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/

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About Genetic Risk & Celiac Disease

23andMe Celiac Disease Risk Markers

[This was a reply to an email question about genetic risk of celiac. I have so much to share here, but so little time for blogging, that I decided to grab this part, and hope to add more of my recent explorations in the future. Not TOO distant, I hope!]


Like so many people, I failed all the blood tests for celiac, despite having a boatload of symptoms. That was why I took the 23andMe test for celiac markers, with the results showing 4.07 times the normal risk of celiac. In the general population, risk is 0.24%; mine was 0.96%. There are currently 4 known genetic markers for celiac:

* HLA-DQA1 (SNP rs2187668)
* 4q27 (SNP rs6822844)
* 3p21 (SNP rs6441961)
* 3q28 (SNP rs9851967)

I have 3 of the 4, all except the last and least important one, which is what made for 0.96%. Now, ~1% that sounds awfully small, but the genetic risk combines with a variety of other risk factors.

“Estimates of the heritability of Celiac Disease vary. Risk factors other than the SNPs mentioned here include having European ancestry, family history of Celiac Disease, and a personal history of other autoimmune disorders. These disorders include Systemic Lupus Erythematosus, Type 1 Diabetes, Autoimmune Thyroid Disease, and Rheumatoid Arthritis.”

I have European ancestry, family history, and a family history (not personal history) of the autoimmune disorders listed as examples, with a personal history of autoimmune disorders not listed as examples. My diagnosis came from combining all of these:

* genetic risk factor PLUS
* family history PLUS
* ancestry PLUS
* other autoimmune disorders PLUS
* symptoms PLUS
* blinded trial

You see, the inclination of the docs was to read the symptoms as meaning a combination of a bunch of other possible conditions, which they’ve been attempting to treat for 10-20 years. Unsuccessfully. But we kept trying. Believe it or not, this made sense, specifically because, until we had all that information, the risk of the other conditions was higher than the risk of celiac, making it much more logical to explore those options.

They were reluctant to consider celiac, in part because it is a “fad” currently prone to self-diagnosis. Docs rightly tend to mistrust self-diagnoses of current fads, but then every now and then the fad was right! LOL! The other reason they were mistrusting this “self-diagnosis” was because I had atypical presentation of the symptoms. Most folk have primarily gut problems. I had mostly skin. Most folk with celiac related skin problems have those show up on limbs and back. Mine were worst on my face. Medically, it didn’t LOOK like celiac or dermatitis herpetiformis. They weren’t sure what it was, but it didn’t look like what it turned out to be. So you really can’t blame the docs.

But when you combined all these risk factors, you ended up with roughly 1/4 risk instead of 1/100. Big difference. Then the blinded trial tipped the balance. When you have someone with a 1/4 risk of celiac and symptoms and they pass a blinded trial, well, the reluctance to diagnose celiac faded.

EDIT:

I am adding a link to the article citation which was referenced in the test results. For those who want to explore more deeply.

van Heel DA, Franke L, Hunt KA, Gwilliam R, Zhernakova A, Inouye M, Wapenaar MC, Barnardo MC, Bethel G, Holmes GK, Feighery C, Jewell D, Kelleher D, Kumar P, Travis S, Walters JR, Sanders DS, Howdle P, Swift J, Playford RJ, McLaren WM, Mearin ML, Mulder CJ, McManus R, McGinnis R, Cardon LR, Deloukas P, Wijmenga C.
A genome-wide association study for celiac disease identifies risk variants in the region harboring IL2 and IL21.
Nat Genet. 2007 Jul;39(7):827-9. Epub 2007 Jun 10.
http://www.ncbi.nlm.nih.gov/pubmed?term=17558408

AT LAST!!

I started this blog on May 15th. On May 24th came my first post about my trials and tribulations with trying to get a celiac diagnosis. Well, LOOK AT THIS:

Pic of the day - At Last!!!

OK, now between May and now, there have been a lot of changes. The big one has been that my primary care doctor moved to another country. That is kind of a biggie when it comes to moving forward with any kind of health questions. 😉

I was assigned to a new doc, and wasn’t any too sure about this, since I knew nothing about the person. I was thinking about possibly switching clinics, since I knew more primary care folk I don’t trust at my current clinic than folks I do trust, and there are a couple who I wouldn’t trust to throw me a lifesaver if I fell overboard in a boat. They would either think they knew a better way, or they’d be busy asking other people’s advice and not listening to me. So I’ve been judiciously reserving judgment.

