A FLAW in a widely used 鈥済ene chip鈥� has stopped some research projects dead
and set others back many months. The problem raises concerns about how far
researchers can trust this technology and the publicly available genome data on
which it is based.
Affymetrix of Santa Clara, California, makes the lab-on-a-chip in question,
which allows researchers to screen and identify thousands of mouse genes in
hours, and helps them with experiments on everything from ageing and behaviour
to gene therapy and neurodegenerative diseases.
鈥淭his hits us pretty hard,鈥� says Andrew Brooks of the Functional Genomic
Center at the University of Rochester Medical Center in New York. 鈥淲e have been
using these arrays for some time. So papers have been written, grants have been
submitted and people have followed up results.鈥�
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The chip, called the GeneChip Murine Genome U74 Set, is an array of thousands
of known sequences of DNA, which act as probes. If a sample contains a
complementary sequence, it will bind to the relevant probe on the chip and light
up.
To design the probes, Affymetrix used data from a public mouse genome
database. But it misinterpreted some sequences because of uncertainties about
which way round some DNA fragments are in the genome. This led to faults in 25
per cent of the probes in arrays A and B of the chip and 60 per cent of the
probes in array C.
The company has sent out masks to screen out the bad probes, so that good
data can be reanalysed, says Brooks. It has also promised replacements in three
months.
鈥淔rom a scientific standpoint, we鈥檒l grow from this,鈥� says Brooks. 鈥淥ther
companies will take a harder look at information they are using from public
databases.鈥� He is confident that Affymetrix is on the way to rectifying the
problem. 鈥淭he only downside is that it鈥檚 going to take them time to do it
谤颈驳丑迟.鈥