When I Need You, I Just Close My Eyes

Dear Grandpa,

We're coming up on the sixth year without you here. I have to admit, I find myself missing you at the oddest of times. When a moment of silence intrudes upon my day, I think of the times I didn't say enough to you. Years could roll past before I'd even consider visiting. Like every young person, I was busy. So very busy doing nothing and getting nowhere. While you weren't always in my sight, you were always in my heart. You still are. Nowadays, you are almost always on my mind.

Two peas in a pod; that was us. No one was more hard-headed and stubborn than you, until there was me. You seemed to take conversations as a challenge to mentally wrestle me into a defeat, but I would never give up. No matter the subject, if you took the pro, I was the con. If you derided something for being useless, I had to extol it's intrinsic worth. If you changed your mind, so did I. And I always had to use big words. Not because I thought you were stupid. No, you were never stupid. But I had to substitute vocabulary for the size and age (wisdom?) you brought to the table. I didn't think about how it may have hurt you to have a grade-schooler outstrip you in debate. And to an outside party, I'm sure they thought I was tearing you down. But you and I knew. I could see it in your face. You enjoyed the fight. You were proud of me. And I was proud of you.

I still am very proud of my grandpa. I speak about you often. I tell stories about my childhood, always with a prejudice to stories about you and me. I doubt anyone has more shaped my outlook on life than you. And who better? Born in 1927, the first child of an unmarried mother, you began life in difficult times. You were the grandchild of a farming family, so hard work would not be a stranger to you. Which would be good practice; you were barely a man when war found you. Or did you find it? You entered the U.S. Army and became a Ranger. Dad tells me you were a driver for General Patton and that you stayed in France during the war. He also says you were in Germany for reconstruction. I've filed a request for your military records.... I wonder what I'll learn or confirm? I have pictures of you from the war. Dad found an envelope with my name on it when he was clearing your house. Inside were some unmarked photos of half toppled buildings. And one of you. Where were you that day? Who were the young men in the photos with you? What story did you want to tell when you took these? How I wish you were here to tell me now.

You know I've always loved history. And getting me to shut up was never easy. Now I never shut up about family history. And you've been one of my favorite subjects. Not that you've been easy to find, mind you! I've located your birth certificate.... well, a transcript. I have to get Kentucky to send me a copy. Not that it will list your father's name. Your mother listed you under her maiden name, leaving me a mystery to solve. You were living with your maternal grandfather during the 1930 census. He told the enumerator your last name was Berrio. But we both know what a dead end that is, don't we? Auntie tells me that you told her about confronting a man named Berrio, only to find out he wasn't your father. He gave you another man, Estes, but that man denied you too. I wonder if that hurt you, hardened you. I've heard that when you joined the army, you had to request a delayed birth certificate, and that you chose to stick with your stepfather's name, Gibson, when you had the chance to change it. You were used to the name? Or did you love your stepfather? Dad tells me he remembers his grandfather as being very unkind and cold to you and your children. Dad says that your stepfather didn't consider you family. But is that the truth or is dad remembering his own coldness? You wouldn't believe the number of conversations I have with him about family. In one breath he's "blood doesn't define a family" and in the next it's "I don't care about that side, they aren't really blood related". But you know dad, he's right today and he's right tomorrow. He got that from you. And so did I.

I'd love to be more right about you. If I had just one more day, I'd ........... who am I kidding? I'd like to say I'd ask you all sorts of questions and pull out photos and have you identify everyone. I'd like to say I'd ask you point blank about your military career and your marriage. I pretend I'd have the guts to ask you about losing your first daughter, Evelyn, when she was only 9 hours old. I imagine the brickwalls of my family history tumble. But we both know what our one day would be. You'd make your famous cookies; I'd eat until I was sick. I'd remark on some little factoid I had learned, you'd call me Miss YellowPages. Naturally, and almost instinctively, I'd correct you. YellowPages are for phone numbers. I'm an Encyclopedia............ and we're off to the races. Then dad would have to "separate the kids", although we wouldn't understand what all the fuss was about.

After all, we're just talkin'
-Ana

Can't spell Promethease.com without T-E-A-S-E

When you get into the meat and potatoes of genetic genealogy, you will find there are many good DNA tools that can help you in your research. Some require your raw results added to their servers, others have a tool you download and use on your own. Some share your information with others, some don't. I could spend every day talking about all that is out there for you to explore.

