Tag Archives: 23andme

Ralph Pethica: Improving My Fitness With Genetics

1_RalphPethica_QS Talk 2014 Powerpoint

One interesting aspect of personal data is how it can reveal what is unique about you. Nowhere is this more true than with genetic information coming from DNA testing kits. However, people are still at an early stage on how they apply that information to their lives. Ralph Pethica, who has a PhD in genetics, was interested in what his DNA could tell him about how to train more effectively. His findings were presented as an ignite talk at the 2014 QS Europe Conference.

What did Ralph do?
Ralph loves to surf. When it is the off-season, he trains so that his body will be in good condition for when the warm weather rolls back around. He used genetic research to inform how he designed his training plans.

How did Ralph do it?
Ralph used a 23andMe kit to find out his genetic profile. He researched those genes that have been found to have an impact on fitness to see his body should respond to exercise. For example, did he possess genes that gave him an advantage in building muscle with resistance training? He then modified his training routines to take advantage of this information and monitored his results (using the Polar watch and a Withings scale) to see whether his assumptions held up.

What did Ralph learn?
Ralph found out that he has genetic disadvantages when it came to strength training. This told him that progress in this area depended more on his lifestyle. In particular, he found that eating immediately after working out was important.

When it came to cardio exercise, he had a number of genetic advantages. The unexpected downside to this is that his body adapts quickly to any training regimen, resulting in a plateau. To get around this, he varied his training plan and monitored his results. On one day, he would cycle at a steady rate, while the next, he would use high-intensity intervals. His body seemed to respond to the varied training plan and he hit fewer plateaus. Without knowing which genes he possessed, and reading current research on those genes, it is unlikely that he would have discovered these effective customizations to his training plan.

Ralph has taken what he’s learned and built a tool called Genetrainer to help people use their genetic information to inform their fitness plains. You can check it out here.

Tools: Genetrainer, 23andMe, Polar RCX5, Withings Smart Body Analyzer

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Mark Drangsholt: Deciphering My Brain Fog

One of the benefits of long-term self-tracking is that one builds up a toolbox of investigatory methods that can be drawn upon when medical adversity hits. One year ago, when Mark Drangsholt experienced brain fog during a research retreat while on Orcas Island in the Pacific Northwest, he had to draw upon the self-tracking tools at his disposal to figure out what was behind this troubling symptom.

Watch this invaluable talk on how Mark was able to combine his self-tracking investigation with his medical treatments to significantly improve his neurocognitive condition.

Here is Mark’s description of his talk:

What did you do?
I identified that I had neurocognitive (brain) abnormalities – which decreased my memory function (less recall) – and verified it with a neuropsychologist’s extensive tests.  I tried several trials of supplements with only slight improvement.  I searched for possible causes which included being an APOE-4 gene carrier and having past bouts of atrial fibrillation.

How did you do it?
Through daily, weekly and monthly tracking of many variables including body weight, percent body fat, physical activity, Total, HDL, LDL cholesterol, depression, etc.   I created global indices of neurocognitive function and reconstructed global neurocog function using a daily schedule and electronic diary with notes, recall of days and events of decreased memory function, academic and clinical work output, etc.  I asked for a referral to a neuropsychologist and had 4 hours of comprehensive neurocog testing.   

What did you learn?
My hunch that I had developed some neurocognitive changes was verified by the neuropsychologist as “early white matter dysfunction”.  A brain MRI showed no abnormalities.  Trials of resveratrol supplements only helped slightly.   There were some waxing and waning of symptoms, worsened by lack of sleep and high negative stress while working.  A trial with a statin called, “Simvastatin” (10 mg) began to lessen the memory problems, and a dramatic improvement occurred after 2.5-3 weeks. Subsequent retesting 3 months later showed significant improvement in the category related to white matter dysfunction in the brain.  Eight months later, I am still doing well – perhaps even more improvement – in neurocog function.

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23andMe Sets Growth Goal Of One Million Customers, Reduces Price to $99

23andMe, a wonderful annual sponsor of the Quantified Self, has some exciting news to share with us. Check out this letter from 23andMe’s CEO Anne Wojcicki below!

