Category: Hobbies

These are things I enjoy doing.

What Else Can I Do With My 23andMe or AncestryDNA Data?

DNA StructureSeveral months ago I bought 23andMe’s Personal Genomics test kits for my wife and myself.  23andMe is a DNA analysis service providing information and tools for individuals to learn about and explore their DNA. Using an Illumina HumanOmniExpress-24 format chip, 23andMe detects single nucleotide polymorphisms (SNPs).  23andMe then analyzes the SNP data and provides reports on ancestry composition (what countries/regions your ancestors most likely came from).  Prior to November 2013, 23andMe also provided health risk analysis (certain cancers, risk of heart disease, response /reaction to various medications) and physical trait probability – from eye color to ear wax type.

My 23andMe Ancestry Composition

Uncle Sam Knows What's Better For You Than You DoSadly, the US Government (Food and Drug Administration – FDA) has forced 23andMe to stop selling its health risk service, as the FDA considers the interpretation of DNA data a medical device.  Apparently the nanny state government has again decided that they are the only ones who can save us from our fearful, ignorant, incompetent selves.  If you want some very clear arguments on why the FDA is overstepping their regulatory boundaries and doing more harm than good in limiting the ability of consumers to purchase personal genomic information from whom they choose see this letter: https://slatestarcodex.com/2013/11/26/a-letter-i-will-probably-send-to-the-fda/.  While the science may not be perfect (but is fast-moving), the combination of innovating firms, big data analytics, and affordable individualized medicine is powerful.  Damn poor timing by the FDA to shut it down….

Fortunately, my wife and I were able to engage in unregulated commerce with 23andMe and got our health risk and trait analysis completed before the FDA ruled on my incompetence as a medical consumer to evaluate data and then to discuss my genetic findings, along with my lifestyle, habits, and environmental health factors with qualified medical professionals of my own choosing.  So now I have some data points about what medical condition might kill me (spoiler alert: you will die someday, of something), unless something else kills me first (a much more probable car accident, falling off a ladder, a giant sinkhole opening up and swallowing me into the Earth from which I came, poisoning by my wife for one to many snarky comments – the possibilities are endless!). You see, having access to this information is important to me as one of my parents was adopted, so next to nothing is known about their biological family’s disease history, other than knowing that the biological father died at age 49 due to some sort of medical condition (i.e. not an accident).  I also have an adopted sibling who knows even less than I know about my biological grandparent’s family (more on adoption and DNA here: https://dnaadoption.com/Home/CanDNAtestingreallyhelp.aspx).   Just before Christmas, I bought a SNP test for this sibling – this time from Ancestry.com (23andMe’s ability to sell was in question at the time, although I am hopeful that they will obtain the FDA’s permission to resume marketing their health analysis service soon).

Since receiving my results, I have explored several ways of using the data to better understand myself, my health risks, my ancestry, and to find possible relatives based on DNA data.  My sibling has since received their Ancestry.com DNA SNP analysis results so I thought I might share publicly what I have discovered you can do with your own SNP DNA analysis data – whether from 23andMe, Ancestry.com’s AncestryDNA, FamilyTreeDNA or other providers of personal genomic services.  The good news is that your raw data is valuable and able to be used to report on ancestry, health risks, medication responses and physical traits at a variety of services beyond the services that 23andMe and AncestryDNA provide (can’t stop progress, FDA).  Here’s several ways you can make greater use of your DNA data.

Health Risks and Traits


While 23andMe is not currently able to provide health risk analysis due to the FDA’s shortsighted actions, you can still have your 23andMe Raw Data analyzed by other sites.  Some of these sites use 23andMe findings in their own analysis.  Before you get too deep into the health risk bit, remember that this is not an exact science.  There are many factors beyond SNP variations that determine your health risks, including behaviors (smoking, alcohol consumption), nature (radon exposure, a parent with Agent Orange exposure), or nurture (diet as a child).  Some of these non-genetic factors may introduce more risk of a disease or condition than simply having a variation in a certain SNP.  Results are not a guarantee that you will have the illness identified; you are only seeing a probability or risk.  If normal probability of a disease is one in a million, and your risk is 3 times higher, that’s still a pretty small number.

The most detailed health reporting tool is SNPedia’s Promethease.  Promethease analyzes your raw data and matches the data points that you upload with entries in the vast SNPedia database to provide a detailed report of variations that are tied to health risks and other traits.

