Archives

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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Free health results from your DNA test for the rest of 2019

Dec28

There is a third party site which will analyze your DNA test results for health information called Promethease which is FREE until the end of the year as a gift to us from MyHeritage who has acquired that site. You can even upload several tests from different companies for the same person to get a more complete picture.

Looking at your results takes some getting used to. It is a fairly geeky interface but here is a video that explains it.

 

They only keep the report for 45 days, but you can download it to your computer for future viewing.

Please be aware that the problem with trying to get health results from your DNA test is that so little is yet known. While some of the most damaging mutations are well documented there are hundreds more that might or might not be a problem. Most evidence is from correlation studies which are not necessarily definitive or large enough to be statistically significant.

On the front page you may quickly agree to many terms and conditions but please read and understand this one,

“I realize that most published reports about DNA variations explain only a small part of the heritability of a trait, and they also don’t take into account how different variants might interact. In addition, published reports typically ignore environmental, dietary, microbial, medical history and lifestyle factors, any or all of which may well affect my true risk for any trait or disease. “

Reading some of the information Promethease shows for your genes can be scary but don’t be alarmed. Most of these results are just saying that you might have an increased tendency for a specific condition but please remember that genes have to interact with each other and your enviroment so most are not destiny by themselves.

Here is an example of how it works:

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Are you genetically resistant to AIDS?

Jan17

There is a gene called CCR5 that can have a variation that prevents AIDS. You need to have two copies, one from each parent, to be immune to AIDS. If you have only one copy, your resistance is increased. The current theory is that this mutation became prevalent in Europeans after the ravages of smallpox or perhaps the Black Death and was selected for, since it is presumed protective against those diseases. It is more frequent in Northern Europe than Southern, but is found as far south as North Africa.

from wikipedia – By US National Institutes of Health – National Institute of Allergy and Infectious Diseases – US National Institutes of Health – National Institute of Allergy and Infectious Diseases, Public Domain, Link

The down side is that this CCR5 change may increase your risk of an abdominal aortic aneurysm and put you at risk for complications from various viruses like West Nile or tick born encephaliitis. Wikipedia has an excellent and detailed article about CCR5 here.

This AIDs protective variation is actually the loss of 32 alleles (so it is called delta 32) on chromosome 3 at location 46414947.

It is that change that the Genetics researcher He Jiankui claims to have made on two embryos in China using CRISPR technology which has caused such an uproar around the world. Click here for the NPR article about that which mentions that their father is HIV positive.

If you have tested your DNA at 23andme, you can check your own CCR5 for the delta 32 variation which is known as i3003626 there. Here’s how

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Going Gluten Free: What Does Your DNA Say?

Sep22

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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MTHFR – hype or a problem?

Jun12

There have been so many claims in the alternate medicine arena about health problems caused by variations in the MTHFR gene that I was not surprised to get this request from a favorite cousin:

Could you please check to see if there is information in my Ancestry test that tells you whether I have a bad version of the MTHFR gene?

Like many genes, the MTHFR is made up of a long DNA chain including many SNPs (Single-nucleotide polymorphisms), pronounced “snip.” SNPs are places where a single letter in the DNA code often changes to another letter. Since these can vary from one person to another they are useful for figuring out ethnicity. However some variations can have health effects. Typically you would need more than one variation to greatly increase your risks of specific diseases, but not always.

MTHFR location on chromosome 1 from the NIH page about it

So what does the MTHFR gene do? It has the instructions for making an enzyme critical to turning the amino acid homocysteine to another amino acid, methionine, a building block for making proteins. That is a simplification; click here for the full explanation from the National Library of Medicine (NIH).

One health condition, known as homocystinuria, causing blood homocysteine levels to be too high, is caused by variations in this gene. However that can easily be addressed with certain vitamin B supplements. Geneticist Charis Eng discusses why a DNA test is not needed to diagnose or treat this at https://health.clevelandclinic.org/a-genetic-test-you-dont-need/

Selection Panel on right at Promethease

The genetic cause is not simple, according to the NIH at https://ghr.nlm.nih.gov/gene/MTHFR#conditions – “At least 40 mutations in the MTHFR gene have been identified in people with homocystinuria, a disorder in which the body is unable to process homocysteine and methionine properly.”

So can I answer my cousin’s question? There are several SNPs in the MTHR that have been intensely studied, maybe these were tested in her Ancestry.com test.

My advice to her was to upload to Promethease.com which will analyze this nicely for her. When you look at the report, type MTHFR in the box labeled Genes (outlined in red in my image here) and let it tell you your risks.

Of course I still had to figure out whether I could find the most interesting MTHFR SNPs in the raw results. If they are not there, then Promethease will not be much use.

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