Today we’re announcing some big news. I don’t want this moment to go by without a note of gratitude to our customers and those who have been advocates for 23andMe over the years.

We have come a long way together.  Because of you we pioneered the use of personal genetics.  You are helping us establish a new medical era that is defined by wellness, disease prevention, and personalized care.  You also helped us create a novel research platform.  By leveraging online tools, social networking and crowd sourcing, and combining them with genetics, we created a platform that has set the stage to transform the way pharma companies and academics do health and wellness research.

We want to do more.

23andMe has raised more than $50 million in new financing with the goal of reaching one million customers.  To help us reach our goal, we are happy to announce today, that we are dropping our price to $99.

One million customers can be the tipping point that moves medicine into the molecular era.  Hundreds of you have written to us about how genetic information changed your lives and, in some cases, saved your lives.  We believe genetics should be an integral part of health care and we will work hard in the coming year to help genetics become part of everyone’s health and wellness.

A community of one million individuals will also benefit the world.  A genetic data resource of this magnitude has enormous potential to address unanswered questions related to the contributions of genes, the environment and your health.  Understanding these factors and their interactions could lead to major improvement in diagnostics, preventive medicine and therapeutics [Collins NATURE | VOL 429 | 27 MAY 2004].

This change is not just about a new price point for personal genetic testing. It is about an ambitious plan that could transform medicine for generations to come.

If you have questions about the new pricing please go to our FAQ or email your questions to customercare@23andMe.com.

Posted in News and Pointers | Tagged , , , | 4 Comments

Toolmaker Talks: Bastian Greshake (openSNP)

We talk about very frequently here on the QS website about tools, methods, and systems that help us understand ourselves. When it comes to the self there may be nothing more fundamental to understanding our objective ourness than our basic genetic makeup. Many of you have probably undergone or have thought of using Direct-To-Consumer genetic testing to better understand your phenotypes, disease risk, or even your ancestry. That’s all great, and I’ve spent a lot of valuable time combing through my own genetic data, but like most data true power lies in large datasets that provide observations across many individuals. So how do you participate in that type of sharing and learning? Enter the team at the openSNP.org. Today we talk with Bastian Greshake, one the developers behind the openSNP project.

How do you describe openSNP? What is it?

The too long, didn’t read version: A open platform which allows people to share their genetic information and traits, which are suspected to be at least partially genetically predisposed, which also tries to annotate those genetic variants with primary scientific literature. The data can be exported from openSNP through the website or through APIs, making it easy to re-use the data.

A longer version: openSNP has basically two target groups and users may as well fit in both categories.
First there are customers of Direct-To-Consumer (DTC) genetic testing like 23andMe who want to share their genetic information with the public for various reasons. Those can use openSNP to release their genetic data into the public domain using the Creative Commons license which is applied to the data uploaded and entered in openSNP.
As genetic information is interesting but not very useful to analyze the effect of genetic variants on bodily traits those users can also enter information about traits which might genetically influenced and create new possible categories which all other users then can enter. Those traits range from the more obvious ones, like eye and hair color, to more exotic ones like political ideology. A few weeks ago we also created a method for  users to also connect their Fitbit accounts to openSNP to make the collection of data easier and more standardized. The genetic effects on activity, sleep habits and weight loss/gain can more easily be analyzed in this fashion.

We also mine the databases of Mendeley, the Public Library of Science and the SNPedia to annotate the genetic variants users carry. This allows customers of DTC testing to find out what the recent scientific literature is able to tell them about their genetic variants. While the SNPedia is a crowd-curated Wiki, Mendeley and the Public Library of Science link back to primary literature, in the latter case even to Open Access literature which is full text available for everyone.

The second group of users who are interested in openSNP are scientists and citizen scientists who are interested in using the data for their own studies, be it to figure out what genetics can tell us about our ancestry or which effects single variants have on disease risks or other traits. The data can be downloaded from openSNP in bulk or more granularly accessed through a JSON-API and the Distributed Annotation System, a standard in Bioinformatics, which for example is used to visualize the data.