To get started with Promethease, head to https://promethease.com/, accept the terms of use and upload your raw data as downloaded from your test provider.  The cost is $5 – you’ll be prompted for payment as you step through the interface.  After about 15 minutes you’ll have a very detailed report generated.  The reports can be a bit overwhelming.  Check out this YouTube video for help on reading and manipulating your report.  Your Promethease report is not kept online forever, so be sure to download a copy of your report (it is a big HTML web page) so you can reference it later.

You’ll want to experiment with filters on your Promethease report to eliminate findings of bad repute or low quality.  Talk to your doctor about the findings in the report (take a copy with you).  Some doctors don’t quite know what to do with consumer-driven genomics, but good doctors will take an interest in the data and help you understand what the findings mean to your long-term health plan.

Sample Promethease Report

If you used 23andMe, another option for interpreting your health risk is through the Livewello app (https://livewello.com/23andme).  Livewello provides an easy-to-read report on the variations found in your DNA.  Findings in the report are linked to SNPedia, NIH, 23andMe and other sources to help you better understand the finding.  You’ll pay $19.99 for the Livewello app.  Some of my Livewello 23andMe health findings are pictured below:

Livewello DNA Findings Chart

Interpretome (https://esquilax.stanford.edu/) is another web-based tool that provides analysis and reporting on health risk, ancestry, and Neandertahal makeup using your 23andMe or Lumigenix raw data.  You’ll have to convert your Ancestry.com AncestryDNA data to 23andMe format to use Interpretome (there’s an Excel spreadsheet with a macro that can do the conversion here: https://boards.ancestry.com/thread.aspx?m=132&p=topics.dnaresearch.autosomal&dc=50). To get started, click the ‘Begin Exploring’ button in the upper-right hand part of the page.

Ancestry & Relative Finding

It is natural for humans to long for a sense of belonging – a sense of where we come from and a knowing we have a small place in the history of our species after we take our final breath.  I’ve taken an interest in genealogy for this reason – it gives value to the history of those who came before me in creating the today that I live in and gives me a sense of contributing to the future of my family and the human race (as an aside, I just finished reading The Rational Optimist – when I overlay the themes in the book with genealogy I see a greater degree of connectedness in this grand journey of humankind on this earth).  So it is only natural to seek out those who share a bit of our common heritage as relatives, adopted or not.

Using DNA analysis as a method of finding ancestry and locating close as well as distant relatives is possible through comparing a DNA sample against samples known to be from a specific country or region.  If you share some common bits of DNA with those known samples, it is a safe bet that you share common ancestors from the same region as the known sample.  Locating relatives works in much the same way – the more shared DNA data points, the more likely you are to share a common ancestor.  The more shared DNA, the closer that common ancestor is to the matches.  Using triangulation, you can determine where those ancestors live on the family tree (If you and 4th cousin Joe share certain bits of DNA, and Joe and Jane (a 3rd cousin to you) share certain strands, you can begin to identify where that common ancestor is.  So the more data points (that is, the more people who share their DNA), the better for identifying relatives.

My 23andMe DNA Relatives

The cousin level (2nd, 3rd, etc.) is a guess based on how much shared DNA you have.  Remember that you have 32 great-great-great grandparents.  If someone is your fourth cousin, that means they share one of those great-great-great-grandparents with you.  (see this Wikipedia article for information on cousin distances: https://en.wikipedia.org/wiki/Cousin).  Take it several more generations and you find that you have 4096 10th-great-grandparents – a common 10th-great-grandparent between two people means that you share one of those 4096.  There is a good chance that you won’t be able to ever find out who that common relative is.

23andMe has located several close relatives based on my own DNA tests (My Ancestry.com DNA results are pending) based on shared bits of DNA with others in their own database.  Ancestry.com does the same – matching individuals in their own database.  There is no way currently to upload your Ancestry.com DNA data to 23andMe or vise-a-versa.  If you want access to either 23andMe or Ancestry.com DNA relative finder databases, you’ll have to take a test with that company.  Fortunately, the test is fairly cheap at both sites, so take both for access to both databases.

There are also 3rd party sites where you can upload your 23andMe and AncestryDNA raw data for analysis and comparison against other individuals in the database.  Using these services casts a wider net in a deeper pool when it comes to finding possible relatives.

