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Do my genes suggest I should drink less coffee?

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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Using Spreadsheets

In recent discussions with a few of my genetic genealogy students, I discovered that many need some help with understanding how to use spreadsheets. So I went looking and found a series of excellent youtube videos that even taught me a few things. Here is the first one in the series.

He uses OpenOffice Calc which is free and happens to be the spreadsheet that I use.

The basic idea of a spreadsheet is to make a list of things that you want to keep track of, with the information about each of them listed next to them in columns. As you use it, you may decide to insert more columns, the things you are tracking for each, or more rows, the items you are interested in. You can also delete any of these and best of all, sort them.

For DNA tracking purposes, the only other important function to understand is formatting cells so that the numbers don’t surprise you by turning into dates or fractions when you do not want them to. Click here for a recent article claiming that 20% of scientific papers on genes contain gene name conversion errors because of this type of reformatting!

Personally I reformat the start and stop points to have commas so I can read the numbers more easily and make the centimorgans column (genetic distance) default to two decimal places so that they line up well. I also change the font to Arial.

Suppose you want to keep your match list in a spreadsheet. There are many articles on this blog that explain how to do that. Use the tag DNA spreadsheets to find them by clicking here – http://blog.kittycooper.com/tag/dna-spreadsheet/
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Using an ahnentafel and the DNArboretum tool

There is a new tool, a chrome add-on called DNArboretum, that will generate an ahnentafel ancestor list from a Family Tree DNA tree or from the old format 23andme tree (not myHeritage).

An ahnentafel is a very clever and condense way to show all your ancestors. When trying to match up with a DNA relative it is particularly useful since you can quickly scan their ahnentafel for places and names in common. Obviously it would be better to automate that comparison but with misspellings and Norwegian names that has not worked well for me. However it might work for you, so click here for my blog post about how to use automation to compare GEDcoms.

MyAhnentafel

This is part of my ahnentafel as generated by DNArboretum from my tree at Family Tree DNA when logged into another account there. I clicked on my great grandmother Maren Wold and it bolded all her ancestors and descendants. Note that my parents are missing because they are marked private.

Sue Griffith of Genealogy Junkie has blogged in detail about how to install and use this tool at
http://www.genealogyjunkie.net/blog/dnarboretum-a-great-free-google-chrome-extension-for-viewing-trees-on-23andme-old-style-trees-and-ftdna

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Organizing DNA results with your Genealogy: WIKItree.com

While I have many spreadsheets that I use to analyze DNA results, what I also want is a field in my genealogy program where I can put simple DNA information like haplogroups, where the person tested, and the GEDmatch id number.

To my delight, the free online one world tree at WIKItree.com has all those features. Plus you can see whom you might have gotten your X DNA from, as well as your Y and mtDNA ancestral lines. Another feature is that a person’s profile page shows the tests of relatives that are related by DNA. Here is my mother’s page:

WikiTreeGretchenSmll
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Mapping an Ancestral Couple: a Backwards Use of my Segment Mapper

Sometimes I wonder if the interest in genetic genealogy runs in our DNA. I have found many more new cousins with autosomal testing that are descended from my WOLD line than in any other family. Yes they all had lots of children until recently, but so did the Munsons and the Skjolds.

So I decided to make a picture of the HIR (half identical region) DNA segments that I know come from my great-great-grandparents Jørgen and Anna Wold of Drammen, Norway. To do this I made a CSV file with a list of all the segments that are just from those ancestors. I put the first names of the group of matches in the column that would be the MRCA in the usual style segment map. I have to give credit to my distant DNA cousin (on the AJ side) Israel Pickholtz (he blogs too) for this wonderful idea of making a reverse segment map. Below is my picture of Wold DNA created with my DNA segment mapper tool. Click the image to go to the actual html page which will show the centimorgan values and names when you put your mouse on a colored block.

WoldDNAsmllThe use of two lines is arbitrary; I could have used three or four. The DNA segments shown are not separated into lines for Anna and those for Jorgen. Where that was possible, I had intended to do it with colors, but did not get to it, next version. Knut, OK, Nancy and Aaron are on Anna’s side while Susannah, her mother, and Lester are on Jorgen’s side only.
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