just one side (the m_ file) in a spreadsheet for use to keep track of my research. However M-O-M does not work for the tree files (aka the a_ file – actually it has a list of ancestors and which trees they are from).

Sometimes it is good to be a programmer. I have put together a new tool that you can use with a list of matches, for example the match file from M-O-M, to create a new tree file with only those trees that are for the matches in the match file. Then you can upload that match file and the new tree file to DNAgedcom for use in GWorks.

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New Compact Chromosome Browser on GEDmatch’s GENESIS

Today GEDmatch launched a version of my segment mapper which is integrated with their database. It can be used as a way to easily visualize multiple matches on GENESIS. This first version shows how everyone compares to the first person on the list, like the current 2D chromosome browser but more compact. Also each color is a person.

My Munson cousins in my new compact segment mapper at Genesis

Above is the screenshot of my Munson cousins which even shows one of the boxes that appears when the cursor is placed on a segment. Click on this image to see a copy of the html version (edited for privacy) where you can put your cursor on any segment to see the details. (N.B. when you put your cursor on a segment and the information pops up via javascript that is called a mouse over in geek speak. )

One way to get a display like this at Genesis is to check the boxes (tier 1 only) next to your best matches in the one-to-many (up to 40 of them) and then click the button “Visualization” at the top of the page. Another way to get there is to use the Tier 1 tool “MultiKit Analysis” and select the kits you want to look at. Remember the first kit listed is the one that all the others will be compared to.

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