Chip chop

 作者:钮圩祸     |      日期:2019-03-07 09:18:00
By Anil Ananthaswamy A flaw in a widely used “gene chip” 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. The chip 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. “This hits us pretty hard,” says Andrew Brooks of the Functional Genomic Center at the University of Rochester Medical Center in New York. “We have been using these arrays for some time. So papers have been written, grants have been submitted and people have followed up results.” 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. “From a scientific standpoint, we’ll grow from this,” says Brooks. “Other companies will take a harder look at information they are using from public databases.” He is confident that Affymetrix is on the way to rectifying the problem. “The only downside is that it’s going to take them time to do it right,