The genotyping will be done through 23andMe. We will order you a gift kit which will be delivered to your address. These gift kits include prepaid access to the 23andMe website for 12 months, so you can check up on the latest findings about your genetic variation as well. After this 12 month period, those features will expire automatically, you don’t have to cancel any subscriptions.

Our application form contains some standard questions (Where do you live? Does 23andMe deliver to your country? etc.) but also some details about your motivation, why you want to make your dataset available to the public and why your data might be of great interest (For example: Do you have a rare disease where research is lacking?). Additionally, we will also try to get people genotyped who are currently under-represented in publicly available data sets. Most data up to now is from WEIRDs: Western, Educated, Industrialized, Rich and Democratic people (most are probably male, too).

We would like you to deposit the final raw data, which you will then be able to download from 23andMe, into the openSNP database, ideally along with some phenotypic information about yourself. So please think about the possible consequences which may arise by doing so before you apply for one of the genotypings. The application process has some questions about possible consequences as well (just so we get a feeling of whether you know what you are doing). If you get your results, but then find the results too problematic to publish: That is fine. We are aware of this possibility and while it would suck for us as it means less data, you are the one who has the last word in this matter. Some information that might make you a bit more comfortable with the idea of sharing data: We won’t release the names of any applicants (whether successful or unsuccessful) and you can sign up to openSNP using a pseudonym, plus we don’t log any IPs used to access openSNP.

tl;dr

We offer you the chance to get genotyped through 23andMe for free if you are willing to share the data with the public. Here’s the planned schedule:

• Until 03/25/12 23:59 o’clock you can apply for a genotyping using this application form
• We select the lucky winners between 03/26/12 and 04/08/12 and get in contact with every applicant.
• Mid-April: You should receive the 23andMe-kits in your mail.
• End of May: You should receive the results of the genotyping, so you can upload the results to openSNP.

If you’ve got any questions regarding the application process, the schedule etc., just let us know using the comments or write us an email to info@opensnp.org. We will try to answer all of your questions as fast as possible.

Good luck,
wishes your openSNP-team!

The next video shows you how you can use the openSNP-frontend to enter your phenotype-data, what kind of information the individual SNP-pages can show you and how you can subscribe to the openSNP-RSS-feeds to be notified about the latest genotyping-files etc. A small new feature which is missing from the video as we implemented it after recording the video: The news-page features a tab that includes the latest publications on the SNPs we have in the database. And for all info-junkies: You can also subscribe to the latest publications using RSS.

The last video shows how you can query the APIs which we have implemented. Bonus-Content: This video includes the first preview on how you can use the Distributed Annotation System to visualize individual genotyping files! In short: You can use http://opensnp.org/das/sources to get a list of all DAS-sources we have with openSNP. Each source represents all SNPs we have of a single user, regardless of how many genotyping files a user has provided.

If you want to use a DAS-source in a genome browser, for example in MyKaryoView you can use the features-commmand of DAS. The link for this is http://opensnp.org/das/$user_id/features, where you have to replace $user_id by the ID of the user you are interested in. If you want to query SNPs between chromosomal positions using DAS you can use http://opensnp.org/das/$user_id/features?segment=$chromosome_name:start,stop. So http://opensnp.org/das/1/features?segment=1:1,1000000 will give you all my SNPs on Chromosome 1 between position 1 and 1000000.

If you want to see an example for a visualization using DAS look at the video below. The DAS features are still experimental. I will attend this DAS workshop to get some help with the final implementation, so if you have suggestions: Please let us know!

Enjoy playing around with this features. As usual: Let us know if you find any bugs we have missed!

Let’s start with the user-index, which can easily be accessed at http://opensnp.org/users.json. This includes the complete list of all openSNP-users and their names, their unique user-IDs and all the genotyping-files (with the unique genotype-IDs and the download-links). We hope that this makes an ideal entry-point if you are looking for genotyping-files and the user-IDs to further query the openSNP-database.

If you want to get genotypes of single or multiple users for a given SNP you can use the JSON endpoint at http://opensnp.org/snps/json/$snpname/$userid.json. Just replace $snpname by the Rs-ID you are interested in and $userid by the unique ID of the user you are interested in. For example: http://opensnp.org/snps/json/rs9939609/1.json gives you my genotype at Rs9939609. If you are interested in the genotypes of multiple users you can concatenate this into a single query by either using commas to provide multiple User-IDs (for example http://opensnp.org/snps/json/rs9939609/1,6,8.json) or by giving a range of user-IDs (for example http://opensnp.org/snps/json/rs9939609/1-8.json).

Similarly you can access all phenotypic information of a given user by using http://opensnp.org/phenotypes/json/$userid.json. Again: Just replace $userid by the unique ID of the user you are interested in. For example http://opensnp.org/phenotypes/json/1.json gives you all the phenotypic information I have entered about myself so far. Concatenating multiple users into one query works just as for the SNP/User-combinations by using commas (http://opensnp.org/phenotypes/json/1,6,8.json) or ranges (http://opensnp.org/phenotypes/json/1-8.json). In any case: If you request data of users or user/SNP-combinations that don’t exist the JSON-hash you will get back includes the key “error”, just like this.

