Personal Genomes in Clinical Care. Quake paper is a waste!

With all due respect to the scientists involved in analyzing Stephen Quake's genome in clinical context.

You did a major league $h!tty job.

No offense.

I can only assume this based on what you reported in the lancet paper.

Start by asking yourself.

"Is Stephen healthier because of what that genome and clinical assessment added to his care?"

I am speaking precisely on this topic at the Consumer Genomics Conference on June 3rd at 830 AM. So I will hold off on all my arguments....But,

The Paper
even says

"We noted that most of the sequence information is difficult to interpret, and discussed error rates"

Ummm, ok. Nice counseling session.

"patients with whole genome sequence data need information about more diseases with a wide clinical range"

Perhaps that person could actually be a physician, maybe a generalist?

"For this we offered extended access to clinical geneticists, genetic counsellors and clinical lab directors"

Nice! Joubert's is not Gilbert's is not Plavix. Thanks for stopping by.

I did appreciate that your paper calculated pretest probabilities. Unfortunately these were based on a pedigree which had no ethnicity and incomplete clinical data.

1. No Glycohemoglobin to evaluate for diabetes risk or maybe even diagnose it
2. No Iron Studies to evaluate for Hemochromatosis, yet you state genes may set him up for it.
3. No documentation of a physical exam including DRE for prostate hypertrophy/cancer or PSA
4. No dietary history? No Smoking history? No social history?

Shall I go on?

You show increased risk for Diabetes post test as well as prostate cancer, obesity, CAD, MI, Asthma, NHL, RA (no ESR/CRP/CCP?)

You projected an increased risk for 7 and decreased for 8. Yet no Assessment of MCI etc in Alzhemiers disease? My god, you did a stress test in an asymptomatic patient who exercises daily.

"Although the methods we used are nascent, the results provide proof of principle that clinically meaningful information can be derived about disease and response to drugs in patients with whole genome sequence data"

Translated: We made up a system and used novel DNA results to hypothesize about disease risk using research fellows, computer programs an excellent cardiologist (Not a GP) and an Echo machine.......But we skimped on the physical exam, use of primary care doctors, complete blood counts and other clinically useful testing and procedures.

I admire your efforts, but

A. You have missed the boat in using not all the tools at hand
B. By being Genome-centric, we miss the clinical picture.

"Although no methods exist for statistical integration of such conditionally dependent risks, interpretation in the context of the causal circuit diagram allows assessment of the combined effect of environmental and genetic risk for EVERY individual"

Translation: Nothing exists statistically to evaluate disease interaction and how it may increase risks of interlinked disease.

Ask yourself, "What have we done to make Stephen Quake healthier from this test?". Other than hype the use of a genome clinically?

This paper was all genome and NO CLINICAL ASSESSMENT!

The Sherpa Says: The only thing of note that is important here is the CYP2C19 data.......
I have seen abnormal CGH data in a child with severe developmental delay come directly from a high functioning mother who was a power litigator. The genome scan as it stands now is noise. It also requires a full team a month to intepret. Clearly not ready for medical prevention or prognostication, sorry.

New play about Marinetti and Mayakovsky in Minneapolis (May 14-23)

M²: Mayakovsky and Marinetti

May 14 – 23, 2010
Open Eye Figure Theatre, Minneapolis

Presented by Theatre Novi Most:

In the first decades of the 20th century, Vladimir Mayakovsky and Filippo Marinetti were among the rebellious few who saw, in the automobile and modern warfare, the pinnacles of human creativity and ingenuity. They were the naughty, foolish, self-crowned kings of Futurism — and they agreed on virtually nothing. Set in our near future, M(2) sees these two magnetic personalities meet again to relive the past and finish unfinished arguments. Based on historical letters, poems and texts by Mayakovsky and Marinetti.

Written by Vladimir Rovinsky with Felip Costaglioli
Directed by Lisa Channer & Vladimir Rovinsky

CAST
Vladimir Rovinsky
Stephen Pearce
Sasha Gibbs
Billy Mullaney
Julianna Drajko

DESIGNERS
MULTIMEDIA David Steinman
SOUND Dan Dukich
LIGHTS Robert Perry
COSTUMES Amanda McGee

Presented at Open Eye Figure Theatre
506 E. 24th St., Minneapolis, MN 55404

General admission tickets are $12.
Student tickets are $10.
For tickets, please visit http://www.theatrenovimost.org

more info

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Landslide on Mars triggered by an impact | Bad Astronomy

mars-impact-avalancheUniverse Today is reporting that a recent landslide on Mars looks to be triggered by a small (under 1 meter) rock hitting the surface of the planet. The landslide is less than three years old, and a new impact crater near the top appears to be the culprit.

