The Great Paternal DNA Quest

An innocent enough comment made by my sister last summer led to a great journey in my genetics and genealogy research. It also may eventually lead to me breaking down a “brickwall” that surrounds my third great grandfather Alfred Adams. Beside that, it’s a great story.

One of the things that genealogists always bemoan is the regret over missed opportunities to talk to our parents, grandparents and in my case great-grandparents about their ancestors. I’d give anything to have 2-3 days with my grandparents and a tape recorder. With the advent of DNA testing and genetic genealogy, genealogists are now realizing how important testing older members of our family is.

I’ve covered it in greater detail in other posts but the type of DNA that most people test for is called autosomal DNA. It is made up of Chromosomes 1-22. (X and  Y DNA are handed down differently to males and females) Autosomal DNA is split apart down the middle, chopped into segments,  mixed around and then recombined with every new baby. Each of us inherits 50% of our DNA from each of our parents. But that’s where that rule ends. The 50% I got from my dad could have been 90% from my paternal grandmother and only 10% from my paternal grandfather. My sister could have had 30% from my paternal grandmother and 70% from my paternal grandfather. The same thing takes place on the maternal side. We get 50% from each parent. It’s random what the percentages are once you go past the parent to child level. That process is what allows us to evolve as species and it keeps us all from being twins.

All human beings have about 3.2 Billion nucleotides (points)  on their 23 pair of chromosomes. Over 95.5% of that DNA is identical in every person on earth.  It’s the  4.5% that makes us unique as individuals.

These testing companies take a “snapshot” of about 700,000 individual locations on the 23 sets of chromosomes that are known to have differences between people. These are called single-nucleotide polymorphisms or SNPs.  They use those SNPs to determine genetic matches among other test takers, to breakout your heritage and to identify traits and potential health issues.

Autosomal DNA is very good at identifying people with common ancestors out to about the 3rd-4th cousin range. After that, it’s hit or miss if enough DNA will remain to be able to detect the match. When you are trying to identify a connection via DNA, the closer in generations you can get – the better off you are. Since I’m trying to find out where our earliest known Adams ancestor came from, any movement upward the family tree toward my third great grandfather Alfred will help.

adams line

The comment my sister made back last summer was that she wondered if the hospital still had any of the blood samples or biopsies from when my dad was admitted prior to his death in 2014. It had never crossed my mind.

The next day, I started making phone calls. Not only did the hospital have biopsy sample blocks and slides on my dad, they also had some samples from my mom from back in 2007.  She passed away shortly after those samples were taken. We found out what the requirements were to obtain those samples (they vary by hospital, city and state) and we went through that process. In Arizona and that particular hospital it was incredibly easy.

I knew that we were probably only going to have one opportunity to extract and process this DNA (if we were lucky) and I didn’t want to waste it. With the advancements in genetic processing and testing,  I’m fairly certain that within the next few years we’ll all be getting our entire genome mapped. Not only that but the prices will drop to about the same as what is currently being charged by the big 3 (Ancestry, Family Tree DNA and 23andMe) to test just those 700,000 points.

I decided to have my parents’ entire genomes run. I contacted the folks over at http://www.fullgenomes.com to see what they recommended. They (Justin Loe) suggested a lab that handles paraffin embedded samples and extracts DNA from it. That lab, http://www.omegabioservices.com , and  Dr. Weining Tang worked wonders. My mother’s sample was unusable because it was only pathology slides and those had been fixated. My dad,  however,  had a section of tissue that had been preserved using paraffin infusion. That process degrades the DNA but Dr. Tang felt they  could extract enough quality DNA to be able to use it for the  whole genome test that FGC was going to run on it.

I received the results last Friday. Let me warn you. A full genome is a ton of data. The raw data file was  39 GB in size. That’s the equivalent of a three hour movie in 1080P (Blu-ray)  quality. It’s a mountain of data.

I extracted out the  Y DNA and mitochondrial data first.  I found out that my paternal grandmother was U5 (U5b2a1a1),  one of the oldest Maternal haplogroups.  I already had done my  Y DNA so I wanted to look for any changes that happened between my dad and I.  Those minor mutations are what make branches in the  haplotree. Myself, my father and my son have all been mapped.

All this really was neat info but it wasn’t helping me do what I wanted to do. I wanted to get a generation closer to Alfred Adams to see if we could break through that brick wall.

I knew the solution wasn’t difficult.  I just had to write a program that would search through that huge mountain of data and pull out the data on just those SNPs that are tested by Ancestry, FTDNA or 23andme and create my own file. I could then upload that file to gedmatch or even potentially family tree DNA. Thankfully, none of that was necessary.