GEDMatch is a great open tool.  Uploading your data to GEDMatch is quick, easy and free.  Processing takes some time (weeks for me, but it seems to be going faster now).  Once your sample is analyzed, you can log in and see matches.  GEDMatch has triangulation tools built in, as well as many other powerful analytic tools.  I’m just getting started with GEDMatch, so I can’t provide too much as far as instructions go.  The picture below shows some of my GEDMatch cousins.

gedmatch one to many results

I also uploaded my data to FamilyTreeDNA (FTDNA).  FamilyTreeDNA provides several different DNA tests specific to males or females (looking specifically at X or Y chromosomes), as well as tests that look at your maternal or paternal DNA details.  For $69, you can upload your AncestryDNA or 23andMe DNA results to FamilyTreeDNA.  That data will be analyzed and compared to their large database of individuals to find possible relatives.  The picture below shows some of my FTDNA relatives.

My FTDNA Relatives

There are many other ways to analyze, interact with, and compare your DNA test results besides those I have listed.  The following sites offer far bigger lists of tools, sites and databases you can use, as well as tips on how to get started.

Feel free to leave a comment below if you have any other resources or tips for using your raw DNA data.

Fatherlessness

I have finally picked back up The Way of the Wild Heart and started reading it again.  It seems an appropriate week to start reading the book again since it is just past Father’s Day and in light of an exchange with my sister on her blog regarding our own father and our relationship with him.  I’ve been in a bit of a funk lately, and I’ve been struggling to figure out why.  I’ve been exercising, have a great new job that just seemed to come to me instead of me trying to force something that just wasn’t right, and am daily in awe of my children.  I started to put my finger on the problem yesterday during a long run – I am lonely.  Damn lonely.  Not in solitary confinement, I don’t get to see anybody type of way, but a more primal way – a lack of masculine initiation, validation, and companionship way.  Many of the guys that I had developed a real friendship with – men who could mentor me, walk with me, understand me – have left.  A couple to Tennessee for promising new jobs, one who up and left on a grand adventure to LA, one left behind at a job where things just got nutty, and one who is currently deployed.  And this has left me coasting, not living like an adventurer – someone who leads other men, or a strong guide for his own son’s masculine journey, or a husband passionate about loving and uplifting his wife.  It’s not like I am a bad person or really any different from most men.  It’s just that I can see that something is missing – the something is what John Eldredge calls fatherlessness.  He puts it like this in chapter 2:

Whatever life has taught us, and though we may not have put it into these exact words, we feel that we are alone.  Simply look at the way men live.  If I were to give an honest assessment of my life for the past thirty years, I’d have to confess the bulk of it as Striving and Indulging.  Pushing myself to excel, taking on the battles that come to me with determination but also with a fear-based drivenness, believing deep down inside that there is no one I  can trust to come through for me.  Striving.  And then, arranging for little pleasures along the way to help ease the pain of the drivenness and loneliness.  Dinners out, adventure gear.  Indulding.  A fatherless way to live.

That sounds a lot like me – pushing to create meaning and find pleasure but constantly feeling a lacking sense of fulfillment, in the deepest sense.  And that’s what struck me in Tom Wolfe’s quote from The Story of a Novel:

The deepest search in life, it seemed to me, the thing that in one way or another was central to all living was a man’s search to find a father, not merely the father of his flesh, not merely the lost father of his youth, but the image of a strength and wisdom external to his need and superior to his hunger, to which the belief and power of his own life could be united.

My sister laid out a bit of history on my dad, and certainly, there is more than the one final blow of abandonment that she wrote of.  Dad did some things right and some things wrong, and I’m sure most of what he did – good and bad – was right out of his own father’s playbook.  I suspect if I were to ask my dad the big question, “Do you have what it takes?” his answer, after peeling away the defensiveness, anger and nearly endless ways to prove his abilities and worth his answer would be “no”.  But I think he did well enough with me that I could probably answer a resounding, “I don’t know if I have what it takes.”  And I hope that I can help my boys be able to answer “yes.”

I am trying to be more purposeful in initiating my sons into the world of masculinity, even though they are only 2 and 1 years old.  I want them to know that they have what it takes – and that I believe that about them and will help them in their journey.  I’m sure my sons will feel that primal bond to me as a father and to their grandfathers and great-grandfathers.  And through that bond, they will undoubtedly inherit some of my flaws – my temper, my self-doubting, and my insecurities.  And I think that Eldredge has it right when he writes that,

Being a father is a noble undertaking, and a terrifically hard one.  A “hazardous conquest,” as Gabriel Marcel wrote, “which is achieved step by step over difficult country full of ambushes.”…  If our earthly fathers faltered along the way, it may have been that the country they were asked to travel was more difficult than we know.  The longer we live, the more I think we will see our fathers’ failures with compassion, and-I hope- we will see all that was good in what they were able to offer.”