But I won't.

I'm actually getting ready for a break from DNA. I've been working so hard on it for so long that I think I'll go insane soon. I've upgraded my brother's FTDNA kit to an autosomal test and with that and my maternal cousin's test, I've not only been comparing our matches, but also mapping our shared segments. My parents share a line (or two), so there is expected overlap. But I figure where my brother and I share a segment and my maternal cousin doesn't is a good place to start for paternal matches. It's still possible the segments are part of the shared line or maternal material my cousin didn't get, but there has to be something that is exclusive to dad, right? I mean, what are the odds that I got only his mother's DNA? Things to make you go crazy.....

Which leads me to my last DNA post for a bit. And I promised to tell you about a tool that cost you only $5 and was a bit of fun. I will warn it may drive you crazy if you let it. The website is Promethease.com. What does Promethease give you for $5? Well, you upload your raw results and they spit back a chart of the good, bad and indifferent in your DNA. You see, ever since we could code DNA, scientists have been researching what segments control what in our bodies. So there are thousands of published works on cancer risk, heart disease, mental issues, immunities, drug interactions, etc. and this tool tells you what studies have said about alleles you carry in your DNA. Now, does that mean you have or have the potential to have a disease listed? Meh. This isn't a medical test. It's using published work that may or may not have a bias in it's research. If you're looking to solve medical mysteries or gather information prior to having children, go see a medical professional and get a "real" test done. If you just want to have a bit of fun, let's hop right in!

So I ran the tool and got my results in about 10 minutes. After playing around a bit to see what I was looking at, I reviewed my results:

My Good

• I have a lactose tolerance due to a European gene. Cool. I like milk.
• I am difficult to hypnotize. This is true. I have actually had people attempt to hypnotize me with no success.
• I have a resistance to HIV. Now, this one is awesome, because the theory is that this is actually an indicator of immunity against the plague. I apparently would've had to have had a relative who contracted and survived the plague in order to have this passed down to me. I've also done my maternal cousin's results and he's got a higher frequency than I, which means both of his parents carried this allele, whereas only one of my parents did.
• I have lowered odds of going bald. Good to know. Oh, but my bad includes increased risk of baldness. Well crap on a cracker.

My Bad

• Increased risk of cancer (breast, lung, and prostate). Weirdly, I have also a decreased risk of cancer in other alleles. So this one's a wash, apparently.
• Increased risk of diabetes. I'm pretty sure my obsession with fast food and aversion to physical activity increases my risk of diabetes anyway.
• Increased risk of Crohn's and IBS. Interesting considering those diseases do actually run in my mother's side.
• Increased mental disorder risks including dementia, bipolar disorder, depression, and suicide. On the other hand, some of these are also linked to higher intelligence and creativity. Well I am awesome. Sometimes crazy awesome.

My Indifferent

• Once again, this tool tells me my eyes are blue. I've already informed the creator that my eyes are brown.
• Sensitivity to sunlight. I do burn easily. I avoid direct sunlight like a vampire.
• I have impaired motor skills. I don't know about that.... well, my reflexes are a bit slow. And sometimes I'm a klutz.... but "impaired"? little harsh.
• Loss of short term memory. This one yes. A thousand times yes. It's not an all the time "Finding Nemo" Dory thing. But I do have trouble retaining information the first time through. And names? Forget it. If you tell me your name, I've already forgotten it before we're done with the handshake.
• Curly hair. Nope, straight.

This is just a small portion of the report. You get a zip file that has the report itself, then there is a data folder that will show you medical conditions, how medicine affects you, and other things studies claim to have found that are a bit complicated. Each one of these results will come with a link to more information about the allele and the studies that "found" these conditions. Read the studies. Like I said, some will have a bias in their research. Just like any other source, you have to evaluate the informer as much as the information. That's why this should be a "just for fun" kind of thing. If you're one of those people that worries over every news story about Ebola even though you weren't anywhere near the outbreak city (or state), then don't use this site. You'll just worry over every little thing. To be sure, I'm no more worried about my risks of heart disease than I was before. And I'm not going to start kissing rats or engaging in risky behaviour just because I'm supposedly carrying a plague/HIV immunity. Again, if they can get my eye color wrong, how right can they be about my arthritis risks?

