What's the biggest limitation to next-gen sequencing?

18% Library preparation
17% Read length
13% Multiplexing
45% Data storage/analysis
5% What limitation? It's a perfect process already.

Audience/reader poll results from GenomeWeb's daily newsletter. These results are from last week's poll.

..."Not a single state posted a decrease in obesity, and three of every ten children living in 30 states are overweight or obese, said Jeff Levi, PhD, executive director of the Trust for America's Health, which compiled the "F as in Fat" report with the Robert Wood Johnson Foundation.

Overall, two-thirds of Americans are either overweight or obese, the report found.

Americans' access to healthcare, the $ costs of healthcare reform, swine flu colonizing the world over - all of these are far less frightening than the fact that we are greedily committing suicide-by-caloric-intake.

We are, quite literally, eating ourselves to death.

Before you read the coverage, fix your gaze on this beauty of a closing sentence:
"By way of contrast, in 1991, no state had an obesity rate above 20%."

In less than 2 decades, states obesity rates continue to rise by 1+% PER YEAR and NOT A SINGLE STATE posted a decrease in obesity rates over the past year.

Forget outsourcing. Forget the innovation economy. Forget fixing science/math education. If we don't focus on fixing obesity NOW, in 3 more decades there won't be enough of a workforce left to worry about the economic viability of this federation of states.

More really scary stuff from Medpage coverage of the Robert Wood Johnson Foundation's frightening "F as in Fat" report:

"Sixteen states experienced an increase in obesity rates for the second year in a row, and 11 states experienced an increase for the third straight year.

Moreover, America's vast waistline is "a big contributor to the skyrocketing healthcare costs in the U.S. How are we going to compete with the rest of the world if our economy and workforce are weighed down by bad health?" Dr. Levi asked.

Mississippi was once again the fattest state with 32.5% of it adult residents obese. But Mississippi was not an anomaly in the region -- eight of the top ten states are in the South.

Here are the report's top 10-ranked by percent of obese adults:

Mississippi (32.5%)
Alabama (31.2%)
West Virginia (31.1%)
Tennessee (30.2%)
South Carolina (29.7%)
Oklahoma (29.5%)
Kentucky (29.0%)
Louisiana (28.9%)
Michigan (28.8%)
(tie) Arkansas (28.6%) and Ohio (28.6%)
According to the report, adult obesity rates now exceed 25% in 31 states and exceed 20% in 49 states and Washington, D.C."

"Principles of Open Source software did not prove to be useful in open drug development. ... Crowdsourcing will not advance quantum physics," he writes. "Open Science in its fullest form is not an issue that scientists can truly solve by themselves."

Open Science's Greatest Need Is ... Non-Scientists? | The Daily Scan | GenomeWeb

Please read the great post examining models of 'open science by Pawel.

While I agree with much of the chewy content goodness, I'm not sure I can sign on to the bit about 'principles of open source software did not prove to be useful in open drug development' being entirely true.

The capability for open source to be useful in things like crowdsourcing new theories of genetics+anthropology (genoanth) in addition to drug development hasn't been proven, but it certainly hasn't been disproven.

Especially in health analytics/personal biometrics ("Me-trics" or the #quantifiedself) Joe the Plumber hasn't had access to the kind of data about ourselves (much less others) that we'd need to share and contribute to an open-source public health development initiative.

Cancer-survivor communities like ACOR (@gfry, @ePatientDave thanks again for the heads up here) COULD in theory be used to open-source new treatments. In fact, the community/listserv members ARE using the list this way, but the 'establishment' isn't paying much attention.

PatientsLikeMe.com, however, has made open-sourcing one's health data relatively easier, lowering barriers to entry by putting metric tracking/analytics tools in the hands of patients.

Despite my fan-girl-ism for PLM, there are issues with the service, which isn't 'pure' opensource (in my opinion) - I cannot opt out of having my data anonymized and sold, and I can't demarcate if it's used for corporate gain versus nonprofit research purposes. I also can't throw my data open for the world to use/view at will if I so choose.

If I was designing an open-science, open-source health development initiative (product or drug), I'd go after a software installlation like that offered by Palantir Tech. Then I'd recruit survivors and start sharing data nodes. Then I'd motivate the community to go to work analyzing the hell out of the data intersection points for sparks of potential relevance. Then each promising x+y would have to be examined for causation/correlation.

If I wanted to cure a disease like Parkinson's, or even come up with EBP support (and EBP here would really be E2BP, for Evidence-based practice+ Experiential-based practice) for a new clinical guideline to impregnate into real-world practice, this is how I'd go about it.

I digress. But Pawel Szczesny (Freelancing Science) is right about one very big issue here - open science (or open source, or open health) absolutely require participation outside traditional professional gradients to succeed.

Talent without a pedigree counts for something here. Let's make sure we don't continue to make the mistake of discounting the value of experiential knowledge, which is open science (and 'open health's) most underutilized asset.

Then a new technology emerges and creates the possibility for a radically different organizational architecture, using an entirely different combination of skills and relationships. The only way to get from one organizational architecture to the other is to make drastic, painful changes. The money and power that come from commitment to an existing organizational architecture actually place incumbents at a disadvantage, locking them in. It’s easier and more effective to start over, from scratch.

Link via @ahier.

On Wednesday, July 1, 2009, Obama will be holding an online town hall meeting on health care reform to answer some common questions. People can submit questions via Facebook, YouTube, and Twitter (twitter hashtag: #WHHCQ)

President Obama will answer common questions. If enough of us ask, maybe we will get a verbal commitment from Obama to support our health data rights.

Here are a couple of twitter examples:

Obama, will #hcreform support my right to access and use #myhealthdata ? #WHHCQ

Hi Prez Obama! Will #hcreform support humans’ access to their own health data, kinda like how they access their pet’s data? #WHHCQ

Please RT. Wednesday July 1st on Twitter. #WHHCQ.

Participate in President Obama's online town hall meeting on healthcare reform. Let's storm the tweetstream folks.

Surely you can donate 140 characters?