Both groups can profit from the commenting features which allows users to communicate about traits and individual genetic variants. The internal message system of openSNP also facilitates further communication, for example to share details about shared traits and diseases or to allow people who want to use the data to get back in touch with the people who uploaded the data. The latter one enables the direct exchange between those two user-groups in a bidirectional way: Researchers can ask questions about traits and people who have shared their data have a back channel as well and can get notified about the results researchers have made.

What’s the backstory? What led to it?

It more or less began with me getting my genetic information analyzed by 23andMe myself. After I received the results I published the data in a git repository on GitHub to make it available for others who might benefit of having more data. As I started to dig deeper into my own results and the raw data I wanted to have more data sets myself, to be able to compare the results. But unfortunately there wasn’t a single resource for such data. Some people also had published their data on GitHub, others on their own websites, collected publicly available data sets in a Google Spreadsheet or participated in projects like the Personal Genome Project.

This was quite frustrating: Finding the data was hard and it most often there was no additional data about traits attached. And more often than one would expect there was also no way to contact to people who made the data public. So the idea to create a platform to solve this problem grew and I contacted some friends to see if they were interested in doing such a platform, just for fun. We started out with the basic idea of creating a platform where people could upload their genetic data along with some traits they have. A couple of weeks after we started to work on the project we stumbled upon the APIs of Mendeley & the Public Library of Science and thought it might be cool to include additional data about the genetic variants as well. During the development we came up with more and more features, like the openSNP APIs. All in all the project is still growing and we’re working on adding and refining features.

What impact has it had? What have you heard from users?

We submitted the first release of openSNP to the 2011 PLOS/Mendeley Binary Battle, a competition interested in creative ways to use their APIs and won the first prize. We also secured a small grant from the German Wikimedia Foundation, which allowed us to genotype over 20 people, mainly from underrepresented groups, to diversify the available data. Those persons have now released their genetic data on openSNP as well. Right now we have over 250 genetic data sets on openSNP and just short of 600 registered users. Those numbers don’t sound to impressive in the age of one billion people on Facebook. But to put it into perspective: Genetic testing is still a niche thing and before openSNP was released there were about 40-50 of those data sets publicly available.

The feedback of our users has been very positive. Many users come up with new ideas for features they like to see added and we are really open to those suggestions and critiques. Many of the API methods, which are now implemented (and the whole Distributed Annotation System), are only in place because user let us know they wanted them. I know of users who are actively using openSNP to learn more about their test results and are in an active exchange with other users with similar traits. And while the amount of data we have so far doesn’t really allow scientifically sound studies there are already people using the data, for example there are users who run their self-written analysis-tools over the openSNP-data sets and report the results back to the users, which is amazing.

What makes it different, sets it apart?

Of course we’re not really the first to think of such an idea but are more or less a remix. For example 23andMe themselves do use the data of consenting customers for studies. They also provide questionaries about traits which users can take. But this data isn’t available to the public, due to (perfectly reasonable) concerns in terms of privacy, bio-ethics and liability. On the other hand there are projects like the Personal Genome Project, which publishes traits and genetic data of participants into the public domain. But due to similar reasons like with 23andMe the participation in the project isn’t open to everyone.

We feel that informed individuals should be in the position to share their data with the world, like they are already doing on their own websites, in an easy fashion. And of course we’re targeting a slightly different group: Probably over 150,000 people are customers of some DTC genetic testing, this is a huge potential data source which could be used to help us understand new and exciting things.

What are you doing next? How do you see openSNP evolving?

We’re still developing and refining openSNP. One of the biggest problems right now is the quality of the data for the additional traits. We have kept the process of adding data really open on purpose, to make it easy for people to provide additional information about themselves. Unfortunately this has the side-effect that the quality of the descriptions varies wildly. Those problems start of with regional idiosyncrasies: Is it “Eye Color” or “Eye Colour” and are you using the metric or the imperial system of units? And is your eye color blue or “Indeterminate brown-green with a subtle grey caste”? This granular data can be very useful, but for many applications it can be too specific. With the implementation of the Fitbit API we’ve taken a first step to keep the entering of data simple but unified at the same time. And we’re currently looking into other ways of how one could counter problems like this.

