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Automatic Clustering from Genetic Affairs

My genealogy groups are buzzing with excitement about a new tool from Genetic Affairs to automate the clustering of your DNA matches. This takes the Leeds method concept to another level.

Everyone is posting pretty cluster pictures like the one below that I made for my perfect cousin, the star of many of my blog posts. This is a table where each DNA match is listed on the top and side; then if they match each other, the box is colored in with the color for that cluster. The chart is sorted by cluster. The idea is that each colored cluster shows descendants from a probable great grandparent couple of yours.

The gray boxes show where people match others outside the cluster which can often happen when families intermarry more than once or when they are first cousins enough times removed to have been in the second or third cousin group by DNA but are related to more than one set of great grandparents.

Automated clustering is useful because it puts your DNA relatives who are related to each other into visual groups so that you can quickly see which line a new match is related on. The picture is pretty but the workhorses are the charts for each cluster shown below that image when you scroll down. Here is the privatized one for my “perfect” cousin showing our MUNSON cluster.

Each name can be clicked to go to that Ancestry match page plus much useful additional information is shown next to the username: how many cMs shared, how many matches shared in the whole group, cluster number, how many people in their tree, and the notes you made for that match.

The image and charts are from the HTML file which arrived via email from Genetic Affairs after I requested automated clustering for my cousin’s Ancestry profile, which is shared with me there. You have to save the html file to your computer and then click on it to view it. When it first comes up, it is a mish-mosh sorted by name, but then it resorts itself by cluster. Fun to watch. Click here for the step by step of how to use this tool from the Intrepid Sleuth. It can also cluster matches from other sites like 23andme.

I decided to try it on an unknown father case I had not gotten around to working on yet, to see if it succeeded in speeding up the process and it did, to under an hour! A new record.

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Collecting Family Trees with Automation

Did you know that there are chrome add-ons that can collect pedigree trees from many genealogy sites and DNA testing sites? These tools can collect a tree of ancestors as an ahnentafel list which is a very useful and compact format to scan for common ancestors and locations.

Click here for my post explaining an Ahnentafel list and the tool DNArboretum to create one from a tree at Family Tree DNA.

The pedigree view of a family tree on Ancestry.com or MyHeritage can also be collected into an ahnentafel list with another chrome add-on, a tool called Pedigree Thief (click here to download it).

Saving a new cousin to my tree

When it is just a few new relatives at Ancestry, you don’t need those add-ons. After all, it is easy to use the Tools menu on the Profile Page of the ancestor you want from a tree at Ancestry.com to copy over a few people. In fact, if you copy one person over, you can click back to the original tree and copy them again in order to get their whole family group, just like in an Ancestry hint. I do recommend that you check sources and make sure that this is good information. Even if you are making a Quick & Dirty tree (Q&D) for an adoptee, it is best to check it over, as some trees on Ancestry.com are quite unrealistic with parents born after their children and other such errors.

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When the DNA says your parents are related

One of the first things I do when helping someone with their DNA results is to check if their parents are related. This can explain unusual patterns of matches, for example, all seemingly from one side.

GEDmatch.com has a nice tool called “Are Your Parents Related” (AYPR) in the”Analyze Your Data” blue panel (middle right of page) which looks for places in the specified kit where the DNA is identical on both chromosome pairs, maternal and paternal. This happens when you inherit the same segment of DNA from each parent because they are related. We call this a homozygous run which is a fancy way of saying a stretch of identical DNA on both sides.

CeCe Moore specializes in helping people who make this discovery. Click here for the informational brochure she helped Brianne Kirkpatrick, genetic counselor, create. It includes where to get emotional support.

My goal is to help you figure out what the DNA means yourself. Can you deduce what the relationship of those parents is? Well a very simple rule of thumb is to multiply the shared DNA from AYPR tool by four and look up that new total at the DNA painter calculator for the possibilities. Then do further family DNA testing to confirm.

Why does this work? Let’s look at the numbers. Suppose your parents share 25% of their DNA. They will pass about half of that to you, so 12.5%. However only about half of that will be the same DNA so it will show up as about 6.25% on the AYPR tool.

Look at the image. The total is 215.3 when you multiply by 4 you get 861.2. You might look that up before you read on …

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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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