Tag Archive | SNP

Why Y?

Jun15

Father’s day is always an occasion for the DNA testing companies to offer discounts on their kits and this year is no different. Give Dad a DNA kit is the message. Why should you? Well his autosomal DNA might find cousins you had lost track of, discover ethnicity you were curious about, or solve an unknown parent mystery. After all, he is one generation closer to your ancestors. I tested my late father long ago and am grateful to have that information. Click here for my evaluations of the different autosomal testing companies.

Dad and I in about 1953 (he was in the Air Force)

Only men have a Y chromosome and there are tests for just the Y. Those tests can give you information about your surname and your deep father line ancestry. Family Tree DNA is the place to test just the Y although both LivingDNA and 23andme will give you a high level Y haplogroup, plus there are tools to determine the haplogroup from an AncestryDNA or MyHeritage test (discussed at the end of this post).

If you know what a Y haplogroup is you can skip this paragraph … The 23rd pair of chromosomes is an XX for a woman and an XY for a man. The problem or benefit is that there is no second Y for that Y to recombine with. Thus unlike the other 22 chromosomes a man’s parents give him, the Y is unchanged from his Dad’s and his Dad’s and his Dad’s and so on, except for mutations. Those little changes accumulate over thousands of years and allow scientists to catalog the Y and trace the migration of mankind around the globe. Each set of Y mutations is assigned to a haplogroup, and subgroup, which can tell you where your ancestors came from thousands of years back. Here is the latest diagram from the
wikipedia article on Y

Y haplogroup world expansion – start at the big Y in Africa (A was the first haplogroup) -image from wikipedia by Maulucioni [CC BY 3.0 (https://creativecommons.org/licenses/by/3.0)]

If you are of European origin then click here for the Eupedia articles on each haplogroup.

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Do my genes suggest I should drink less coffee?

Jun24

Whenever a new study is published linking a specific gene or SNP to a particular trait or health risk I go rushing to my DNA results to see what I have, so I thought I would share how I do that.

My latest worry is my coffee drinking habit.

There are so many coffee and caffeine studies that I am totally confused about what I should be doing. One caveat is that most of these studies are far from comprehensive and all of them need to be taken with a grain of salt. Have they really factored out all the other possibilities that could cause this result? Let’s face it, it’s early days yet in understanding what specific genetic variants do.

Personally when I read one of these articles, the first thing I do is google that gene name to find the associated SNP’s “rs” number so that I can find that variant in my results. For example let’s look at  rs762551, a SNP involved in the metabolizing of coffee.

While it is easy to look up a gene or SNP if you have tested at 23andMe or GENOS by using their browse raw data functions, what if you have only tested at Ancestry.com? Or Family Tree DNA, which has deliberately chosen not to test health related SNPs?

It’s actually pretty easy to look up a SNP in your raw data if you have downloaded it.

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How to figure out what Y SNPs are tested at 23andme

Feb23

Those of us who are tested at 23andme and have also done the Y STR test at family tree DNA may wonder when some family tree DNA project manager says “Test SNP so and so” whether that SNP is already tested by 23andme. This post explains how to figure that out. If I have already lost you, then this post may just be too technical or else not your cup of tea. To better understand Y testing read this Y lesson by Kelly Wheaton.

For a good explanation of what a STR versus a SNP is, read Roberta Estes’ post – http://dna-explained.com/2014/02/10/strs-vs-snps-multiple-dna-personalities

So to figure out which SNPs my Dad has already tested, I first created the L11 subset image below of the R1b Y haplogroup SNPs from the beautiful diagram created for R1b by Mike Walsh because I need visuals:

R1bL11

Back to the original question. My Dad is an R1b etc and 23andme uses a four year old haplogroup designator rather than the current ISOGG R haplogroup listing. A visitor to this blog suggested that we test DF100 because that is an interesting subclade we may belong to since we have these SNPs according to 23andme: L11/PF6539/S127, L52/PF6541, P310/PF6546/S129, P311/PF6545/S128.

The diagram shows that the possible downstream SNPs for Dad are U106, DF100, and P312. So how to find out if they are tested at 23andme? Since the haplogroup at 23andme shows L52 as the last SNP can I assume the others are tested?

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Finding Distant Relatives with Autosomal DNA Testing

Jan14

Maybe you tested your DNA to prove or disprove a genealogical theory. Or maybe you tested to check on your health risks or carrier status. But now you see all these possible 3rd to 5th cousins in your family finder or relative finder lists and you wonder if you are related and if you can find that relationship. Perhaps you contacted a few and had almost no responses.

DNARelativesSampleSYes you are probably related, but without both of you having a good paper trail you would be most lucky to actually find that relationship. It is likely to be further back than suggested if your ancestors were at all endogamous. Just living in the same location for a few hundred years can lead to much inadvertent intermarrying and more common DNA than degree of relationship would expect. So autosomal DNA testing is no genealogical shortcut. Some of the people you contacted already know this, so if they saw no common surnames or places on your profile they may have lost interest.

So be prepared before contacting those likely 3rd to 5th cousins.

  1. Have an easily readable pedigree chart in both PDF and online format (GEDmatch can do the latter, more on GEDmatch later)
  2. Another good tool is a list of about 12 generations of ancestors by place name. Much easier for a possible relative to scan.
  3. Do some reading on the basics. UPDATE 9-sep-2018 See my article – http://blog.kittycooper.com/dna-basics/
  4. Try to talk some close relatives into testing so you have more data to work with
  5. Last but not least, make a decision on how much time you want to devote to this project … warning it can be addictive

If you want to do the minimum, then scan the localities and surnames of these possible cousins and contact the ones with surnames or place names in common with you. Indicate in your message that this is the reason for contact. Include the URL for your pedigree or family site and offer to send the PDF files. Include your email address if you are using the 23andme messaging system. The more directed the contact, the more likely you will hear back. I recently went through and cancelled some of my early invitations and send new improved ones on the lines above and got four new shares.

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