It is probably useful in this time of economic uncertainty, when many of the charities that fund medical research are watching their money disappear down the holes that have opened up in the banking system, to have something to fall back on.
Dr Peter Campbell, a researcher at the Wellcome Trust Sanger Institute in Cambridge, at least has his medical degree, complete with clinical training, to support himself if things go belly up.
That’s not likely to happen to the world’s largest charity, and Campbell also has a statistics degree if clinical haematology is not of interest. For the moment, he is working with the Institute’s renowned Cancer Genome Project, analysing the data that is being generated in enormous volumes from the project’s quite remarkable and prolific work on sequencing the genomes of tumours.
The main aim of the project, Campbell says, is to document and catalogue the mutational profile of human malignancies. Up until now, that has predominantly been done through medium-throughput sequencing of PCR products.
“There’s a laboratory pipeline for generating PCR products and automating the sequencing,” he says. “And we’ve got a series of informatics tools that analyse the capillary sequencing data with the aim of identifying somatically acquired variants. That’s been the major thrust of the project for the last five or six years – developing the tools that underpin that effort.”
The group has also made a substantial effort looking at copy number variations through the use of oligonucleotides microarrays, an effort that is nearing completion, and more recently the group has been investing heavily in new sequencing technologies and the application of those to cancer genomics.
One of those new technologies, Illumina’s Solexa sequencing platform, will be the topic of his talk to the Australasian Microarray and Associated Technologies Association’s (AMATA) conference in his hometown of Dunedin, New Zealand, in November. There, he will talk about how using genome-wide, massively parallel paired-end sequencing has caused a revolution in our understanding of the cancer genome.
In April this year, Campbell and his team published a paper in Nature Genetics reporting multiple germline structural variants and somatic rearrangements to the base-pair level of resolution in DNA from two individuals with lung cancer. “The results,” they wrote, “demonstrate the feasibility of systematic, genome-wide characterisation of rearrangements in complex human cancer genomes, raising the prospect of a new harvest of genes associated with cancer using this strategy.”
For Campbell, who has to analyse the data, the amount being extracted from these new technologies is phenomenal. “It’s perfectly set up for identifying rearrangements in DNA sequencing because you get millions and millions of sequences,” he says.
“At the moment we are getting 30 million sequences per run – you get 30 million sequences and you get 35 base pairs from either end of a fragment that can be up to 500 base-pairs long.
“We are now looking at using fragments that are up to 5kB long. If you randomly shear your genomic DNA so these fragments are randomly scattered across the genome, then 30 million reads give you three or four times coverage of the genome. So you should in theory have three or four of every rearrangement in that genome, and that’s only from a single run.”
The question then becomes, what do you do with all of that information and how do you make sense of it? “Ultimately, you are looking for recurrence,” he says. “For example, we are interested in finding fusion genes that are involved in a number of malignancies. If you see a chromosomal rearrangement or something that gives rise to the same fusion event in more than one cancer, then that gives you some confidence that what you are looking at is the genuine driver event rather than a random genetic change.”