I asked around a lot. Many people told me that the doc I’d been assigned to was mentored by my previous primary care doc (who is the first doc I trusted and who has earned that trust by both listening and saving my life a couple times). People told me the new doc is geeky, like me; that he’s interested in e-patients, like me; that he’s open to using email for communication about minor issues; etcetera. So I made a “new patient / establish care” appointment, which takes a while to get. That was today.

I was very careful preparing for the appointment. After all, I have longstanding complicated unresolved health issues. I’m a participant in this PGEN study, and some docs really aren’t into that. And I’m aggressively self-educated about my own health issues. I’m a medical librarian. I’m a really GOOD medical librarian. I specialize in systematic review searches. I have both co-taught on this topic with Cochrane folk, and am on Cochrane review teams. Docs will tell you there is no worse patient than another doctor, or another healthcare provider. Well, they might make an exception to that guideline for me, and if not, I’m darn close to being just as awful.

A few months ago one of the docs I work with was chatting with me. I was rambling on at fairly high speed about some of the new research in her area of interest, or something like that. She hadn’t seen it yet. When we changed topics, I did the same thing in the new topic. She just looked at me with a combination of humor, horror, and awe in her eyes, and asked, “What kind of doctor has to deal with YOU as a patient?” I told her, and she said, “Thank goodness! He can handle it!” Of course, that was before I found out he was moving to another country. Oh. A new doctor? Oh. Uh oh.

For this first meeting, I established my priorities, and clustered them: celiac/skin; MTHFR/folate; osteoporosis/HRT. I made notes in my phone. I printed off a highly selected subset of pages from the genetic studies. I brought copies of a couple other articles just in case. I researched the available expertise on celiac in the system. I hunted down the newest clinical guidelines for diagnosis of celiac. I reviewed the guidelines. I reviewed the articles by the only in-system clinician who remotely comes close to being a celiac “expert.” I made two copies of everything I planned to share with him. I went through the list, & cut it in half. I then hid my copies, and my extra back up single articles. I debated bringing my box of vitamins, but finally decided to. The nurse was glad, which made it ok.

The doc had a student with him today, an MD/PhD fellow. She and I had a lovely chat, but it became rapidly clear that this was too complicated for the amount of time available, so she passed the baton along to him. Because of the time crunch, the conversation was rapidfire, with lots of interruptions back and forth. It wasn’t the best communication I’ve ever had with a doc, but it was far far from the worst, also.

His top priority was the osteoporosis. That’s fine. So we talked about bisphosphonates for a while, and why I don’t want to take them. It’s a risk/benefit issue. I’m not persuaded that I’m badly enough off for it to be worth it to me to take them. I could bore you with the details, but to make it short, this is an area where I’m not an expert, but I know a lot of folk who are, and I’m able to talk about bisphosphonates moderately intelligently. What was important for me was for the doctor to believe that. I was able to show that I’d read some of the same literature that he had, and this helped (I hope) establish some sort of credibility baseline for me. (The genomic content came into play a few moments later, with the doc deciding that the potential value of the HRT is just not worth the potential risk of DVT, given my genetic scan results, and he has me tapering off it.)

Then he was willing to take a look at the genomic info I’d selected out. Some of these we’ll have to deal with later. He and I agreed that most of what healthcare currently knows about MTHFR is suspect and insubstantial. He asked why I’d decided it was important. I pointed out some superficial similarities between my body type and the more severe form of MTHFR; showed him my brief distillation of Pubmed searches on emerging trends in MTHFR research; and then emphasized that a major driver was my constant craving for foods high in folate. Since he was already doing bloodwork, he agreed to add in the baseline test for a few vitamins and minerals.

We have a long talk about the skin issues and antibiotics and dermatitis herpetiformis and rosacea and celiac … what to do, and why a diagnosis matters if it doesn’t change my determination to remain gluten free. My computer crashed so I’m going to just wind this up now and perhaps continue another day. The end point is that the genomic tests DID change my healthcare practice. I walked away with a piece of paper that says I have a celiac diagnosis; we are removing the HRT; and I have the docs OK to start folate supplementation once I have my labs drawn. Pretty good starting point!

Interviewed at Patients Like Me

This was originally posted at:

Learning Your Personal Genetics: An Interview with PGen Study Participant PF Anderson
http://blog.patientslikeme.com/2012/06/29/learning-your-personal-genetics-an-interview-with-pgen-study-participant-pf-anderson/

They have more there, and more interviews planned, so please check out their blog!

