Capillary Electrophoresis: choosing your machine

Sample capacity is at the heart of the decision on what capillary electrophoresis system best fits a lab's needs.

Some instruments have a high-throughput capacity, while others don't.

At the high-throughput end of the scale, Dr John Forster explained his decision to purchase an Amersham MegaBACE 4000 instrument for new plant genomics company AgGenomics as being the high capacity.

The facility already had a MegaBACE 1000 in place, as well as an ABI Prism 3700, but the 384-capillary capacity was the drawcard, said Forster, who is the technical manager at AgGenomics.

According to Forster, AgGenomics uses its instruments for sequencing and genotyping, using methods including microsatellite marker and SNP analysis.

"We get good on-the-ground support from Amersham in Melbourne," he said, explaining that the company had assisted with protocol development and had also helped AgGenomics run courses on the instruments.

At the other end of the scale, Dr Ted Edkins from the Molecular Genetics unit at Perth's Princess Margaret Hospital chose a Beckman CEQ2000 eight-capillary sequencing unit because it provided automated sequencing functions at a relatively small capacity.

"It's a marvellous machine, but a bit too big for doing smaller scale work," he said.

He explained that he knew it would be under-used when he purchased it, but wanted an automated system for sequencing and genotyping, which meant it had to be capillary electrophoresis.

"This instrument is a compromise," Edkins said, adding that the lab would eventually catch up with the capacity.

Edkins said he believed an underexploited niche was the use of automated systems for sequencing and genotyping on a small scale. His lab is primarily involved in detection of genetic diseases like cystic fibrosis in families and has no use for high-throughput systems.

Another small-scale user is Charlie Bell, a molecular geneticist at CSIRO Forestry and Forest Products. His lab has two instruments, a Beckman CEQ2000 with eight-capillary capacity, and an ABI Prism 310 with a single-capillary capacity.

"I'm not sure I'd claim that one is better than the other," Bell said, explaining that the lab bought the Beckman because it had a bigger capacity.

"We went for a capillary machine as it has much less technical requirements than a slab-gel machine," he added.

Bell's lab is using the instruments primarily for fragment analysis as well as a small amount of sequencing.