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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Lessons from Gaucher Disease and MTHFR Deficiency

Second Life: Relay for Life 2007: Angel in the Cherry Blossoms

A friend of mine was diagnosed with Gaucher’s Disease this week. (Gaucher is pronounced the French way, Go-Shay.) For most folk this would be a bad thing. For her, it was a gift. It reminded me of when I finally got my celiac diagnosis. I’d been sick at varying levels for at least 20 years. Finally having a diagnosis and being able to DO something about it was … unimaginable. Imagine eyes raised to heaven, and angels singing with serene beauty. A sense of humble joy, and relief.

Then, for me, finding the MTHFR aspect, and realizing it isn’t entirely clear where the celiac leaves off and the MTHFR begins, or visa versa. They seem to be pieces in the same puzzle, interacting in ways that are not necessarily straight forward. The MTHFR in particular is complicated, since it has been overlooked and neglected by the healthcare system until very recently, and like celiac in the USA, is often overlooked.

Well, surprise! Gaucher has some real similarities to this scenario. Like MTHFR deficiency, Gaucher disease has a very rare and severe (read: deadly) manifestation, AND a milder version often overlooked or misdiagnosed, but often disabling. Both Gaucher disease and MTHFR deficiency involve a genetic profile that creates a lack of an enzyme needed to break down a chemical in the body. Lack of the enzyme and inability to break down the chemical compound means that the body ends up with too much of something it doesn’t need and doesn’t want, and not enough of something it does need. And, for both these conditions, that imbalance then causes a wealth of confusing symptoms and a poverty of health and ease.

For MTHFR deficiency, the enzyme needed is Methylenetetrahydrofolate reductase (MTHFR). (Duh. Obvious.) MTHFR, when you have the right stuff, converts homocysteine (toxic, as in bad for you) into methionine (essential, as in something your body needs). Too much homocysteine is related to a lot of difference diseases, most commonly heart disease, nervous system and psychological diseases, and osteoporosis and fragile bones. Recently, there is research showing that too much homocysteine might be related to a number of cancers. There’s plenty more, but that gives you the idea that this can be trouble.

For Gaucher disease, the enzyme needed is the lysosomal enzyme glucocerebrosidase. That’s a mouthful, but I bet my friend manages to learn to make it roll off her tongue easily in no time! Just as with MTHFR, not being able to break down the chemical, means you end up with too much in your body, and then that causes damage. For Gaucher, instead of getting too much homocysteine, you have too much in the way of glucocerebrosides. What is supposed to happen with the glucocerebrosides is that they are broken down into the sugar called glucose and a fat called ceramide. Your body knows how to use those. But a person’s body kind of chokes on the glucocerebrosides. The cells that are supposed to break them down (a type of white blood cell called macrophages) actually get bloated and confused, and stop doing what they are supposed to do. In case you don’t already know, white blood cells are part of your immune system, so with the macrophages in trouble, that means EVERYTHING is in trouble, but especially the spleen, lungs, kidneys, and often the brain. Talk about scary! Early signs include anemia, easy bruising, bone pain, and easy fractures. Those early signs of Gaucher are coincidentally also sometimes early signs of celiac disease and MTHFR deficiency, BOTH. See why it is so hard to diagnose these things?

Here’s another similarity, but this one between me and my friend’s diagnoses, rather than the diseases. Both both of us, the symptoms we showed were not the expected presentation. We had the disease, but the docs missed it for years simply because what they were trained to look for was different from how it manifested in our bodies. Let me try to say that a different way. The symptoms for both of these come from the build up of the bad stuff in our bodies, but that build up can cause things to break down in more than one way. For most people, certain things break down, but for both of us the stuff that broke down was unusual. These are the kinds of diagnoses that make perfect sense after the fact. Hindsight is always 20/20, right? For my friend, her family had approximately the same symptoms for five generations, and no one ever figured it out. For me, we are less sure, and less clear, but I see echoes of my symptoms in old family stories. I wish I could go back in time and tell my beloved grandfather to change his diet so that he wouldn’t die crippled and in pain.