When it came to this tool, I found myself interpreting the results through what I already knew about my family medical history. And maybe that's the best way to look at it. I mean, ideally I should be using the information to find new clues to unknown issues, but I get less stress by just using it as a confirmation of what I know. In the medicine interactions area, it suggests that I have an increased risk of liver damage if I use Tylenol. Well, I do use Tylenol. So should I stop based on this test? Not really, no. I had an injury that sent me to the hospital right after I received my results. The doctor told me to take some Tylenol and rest until the pain went away. I asked him if I could take aspirin and he said that it would thin my blood and that was a greater risk to my condition at the time. After talking to him about my Promethease results and reading the studies involved, I've not changed my Tylenol routine. But I will admit that sometimes, right before I take that little pill, I hear a voice in the back of my head saying, "We really need to switch it up every now and again. Just to be safe."

But then my short term memory fails and I forget all about that silly little voice,
-Ana

Third Party DNA tools: Gedmatch.com

I feel lazy. I haven't written in this blog in a month and I feel terribly lazy. However, I've been terribly busy. Why? Well all these wonderful DNA matches keep rolling in! I received my AncestryDNA results for my maternal 1st cousin and have been putting his results into a spreadsheet with my results to see where we *don't* overlap so I can focus on cousin matches that are probably exclusive to my father (my parents do share an ancestor, so there is a lot of overlap!). It doesn't help that Ancestry doesn't have any way to look at the chromosome data so I can see where I match my matches. It doesn't help that I can't look at how my matches match others to see if there is a pattern. And it really doesn't help that I can't easily compare how many matches my cousin and I have in common.

Enter Gedmatch.com!

Gedmatch.com is a volunteer-run free website that allows you to upload your raw autosomal DNA data from AncestryDNA, 23andMe, and FTDNA to use their host of tools. I will start off with the warning that they are so backlogged with new uploads that they aren't accepting any new ones until mid-August (currently the 15th). But I've put off this post for so long, that I think it's best to just let you know about all the features and let you get ready. So what does Gedmatch do that's so special? Why will you be sitting on the edge of your chair waiting for August 15th?

One to Many
The first option for analyzing your data is the "one-to-many". This option allows you to compare your data with the entirety of Gedmatch's database. Now, I'm going to take a moment to mention IBS and IBD. Inherited by Descent (IBD) is the term used when your DNA matches someone else, because you've inherited the DNA via a common ancestor. Inherited by State (IBS) is when your DNA shows a match, but is most likely due to just random jumbling of DNA that looks like someone else's DNA. How do you know if your match is IBS or IBD? General rule of thumb in genetic genealogy: a DNA segment must be at least 7cM (centiMorgans) long in order to be IBD. Now, 7 cM is terribly small. To put it into perspective: a sibling will have 2350cM in common with you. A 1st cousin will have 800 cM, 2nd 200....by 5th cousins, there's only 25cM in common! So a segment match of 7 is going to be way back there. If you're looking for close relations, you'll want to look at larger segments.

Why is that all important? When you go to the "one-to-many" tab, you'll be asked what you want the minimum length of autosomal DNA segments to be for your matches. It's default setting is 7cM. Go no lower. A second length option you have to set is for the X chromosome. Now, there is value in an X chromosome match. If you match a male on his X chromosome, then your focus should be the maternal side of his tree. The default value for the X is 3cM, however. This tool will pull up any matches of autosomal DNA of 7cM OR 3cM on the X chromosome. So you could end up looking at a lot of matches that are high on the X chromosome, but below the threshold on the autosomal DNA. Does that mean you aren't related to them? Not entirely. The problem is that the X chromosome isn't gender specific. Yes a male has only one X and gets it from his mother, but his mother got one from her father as well as her mother. So the variety of ancestry makes the X unreliable on it's own (for right now). When you set up your defaults, set the X option higher (30 or more) to filter out any matches below the autosomal threshold. You can always look at those matches later, but your first foray will be less confusing if you leave those bits off. There is also a check box for cross referencing. I won't get into what it is, because it's unreliable. Just don't check that box.

This is the one to one of my best match and myself.
I would focus on the chromosome 2 segment as it
meets the 7 & 700 rule.

