Gedmatch: a DNA geek’s dream site, thanks to The Legal Genealogist

Gedmatch: a DNA geek’s dream site

Posted on August 12, 2012 by Judy G. Russell

Great DNA utility website

It occasionally surprises The Legal Genealogist to realize that not everyone is ready, willing and able to test with every DNA company on the planet, or at least in the United States. Just because doing a full round of tests withFamily Tree DNA, 23andMe, AncestryDNA and others will set you back somewhere in the neighborhood of a grand or more is no reason not to let loose your inner DNA geek, is it?

Oh. Yeah. Right.

There is that little problem of the mortgage and the kids’ school clothes and that doctor bill and…

Sigh… Don’t you just hate it when real life interferes with what you want to do?

So to fill in some of the gaps, at least for autosomal DNA tests, let me introduce you to a wonderful website:GEDmatch.com, with tools for genetic genealogy research that carry a whopping big price tag of exactly zero. That’s not a typo. The site is free, though donations are gratefully accepted and anybody who uses the site really should kick in — it isn’t cheap to provide the kind of computing power Gedmatch provides.

The brainchild of Curtis Rogers and John Olson (a distant DNA cousin of mine), Gedmatch offers a range of utilities that make it a little easier to extract every bit of potentially useful information out of your autosomal test results. Autosomal DNA testing, remember, is the kind that works across gender lines so you don’t have to find a direct male line from father to son to son (YDNA or Y-DNA¹) or a direct female line from mother to daughter to daughter (mitochondrial DNA or mtDNA²). It particularly helps you identify cousins with whom you can share research.³

To use the site to full advantage, you need to download your raw autosomal DNA test results and match lists from your testing company and then upload them to Gedmatch. Both Family Tree DNA and 23andMe make raw data available — AncestryDNA does not — and directions for downloading are on the Gedmatch site. Gedmatch works with the raw results from deCODEme as well. And you can upload a GEDCOM with your family tree to see if you can identify common lines, using technology to help with traditional paper-trail genealogy too.

Although you do have to provide your email address and the exact name you used with your testing company, you don’t have to use your name publicly. You can be John’s Mom, or CountryCuzzin, if you prefer. You don’t have to make any of your information public if you’d rather not, although the utility of the website is limited if you don’t.

Once you’ve uploaded all the files — and there’s more than one to upload — you’re ready to start playing with the utilities.

First, you can compare your results with the results of all other Gedmatch users who’ve made their results public — no matter what company they’ve tested with:

The results can be sorted by the total amount of DNA you have in common with others, measured in units called centimorgans or cM,⁴ by the longest segment you share, by the number of generations you’re likely distant from your matches and more. Email addresses of your matches may be listed, but can’t be copied-and-pasted to protect them from harvesting by spammers.

You can choose to see information about selected matches in a chromosome browser. Here’s what my results look like against my two uncles and my aunt on Chromosome 1:

And there are several matrix displays available that will display your selected matches not only as they match you but as they match each other, including a very useful option for displaying estimated distance to the most recent common ancestor.

There’s a genetic distance calculator, a relationship calculator, the ability to triangulate on match results to see how you and your match relate to others, a tool for checking to see if your parents are related to each other, and more.

One of my favorite tools is a quick and easy tool labeled “People who match one person, but not the other …and people who match the same 2 people.” I use it to see others that I have in common with a match, and it quickly produces a chart showing information as to how each of us compares to each common match. The chart does have email addresses, deleted here in this example showing matches I share with an uncle.

There’s more than enough here to satisfy your inner DNA geek. You can phase data — if you and one or both of your parents have tested, this utility will help identify what portions of your DNA came from which parent.

And there are six different options for displaying admixture (ethnicity or deep ancestry) data — and each of the six has options galore. Here’s my admixture under just one of those options:

If that’s not enough, you can even get your very own personal chromosome painting:

For anybody interested in learning more about DNA, or even just playing around with results, this is one cool set of utilities. Kudos to Gedmatch, a DNA geek’s dream site!

---

 
SOURCES

1. ISOGG Wiki (http://www.isogg.org/wiki), “Y chromosome DNA test,” rev. 23 Jul 2011. ↩
2. ISOGG Wiki (http://www.isogg.org/wiki), “Mitochondrial DNA,” rev. 30 Jul 2010. ↩
3. ISOGG Wiki (http://www.isogg.org/wiki), “Autosomal DNA,” rev. 8 Feb 2012. ↩
4. ISOGG Wiki (http://www.isogg.org/wiki), “Centimorgan,” rev. 24 Jul 2010. ↩

Share this:

• Google +1
• Facebook
• Twitter
• LinkedIn
• Email

This entry was posted in DNA. Bookmark the permalink.

Gedmatch: a DNA geek’s dream site | The Legal Genealogist

'via Blog this'

Why I’m a Neanderthal, and You Could Be Too, courtesy of Altucher Confidential

I haven't gotten my 23andme results yet.  Yikes!  I like his columns, maybe you will, too.

Why I’m a Neanderthal, and You Could Be Too

• Posted by James Altucher

Tweet

My rating

I’m forgetting a lot of things today and it’s causing me to panic. But more on that later. I just got my results from 23andme.com.

(23andme started by Sergey Brin’s wife, Anne Wojcicki)

Do you know the site?

Here’s what I had to do. They shipped this vial to me and I had to spit into it until it was half full. You ever try spitting for five minutes. There’s something sexually unpleasant about it.

Then I had to put the vial in a carefully sealed box. I live in New York State which apparently is the one state in this great republic we live in where you it is illegal to do any sort of genetic testing. What’s up with that Andrew Cuomo? Do you have something to hide? I can’t mail this vial from New York.

