Sunday, February 10, 2013

Marseille Police Facing $1.3 Million Price Tag for Three Genomes

The city of Marseille, France, is considering a very peculiar scientific conundrum: one of two identical twins is a suspect facing sexual assault charges, but standard DNA testing doesn't have the resolution to differentiate between the two:
One expert told the French newspaper La Provence: "For a normal analysis, we would compare 400 base pairs [of nucleotides] which make up DNA."  In the case of identical twins, he added, "We would be looking at billions."
It's implicitly assumed that three whole genomes worth of sequencing (two for the twins, one for the evidence) are being considered to resolve which twin was the culprit.  However, the price tag is exorbitant:
Police have been told it would cost upwards of 1m euros (£850,000, or CAD$1.34 million) to conduct an ultra-sophisticated genetic test that would be able to tell one set of the twins' DNA from the other.
I have no idea where they're getting their cost estimates from.  Some lab in France is going to walk away with a tidy sum as whole genomes do not cost that much to run (I'll be generous and say that they're under $10 thousand each in Toronto; and at reasonable depths of coverage the cost can be half that).  The only explanation I can think of is that they're including the cost of an Illumina HiSeq in the price, maybe even two in case one breaks down during the investigation.

Though I'm pretty convinced that the Marseille police department needs the genome sequences on these twins to base their evidence, it's also known that chip based analysis of monozygotic twins can identify hundreds of Single Nucleotide Polymorphisms differing between the pair.  One study identified 477 different variations among 500k examined.

That's not to say that whole genome sequencing will make their job any easier, despite the higher resolution and price tag.  One recent report sequenced three sets of twins, but failed to find any gene copy number variations or SNPs that differed between paired siblings, while another report examined the genomes of nineteen sets of twins for copy number variations using chip-based technology did.

The Affymetrix 500k SNP chip arrays, like the ones used in the first study, cost a few hundred dollars to run.  So again, I'm puzzled as to why the police in Marseille received such a wild estimate for this project: the data analysis will surely cost more than the sequencing, but $1 million dollars?  No way!