Nice try, I guess

I swear I haven’t been drinking, Officer. It was my gut flora!:
[Via NCBI ROFL]
Endogenous ethanol ‘auto-brewery syndrome’ as a drunk-driving defence challenge.

“For various reasons, the reliability of the results of forensic alcohol analysis are often challenged by the defence. One such argument for acquittal concerns the notion that alcohol could be produced naturally in the body, hence the term ‘auto-brewery’ syndrome. Although yeasts such as Candida albicans readily produce ethanol in-vitro, whether this happens to any measurable extent in healthy ambulatory subjects is an open question. Over the years, many determinations of endogenous ethanol have been made, and in a few rare instances (Japanese subjects with very serious yeast infections) an abnormally high ethanol concentration (> 80 mg/dl) has been reported… …With reliable gas chromatographic methods of analysis, the concentrations of endogenous ethanol in peripheral venous blood of healthy individuals, as well as those suffering from various metabolic disorders (diabetes, hepatitis, cirrhosis) ranged from 0-0.08 mg/dl. These concentrations are far too low to have any forensic or medical significance. The notion that a motorist’s state of intoxication was caused by endogenously produced ethanol lacks merit.”

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I had never thought of this excuse. So the driver is really drunk because of his intestinal bacteria. Right.

Of course, the law is driving while intoxicated. It never states HOW one became intoxicated. I would think that the judge would not care whether the high alcohol level came from drinking or from bacteria. The driver is still impaired and should not be driving.

Technorati Tags: Science

Complex applications often require significant testing

There’s many a slip ‘twixt spit and SNP: errors in personal genomics data:
[Via Genetic Future]

Peter Aldhous has a great piece of detective work in New Scientist, which has revealed a bizarre and sporadic glitch in the online software provided by personal genomics company deCODEme to allow customers to view their genetic data.

The glitch appears to be restricted to the display of data from the mitochondrial genome (a piece of DNA with a special fascination for genetic genealogists, since it is inherited almost exclusively along the maternal line). On several separate occasions the deCODEme browser presented Aldhous with a mitochondrial profile that was spectacularly wrong, differing from the profile in his raw data at 44 out of 93 positions.

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It looks like the software glitch may have been fixed but it required some very astute observations by a knowledgeable user. And this case was pretty obvious with so many errors present.

What would happen with errors that are more subtle? Particularly when the data may be used to make medical decisions? I figure that these things will be worked out eventually but in the meantime, there will be a very strong need to carefully vet the results from applications such as this.

Technorati Tags: Bioinformatics, Science, Technology

The Wild West for sequencing

Complete Genomics back in action after 6 month funding delay:
[Via Genetic Future]

Complete Genomics is finally back on the road towards fulfilling its promises of $5000 human genome sequences, after delays in obtaining funding for a massive new facility pushed back its plans by six months. The $45 million in funding it announced this week will be sufficient to build the new Silicon Valley facility, which the company claims will have the capacity to sequence a staggering 10,000 genomes over the course of 2010.

Complete Genomics is an unusual creature in the second-generation sequencing menagerie: instead of aiming to generate revenue by selling machines to researchers and biotech, Complete has an entirely service-driven business model. Basically, it aims to create a series of extremely automated sequence factories with a single input (human DNA) and a single output (an accurate and comprehensive list of all of the variants present in that sample’s genome), operating on a massive scale. All of the steps in between will be performed using in-house sequencing technology and analytical software.

It’s an audacious plan – but clearly it’s a plan with sufficient plausibility to convince investors to cough up $45 million in the middle of a major venture capital drought. If Complete can meet their ambitious goals for 2010 they stand to gain pole position in a field where the pay-offs are potentially massive, as the preferred providers of the raw genomic material for the new field of personalised medicine.

So, will it work? I spoke on the phone to Complete Genomics CEO Clifford Reid and company director Alex Barkas about their plans over the next 18 months.

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$5000 for accurate, whole genome sequences really changes the ball game. This makes it very easy to envision this process becoming very common. There are a lot of big ifs here that have to be overcome.

My worry with some of this is that we are talking about having great accuracy calling over 3 billion bases. In a commercial setting there are going to be pressures to take some short cuts . These companies will need careful vetting of their procedures and have strong quality control to assure accuracy. It would be a shame if someone makes medical decisions based on inaccurate information.

but if they can do this, we are entering a new era for human genomics.

Technorati Tags: Bioinformatics, Science