I am learning to see my father in that way, and I hope to God that my boys can say the same about me.  I need fathering still – from my earthly father, from the men that I surround myself with, and from God – I am an unfinished man.  And because we live in a fallen world where thorns and sorrows grow, I have to start my understanding of masculinity in God.  I have previously read this verse and thought it sounded rather wimpy.  But maybe there is more strength behind it than I previously read:

Because you are sons, God sent the Spirit of his Son into our hearts, the Spirit who calls out, “Abba, Father.”  So you are no longer a slave, but a son; and since you are a son, God has also made you also an heir. (Gal. 4:6-7 NIV)

Oatmeal Cake and Emerald Sequins

My sister posted a note on a family breakfast favorite: ‘Oatmeal Cake’.  As she recalls, we first learned of Oatmeal Cake (a wonderful breakfast dish that my wife refuses to serve me because of the high fat content) at a retreat center up in the mountains of north central Pennsylvania.  Maybe the low-fat version that Pamela posted could actually get made in the Townsend household?

Mount Zion Retreat Center

The memory of Oatmeal Cake reminds me of the couple times we did go as a family to the retreat center.  It was a beautiful location and a nice change to catch up with a childhood friend, Chip.  I remember climbing the mountain, a tree that grew up between a massive rock, splitting it in two, and the good food.

sequinsOddly enough, however, the most vibrant memory I have of the place is that of old lady perfume and emerald colored sequins.  During one of our visits to the retreat center there was a group of old ladies also staying there.  They invited us kids in for arts and crafts time where they were making some little contraptions out of emerald colored sequins.  To this day, certain old lady perfume and seeing emerald green sequins in craft stores takes me back in time, as though I am being yanked into an alternate reality, like no other memory trigger I have.

Isn’t it funny how some things have the power to trigger such seemingly random memories in such a powerful way?

Book Study

My buddy Wade has invited me (and a bunch of other guys) to join in on an interactive book study centered around The Way of the Wild Heart: A Map for the Masculine Journey, by John Eldredge. Basically, we read the book simultaneously and post comments, thoughts, etc. on each chapter on our blogs.  I like the idea and plan to participate.  I have already read Wild at Heart: Discovering the Secret of a Man’s Soul, as has my wife, Stephanie.  I dare say that Wild at Heart was more influential for Stephanie, helping her understand the often confusion things that I do because of my man-ness (not an excuse, just an explanation).  I am working on The Secrets Men Keep: How Men Make Life and Love Tougher Than It Has to Be now, but will jump right into The Way of the Wild Heart: A Map for the Masculine Journey as soon as I finish up and look forward to a discussion with other guys trying to understand manhood and who we are called to be as mean in the world, nation, with our families as husbands and fathers, and in our own minds.  Wade has always been a source of encouragement for me and I look forward to this experiment with him and the rest of the guys joining in.  Feel free to join in if you want!

Cranberry Beer Bread

sacranberryRound-about Christmas time I start to see the Samuel Adams Winter Classics Mix Pack on store shelves.  I love all but one of the 6 selections in the Mix Pack (especially the Old Fezziwig Ale – the Christmas cookie of beer).  The one that I don’t care for is the Cranberry Lambic.

The Samuel Adams website descibes the Cranberry Lambic this way:

Samuel Adams® Cranberry Lambic is a fruit beer that draws its flavor not just from the cranberries it is brewed with, but also from the unique fermentation character imparted by the rare wild yeast strain. The result is a flavor rich in fruitiness and reminiscent of cranberries and bananas, cloves and nutmeg. The yeast fermentation also will create a slight sourness on the sides of the palate, a signature of the original Lambic style which, with the subtle cereal note from the wheat malt, remind its drinker that, as fruity a beer as this is, it is still a beer.

I found the brew to be just too juicy and sweet and as a result always end up with several bottles tucked into the back of the kitchen cabinet.  I tossed a couple this past September that were left over from the previous year’s Yule celebrations, and let me tell you….. phew…. a super sweet fruit beer just doesn’t keep.  I nearly gagged as I poured the thickened, chunky, and just plain spoiled beer down the drain.  And it broke my heart.  I hate waste, especially a wasted beer.

