Pages

September 08, 2006

Update on work towards $1000 genome sequencing

Currently it costs about $1,000,000 to sequence the genome.
A target is to sequence the genome for $1000 by 2014 (and $10,000 by 2009).

In 2005, Jay Shendure used off-the-shelf parts to determine the order of all the DNA bases in a bacterial genome, at 20 times the speed and one-ninth the cost of traditional DNA sequencing. Shendure is now building on polony sequencing, a method developed in George Church’s lab at Harvard. Shendure spreads millions of tiny beads on a glass slide, each attached to a small DNA fragment. He then adds fluorescently labeled DNA bases. The bases bind to short, complementary DNA sequences, and a standard fluorescence microscope records which base is at each position on a fragment.

Shendure next plans to use the technique to sequence the genome of a lung tumor in order to identify the genetic mutations that caused it.

Related articles:
Past review of costs for DNA sequencing

Commercial process for sequencing

The economist recently looked at synthetic biology It has a chart that looks at pyrosequencing (almost a billion sequences per person per day), ABI sequencers (About 5 million per person per day), EGEA gene writer (About 5 million per person per day) and ABI sythesizers (about 200,000 per person per day).

The article describes work to increase the number of amino acids that can be assembled into proteins. At the moment only 20 are used routinely in biology, but chemists can make thousands of others. Proteins containing those “non-biological” amino acids would have novel properties, and some of those properties might be useful. Lei Wang, of the Salk Institute in La Jolla, California, is trying to extend the amino-acid parts set. Dr Wang's starting point is the redundancy of the genetic code used by nucleic acids. This code is spelled out in the genetic “letters” A, C, G and T, which correspond to chemical sub-units of nucleic acids. The letters are grouped into three-letter “words” known as codons, meaning that there are 64 of them. All but three of the codons correspond to particular amino acids, and the order of the codons in the nucleic acid corresponds to the order of the amino acids in the protein. The remaining three are signals that the protein is complete.

Dr Wang has managed to reassign one of the stop codons in E. coli, the bacterial workhorse of geneticists, to recognise an unnatural amino acid. This can now be incorporated into proteins made by the bacterium.

0 comments: