Good Lord, People, 23andMe is NOT Dead!

23andMe

Good Lord, people, 23andMe is NOT dead! Or closed, or no longer taking orders, or anything like that. I hear this a lot.

“You know, I always wanted to get my genome tested. I was going to try 23andMe, but then the FDA shut them down. Oh, well, missed my chance. [sigh]”

NO! You did NOT miss your chance. Firstly, 23andMe is not closed for business. They still will take your money and your sample. They still will analyze the sample and give you results. From what I’ve been seeing in the results from folk I’ve been helping to look at their data, 23andMe seems to be running the test exactly the same way they always did, for the same SNPs.

They simply are, at this time, not offering their health reports to new customers. It isn’t the data that has changed – it iw what analysis is shared with the customer. Old fogies like me who got their tests done before the FDA folderol” still have access to our old 23andMe health reports, and they continue to improve them.

I have heard nothing to indicate that 23andMe are not working with the FDA to try to make it possible to release health reports again in the future. Issues around that get complicated and I’m going to save them for a later post. Right now, what if you wanted a test for some genetic health information? Can you do it? How long will you have to wait to find out the answers to your health questions?

You can still do it. It isn’t as easy as it was before, but it can be done. I’ve been spending a lot of time talking people through how to do this, and it is time to write it down. If nothing else, it will save me time. This will be the short short version, and I can answer more detailed questions and describe specifics, maybe give an example or two or three.

FIRST, THE DISCLAIMER

Risk is Not Just Genes

Making sense of genetic information is complicated even for experts, which most of us are not. Of course, part of the irony of looking at genetics for health conditions is that most of the time what causes the condition is not just the genetics, but genes PLUS something else. If you don’t find the genes for something, that doesn’t mean you can’t get it; if you do find the genes for something, it doesn’t mean you will get it. It is hardly ever a case of this=that.

What Does Risk Mean, Anyway?

There is also the challenge of figuring out how important the risk is, and whether or not to do something about it. So, my personal risk of celiac disease is over 4 times normal. Wow! That sounds like a lot, doesn’t it? But 4 times normal for celiac risk is still only 1 in 20 people, because normal is about 1 in a hundred. I know someone with celiac risk 17 times normal, which is 1 in 4 people. That’s getting to be pretty serious! But, while celiac is dangerous, it isn’t one of those conditions that is immediately deadly or painful. And my friend still has a 3 in 4 chance of NOT getting celiac, and that is a lifetime risk.

On the other hand, my risk of venous thromboembolism (VTE) is 1.5 times normal. That doesn’t sound like much does it? It’s higher, but only a little bit. So we don’t really need to worry about it, do we? Well, yes. VTE can kill you on the spot, and it is incredibly painful. And normal is 1 in 10 people for lifetime risk. For me, the risk is closer to 1 in 7.

Given that, according to 23andMe, my genetic risk of celiac is roughly 1/20 and my risk of VTE is 1/7, and adding in the comparative dangers of the two diseases, my docs got all excited about the VTE, and not terribly about the celiac. I hope you understand why now, and also a bit more about why genetic risk is complicated.

On Asking for Help

Last part of the disclaimer.

For both of these, celiac and VTE, 23andMe looks at SOME of the genes and SNPs known to be associated with the condition, but not ALL of them. So whatever 23andMe tells me about risk is only part of the picture. It looks at the most important genes, but is still only part of the picture. That’s why you need experts to put all the pieces together, and get more information to fill in the gaps from the 23andMe test.

Everyone always says, “Ask your doctor,” when it comes to finding something puzzling, confusing, contradictory, or worrisome in your genetic tests. I did, and found that most of my doctors didn’t have the expertise to make more out of it than I did. Some poohpoohed the 23andMe results, others made clinical decisions based on them without verifying with other tests, some asked for more medical tests to expand upon what 23andMe had, and one said, “You know more about this than I do, but I’m going to learn.” Here is a quote from an NEJM article a few months ago about the risks and benefits of trusting direct-to-consumer personal genomic services such as 23andMe.

“Clinicians will be central to helping consumer–patients use genomic information to make health decisions. Any regulatory regime must recognize this reality by doing more than simply adding the tagline on most consumer ads for prescription drugs: “Ask your physician.” That is insufficient guidance unless your physician has ready access to a clinical geneticist or genetic counselor.” Annas GJ, Elias S. 23andMe and the FDA. N Engl J Med 2014; 370:985-988. http://www.nejm.org/doi/full/10.1056/NEJMp1316367

Some of the personal genomics service offer phone-in access to genetic counselors. I tried that, and didn’t get helpful answers there, either. Even worse, one of the answers I got was blatantly wrong. It may have been just the genetic counselor who I happened to be talking with, so don’t judge the whole profession by that one person, but do be prepared to keep looking for info if needed. Where I found the most helpful information was in the 23andMe forums, BUT a lot of the info there was unreliable, and I had to sort out what was helpful and what wasn’t.

