Low cost genomics

08 November 2009
Posted by Chris Smith.

As we discover more genes that make us susceptible to developing certain disease or reacting the wrong way to certain drugs, the race is on to come up with very fast systems that can read DNA sequences and at very low-cost.

DNA fragmentIt's fair to say that prices have come down a bit since the 100 million US dollar spend that was required to complete the official human genome project, but US $2000 to do the same thing seems almost unbelievably cheap. But that's roughly the price quoted in a paper published in the journal Science from a California-based company called Complete Genomics, who have developed an ingenious method of sequencing genetic material very quickly and very accurately.

Their teachnique involves first cutting DNA into short segments about 400 genetic letters long and then linking small numbers of the segments together using special "adapter" sequences, which are artificial pieces of DNA containing a specific sequence of genetic bases.

The result is a collection, known as a library, of small circular DNA molecules representing the entire genome. Next, a single strand of the DNA is copied using an enzyme called Phi29 polymerase, which generates long coils of DNA called "nanobundles". One billion of these nanobundles are then dotted individually across a special chip about the size of a microscope slide. The surface of the chip is prepared in such a way that it binds to the nanobundles, locking them in place.

Then, to read the DNA sequence, a series of special colour-coded probes are added to the slide. These contain sequences that recognise and bind to the adapter DNA and to the adjacent genomic DNA. When a probe matches one of the genetic letters in the genome it lights up and is "read" by a laser before being washed off and the process repeated to read the next letter.

In this way, one by one, different probes are used to interrogate the DNA sequence letter by letter. This process is repeated many times to read the DNA sequences in the millions of nanobundles. As this is going on, a computer programme is logs the emerging genetic messages and working out which bits overlap with which to piece back together the complete genome.

The result is a highly accurate genome sequence that can be produced rapidly and cheaply.

The team have checked the technique by sequencing three human genomes. According to Cliff Reid, the CEO of Complete Genomics, "We've demonstrated that it's possible to accurately and affordably sequence and detect variants across entire human genomes.

This high-quality, cost-effective approach to genome sequencing will allow researchers to study complete genomes from hundreds of patients with a disease to advance the understanding of the genetic causes of that disease, with an end to preventing and treating common human ailments." Dennis Ballinger, vice president of Complete Genomics, also highlighted the speed and cost effectiveness of the platform. "The nearest competitor to what we're doing currently costs $40,000 per genome and takes 8 weeks. That's twenty times more expensive and 8 times as long as us."

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