We’re also looking in more data sources to annotate the genetic variants listed in openSNP, to provide even more information for customers of DTC testing. And we’re also working on making our APIs more powerful. With the rOpenSci package there is already a great library which makes use of the APIs in the current state, but of course we would like to see more of those libraries.

And it’s hard to say in which direction openSNP will evolve as we are a bit dependent on the DTC genetic testing industry. More and more data, like Whole-Genome or Exome Sequencing, is generated and we are working on reflecting those changes on openSNP as well. And we’re open for any suggestions. So if you find that a feature is missing you should let us know, we will try to work out a way of how this might be usefully implemented.

Anything else you’d like to say?

First of all: We know, genetic information is sensitive and depending on where you are living there might not even be laws to protect you from discrimination based of your genes. Other countries, like the US with the Genetic Information Discrimination Act (GINA), have some mechanisms against this, but even those might not offer total protection in the end. And you should also keep in mind that your genetic information does not only give away details about yourself, but by design also about the next of kin. I think this is really important. If you are thinking about publishing your genetic data please keep those issues in mind. And if you come to the conclusion that this isn’t for you as you have to fear negative repercussions or just have a gut feeling of not really wanting to publish the data: Please don’t do it.

And what I also can’t stress enough is that openSNP is developed and run by a team of about four people and we are all doing this in our spare time as a fun project and as community service, without compensation. Some of us have day jobs, others are still studying and some even do both. So while we are doing our best to keep everything running it might sometimes take a while. But if you feel like contributing to the project please get in touch with us. We’d love to have more people in on this.

Product: openSNP
Website: www.opensnp.org
Price: Free

Authors note: Data sharing, especially genetic data, is a very sensitive topic in our community. I want to fully disclose my bias towards openness and sharing. I believe that our kindergarden teachers had it right when they taught us that sharing is one of the fundamental human traits we should all cultivate. To this end, I have participated in openSNP and you can view my genetic data here and my Fitbit data here

This is the 18th post in the “Toolmaker Talks” series. The QS blog features intrepid self-quantifiers and their stories: what did they do? how did they do it? and what have they learned?  In Toolmaker Talks we hear from QS enablers, those observing this QS activity and developing self-quantifying tools: what needs have they observed? what tools have they developed in response? and what have they learned from users’ experiences? If you are a “toolmaker” and want to participate in this series, contact Rajiv Mehta or Ernesto Ramirez.


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So, you think you can science? The search for the next CitSci study!

Fat-rich Thanksgiving preparations have got me thinking an awful lot about my first citizen science study, Butter Mind, in which participants ate half a stick of butter, the equivalent in coconut oil, or nothing, and then performed a simple math test.

Butter Mind ran from October 23rd to November 12th. Unfortunately, we were unable to determine in this three week period whether butter or coconut oil improved math performance – the “practice effect” was too large.  However, I did find that butter helped me wake up feeling more refreshed!  Now, I’m looking for something to try next… pork belly, perhaps?

For me, Butter Mind was worth it simply to interact with other fun, curious folks. A total of 42 participants and 2 study organizers signed up. We did math, ate butter together (so to speak), and chatted about topics such as Seth Robert’s Shangri-la Diet, food allergies, and what our favorite butter/coconut oil recipes were.  I feel there is a lot more room for people to benefit from sharing lifelogging details.

In that vein, I’ve created a forum on Genomera for ex-Butter Mind participants to share their thoughts and experience self-tracking.  [Genomera is still in beta; if you would like to access the forum, email eri@genomera.com.] I will also be holding a tweet-up in the Bay Area (date tbd) to meet and chat with our local participants.