So, my recommendation is, absolutely DO ask your doctor, ask a genetic counselor if you can, but that might not be enough. You might need to do more research on your own, or find someone you trust to help you with this.

What Good Is It?

So, what good is it then? It gives you clues. Like a detective, you take the clues and look for more information, or ask for more thorough testing, or raise questions that weren’t being asked or addressed before. Some of the clues will be red herrings. Some of them may lead you to a prized solution. For me, these clues ended up dramatically improving my quality of life, and may have even saved my life.


So, now, the short short version. And PLEASE, if someone more expert than me with genomic data reads this and spots any errors, please say so!

PART ONE

1. Get your 23andMe test done.

Pic of the Day - PGenPGEN, Take 2

2. Log in at the 23andMe web site when you are notified that your results are ready.

23andMe

3. Click: Browse raw data.
23andMe: Getting to your raw data

It should look like this:

23andMe: Browse Raw Data

4. Click: Download raw data.
23andMe: Download Raw Data

5. Complete security procedure (log in again, answer security questions, etc.). It should look like this.

23andMe: Downloading Raw Data

6. Answer the question about what type of data and format you want. NOTE: I always choose ALL DNA, unless you have something else specifically in mind.

23andMe: Downloading ALL Your Raw Data Or ...

7. Find the file (which will be named something like genome_Firstname_Lastname_Full_12345678901234.txt)

PART TWO (A): Easier Way

Genetic Genie

Now you have choices. You can dig into the information the easier way, or the less easy way. Let’s start with the easier way.

1. Select a tool to do what you want with your data. There are LOTS of tools people have built to do useful things with 23andMe data files. One of my favorites is Genetic Genie, because it tells you about the MTHFR gene which has become so important in my life. I also am spending a lot of time with Promethease because it is so complete compared to most other 23andMe analysis tools. Lets start with these.

2. Go to the tool of your choice, such as:

Genetic Genie: http://geneticgenie.org/

Promethease: http://www.snpedia.com/index.php/Promethease

3. Follow the directions at the tool, but this almost always requires you to upload your 23andMe data file. Here are more details about doing this with Genetic Genie.

4. Last come what is always the tricky part — making sense of the information you get. That’s worth several posts, but for starters the main point to remember is that the 23andMe test is a place to start, not a final answer. In Genetic Genie, the code, analysis, and text are written by engaged amateurs, not by doctors or genetic counselors. They worked hard, collaborated with a lot of other people, and did a lot of research, but it isn’t going to say the same things your doctor might.

More Tools

23andMe: Tools for Everyone http://www.23andyou.com/3rdparty
NOTE: When 23andMe took out the health reports, they also edited this page to remove links to tools that provide health data from 23andMe data. So, this is interesting and useful, but not sufficient. You’ll have to look somewhere else for most tools.

23++ Chrome Extension: Get more from your data:
http://23pp.david-web.co.uk/getting-more-from-your-data/

Confessions of a Cryokid: Top 10 things to do with your FTDNA raw data (2011) http://cryokidconfessions.blogspot.com/2011/06/top-10-things-to-do-with-your-ftdna-raw.html

Genetic Genealogist: What Else Can I Do With My DNA Results: http://www.thegeneticgenealogist.com/2013/09/22/what-else-can-i-do-with-my-dna-test-results/

International Society of Genetic Genealogy: Autosomal DNA Tools: http://www.isogg.org/wiki/Autosomal_DNA_tools

Resqua: Q: What should I do after generating my Gene variance report? http://resqua.com/100005927200207/what-should-i-do-after-generating-my-gene-variance-report

Think Exponential: Get SNPd! http://thinkexponential.com/2013/01/10/why-you-should-get-snped/

PART TWO (B): Less Easy Way

Linking Disease Associations with Regulatory Information in the Human Genome

Actually, there are a LOT of different “less easy ways.” You can open the raw data file in a text editor and search manually for specific pieces of information. Or, if you code, you can write a little program to do some of the hard work for you.

Basically, it comes down to doing a lot of research, the hard way, by hand. But, believe it or not, I am doing it. I’ve had a lot of help from people who offered tips or comments in the 23andMe or MTHFR.net forums, on Facebook, on Twitter, and comments on these blogs. I am NOT an expert, but like most readers of this blog, just someone who wants or needs to know more. This is what I’ve learned and figured out on my own, offered as an example, nothing more.

