genomeboy.com

Complete Genomics may be a one-trick pony, but as Paul Simon would say, it turns that trick with pride:

Reid also took issue with the idea that CGI is a services business. “It’s not a services business — you can’t call us up and ask for services – we have a data business. This business is enabled by a dramatic new development in this industry. There is finally, for the first time, one organism, one type of data that can be produced in a standardized mechanism — it’s called a human genome.”

Reid draws a strong analogy to Google. “Google has one type of data called web documents, and produces one type of report called sorted list of documents, based on your query. We’re doing that for genomic data, taking the one type of data – the human genome — building a huge Google-like proprietary back end, that can take one input – human DNA – and produce one standardized output, a human genome report, a sorted list of variants. That is all about economies of scale.”

Let’s let Dr. Frank Baxter inaugurate the start of a new school year:

The standard treatment for infection with the hepatitis C virus is a grueling 48-week course of the antiviral drugs interferon and ribavirin that gives some patients flulike symptoms and severe depression. The treatment varies in its effectiveness, being much more successful in Americans of European descent than in African-Americans.A Duke University team has now uncovered the principal reason for the disparity between the races. It lies not in differing compliance to the treatment or access to health care, as some have assumed, but in genetics.Using a genetic test called a genome-wide association study, the Duke team, led by David B. Goldstein and John McHutchison, found that the coding at a single site on the DNA, out of the three billion sites in the human genome, made all the difference in people’s response to the treatment.

I suppose it’s all about what questions one chooses to ask.

[Hat tip: Linda]

The physicians and hospital leaders from Cedar Rapids told us how they have adopted electronic systems to improve communication among physicians and quality of care. Last year, they decided to investigate the overuse of CAT scans. They examined the data and found that in just one year 52,000 scans were done in a community of 300,000 people. A large portion of them were almost certainly unnecessary, not to mention possibly harmful, as CAT scans have about 1,000 times as much radiation exposure as a chest X-ray.“I was embarrassed for us,” said Jim Levett, a cardiac surgeon and the head of a large physician group. More important, the area’s doctors and clinics are turning that embarrassment into change by seeking out solutions to reduce the expense and harm of unnecessary scans.

That number of scans in Cedar Rapids may seem shocking, but there is nothing surprising about it. Nationwide, we do 62 million CAT scans a year for 300 million people. So Cedar Rapids’s rate was actually better than average. But all medicine is local. And until a community confronts what goes on in its own population — to the point of actually seeking the data and engaging those who can solve the problem — nothing will change.

James D. Watson on the Tropic topic of cancer:

Restarting the War on Cancer has to start at the top: in 1971, Congress decided that the president, not the head of the National Institutes of Health, should appoint the director of the National Cancer Institute. Yet like all too many outposts of the White House, the institute has become a largely rudderless ship in dire need of a bold captain who will settle only for total victory.

There’s been a fascinating back-and-forth going on in the genome blogosphere about the pre-publication of the Applied BioSystems (i.e., Life Technologies) whole-genome sequence of a Yoruba, the seventh published whole human genome (is this still correct?), although the Yoruba one was done twice. At MassGenomics last month, Dan Koboldt took the paper’s authors to task for not offering a comparison to Illumina’s earlier sequence of the exact same genome. ABI’s Kevin McKernan responded in the comments. Meanwhile, in a guest post at Genetic Future yesterday, Luke Jostins suggested that ABI’s paper was not entirely cricket (links by me):

What follows is idle speculation, and thus (hopefully) not slander. My guess is that SOLiD is attempting to reposition itself as the Low Coverage Sequencing Company. They have still failed to topple Illumina as the market leader, and I expect that they think if enough people start thinking of SOLiD as “the guys who did a good quality 18X genome”, all the people who found the low coverage 1000 Genomes Project work sexy will start looking to SOLiD. But to do this, they had to fudge a few things: get the coverage down by cutting out lots of reads, obfuscate the low quality of heterozygous calls, and give an overenthusiastic estimate of how cheap their technology is.

Ouch. And I thought the direct-to-consumer genomics debate was rough.

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As Jason notes, filmmaker Marilyn Ness has taken on the unenviable task of making a documentary about the Personal Genome Project. I reckon the only thing crazier would be writing a book about it.  Anyway, I happen to think this webisode in particular captures George Church’s ch’i and his whole family’s remarkable ability to live in the moment. And I think this clip hints at—and I say this with nothing but affection—what unrepentant dorks the ten of us are.