A team of researchers at Harvard Medical School led by George Church has developed a new and relatively inexpensive method to DNA sequencing that utilizes readily available tools and reagents.
The Harvard team reported its results in Science in the same week that researchers at 454 Life Sciences published an alternative method for DNA sequencing in Nature. Its technology has been licensed to Agencourt Bioscience Corporation.
Unlike the 454 approach, the method developed by Church and colleagues is a form of DNA resequencing – that is, it requires a reference sequence with which to compare the new sequence, because each fragment of DNA sequenced is so short. Nevertheless, many likely lab applications – from genotyping haplotypes in a disease study, searching for mutations in cancer resistance, or as in the Science paper, identifying microbial strain variants – would fall into this category.
Church calculates that his group’s method offers a ninefold reduction in the theoretical cost of sequencing a human genome – from an estimated $20 million to about $2.2 million. “These developments give the feeling that improvements are coming very quickly,” says Church. “The [desirable] cost of $1,000 for a human genome should allow prioritization of detailed diagnostics and therapeutics, as is already happening with cancer.”
The Harvard group tested its method by sequencing a novel strain of the bacterium Escherichia coli. Similar to 454, the method relies on elongating small DNA fragments on tiny micron-diameter beads. Church’s group packs some 14 million DNA-coated beads onto a slide the size of a dime.
The Church method adapts a commonly available microscope with a digital camera. Short nine-base tags, with each of the four bases present at a specific query location, are ligated onto the bead-attached DNA fragments. Each tag has a different fluorescent dye attached, depending on the base at the query position. The fluorescence data are recorded, and an algorithm aligns the short DNA sequences onto the appropriate reference sequence. The authors append detailed supplemental material, methods, and pricing to allow other researchers to assemble similar sequencing systems.
The Harvard group sees ample room for improvement, in part by increasing the density of beads on a slide. They write: “We collected ~786 gigabits of image data from which we gleaned only ~60 megabits of sequence. This sparsity – one useful bit of information per 10,000 bits collected – is a ripe area for improvement. The natural limit of this direction is single-pixel sequencing, in which the commonplace analogy between bytes and bases will be at its most manifest.”
Featured Report: Shendure, J. et al. “Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome.” Science online 4 August, 2005. DOI: 10.1126/science.1117389