Critical Background

23andMe gives SNP-based data. SNP stands for single nucleotide polymorphism. Polymorphism means something that can be itself but in different ways, our eyes are eyes whether they are blue or brown or hazel or violet or any other natural eye color. I won’t give an introduction to genetics here, but there are several online resources that explain these ideas, with one of the best resources being Genetic Home Reference from the US government. Depending on how much you want to know, you may wish to take the Coursera courses Introduction to Genetics and Evolution (Duke U) or Experimental Genome Science (U Penn).

1. What SNPs do you want to know about? Check here:

RegulomeDB (Stanford): Linking Disease Associations with Regulatory Information in the Human Genome: http://regulomedb.org/GWAS/

I have also found SNPs of interest in research articles, PUBMED, and other places, but this is a good start. The SNP identifier (what you need) will look something like this:

rs2187668

2. Find out which polymorphism is the one considered “healthy” or “normal”, and which one is the one associated with risk of disease? These maybe called “risk alleles” or
simply polymorphisms.

For example, for SNP “rs2187668” (one of the celiac risk SNPs) the risk indicator is (T), while the normal is (C).

3. Open your 23andMe raw data file in a text editor, like WordPad (Windows) or TextEdit or TextWrangler (Macintosh).

4. Search for the SNP you want to know about. The data will be in four columns:
– RSID
– Chromosome
– Position
– Genotype
You need to know about the first and last columns, RSID and Genotype. It will look a little like this.

rsid…..chromosome…..position…..genotype
… [many other rows of data] …
rs2187668…..6………32605884…..CT

So, this person (me) has for that SNP one risk allele “T,” (which I happen to know is from my dad, by comparing it to his scan) and one normal allele “C,” (which must, by default, be from my mom, since for every gene pair we have gotten one from each parent).

5. Repeat for all the other SNPs associated with the condition you are researching.

6. Search for more information and articles about those SNPs, the condition, and more. You can’t make sense of this without more information. And ask lots of questions.

More Tools

ENCODE:
About: http://www.genome.gov/encode/
Data: http://genome.ucsc.edu/encode/

ENSEMBL Genome Browser: http://useast.ensembl.org/

OpenSNP: https://opensnp.org/ OR https://opensnp.org/snps/

SNPedia: http://www.snpedia.com/

UCSC Genome Browser: http://genome.ucsc.edu/

Advertisements

What the Heck is MTHFR Deficiency?

Mother and Baby

The first item on my report was … that I am a carrier for a genetic condition. Whoa! Really? The next question was, “What the heck is MTHFR Deficiency?”

I dug around a bit online and found out this is, shall we say, not a bit deal. One of my first steps is usually to try to find out other names for whatever it is I want to know. Another name for this is Methylenetetrahydrofolate Reductase Deficiency. Ie. Methylene-Tetra-Hydro-Folate Reductase Deficiency. It is also associated with Homocystinuria, and some people call them the same thing (but that seems to not quite accurate). The short version is this is really common, and even if you have it usually it isn’t very serious. Chances are you could have it and never know it.

They say 45% of white Americans will have at least one copy of the various genes that are associated with this. I have two copies, but of two different versions. That probably means that both my parents had one, but might not. I don’t know enough yet to make sure, and would have to get more information. I don’t know enough to understand if the two versions are on the same gene (a copy from each parent) or if they are involving multiple genes with related effects. If both my parents have it, then my other siblings probably all have at least one copy, which wouldn’t be a big deal if it was true. When it is most important to know about this is when you are having kids, and all my sibs have had all the kids they are going to. The public info about this points out that the main solution is to take vitamins with folic acid in them while pregnant, and since they recommend that for everyone anyway, you’re covered as long as you follow standard medical advice.

Here is the link, out of all the ones I looked at, which had the most helpful information for me.

Counsyl: MTHFR Deficiency: https://www.counsyl.com/diseases/mthfr-deficiency/

What was interesting for me was when I started looking at the Homocysteinemia aspect of it.

Pubmed Health: Homocystinuria: Cystathionine beta synthase deficiency: http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0002179/#adam_001199.disease.symptoms

I fit bits and pieces of the description. Obviously, I’m not intellectually disabled, but I do have:
– High arches of the feet
– Knock knees
– Long limbs
– Nearsightedness

These all could be attributed to other causes as well, but I found it curious. I have particularly strange feet (at least according to shoe salesmen), and limbs so long that none of the normal ergonomic guidelines apply to me. I am also mentally noting that they say to be particularly careful of blood clots for people with this condition. As far as we know, I don’t have the condition, but this is something I’ll want to share with my doc and discuss. I’ll also want to talk about this with my kids and siblings, even though it is not a reason to worry.