This are all the options you can supply by using our JSON-endpoints right now. There are no API-keys and no rate limits. We will just see how it turns out and if any limiting of the access will be necessary in the future. We hope that this will allow more easily reusing the openSNP-data and you maybe have already some nice ideas for remixes/browser plugins/younameit. If you have any requests, which kind of JSON-endpoints you need or would like us to add, just let us know. We are currently experimenting with this JSON-stuff and are open for any critique, comments, ideas etc. If you want to help us to implement further features into openSNP: Please do so, we are open for everybody who wants to participate and want to invite you to do so. The source code is freely available and there is a Google Group/mailinglist where we discuss bug-fixing, new features etc. So you might want to join us there.

For those of you who speak german: You might be interested in our talk on the privacy implications of the coming post-genomics era, which we gave at the 0. Spackeriade. You can watch it on YouTube as well or download the video. Again: The slides can be found at SlideShare or as LaTeX-sources on GitHub.

Thanks for all who helped on the slides, gave us their feedback and of course all of you who approached us after the talks – in real life or via email – and had some ideas for new features. We already started to work those. Stay tuned to see some changes on openSNP in the next weeks.

Additionally Philipp and I will be in Berlin between 12/27 and 12/31. As we have mentioned before we will give a talk on openSNP and crowd-sourced genome-wide association studies at the 28th Chaos Communication Congress. The talk will be on 12/28 at 11 pm. This talk will be in english and there should be day passes, so if you are in town you can pay us a visit. If you are If you’re able to speak or understand German you can also pay a visit to the 0th Spackeriade which takes place on 12/29. We will talk about the implications of the post-genomics-era on privacy.

Thanks again for all your support, for voting for openSNP in the different contests we have entered, for sharing your data with us, for finding bugs, for spreading the word. Have some nice holidays and maybe we’ll see some of you for a beer in Berlin.

They have pledged up to 7000€ for ideas that promote open knowledge and open science – naturally, we had to apply!

What we’re trying to do with the money (if we win) is to give out free genotypings to people who can’t afford them, but still want to participate in the research. We could give out up to 35 genotypings with the money. Of course, just because we give anyone the money to get genotyped doesn’t mean that they have to publish it – we can’t force you to reveal potentially damaging information about you.

To win this contest we need your vote – you can vote here, the page is in German but you only have to activate the radio-button for project “02-Open (Citizen) Science durch mehr öffentlich verfügbare Genotypisierungen” (that’s us, translation: “Open (Citizen) Science through more openly available genotypings”) and then press the submit-button on the bottom of the page. You don’t necessarily have to supply any of the additional information (which seems to be for their statistics), but if you speak or write German I’m sure they would appreciate the input!

We’re thrilled to have won the Mendeley/PLoS Binary Battle and we’re sure we couldn’t have done it without you guys. Thanks for your votes & your continuing support!

The openSNP-team

We also want to send our congratulations to PaperCritic, which came in second, and rOpenSci which is the second runner up. Both are definitely worth a look (as are all the other entries of the binary battle as well). It is really great to see what creative minds can build with open data and open APIs.

As Philipp is currently writing his master thesis (and I’m also working for the last exam of this year) there hasn’t been much new in terms of features in the last weeks. But this should end in a week or two and we already have some plans. And we are also applying for some small funding via the german Wikimedia Foundation and their WissensWert-contest, which funds projects that support open knowledge. We are trying to get the funding in order to get data of more people who are into sharing their data genotyped (and may lack the financial resources to get it done). This could lead to some more data sets on openSNP.

Thanks a lot ! And if you have any questions: Just contact us, we are really looking forward to get in touch with you.

If you want to help us, give us your vote and spread the word. Thanks a lot!

We have finally taken the time to analyze some of the results of the survey on sharing genetic information we did before we started working on openSNP.

Some general information: Overall 229 people participated in this survey. About 25% of participants gave their chromosomal sex as XX, 74% as XY and there are no differences in terms of usage of DTC-companies between those groups. The mean age of the participants is ~33, the youngest being 15, the oldest being 70. Over 80% of participants gave their ethnicity as caucasian.

Nearly 40% of all participants have already used a DTC-company to get themselves genotyped, further 30% plan to do so while 30% don’t plan to get genotyped. This high amount of participants that got themselves genotyped seems to be the result of the ways we spread the survey: We posted it at the 23andMe-community, sent it to the DIYBio-mailing list and some bloggers out of the fields of genetics/personal genomics also wrote posts on the survey (again: Thanks a lot for your support). We also spread the survey using Twitter, Facebook and Google+. We chose this approach as our goal was not to survey a representative sample, but to assess the demand for a service like openSNP.