Go to the UT article to get details. And look at the bigger version there of the image taken by the HiRISE camera; there’s a much larger crater near the bottom of the slide, and you can see where the dust rolled into it and up the far slope of the crater wall, but only partway! It’s yet another amazing shot of the dynamic surface of this nearby world.


Moon Walkers Briefed On Internal NASA Study Results (Update)

Keith's note: ESMD AA Doug Cooke briefed Neil Armstrong and Gene Cernan today via telecon on the results of NASA's internal exploration working group studies. No word yet as to when the rest of us will learn what Doug told Armstrong and Cernan - perhaps next week a this Senate hearing on 12 May?

Reshaped spaceflight plan gains support, MSNBC

"Nelson has arranged a high-profile Senate hearing on the future of U.S. human spaceflight for May 12, just two days before the shuttle Atlantis is scheduled to lift off on its final trip to the International Space Station. Among those who may testify are Apollo astronauts Neil Armstrong and Gene Cernan, the first man and the last man to walk on the moon."

Keith's update: The witnesses for Wedensday's hearing have been announced: Holdren, Bolden, Armstrong, Cernan, and Augustine.

Bill Gates Funds “the Most Benign Form of Geoengineering”: Ships That Spray Seawater To Seed Clouds | 80beats

cloud-seedingBill Gates is getting serious about geoengineering. Back in January, after the failure of governments at the Copenhagen Climate Change summit to do anything serious, the billionaire former head of Microsoft announced he’s give nearly $5 million of his fortune to fund research into geoengineering projects. Recently he announced his first concrete foray into the field: giving $300,000 to project that would spray seawater into the sky, seeding clouds that would hopefully block some of the sun’s UV rays.

The machines, developed by a San Francisco-based research group called Silver Lining, turn seawater into tiny particles that can be shot up over 3,000 feet in the air. The particles increase the density of clouds by increasing the amount of nuclei contained within. Silver Lining’s floating machines can suck up ten tons of water per second. If all goes well, Silver Lining plans to test the process with 10 ships spread throughout 3800 square miles of ocean [Inhabitat].

Most of the major geoengineering ideas that have been proposed—launching a reflective shield into space, artificial trees to pull carbon dioxide out of the air—are extremely expensive and difficult.

However, a study last year calculated that a fleet of 1,900 ships costing £5 billion (about $7.5 billion) could arrest the rise in temperature by criss-crossing the oceans and spraying seawater from tall funnels to whiten clouds and increase their reflectivity [The Times].

Unlike, say, seeding the sea with iron, seawater spraying doesn’t involve dumping additional material into the environment, so it would require less arduous permit-getting to test. And as opposed to the plans to put particulates in the clouds, seawater spraying would be easier to shut down and wouldn’t affect weather patters for quite as long.

Armand Neukermanns, who is leading the research, said that whitening clouds was “the most benign form of engineering” because, while it might alter rainfall, the effects would cease soon after the machines were switched off [The Times].

Related Content:
80beats: With $4.5 Million of Pocket Change, Bill Gates Funds Geoengineering Research
80beats: Bill Gates Patents a Device Aimed at Halting Hurricanes
80beats: Iron-Dumping Experiment Is a Bust: It Feeds Crustaceans, Doesn’t Trap Carbon
DISCOVER: 5 Most Radical Ways to Squelch a Climate Crisis (photo gallery)

Image: John McNeill


NCBI ROFL: Teaching may be hazardous to your marriage. | Discoblog

"Kenrick et al.'s experiments demonstrate that men who view photographs of physically attractive women or Playboy centerfolds subsequently find their current mates less physically attractive and become less satisfied with their current relationships. What then would be the cumulative effect of being exposed to young, attractive women on a daily basis? Would there be any real consequences to the men's dissatisfaction with their relationships? Secondary school teachers and college professors come in contact with more young women at the peak of their reproductive value than others do. The analysis of a large, representative data set from the United States indicates that, while men in general are less likely to be divorced than women, and secondary school teachers and college professors in general are less likely to be divorced than others, simultaneously being male and being a secondary school teacher or college professor statistically increases the likelihood of being divorced (p <.05)." Photo: flickr/anyjazz65 Related content:
Discoblog: NCBI ROFL: Boys and girls, please open your textbooks to page 69…
Discoblog: NCBI ROFL: Why Facebook is ruining your marriage.
Discoblog: NCBI ROFL: An ecological study of glee in small groups of preschool children. WTF is NCBI ROFL? Read our FAQ!