Now, for the big announcement! Genomera is holding a competition for “Next Citizen Science Study.” (Details after the jump.)  The lucky winner will have their study hosted on the Genomera platform and will receive a 23andMe Complete Edition ($499 value).*

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23andMe, Alzheimer’s disease, and ApoE

Like other early 23andme customers, I’ve been struggling to find something interesting to do with my genetic results. After quickly learning [what kind of earwax](http://www.nytimes.com/2006/01/29/science/29cnd-ear.html) I’m predisposed to have, the path fades out amidst a tangle of SNPs.
Here’s an example of a typical quest, and its results.
It is well known that particular variants of the ApoE gene, which is found on chromosome 19, are associated with an [elevated risk of Alzheimer's ](http://www.nia.nih.gov/Alzheimers/Publications/geneticsfs.htm)disease. Other variants are associated with reduced sensitivity to statins, which are commonly used to lower cholesterol in patients at risk for heart disease. [Lab Tests Online](http://www.labtestsonline.org/index.html) provides a good, brief description of how [genetic testing of the ApoE gene](http://www.labtestsonline.org/understanding/analytes/apoe/test.html) can be used in mainstream medical practice.
Reporting an upcoming Wired story on a different topic, I recently visited an M.D. outside Denver who takes an aggressive approach to longevity treatment, and found that he routinely orders ApoE tests for his patients, as part of a panel of 11 genetic markers that costs about $500. He told me that if I wanted just the ApoE results, I could get them for about $90.
But who needs to pay by the gene when you’ve got 23andme? More than 600,000 SNPs for $1000 bucks is awfully cheap compared to $90 for a single genetic test, or so it seems.
I began hunting around the Web. I quickly discovered that I was following in the footsteps of Mark Fletcher, also an [early 23andme adopter](http://www.wingedpig.com/archives/2007/12/23andme_results_266.html). When I read Fletcher’s entry, I knew I had found a fellow traveler. Like me, Fletcher immediately wrote to 23andme upon getting his results, asking if he could download them in a more convenient format for analysis. He got the same email back that I did:
> At this time 23andMe does not have a way to give customers their genetic data on a CD, flash drive or other downloadable or stored format. But we are working to make that possible, and hope to be able to distribute raw data to our customers in the near future.
> Regards,
> The 23andMe Team
There is of course something unconvincing about this answer. Having launched a company premised on giving consumers access to their genetic data, it is hard to believe that 23andme can’t manage to make this data available in a standard, easily downloadable format. But they are just beginning, so let’s cut them some slack. Besides, we are curious about ApoE.
Like Mark, I first consulted the great [SNPedia](http://www.snpedia.com/). Here, I learned that ApoE variants, known as alleles, are indicated by the following SNPs:
> ApoE2 allele = rs429358(T) + rs7412(T)
> ApoE3 allele = rs429358(T) + rs7412(C)
> ApoE4 allele = rs429358(C) + rs7412(C)
That’s just what I needed to know. I went to 23andme and entered rs429358 into the Genome Explorer. My results:
Then I entered the rs7412 into the Genome Explorer. My results:
According to SNPedia, another SNP, [Rs4420638,](http://www.snpedia.com/index.php?title=Rs4420638) is relevant to my quest. Says SNPedia:
> One form of this SNP is very commonly inherited together with the APOE variant ApoE4 and thus predicts its presence.
So I searched on Rs4420638. My results:
Mark went on a largely parallel journey, ending in similar [non-satisfaction](http://www.wingedpig.com/archives/2007/12/23andme_and_snpedia_267.html).
Mark Fletcher says he spoke to another 23andme user who had a no call at the Rs7412 location. Today I received an email from yet a fourth user who had a no call at this location, too. So far, 23andme is zero for four at this SNP.
Like many early adopters, my interest in sequencing my genome is driven more by intellectual curiosity than by pressing health reasons. So I’m hoping that George Church gets his [Personal Genome Project](http://www.technologyreview.com/BioTech/wtr_16169,259,p1.html) geared up quickly. I’ve registered to participate.
But for now, I’m looking for ways to make my 23andme results more relevant. I welcome suggestions.

Posted in Personal Projects | Tagged , , | 3 Comments