Your results will come in a table. You can hide the autosomal column or the X column if you want to focus on the numbers in one or the other. You'll see the kit number for the match (I'll explain that later), their email if they made it public, and your estimated generations before common ancestor. There is an "L" that is a link. You click on that and you see a list of kits that person matches. You can use that to compare matches you have in common, which could help you figure out what side they match with you. The autosomal and X columns have an "A" and an "X", respectively. You click on those and it shows you the specific segments you have in common with that person. Remember, 7cM is the minimum for IBD. But that's not the only number you need to have in your head. The other is the number of SNPs (single nucleotide polymorphisms) in that segment: 700. I try to remember it as the 7&7 rule. If I find a segment that is 7cM long, I then check if it's 700 or better on SNPs. Often, you'll match a person on one chromosome and meet these parameters and then match them on other chromosomes under the minimum. Those other matches are IBS matches and should be ignored when figuring out all that is here. The best part of this table is that you can select multiple kits and compare them all at the same time. I have 6 matches that all have the same email (uploaded by the same person for different family members). I checked each one and then did a comparison. It was obvious from the segment lengths that two were siblings, one was a parent, one was a cousin and the other two were children of one or the other sibling. A message confirmed this assumption and matching all of them on a specific chromosome helped us to figure out how we connected to each other and other tests that we matched on that chromosome segment. Since the parent was their father, and I matched heavily on his X chromosome as well as the autosomal, then we were able to work on his maternal line to find the match.

One to One, X One to One, Phasing, One or Both, and Specific Segment
The next options on the home screen are "one-to-one" and "X one-to-one" comparisons. These are similar to the results you get when you click those "A" or "X" links on the "one-to-many" results, but you can better control the minimums to fine tune the comparison. To be honest, the only time I use these is when someone in a discussion group tells me their kit number and I check to see if we are matched. Same rules apply: 7 & 700. "One or Both" is the option if you want to find matches for more than one kit. When I finally am able to upload my cousin's raw data, this option will help me find the kits that match us both much quicker than running separate reports and comparing names myself.

Phasing is an option I haven't explored as I'm not a parent, nor has either of my parents taken the test. What phasing does is take one or both parents' kits and compare them to their child's kit to figure out what DNA is mom's and what is dad's. It takes a while for the results to come back (about 3-5 days).

And then there is the "Specific Segment" option. You can put in the chromosome number and the segment start and end points, with the thresholds for minimum length allowed, and a report of kits matching you specifically on that segment come up. I've tried it with the chromosome segments that my closest matches have in common with me, but haven't found anyone with a significant match on that segment other than them. Ah well.

Admixture

Admixture is the fancy name for ethnicity. When you took your autosomal test, the company you chose used their own reference populations and algorithms to calculate your possible ethnicity mix. Now, as I've pointed out before, there's a lot of guess work involved. Let me illustrate the point for you:

The results page for each of these tests has a link to the blog or development data. I recommend viewing those links to get information and details straight from the horse's mouth. Sometimes, if not too overworked, the developer can answer a question; or someone else has already asked your question and received an answer!

These four pie charts show my ethnicities according to four different calculators: MDLP, Dodecad, Eurogenes, and Harappa. You'll note that they don't use the same names for similar areas and that even when they do, the percentages can vary wildly. Eurogenes has a chart of where the populations they use as a reference are from. Does that mean that if I match them, that my family is from there? Not really. It's just a way of defining the area. Just because the "South Baltic" ethnicity uses Lithuanians to define it, doesn't mean my family is from Lithuania. Now, I have records that indicate they are, but because of migrations and border changes, they could be Polish or Russian.... all this calculator tells me is that my DNA has data in common with the Lithuanians that were tested.

I used the K12 for each (save Harappa) to give a fair comparison. That means there were 12 possible categories to have represented in my DNA. Every calculator save Harappa has multiple options as far as how refined the results will be. Eurogenes will go up to 36 categories. Well that means we'll get better results, right? Not really. At some point, you can take your DNA to such a small amount that what you match isn't really proving your deep ancestry as much as reporting noise. Just like the matching needs to follow the 7&7 rule, ethnicity works best at 5% and above. Most people, including the developers of these tools, will tell you that K12 is your fairest bet.

And then there's the test to find Ashkenazi DNA............

This is a comparison of the EU Test and the J Test options. It is recommended by the developer that you compare both as Ashkenazi can show a false positive. My supposed Jewish DNA is very small, so it's more likely than not that it's just noise. I explained all of this to my mother, but she's been convinced for years that we're Jewish, so she clung to this like the last chopper out of Nam and has told everyone how her smart daughter found the proof. Oy vey.