About a month before I got my raw data, Thomas Krahn wrote an open source script to do just what I wanted. I worked with him for about a day to figure out what I was doing wrong and we got it working for me. I now had a raw data file in a format that both Gedmatch and Family Tree DNA would recognize and allow me to upload. His script is at https://github.com/tkrahn/extract23

Thomas also has another role that I want to recommend. He’s over at a company called https://www.yseq.net/index.php Thomas and YSeq have been leaders in SNP and SNP Panel testing for a while and now are even offering full genome sequencing. My family group uses their services to offer a low cost SNP test to potential Adams cousins to see if they’re related. Every interaction I’ve had with Tom or Astrid has been outstanding.

That sentiment carries over to all three of the gentlemen I mentioned in this post – along with everyone that worked on this project for me. Hopefully, the last step in truly a fairy tale ending is me finding out who Alfred’s daddy was. Time to go to work.

Griz

P.S.  – If you are a male with Adams as your surname and if you’d like to see if our lines converge, the test at YSEQ is $17.50 plus $5 shipping. You can order it at

https://www.yseq.net/product_info.php?products_id=35735

P.P.S. There is a website called Gedmatch that offers a central repository and matching service for DNA results from differing companies. They also have a number of tools for DNA / genealogical usage. One of those tools (Lazarus) allows you to recreate a person’s DNA if you have enough close relatives tested. Before I found out about my dad’s biopsy sample, I had tested a whole slew of close family members and run the Lazarus program to create a partial copy of my dad’s DNA. I was a able to get the kit up to 2600 cM before I started introducing errors into it. (I’ll cover that later in a separate post) When I checked the Lazarus kit against my dad’s actually DNA, I only had a total of 75 cM that didn’t match. Not too shabby.

Getting started

I’m sure that you’ve seen the commercials about DNA testing and people finding out all sorts of interesting twists about their family. Although it is a dramatization, it does happen. I can guarantee you that if you dig hard enough into your family’s background, you will probably find some skeletons. With the advent of DNA and matching algorithms, people that test find out all sorts of things.

Here’s a positive example. In June of 2016, I was looking for a hobby that I could do while caring for my wife with Alzheimer’s. Since most of genealogy work is done online now, it seemed the perfect fit. My mom had done a bunch of family research back in the 1990s and early 2000s. Heck, our family even had someone make a book about one of our relatives,  George Fisher. That book contained most of the genealogy for my father’s side so I figured I knew most everything already. I was watching a commercial for Ancestry and thought, let’s do this. I ordered kits for my wife and myself. As soon as I did that, I also started an account with Ancestry and started to recreate my family tree.

The first thing I did was add my mom and dad. I noticed this little green leaf thing next to my mom’s name. I clicked on it and I see this –

This was a picture of my mother at 1 year old. The note on the back was written by my grandmother Peggy (Carly Ethyl Clack) to a J.B. & Cleo. I had no idea who they were or who this person was that had this photograph. The note on the back was talking about my mom and asking if they knew if “Harry” was well. Harry was my grandfather (Harry Andrew Austin) and he had disappeared while my grandmother was pregnant. The note was filled with pain and I just had to learn more.

I contacted the person who had posted it and it turns out I have a whole bunch of close family I never knew anything about. My maternal grandfather had a brother James Austin that went by J.B. His son was still alive and he had two adult children. His granddaughter Julie (my 2nd cousin) had scanned that photograph and posted it.

This was a wonderful example of what can happen when you start on this journey. Julie and I have met in person and I’ve talked with her dad numerous times. We’ve grown very close just over the past few months.

Here comes the word of caution. DNA is rigid and unyielding. We may not always get all the answers from DNA we want but generally it doesn’t lie. If you can’t take all the news that comes, both good and bad, then don’t test. You could find out that your parent is not really your parent. You could find out that you’re adopted and were never told. You could find out that members of your family have done things you’d rather not know about. You could find out that you’re the product of rape or incest.

Here’s the bad example. I have a substantial number of DNA matches with people that are mostly African-American. It is clear that a lot of those situations came about due to slavery and my ancestors being slaveholders. It’s not easy to face that truth, but it’s there regardless. The nice thing is that I’ve become friends with a bunch of my cousins as we search for common ancestors and how we became related.

Genealogy and genetics are truth finding exercises. If truth bothers you, I’d suggest matchbook collecting or some other hobby.

You’re still here and reading. I guess I haven’t scared you off…good. My next post, I’ll cover how to get started, how to pick a DNA testing company (if you are going to test) and a neat app that you can download now to give you a sneak peak at what awaits.

Griz