68% of all participants said they would agree to share data with their DTC-company, no matter if it shared the data with others, 26% would agree to share, given that the company didn’t distribute the data to others and about 7% were not willing to share at all. No real surprise here: Those who have already been genotyped or are planning to get genotyped are more willing to share than those who don’t plan to. It would be interesting to know if people don’t want to get genotyped because they don’t want to share their data with a company (e.g. Don’t trust DTC-companies).

General reasons (not) to share

My girlfriend says I'm not allowed to display the mean of scaled answers, but then again, she also objects to the bars having shadows, so I wouldn't listen to her.

We also asked a few questions on why people would or wouldn’t share their data with others. Each question could be answered by making a selection on a five point scale, ranging from 1 (strongly disagree) to 5 (strongly agree). There are quite large differences in reasons why people would like to share. The most agreed upon answer is to help scientists with their work (mean = 4.53, median = 5), followed by personal benefits (mean = 3.64, median = 4) and curiosity (mean = 3.5, median = 4). Over half of all people strongly disagree with personalized advertising as a motivation for sharing data (mean = 1,72, median = 1).

There is less diversity in reasons not to publish the results, although the median of “fear of discrimination” and targeted advertising show that over half of all participants at least agree on those questions (medians = 4), while the medians of the questions about consequences for closely related and privacy breaches are in general more neutral (medians = 3).

Differences between customers/non-customers?

We also used an ANOVA and Tukey’s range test to see if there are any differences in agreeing/disagreeing on those questions between survey participants who have already gotten genotyped, those who plan to get genotyped and those who don’t plan to get genotyped. On the topics why people would share their data we found significant differences for the questions regarding helping scientists, having personal benefits and curiosity. Participants who have already gotten genotyped do agree more on those questions, compared to those who don’t plan to get genotyped. For out of curiosity and to help scientists this is even true for comparing the don’t plan to-group to the plan to-group, with the latter one agreeing more.

Regarding reasons not to share genetical information we find similar results: Those who don’t plan to get genotyped agree significantly more on all four questions, compared to those who have gotten themselves genotyped.

Summary (tl;dr)

Although there are no big surprises in those statistics, it is great to get some results regarding our own guesses:

• People who are already customers of Direct-To-Consumer testing companies (or at least plan on becoming a customer) are more likely to share their data with the company, even if the company allows others to use the data.
• Customers of DTC testing companies do agree more on questions regarding reasons to share genetical information than those participants who don’t plan to become customers.
• Those who don’t plan to get genotyped do agree more on topics regarding reasons not to share their data than those who are already genotyped.

It seems that participants who (plan to) get genotyped are feeling more optimistic about the benefits of sharing their data with the DTC company as well as the public and see less problems in possible reasons not to share their data with others, compared to those who don’t plan to get themselves genotyped. And the same seems true vice versa, of course: those who do not plan to get themselves genotyped will agree more to questions concerning the risks of sharing, while scoring lower on questions concerning the possible benefits of doing so.

It’s too bad that we can’t find out (given the current survey) if this is more than correlation. Do people feel more optimistic and lose some of their fears about sharing their data, after they’ve gotten genotyped? Or do they get themselves genotyped because they feel more optimistic about it in the first place (which seems more likely to me)?

We will explore the data set a bit more in the future. Do you have ideas what things we should take a look at?

We are participating in the Mendeley/PloS Binary Battle. Over 40 applications that make use of the Mendeley and PLoS APIs were submitted. A selection of 11 submissions will get reviewed by some great judges and those get the chance to win 10.001 US $. Were happy that we made it into this final selection. But you should also check out the other applications, there are some great tools.

We are also participating in the WissensWert-Contest of the german Wikimedia foundation. They fund ideas that make use of open licenses and try to support Free Knowledge with up to 5000 €. We applied for the funding to get some people genotyped that would like to make their results freely available, but lack the financial resources to pay for it themselves (this is a thing we quite often encountered). With the money we could get over 30 people genotyped by a DTC-company. Making those results available to the public would provide a great resource for people who are interested in personal genetics.

Features

There is not much new at openSNP in terms of features, but: Currently we are working on implementing the Distributed Annotation System (DAS) into openSNP. DAS is a protocol that has been around for ~10 years and it allows the delivery of genetic information in a way that can be easily reused and makes remixing the data really easy. For example the UCSC Genome Browser and ENSEMBL make heavy use of it to display sequences, along with their annotation (SNPs, genes, diseases etc.). Rafael Jimenez and Manuel Corpas also use the DAS-protocol for their MyKaryoView, which is a genome browser that is meant to be used with genotyping data.

We are also working on adding support for zipped files, but currently Philipp and I are facing a high workload at our universities. If you are interested in helping out and doing some coding in Ruby on Rails: Feel free to do so. All of our code can be found at GitHub and we have a mailing list.