Eye Color and Rare SNP

In the end, I guess what I'm saying is that the admixture tools should be used for fun, not actual science. Maybe one day, but there's no definitive proof that's going to give us the answers we're looking for without a large margin of error. And speaking of "fun" tools with large margins of error.....

I'm not sure, but I don't think they're blue...

There is an option to see what your eye color is. I know, a mirror works just as well, be quiet and listen. This tool looks at the multiple mutations required to make your specific eye color. If you recall my earlier posts, it's not just one gene that decides if you have blue eyes, it can be dozens. So I checked my eye color and it says they are blue/grey. There's some markers for brown and I'm supposed to have golden irises or some such thing, but the user submitted photo of an eye that matches my DNA is bluish grey. In case you've not seen me before, I have very dark brown eyes. They've lightened a bit as I've aged, but when I was a child they were almost black. I can say that I've now studied my eyes more than I've ever done before and I do see some golden flecks near the pupils. And there seems to be some bluish tones that could lead some to say I have hazel eyes. So maybe as I get older, my eyes will start to go grey like my hair? Why do I find that so cool?!

The other supposedly fun tool is the Rare SNP calculator. This tool looks for SNPs that aren't found in the majority of the people in the database. Why would you want to know about these rare SNPs? Well, if you have something truly uncommon, it could help you connect to others who are part of that small group of people. They would be very likely related to you in order to have received that same rare mutation. There is a warning, however, that you need to take super serious: these rare SNPs can impart medical information! The medical information is based on studies (whether or not they are good studies is up for debate) that claim to connect that mutation with a disease or resistance or increased risk (or decreased risk). Please, don't use this utility as a replacement for talking to a medical professional. First, it's set up very confusing. Second, just because you carry a gene doesn't mean that gene is actively working against you. If you want to know your medical genetic information, see a genetic counselor. I need to also warn you that there is a new option to join the SNP pool. This allows you to compare your rare SNPs directly with others who have joined the pool. You will be able to see their medical information based on their DNA and they will see yours. I see no genealogical value in this tool at this point, so I actually don't recommend using it. It's not worth working yourself up over every cancer gene you have. And it's certainly not worth letting strangers work themselves up over every cancer gene you have.

So welcome to the information overload. Now you know what's been taking me so long! I've got one more utility I want to cover and then I'm thinking a wrap up on this series (I'm getting a bit tired of DNA to tell you the truth). I know I've not covered all you'll need to know about Gedmatch.com, but I have three last points:

1. I've started a discussion group on Facebook for those looking to compare notes and ask questions:
Gedmatch. Discussion Group. Even though Gedmatch is in the title, we'll discuss anything related to genetic genealogy. We've got some files and explanations already up, but no question is discouraged.

2. When you upload your raw data, you'll be given a kit number. It's usually a letter that indicates what company you took your test with and a series of numbers. You need that number to run the tests. You can share the number on discussion groups, but then anyone can input your number and see your matches, so it's up to you. Since this is true of the people who match you, note that uploading to this site allows them to see your matches and compare you to others, but only you will be able to use your rare SNP utility (unless you join the pool). Also, no one else can access your raw data. With that said, this is not for those who want to keep their DNA private. Yes, you don't have to give contact information. But I can take your anonymous kit number and look at your matches. With gumption and time, I could use that information to identify you via family trees and records. It's not easy, so it's not a large worry, but it's something those worried about privacy should consider.

3. This is a volunteer site. They don't charge a membership fee. When AncestryDNA finally allowed raw results to be downloaded, this site crashed twice from the number of people uploading their results. Now it's backlogged and runs the risk of crashing again when it allows new uploads. PLEASE take a moment to donate to the site via Paypal or the snail mail address listed on the site. You don't have to pay, but it's the right thing to do. This site makes using third party genetic tools easier for everyone. They give you a place to compare your DNA to people who took tests from other companies. They ask for nothing. They deserve support. Your money makes sure they can keep the site running and buy the server space necessary to give you as many matches as possible. Our continued support will mean improvements to the site as well! Even if all you can give is a little, give it. Give it twice. When you have a little extra cash and think about all those wonderful new matches you've discovered, give that money to show how grateful you are for this opportunity. Encourage others to give. Donate now so they aren't forced to make it a paid site to keep the lights on! (Don't think it can't happen).

Alright, I'm done for now. Up next is a second third party tool you may enjoy and it's only $5!

-Ana