Forum: A global network of millions of genomes could be medicine’s next great advance. | Beacon
gravatar for William
3.2 years ago by
William4.2k wrote:

Internet of DNA

A global network of millions of genomes could be medicine’s next great advance.

Availability: 1-2 years

Noah is a six-year-old suffering from a disorder without a name. This year, his physicians will begin sending his genetic information across the Internet to see if there’s anyone, anywhere, in the world like him.

Do you think this will happen within 2 years?


This is the technical implementation I think  that they are talking about:

The Beacon project is a project to test the willingness of international sites to share genetic data in the simplest of all technical contexts. It is defined as a simple public web service that any institution can implement as a service. The service is designed merely to accept a query of the form "Do you have any genomes with an 'A' at position 100,735 on chromosome 3" (or similar data) and responds with one of "Yes" or "No." A site offering this service is called a "beacon".

So it just a federated query over multiple large genomics (+ phenotypes) data sets. Full genomes are not centralized, or moved, so privacy is less of a concern.

global beacon forum internet genome • 2.2k views
ADD COMMENTlink modified 3.2 years ago by Mary11k • written 3.2 years ago by William4.2k
gravatar for Istvan Albert
3.2 years ago by
Istvan Albert ♦♦ 76k
University Park, USA
Istvan Albert ♦♦ 76k wrote:

What is important to recognize IMHO is that more data does not actually mean better information. I for one think that we need better and longer reads before it is worth sequencing every genome out there.

We are still in the learning phases of what to do and how to do it. Lots of bad data could be worse than no data at all. It may divert resources from making long term progress to  short term gains.

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by Istvan Albert ♦♦ 76k
gravatar for Devon Ryan
3.2 years ago by
Devon Ryan78k
Freiburg, Germany
Devon Ryan78k wrote:

It's telling that they only get to the privacy issue in the antepenultimate paragraph. That's the reason I would say, no, this won't effectively happen in 2 years (I'll mention that this is in addition to what Istvan wrote). There's rapid evolution in what constitutes informed consent in terms of DNA testing (e.g., see the here) and I can't really see that evolution reaching any sort of steady state in the next year or so. If they want answers, it's faster to just contact a diagnostics company. I was at one about a year ago and they have a database like this of all of their samples that they use for filtering and querying. Since that's a private company with no data sharing the consent wording and legality becomes rather easier.

Some sort of walled garden approach is likely the only reasonable path for this sort of thing. The development of that is going to be tricky and time consuming, given the multiple iterations it's going to end up going through.

ADD COMMENTlink written 3.2 years ago by Devon Ryan78k
gravatar for Mary
3.2 years ago by
Boston MA area
Mary11k wrote:

The day I met Haussler, he was wearing a faded ­Hawaiian shirt...

David Haussler is always wearing a Hawaiian shirt. Last week I saw a talk by him where he put a suit jacket over it, though. Heh.

It was a good talk about how we are going to have to represent all the individual genomes. How currently we have one path we call the "reference" genome, but any alternate paths are treated as "second class citizens" in the software. I think this is an area that those of us on the software end of this debate have to be very attentive about. We need more flexible tools, better visualizations, and huge capacity because of all of this.

ADD COMMENTlink written 3.2 years ago by Mary11k

Hi, any chance the talk is online in video form or summarized somewhere? I'd be interested in hearing more. Thanks!

ADD REPLYlink written 3.1 years ago by Nancy Ouyang170

I don't think it was recorded, but I'll check.

ADD REPLYlink written 3.1 years ago by Mary11k
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