27 April 2011

Let the games begin

Earlier today, Pacific Biosciences (Menlo Park, CA) announced that they are now shipping their commercial single molecule, real-time PacBio RS sequencing systems. In the press release, PacBio claim that their new technology "allows customers to obtain results in less than a day", compared to the week+ it takes to obtain data from other sequencing technologies. While papers, talks, and videos of PacBio technology has certainly created a buzz among researchers, it will be interesting to see how this step affects business. NASDAQ:PACB stock closed at 11.60 today, lower than their $16 starting share price last October when they IPO'd.

26 April 2011

NGS in the clinic

Not quite there yet, but it's a step in the right direction: Whole-Genome Sequencing Reaches Clinic. With a flurry of recent papers on tumor sequencing, it's not surprising that the clinicians predict cancer to be the first major application for NGS in a clinical setting.

As we move forward with the technology, I find it interesting to see how people handle the information that is generated. In the case reported here, researchers did not seem prepared to follow up on this issue:
"Genotyping of the patient's mother and absence of a cancer history in the father suggested that the TP53 mutation had arisen spontaneously rather than being inherited. However, the patient could have passed it on to her children. Studies by Wilson and colleagues along with previous research indicated that defects in TP53can cause or promote cancer.
The researchers reported that they communicated the potential risk to next of kin, encouraging them to seek genetic testing and counseling. However, a confidentiality "firewall" included in the research protocol prevented the research team from learning whether the children acted on the recommendations."

As was seen with direct-to-consumer genomics, it's not always clear how patients, physicians, and family members will use the data, and it is important for researchers to consider the implications of releasing such information prior to actually doing so.

24 April 2011

Happy Easter!

"[Chocolate] bunnies should be eaten ears first, according to 76% of Americans."
Given this Easter Infographic by DegreeSearch.org, I'm not surprised that my local Safeway ran out of Cadbury cream eggs yesterday.

22 April 2011

Big Brother is watching you

iPhone Location Tracker by Alasdair Allan and Pete Warden
The Bad:

"The most immediate problem is that this data is stored in an easily-readable form on your machine. Any other program you run or user with access to your machine can look through it.
The more fundamental problem is that Apple are collecting this information at all. Cell-phone providers collect similar data almost inevitably as part of their operations, but it’s kept behind their firewall. It normally requires a court order to gain access to it, whereas this is available to anyone who can get their hands on your phone or computer.
By passively logging your location without your permission, Apple have made it possible for anyone from a jealous spouse to a private investigator to get a detailed picture of your movements."

Before you start stalking people, note that:
"As far as we can tell, the location is determined by triangulating against the nearest cell-phone towers. This isn’t as accurate as GPS, but presumably takes less power. In some cases it can get very confused and temporarily think you’re several miles from your actual location, but these tend to be intermittent glitches."

21 April 2011

Can't solve a problem? Crowdsource it!

Harder. Better. Faster. Stronger. Daft Punk are not the only people striving from progress. Biotech companies are on the lookout for innovative ways of pushing technological limits, and they're looking outside the company for answers. With prizes of $1 million for each competition with solutions judged quarterly, this exercise in crowdsourcing may prove expensive for Life Technologies, but the payoffs (fast turnaround of innovative solutions that may greatly improve performance benchmarks of new technology) just may be worth it.
Life Technologies Grand Challenges