====================

Pic of the day - First Time This Winter I've Worn a Hat

1. What led you to participate in the PGen study?

The “why,” for me, had three main drivers. First, I’ve been ill for over a decade, and only recently tracked it down to what appears to be celiac disease, but all the blood tests have come back negative for both celiac and gluten-intolerance or wheat allergy. Second, I am both a medical librarian and an emerging technologies librarian. I firmly believe in supporting research both by doing it and also by serving as a subject when appropriate. This project matches my professional interests in several areas, not the least of which has been an emerging awareness of the essential nature of personal genomics and big data to moving research and discovery forward, especially in the areas of rare diseases. Third, curiosity. My family seems to be packed to the gills with various genetic conditions, and I’ve always thought we’d make an interesting study!

2. Talk about the decision to blog about the study as well.

Why blog? Because, assuming that this IS an important area for research to change the lives of real people, then it is absolutely critical to educate, inform, and openly dialogue about the risks and benefits of personal genomics. Some people I talk with are quite worried about some aspects, while others aren’t even thinking about potential risks! I’m in the middle. I know there are risks, I’m aware that the benefits we hope for in the long term aren’t here yet, but I believe we have to start somewhere to get where I hope we’re going, and someone has to take the risks to hopefully shift the balance.

I hope that the more of us do this, and talk about it, that this will help other patients and individuals think through why they would or would not want to learn this. Also, while I am enormously impressed with the WeConsent.Us website for its information about the risks and benefits of personal genomics and sharing personal data, there is something about telling a story from a real person in their own words that has more impact. Hopefully my own thoughts and story will enrich what WeConsent.Us is doing.

3. You recently received your genetic results. What’s that been like?

Frankly, the results so far have been pretty disappointing. There are two branches of the study, one using the testing service Pathway Genomics, and the other using the testing service 23andMe. Each of the two companies runs saliva scans for different conditions, as well as other information. The primary conditions of interest for me were not included in the scan by Pathway Genomics. The results were interesting, but not very relevant. What was most interesting is that, according to the results, for the flock of conditions that run in my family, I am not at risk for ANY of them, including some I am already diagnosed as having. That seems rather surprising, so I am puzzling this over. I suspect that these are actually related to the core condition [celiac disease] that the scan didn’t include.

I am also a little worried that if I share my test results with my doctors, and the results show that I “don’t have” or am not at risk for these various conditions that run in my family, that the healthcare team might be less vigilant in monitoring these. Because of worrying about the risks of my healthcare team misunderstanding the results and needing the celiac test, I decided to actually spend my own money on getting the other [23andMe] scan. I’m nervous about the money, but I really feel that the information from the one test is incomplete without the other, and the risks of the incomplete information undermine the value of the original test.

4. At PatientsLikeMe, you’ve been able to chat with other PGen study participants in the forum. What have you gained from that?

The forum conversations have been fascinating! It is really interesting seeing what sort of questions other people have, their reasons, their assumptions, the information that they bring to the table. Many of the conversations there have triggered new questions for me, and opportunities to learn more.

5. If you had to pick one key takeaway from participating, what would it be?

We aren’t “there” yet, but if we ever want to get “there,” we need to start somewhere, and that’s here and now.

Dancing Genes

I was prowling through the 23andMe site while I’m waiting for results, and noticed that the results will include a whole bunch of information in an area that isn’t my top priority, but which is interesting nonetheless.

23andMe: Ancestry: https://www.23andme.com/ancestry/

Dancing Matt takes a Journey with 23andMe

A friend of mine has gotten this test. Her whole family did, which turns out to really help a lot in deciphering results and figuring out what’s what. They’ve been kind of perplexed because they also hit the wall of “well, genomics just doesn’t know that much yet.” Their family was told they have genetics from a certain tribe of Indians in South America, when they know from their family history that they belong to a different tribe in a nearby area. When asked, the genetic scan company told them, “Well, we don’t have any genetic data from that tribe, and this is as close as we can get.” My friend’s family was offended that the report explicitly mentioned one tribe in particular without substantial supporting evidence. They wanted the gray areas to be overtly noted as gray areas. In some ways, it seems like the genetic reports, by pretending to be more clear than they really can be, are building up a reputation for hype. Hmmm.

Take Two

PGEN, Take 2

Well, I just did it. Sent off the sample for the 23andMe test. While I was waiting, I also finishing contacting all my immediate family members to find out if they had problems with my blogging all of this. I come from an exceptionally intelligent and educated family. They were all in favor of my doing this. I also emailed copies of the Pathway Genomics report to all interested family members (about half). They’re intrigued. Now, it’s waiting to see what the other report shows. I’m feeling impatient.

Curiouser and Curioser (What We Don’t Know. Yet.)