So with both of us having a disease that didn’t “behave right”, how did we end up with our diagnoses? You know mine — personal genomics. It took those genome scans to give the right clues, and then to combine those with some educated guesses about treatments. For her? Well, guess what? It was personal genomic again! Well, how do you figure that? What a surprise. Or maybe it is no surprise that both of us have become rabid evangelical supporters of personal genomics, especially for anyone with mysterious ongoing symptoms or chronic diseases that just don’t seem to get genuinely better no matter what you do.

Since my friend’s diagnosis, a bunch of us on Twitter have been reading up on Gaucher. I stumbled on this article today, and it set off a lightbulb in my mind.

Sidransky, Ellen. Gaucher Disease: Insights from a Rare Mendelian Disorder. Discovery Medicine October 27, 2012. http://www.discoverymedicine.com/Ellen-Sidransky/2012/10/27/gaucher-disease-insights-from-a-rare-mendelian-disorder/

Here is the sentence that rang like a gong.

“It has become increasingly clear that “simple” recessive disorders provide unique insight into the complexities of common diseases.”

Deeper into the article there is a second similar sentence.

“These rare inherited disorders often offer a unique window into seemingly unrelated diseases.”

You start talking about “seemingly unrelated diseases” with celiac and you end up with a laundry list of associated conditions that cover the entire body and every major organ system. Ditto for MTHFR deficiency. And a lot of the conditions are the same ones. And they are also associated with Hashimoto’s Disease, chronic fatigue syndrome, myalgic encephalomyelitis, miscarriages, preterm labor, osteoporosis, bipolar, schizophrenia, depression, migraines, epilepsy, memory loss, cognitive decline and mental confusion, and simple things like joint pain, and weird things like hidradenitis suppurativa, and … and … well, I could go on a long time. I started to draw up a list once, to try to organize them all, but it was a bit overwhelming.

This article about Gaucher disease was describing the same sort of far ranging connections to other diseases.

“Studies of patients with Gaucher disease have led to unanticipated research directions impacting several distinct medical disciplines. Some notable examples include the link between mutations in the glucocerebrosidase gene and the development of Parkinson disease and related Lewy body disorders, elucidation of the role of glucocerebrosidase in skin barrier function and neonatal viability, and the connection between lysosomal transport and myoclonic epilepsy.”

Like Ellen Sidransky, I am now asking if there might be a significant pattern forming here. How many of our chronic diseases are actually caused by a cascade of events deriving from a simple bit of biochemistry gone wrong in our bodies? For me, this was easily addressed with a change of diet and new vitamins. For my friend it won’t be quite as easy (enzyme infusions), but it is still a LOT easier than all the meds she’s been taking and hospitalizations she’s been going through. Quality of life improvement is unbelievable, at least for me. Her treatment hasn’t started, but I expect the same phenomenal improvement in quality of life (QoL).

On the one hand, part of me says, “Why? Why did it have to take so long? Why was it so darned hard to figure out? Was there a point to all these years of struggle and pain?” On the other hand, I kind of ‘get it’, I can see how difficult it must have been to figure out. I still resent all the docs who tried to convince me it was in my head, but I am also so very very grateful that the personal genomics tests have reached the point where they are more accessible, and CAN help people like me. Like my friend. And hopefully, many many more.


A Few Resources

Gaucher Basics: http://www.childrensgaucher.org/about-gaucher/gaucher-basics/

Genome.gov: Learning About Gaucher Disease: http://www.genome.gov/25521505

Science Daily: Macrophages: The ‘Defense’ Cells That Help Throughout the Body: http://www.sciencedaily.com/releases/2010/08/100826141232.htm

NINDS Gaucher Disease Information Page: http://www.ninds.nih.gov/disorders/gauchers/gauchers.htm

More on folate genes, plus exomes, genomes, cancer, and Jay Lake

Veins & Cell Structure

Earlier this month it was National Folic Acid Awareness Week, which is now for me a whole lot more important than it used to be! (That is, of course, because of all the MTHFR stuff I’ve been talking about here.) I wrote a big long blogpost about folic acid and folate over at my main blog, talking about how this is a lot more complicated than I used to think.

