Saturday, December 31, 2011

28c3: Crowdsourcing Genome Wide Association Studies (English)

Crowdsourcing Genome Wide Association Studies

Freeing Genetic Data from Corporate Vaults

It was only a couple of years ago that generating genetic information about individuals was expensive and laborious work. Modern techniques have drastically cut cost and time needed to get an insight into one's genome and have ultimately led to the formation of personal genetics companies – like 23andMe, deCODEme and others – that now offer direct-to-customer genetic testing. With a price tag of those tests starting at about 100 €, the number of people that do such tests is on the rise. By now, 23andMe alone has over 100.000 paying customers, with over 60.000 of them willing to donate their genetic data and to actively participate in research projects by filling out surveys, e.g. on their medical histories. This has resulted in a high-quality dataset with genetic information of 60.000 individuals. The best part: The data has already been paid for by the participants in the research.

Who would not love to get their hands on data like this? Unfortunately, the data sits locked away in corporate vaults, inaccessible to interested (citizen) scientists. But what if we could change this?

We've created openSNP, a central, open source, free-to-use repository which lets customers of genotyping companies upload their genotyping data and annotate them with phenotypes. OpenSNP provides its users with the latest scientific research on their genotypes and lets scientists download annotated genotypes to make science more open...

You can find more below. Also there is explanation about what is crowdsourcing.
Ниже есть продолжение.

...We feel that research projects all over the world and science in general would benefit from a rich, freely available source of linked, genetic data. And although genome wide association studies need a minimum number of participants to be able to find significant variations, it is not necessary to have 30.000 participants in your study. There are many publications with significant results with a total number of participants of less than 5000 individuals. Given the current number of 23andMe customers, one only needs 5 % of them to participate in freely sharing their genetic information together with basic information on some medical conditions or other variations to reach the critical mass to be able to perform simple association studies! While many people have already started to publish their results on GitHub et al. and movements like DIYBio are starting to take off, there are no real efforts to create a repository to centrally collect this kind of data.

But what if one could create an open platform to collect this kind of linked data? Is it possible to perform crowd-sourced association studies to create new knowledge about our genes? With the creation of openSNP we have tried (and are still trying) to find out.

Crowdsourcing is the act of sourcing tasks traditionally performed by specific individuals to a group of people or community (crowd) through an open call.

Jeff Howe established that the concept of crowdsourcing depends essentially on the fact that because it is an open call to a group of people, it gathers those who are most fit to perform tasks, solve complex problems and contribute with the most relevant and fresh ideas...

The term "crowdsourcing" is a portmanteau of "crowd" and "outsourcing," first coined by Jeff Howe in a June 2006 Wired magazine article "The Rise of Crowdsourcing". Howe explains that because technological advances have allowed for cheap consumer electronics, the gap between professionals and amateurs has been diminished. Companies are then able to take advantage of the talent of the public, and Howe states that "It’s not outsourcing; it’s crowdsourcing." A less commercial approach was introduced by Henk van Ess in September 2010: “Crowdsourcing is channelling the experts' desire to solve a problem and then freely sharing the answer with everyone..”.

Crowdsourcing is a distributed problem-solving and production model. In the classic use of the term, problems are broadcast to an unknown group of solvers in the form of an open call for solutions. Users—also known as the crowd—typically form into online communities, and the crowd submits solutions. The crowd also sorts through the solutions, finding the best ones. These best solutions are then owned by the entity that broadcast the problem in the first place—the crowdsourcer—and the winning individuals in the crowd are sometimes rewarded. In some cases, this labor is well compensated, either monetarily, with prizes, or with recognition. In other cases, the only rewards may be kudos or intellectual satisfaction. Crowdsourcing may produce solutions from amateurs or volunteers working in their spare time, or from experts or small businesses which were unknown to the initiating organization...

The difference between crowdsourcing and ordinary outsourcing is that a task or problem is outsourced to an undefined public rather than a specific other body. The difference between crowdsourcing and open source is that open source production is a cooperative activity initiated and voluntarily undertaken by members of the public. In crowdsourcing the activity is initiated by a client and the work may be undertaken on an individual, as well as a group, basis. Other differences between open source and crowdsourced production relate to the motivations of individuals to participate.

...Grover explained in an interview that crowdsourcing eliminates a financial barrier that prohibits most people from participating in art, as "Internet real estate is essentially free." Grover finds that the primary appeal of crowdsourcing is the satisfaction that is obtained through working with a community.

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