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.

Bulls and Bearshit

occupy_wall_street_bull_in_ropesI caught this picture in my Facebook stream and it struck me with such offense the it sickened me.

Here’s my response: Let’s bind up business, take down the bull. Let’s destroy my investments and retirement that I have worked hard to earn and save. Let’s take down the engine of our economy. Let’s make the desire to earn money, to generate wealth, to rise above an act of shame. Let’s elevate inefficiency, mediocrity, and spite of strength to the status of a moral imperative.

I reject this. I reject what it stands for and will do all within my power to fight your false premises. I will work, create, and rise above. I will generate wealth and gain power and influence and not be ashamed.

I will maintain my morals. I will care for the orphans and widows. I will care for the poor and downtrodden in response to my personal moral code. I will fight corruption and theft. I will not corrupt. I will not be stolen from. But I cannot and will not give up that which I have worked for to those that do not work, that do not create, that do not deserve. I will not dumb down my abilities or be less than I can be to balance inequality of income or strength of mind. I will not compromise and I will not be ashamed. I reject this.

Open Reply to a Recruiter

I received the following email from a recruiter today:

Hi Joshua Townsend

Hope you are doing great,

I am currently in search of Network Engineer for an esteemed client and I wanted to contact you to see if you are comfortable and available. Please send me a word version of resume and the best way for me to contact.

If you know anyone, who is available and comfortable, Feel free to pass my contact details to them. Thanks in advance and hope to hear from you soon!

Title: Network Engineer

Duration: 6 month(s)

Location: Richardson, TX or San Jose, CA

Skills:

CCNP, EIGRP, ACE load balancing configurations, L2 VLANs, L3 VLANs, Nexus, Cisco IOS, Spanning Tree Protocol (STP), Rapid Spanning Tree Protocol (RSTP)

Description:

  • Must have CCNP or be almost done with in order to apply!!!!

Job Description

  • Identifies, diagnoses, resolves and documents network problems
  • Create and maintain comprehensive documentation for all implemented networks utilizing MS Word, MS Project, MS Excel and Visio
  • Excellent interpersonal and communication skills
  • Ability to thrive in a collaborative team environment
  • utilizing the company change control process in order to ensure compliance with the organizations data center and security standards
  • Install, configure, maintain network services, equipment and devices
  • Plans and supports network layer 2 and 3 infrastructure
  • Strong analytical abilities and professional office experience needed
  • A thorough understanding of the OSI network model, Ethernet, and TCP/IP networking

A practical level of experience implementing and administrating common TCP/IP-based services, including DNS, DHCP, HTTP, FTP, SSH, SMTP, etc

Technologies
LAN, WAN, TCP/IP, DNS, Latency, QoS, EIGRP, BGP

Equipment
Cisco Layer 2 and Layer 3 Switches – Nexus 5K and 7K and Catalyst 6500E
Supervisor 720
Cisco 3845 Routers
Console Router configuration
Cisco Network Analysis Module (NAM)
Load Balancing (Cisco or third party)
Cisco Firewalls ASA and PIX

Technical Skills and Requirements
1. Certifications: CCNP (CCNP in progress is also acceptable but is based on experience and knowledge level)
2. Education: Bachelor*s Degree in Computer Science, Information Technology or similar
3. Experience with the following systems: Windows, Cisco Systems, UNIX, Linux
4. At least 5 years experience building and supporting complex corporate data centers and networks

5. Excellent presentation, communication & customer interaction skills

Thanks & Regards,
Ashish Kr Verma
OKAYA Inc.
Where Commitment Is A Passion

I usually just press delete on this nonsense, but like political survey calls and door-to-door siding salesmen, sometimes not answering just can’t satisfy.  And plain old no-thank-you answer won’t do – I like to toy around before I bat you away (really, you woke me up early on a Saturday with an annoying doorbell ring, double-knock, ring to ask if I want new siding when it is plain as day that I am super-pleased with the dented up old siding I have).  This was one of those cases….  Here’s my reply:

Hi Ashish Kr Verma,

I hope you are doing great also!
It is so kind of you to wish greatness on me.  The world would be a much better place if everyone just tried to do great (instead of whatever it is the kids are doing these days).  Your hoping for my greatness adds to my general wellness.  I hope my wish for your greatness leaves you well, as well.
You came right out and listed availability and comfortableness important factors in future conversation you you.  Since you have been so forthcoming with me, I’ll cut straight to the point:  I am not currently available – my wife of 8 years can attest to this fact.  I will say, however, that I am quite comfortable – I have a great family, a nice job, a quaint little home, amazing friends, good health, and most of my hair.  I have found that comfort and availability often run counter to each other, and that when they do run together it is often a sign of mental illness, infidelity, or an inherent misunderstanding of the OSI model, if you catch my drift.  If you’ll settle for one of your two qualifying factors for talking to you, I’ll continue to speak towards your 6-month Network Engineer position with an esteemed client in Richardson, TX or San Jose, CA.
As for my skills as they pertain to the job you have described, I can do all of that and more!  The only skill I lack is CCNP.  CCNP is a really hard skill to learn – I’ve heard there is even a test for it! Can you believe that?  I have thought about learning CCNP, so I feel that I might as well be almost done with it (and I hope you’ll agree).
However, because of my low degree of availability and high comfort factor, I am afraid that I may not be the ideal candidate for the 6-month Network Engineer position with an esteemed client in Richardson, TX or San Jose, CA.  Maybe if you had a position:
1.)  close to my Northern Virginia home… let’s just say if I hear more than two songs on the radio on my drive to my current office in the morning it is a bad start to the day – a commute to Richardson, TX or San Jose, CA would really put me in a bad mood, thus inhibiting my ability to fulfill these essential job functions:
  • Identifies, diagnoses, resolves and documents network problems
  • Create and maintain comprehensive documentation for all implemented networks utilizing MS Word, MS Project, MS Excel and Visio
  • Excellent interpersonal and communication skills
  • Ability to thrive in a collaborative team environment
  • utilizing the company change control process in order to ensure compliance with the organizations data center and security standards
  • Install, configure, maintain network services, equipment and devices
  • Plans and supports network layer 2 and 3 infrastructure
  • Strong analytical abilities and professional office experience needed
  • A thorough understanding of the OSI network model, Ethernet, and TCP/IP networking
2.) that lasted more than 6 month(s) – I’m big into commitment, I dig jobs that last years, not months
3.) that more closely fit my skills and interests (you should have noticed I’m a technical manager with a background in VMware virtualization, storage, and Microsoft server systems),
4.) with an awesome company (your client may be esteemed (more like ego-maniacs, am I right?) but my current employer is just downright cool to work for), and
5.) presented it to me in a not so spammy way… I might entertain a discussion with you about it.
But then again, probably not.  I’m really not into unsolicited commercial email, which really is what you sent me (there should be some kinda law about that….). Thanks to you, I am now really turned off by esteemed clients everywhere in Richardson, TX or San Jose, CA.
I guess what I’m really trying to say is “thanks, but no thanks”, Okaya?  I hope you are as passionately committed to removing me from your mailing list as I am to adding you to every spam filter I can find.
Thanks & Regards,
Josh

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)

Fatter than ever

I am 3 pounds heavier now than when I started running three weeks ago. Muscle mass, anyone?

05272009

Widget powered by EveryTrail: GPS Geotagging

I am slowly bumping up my distance, running for longer periods of time, and feeling pretty good about it all (although my knees have been screaming at me the past few days).

Having my BlackBerry Storm with the EveryTrail application for tracking my distance/time/tracks helps, as does music streaming through Pandora on my BlackBerry. And of course, pushing my Everytrail stats to FaceBook, my Blog, and Twitter keeps me accountable to all of you to stick with it.

Running

I have started running again.  Enough of being a fatty.  Today was the 2nd run, and it hurt.  But I’ll probably stick with it – I kinda want to see my boys grow up (despite what my cholesterol says).  Maybe I’ll even throw in some pushups and situps for good measure.

I’m roughly following the Couch to 5k program found here: . Seeing walking intervals in the program makes me not feel so bad about actually having to stop and walk for a bit during my runs.

Here is today’s run:
wednesday run at EveryTrail

Map created by EveryTrail:GPS Geotagging

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!