Curiouser & Curiouser

Wow. Moving along here.

Asked the genetic counselor why the celiac results weren’t included. Turns out that when I took the survey and it said that celiac results would be added to the test, well, the system didn’t check to see which branch of the study I was assigned to. I was assigned to Pathway Genomics, and they don’t HAVE a celiac test in their scan. Oh. They recommended I check out 23andMe. Oh.

That costs a chunk of change. A sizable chunk of change. And I’m in the middle of a small home renovation as a sequel to storm damage. Oh. I have to think about this.

Meanwhile some very interesting conversations happening and questions being raised in the PGEN thread in Patients Like Me forums. And while no one else on Twitter aside from me seems to be using the #pgen hashtag, there are also PGEN conversations happening there. As a direct results of chatting about the PGEN study with another study participant and an interested doctor, we’ve started swapping our data around via email. I mean, we are sharing our genomic scan results. The other patient/participant is in the 23andme branch of the study, but had previously gotten the Pathway Genomics scan, so I got to see how the report has evolved over time for that as well as being given permission to log in and browse around in her results on 23andme. Turns out several of my friends who are NOT in the study have also had these tests run, and those are resulting in more interesting conversations.

This has been fascinating! I’m not going to go into details in this post, but I’ve been very intrigued by not only what information is included but also how it is communicated. Both groups have room for improvement, and there are advantages and disadvantages of each. That will have to be another post.

One of the interesting parts of conversations with other study participants has been picking up things they know that I don’t. Or at least I haven’t heard. One tidbit mentioned was that the MTHFR mutation makes it hard to detox. I did a little searching on this, and the belief is that MTHFR deficiency impairs the body’s ability to process heavy metals. While most of what you find on the Internet about this is from less reputable sites, there are some actual research articles. Not a lot, though.

Pubmed: MTHFR (detoxification OR “heavy metals”): http://www.ncbi.nlm.nih.gov/pubmed?term=mthfr%20(detoxification%20OR%20%22heavy%20metals%22)%20

I was less concerned with that than I was with all the test results for conditions that run in my family for which the genetic scan says I’m at low risk. Let me try saying this a different way. There are all these conditions that run in my family. Lots. But the scan says I’m not likely to get any of them. Hunh? That sounded pretty unlikely. Unless I’m adopted or the test samples were mixed up, something like that. Frankly, I’m the spitting image of my dad and have heard tons of stories about my mom in labor with me. I really don’t think I’m adopted. I think the test has missed something important.

There were several of these results, including conditions that many family members have as well as conditions I already have. I’m a bit worried that if the genetic scan is shared with my doctors and says I’m at low risk for something where I know I have a strong family history, would the doctors perhaps relax and not be vigilant about testing for those conditions?

An added complication was that almost all of the conditions that run in my family that the test says I probably won’t get are diseases that are known to be common in people with celiac. That’s … interesting. The genetic counselor kept saying things like, “Maybe there are other genes for these conditions that we don’t know about yet.” So. Alright. Thinking through this.

Disease X is common in a family.
Disease X has proven genetic component & known genes.
Disease X is associated with a 2nd condition, Disease Y.
Disease Y also has proven genetic component & known genes.

If the genetic test is negative for Disease X, is the person also negative for Disease Y?
If the genetic test is negative for Disease Y, is the person also negative for Disease X?
Does Disease X in some fashion contribute to or cause Disease Y?
Does Disease Y in some fashion contribute to or cause Disease X?
Are Disease X and Disease Y linked in some way, or are they independent of each other, and simply cause similar symptoms?

That’s not all, it gets … complicated. And we don’t know enough, not remotely. So getting the genomic scan has, for me, created many many MANY more questions than answers.

I suspect that the conditions in my family for which I tested negative on the genetic scan actually do have a genetic component that wasn’t included in that test. I strongly suspect, given that they are mostly associated with celiac and celiac was not included in the test, that celiac is the root cause of all of those. Of course, there is no proof, and even if we do the next test, we still won’t know enough. But. But.

There are things in the genetic scan I want to share with my docs. But without the information about celiac, I don’t feel safe sharing the results with my docs. Especially since my wonderful doc who I trust is leaving and I’m trying to find a new doc. Knowing the answer to the celiac question might help fill in some important pieces. If that is negative, it might just make for even more questions and confusion. I kept coming back to how much money it costs. I kept thinking about waiting until I have more money, waiting to see how much money is left after the house is fixed. House vs health. House vs health.

Well, I did it. I went ahead and ordered the 23andMe test. Lord, I hope this is worth it.