So I had to give the box to a friend of mine, Brian, who lives in New Jersey. “I don’t want to give it to him,” I told Claudia the week before. “Why not?” she said, “He’ll just put it in his mailbox.” “He’s going to forget about it,” I said, “and then he’s going to feel pressure to do it and then will feel bad and I don’t want anyone to feel bad.”

Brian came over and Claudia gave him the box. “Why is it sealed wrong?” he said. There were two flaps that were supposed to be tucked under but they were sticking out. The box now looked like this weird paper airplane. Claudia made her usual joke, “James went to get a PhD in computer science and now he can’t seal a box.”

Brian, to his credit, just nodded his head and said, “Got it.” And took the box. A few weeks later he wrote me and said, “Dude, I’m sorry I havent’ sent it yet. I’m putting it in the mail today.”

On Christmas [the day I am writing this] I woke up to a nice surprise with an email saying the results were in. I could now know everything about my genetics. What sort of shit my mom and dad left me in their twisted DNA.

A few months ago I met with a friend of mine who had his genes tested. I asked him what the number one thing he learned was. He said, “I learned that my father is my real biological father.” I was surprised that this was news to him. “Apparently a lot of people cheated on each other,” he said, “and these genetic results are showing people the truth.”

But I did learn that my father’s ancestry is either Bedouin or an Ashkenazi Jew. Or both. I almost like thinking of myself as Bedouin. Like Omar Sharif in Lawrence of Arabia. Either way, my ancestors are either from North Africa or the Middle East.

My mother’s ancestry surprised me. She is all northern Europe. Hmmm. Most people with her “haplogroup” are Scandinavian. I wonder if this means I should get blue contact lenses. I wonder if she knows she’s Scandinavian instead of Jewish.

I’m looking at this in realtime as I write this. They give me three warnings before they let me see the Alzheimer’s information. Ok, Ok, I get it. Most people are wimps and are afraid to find out.

(am I related to Miss Scandinavia? She actually looks like a younger version of my mom a little).

Apparently between the ages of 50 and 79 I have a 14.2 out of 100 chance of being diagnosed with Alzheimer’s as opposed to a normal 7.2 out of 100. Apparently one of my parents was kind enough to give me an APOE 4 gene (the other gave me an APOE 3 gene) which is associated with twice the risk of getting Alzheimers.  Big deal. There are so many potential cures out there and I still have another 35 years to go before 79. And I think I can handle the odds of 86 out of 100 that I won’t be diagnosed. Good for me. In the community section on 23andme there are now support groups for people with the APOE4 gene.

Moving on.

Parkinson’s. Again with the warnings. Ok, I’m at the upper end of average. Average is 1-2% of people get it. I’m at 1.9%. Ok, good. I’ll exercise a lot to get that extra dopamine kicking in.

The disease I’m most likely to get based on my genetics is Type II Diabetes. I have a 38 out of 100 chance of getting it when the average is about 25 out of 100. But there are environmental factors which include obesity so I don’t think I will get it. That’s about it. Oh, I have an increased risk of glaucoma. Which once again proves my dad is my dad. He had it, his mother had it, her mother had it. And so on. We’re all good there.

So the worst that can happen to me is that I go blind, lose my memory, lose my ability to manufacture dopamine, and have a heart attack and/or strike (thanks to the imminent diabetes). The best that can happen to me is that maybe I can call myself a Bedouin. Or a North African. I like that.

Good news for my two daughters: I don’t carry any mutations for breast cancer (Ashkenazi Jews are apparently at higher risk of this). Nor am I a carrier for “Zellweger Syndrome Spectrum” which must be some predisposition to like all movies with Renee Zellweger. No wonder I didn’t like Brigid Jones Diary despite so many others of European descent loving the movie.

(genetically disposed to not like her)

Uh oh. Bad news. I have 3 times the risk of becoming a heroin addict. Which is too bad because I was thinking if I was ever in great pain for something then morphine or heroin would be my drug of choice. Hmmm. Have to file that one away. Can I at least take Percocet? It doesn’t say.

Here’s where they are completely wrong. Apparently I’ve inhererited an ability to “effectively learn from errors”. Hahaha. “People with the GG genotype learned to avoid choices associated with negative feedback relatively easily.” When the Alzheimer’s kicks in it will probably be harder for me, though, so I guess it balances out.

On a side note, ever since I got these test results, I’ve been forgetting things. I wrote to a friend of mine, “maybe I need to write an “Apo4e Cookbook” for people with this gene issue” and she wrote back, “It will be a bestseller because everyone will forget they already own it.” I like that positive way of looking at things.

I got excited for a second. 2.5% of my genome comes from Neanderthals. At last! I knew I wasn’t human. Oh wait. Unfortunately 2.5% is average. We killed them and raped them back in the day and all of us are basically 2.5% Neanderthal.

My kids will probably be surprised to find I have no risk of Tourette’s Syndrome. A lot of times when I randomly think of something embarassing that happened to me in the past, even from 30 years ago, I’ll shout out “No!” by accident. They’ve had to explain to their friends that, “Daddy does this sometimes” and Claudia has gotten used to it. But apparently this is all me, and not from my genes.

Two other things that could affect my life. It turns out I am not likely to be a very good sprinter. I have no working copies of the ACTN3 genotype found in many world-class sprinters. So if a mugger is chasing me my best bet is to just give him all my money and not try to outrun him. I kind of suspected this one already.

Finally, I am genetically disposed to have a higher sensitivity to detecting the smell of aparagus in my urine after eating asparagus. This is true. Thank you 23 and me and God Bless You All.

Why I’m a Neanderthal, and You Could Be Too Altucher Confidential

'via Blog this'