I was poking around in the kitchen last weekend for some tasty treats and found a couple of bottles of Cranberry Lambic from this past Christmas.  Determined not to let them go to waste I quickly came to the conclusion that the best thing to do with them would be to bake – Beer Bread.  A Google search yielded a recipe (I’m just not creative enough to make one up on my own).  The recipe is simple:

Cranberry Beer Bread
3 c flour
2 tsp baking powder
0.5 tsp salt
0.5 c sugar
3 tbsp vegetable oil
12 oz cranberry lambic
0.5 c dried cranberries

Preheat oven to 180ºC/350ºF and lightly grease a loaf pan.
In very large bowl, whisk together dry ingredients. Stir in cranberries. Make a well in the center and add vegetable oil and beer. Stir just until no streaks of flour remain. Pour batter into prepared pan.
Bake 55-60 minutes, until top springs back when lightly pressed. Turn out of the pan and allow to cool on wire rack.

I didn’t have enough dried cranberries in the cupboard, so I went halfsies with the raisins.

The result: a nice sweet bread that was enjoyed with breakfast, and again with dinner.  The kids loved it too.  I have one more bottle of Cranberry Lambic in the cupboard, so I’ll be making another loaf soon.  I plan to use the same recipe for similar breads this summer: I am thinking that apricot beers, Sam Adams Cherry Wheat (this is a Sam Adams fruit beer that I CAN get behind!), and even a chocolate raspberry stout could be used for some great baking experiments.

Grape Pie

Concord GrapesI just finished the last piece of my grape pie. For those of you who have never experienced it, Concord Grape Pie may be the most special treat of the fall season. The hearty taste of concord grapes are sweetened with just enough sugar to let you know that you’re eating dessert (although I have been known to serve it for breakfast as well). I thought I would share the recipe with all of you so you too could partake in Concord Grape Pie goodness.

We all know that a good pie starts with a good crust. I like to keep the crust on my grape pie simple to prevent the pie from being too rich. Here’s how I do it:

Cut together 2 cups of flour (1 whole wheat and 1 white) with 1 cup of shortening.
Add 1 egg, 1 Tbsp vinegar
Add about 5 Tbsp of water with a fork (fork keeps it fluffy)
Roll out the crust on a floured surface. This recipe makes 2 crusts, and the grape pie only uses a bottom crust so save the 2nd for another pie or make some cinnamon pinwheels with it.
Lay the crust in a pie plate and sprinkle it with sugar and milk.
The crust does not need to be pre-baked for a grape pie, but if you ever want to use this for another pie that needs a pre-baked crust, you can bake a single crust of this at 450F for 10-12 minutes. Poke some holes in it before baking to keep it from bubbling.

 

As for the good stuff, preheat the oven to 400F and gather up 4 cups of clean fresh concord grapes (that’s about 2 dry quarts or 1 1/2lbs).

Slip the skins from the grapes, setting the skins aside. If you don’t know how to slip a skin, it’s simple. Squeeze the little bastards until the pulp and seeds pop out where the stem was attached. It’s fun and the kids can help (but the grapes do stain).

Throw the pulp with seeds into a sauce pan and bring it to a boil. Reduce the heat and simmer, uncovered, for 5 minutes.
Transfer the pulp to a sieve or colander with small holes to strain out the seeds. You may have to mush the pulp through the holes with a spoon – don’t waste any pulp, just get those nasty little seeds out. Once you are done, add the skins to the pulp.

Mix 1 cup of sugar, 1/3 cup of flour (white) and 1/4 tsp of salt. To the dry mixture add 1 Tbsp lemon juice, 2 Tbps melted butter, and the grape pulp/skin mixture. Pour all of this into the unbaked pie crust in the pan. Bake it at 400F for 25 minutes.

Meanwhile, sift together 1/2 cup of flour and 1/2 cup of sugar. Cut in 1/4 cup of butter until crumbly. Sprinkle atop the pie and bake it for another 15 minutes.

I like grape pie chilled with Cool Whip (but it is also good warm with Vanilla ice cream).

I am working on variations to the pie. I am thinking of making a thin peanut butter pie with the grape filling on top – peanut butter and jelly pie. What do you think? Do you have other creative uses for Concord grapes? Let me know in the comments.

Bender Brewer

I caught this fun little project on Slashdot today.  Mr. Wood and I have been complacent in our brewing lately.  Maybe a brewing robot is just what we need to kick start a new batch – this is about the right time to get a nice light spring ale started.  I’ll get right on it as soon as I finish the kitchen, bathroom, & living room remodel, the basement cleanup, the baby room build-out, actually have (well, not me so much as Stephanie) Michael, and get through new-born hell.  Come to think of it, a new batch of beer may be just what I need to get through this busy season.

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