Folic Acid, More Complicated Than You Might Think:
http://etechlib.wordpress.com/2013/01/19/folic-acid-more-complicated-than-you-might-think/

You can read it there. Sometimes I feel like the whole conversation about folate is being compromised by the conflation of folic acid with the many varieties of folate, and people misunderstanding that there are differences, and they are significant. The conversation is kind of like the old song, “You say tomato, I say tomahto”, except that the words are different and the concept is being treated as if they are the same thing when they aren’t. Anyone want to write a bad parody?

“You say folic, I say folate.
You say MTHFR, I say MTHFRD1”

The blogpost does go into a bunch of the research and evidence behind folic acid versus folate, and some of the gaps in the research. One of the points is that research keeps moving forward, meaning that what we know and what are best practices are a moving target as well. We do the best we can at any given point in time, but must be flexible and keep trying to learn more and improve not only our own life but the lives of others who might share concerns with us.

I now read a lot of the emerging research on MTHFR, and keep track of it. While doing so, today, I stumbled across two recent articles mentioning problems with folate metabolism (and cobalamine/B12) associated with some other genes.

Update and new concepts in vitamin responsive disorders of folate transport and metabolism. http://www.ncbi.nlm.nih.gov/pubmed/22108709

Novel inborn error of folate metabolism: identification by exome capture and sequencing of mutations in the MTHFD1 gene in a single proband. http://www.ncbi.nlm.nih.gov/pubmed/21813566

Severe Combined Immunodeficiency Resulting From Mutations in MTHFD1. http://www.ncbi.nlm.nih.gov/pubmed/23296427

Both of these mention MTHFD1 as contributing to folate metabolism problems, and that these problems with folate processing are leading to immunodeficiency (meaning that your body can’t fight off disease well or heal injuries). At this point the literature on MTHFD1 sounds a lot like the early literature on MTHFR — it only talks about the most severe problems that can be caused by mutations in the gene. I am wondering if this will turn out to be “the next MTHFR,” a gene for which mutations can have both severe and relatively mild ramifications for patients.

Jay Lake

I am also excited to see that some of these discoveries of new genes with clinical implications are coming from exome scans, and that exome scans and whole genome sequencing are both becoming more common. One of my Twitter friends, Jay Lake, is also a well-known and highly skilled science fiction and fantasy author. Jay is trying to raise funds to have whole genome sequencing to try to find a way to combat the terrible cancer he’s been fighting the past few years. As a person who is self-employed, he doesn’t have the kind of insurance I have, and even my insurance didn’t pony up for even the two small personalized genomic scans I had last year that resulted in turning my life around. Jay had his fifth major surgery since 2008 this week. According to the Kickstarter campaign, “Sci-Fi author Jay Lake has an 8% chance of surviving long enough to see his daughter graduate high school. What does a parent do?” The type of cancer Jay has also runs in my family — colorectal cancer. A lot of people get that, and it tends to go badly quickly. There are many reasons why I would love to see Jay get his genome scanned, and I’m betting it would help more people than just Jay and his family. What do we not learn because of only providing selective healthcare to the have’s? I wonder, I really do.

If you are interested in helping Jay, you can buy one of his books, or donate to one of the campaigns listed below. The incentive prizes alone are pretty astounding. And Jay’s not just laying back and waiting, but has come up with some really creative approaches. That’s why there are a couple different campaigns, with slightly different purposes.

Sequence a Science Fiction Writer: http://www.youcaring.com/medical-fundraiser/sequence-a-science-fiction-writer/38705

Lakeside (A film about cancer in families): http://www.kickstarter.com/projects/1060155945/lakeside-0

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!

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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.