Well, That’s Disappointing

Zera: Environmental Indicators: Face with Tears (Detail)

I’m hoping that I misunderstood something, and that more info is coming later. I received the results — 91 page report! Going to take a little time to dig through it. My immediate response was, there are some real issues with their graphic design, hmmm. They do this clever color-based top-level design for quick scan of the results, but I suspect it isn’t truly visible for persons with color-blindness, and they don’t provide the supporting design for those persons. Rule one of design for persons with color blindness is don’t depend solely on the color to carry the message, combine the color with words or numbers.

Next response was, but … but … but … where’s the results for celiac? When I filled in the survey it said they would include that, but if they did, it isn’t in these results. That was my primary motivator for doing this, and if I don’t get that info, I am suddenly seriously unmotivated. Not that I won’t look at the other parts, but my heart isn’t really in it.

More later, as I explore. There doesn’t seem to be as much information as I’d hoped.

My “Why”, or, Flipping Healthcare & Research Upside Down

Today someone posted a question about this study in the Patients Like Me forums. They wondered if other folk were doing this, and what they thought about it. This was my reply.

Found Words: Question Marks

Hi! I’m participating, and I’m blogging it. I’m both excited and nervous. What do I think about it? I think it is super important. I’m a medical librarian, and this (personalized genomics) is a topic that has come up quite a bit recently. The more I learn about it, the more important I think it is. At the same time, our culture hasn’t exactly caught up with the ideas behind what makes it important. Because I’m blogging it and plan to make as much of the information public as possible, I’m talking with my family. I don’t want to upset them about my making personal genomic info public. Luckily, so far, they get it (but I still haven’t talked with everyone yet).

You see, my family has a boatload of chronic conditions that have genetic associations. We also tend to be outliers when it comes to regular treatments. We have bizarre and unpredictable reactions to medications, ranging from unheard of side effects to completely ineffective to super effective (and supersensitive, too). We tend to be extremely hard to diagnose, and often present with atypical symptoms. Sounds like a mess, doesn’t it?

The modern model of healthcare is ill-suited to patients like me and my family. It focuses on the mean, people whose presentation, symptoms, and response to treatments fit nicely under the standard distribution bell curve, all clustered around the center. Science and healthcare are shifting, though, and a good thing, too! The new direction is personalization — customized, personalized treatments designed to work for YOU and no one else.

I describe it to my family like this. Right now, you get sick, and the doctor gives you a prescription. You fill this at the pharmacy, and get the same medicine that anyone else would get. The same pills, shaped the same, colored the same, tasting the same, formulated the same. Why? Because that is what works for most people, and because there are economies of scale in bulk production. God help you if you have a rare condition or don’t respond well to the normal treatment. There is no monetary incentive to develop treatments for the folk who are off at the fringe, instead of “normal”; there are no “economies of scale.”

With personalized healthcare, the hope is that instead of a common generic prescription, you’ll get a treatment that is customized for you. Ideally this will eventually mean customized based on your genetics, your past experiences, where you grew up, events that impacted the community around you, your personal history, recent events, and more. When you’ve spent a lot of time in a healthcare system that doesn’t do well with “rare” or “outlier”, the idea of a healthcare system focused on personalization and customization becomes very appealing.

But we aren’t there yet. We still need to get there. I watched a lot of the recent TEDMED presentations. One of the main ideas I took away is that to get the model of healthcare flipped from bell-curve to custom, from factory-style care to clinician-patient partnerships, there are a few things that need to happen. A big one is that research on which healthcare decisionmaking is based also needs to flip. Research needs to change from the traditional model of “hypothesis generation, data generation/collection, analysis, repeat” to something we don’t have yet, starting with LOTS of data from LOTS of people (“big data”) as the first step, and then this is followed by new ways of looking at and analyzing data, and new ways of collaboratively discovering important patterns that lead to important questions. Flip. Turning it backwards.

Before any of this can happen, the researchers and scientists need to start with that “big data” I mentioned. To get the data, they need people like us, lots of people like us, to share our data. If people are afraid to share their data, then it is business as usual, “the way things have always been.” If we want it to change, then someone, a few someones, need to go first, need to take the risk, need to show others it’s ok. “Come on in, the water’s fine!”

I don’t expect other people to be blogging about this, but for me, I felt it was important. I work in healthcare, health literacy, emerging technologies … it’s a fit. Not to mention that I work in a unit that supports one of the research teams on this study, so my participation actually supports my job and my community. So that’s for me. I am really hoping that others will also participate. Right now, this is a pretty basic introductory study — who is willing to do personal genomics, why, and what do they do with the info. I’m being an outlier again, by broadcasting the whole experience. They’ll need to hear from the rest of you to get a more balanced picture.

If you aren’t sure about what all this is or does, you might want to take a look at WeConsent.Us which is a website designed to provide a clear, plain language overview of the risks and benefits of personal genomics.