This month’s Genome Technology is the 100th issue of the magazine, and the 6th annual cancer issue. In a brief editorial, magazine editor Ciara Curtin calls cancer The Good Fight and notes that the cover story focuses on “researchers who are using all the tools at their disposal – bioinformatics, metabolomics, sequencing, and more – to better understand the basics of cancer, why people are susceptible to it, and to better treat the disease.”
Systems Biology (?) Fights Cancer
I’m not certain if the title for the cover story (above) is appropriate. The research profiled in the article spans bioinformatics, gene expression, genotyping, proteomics, and other disciplines. Or do I just not understand what “systems biology” means? Either way, the story offered an esoteric view of some of the methods being applied to study cancer. Neil Hayes (of UNC Chapel Hill) and other members of the Cancer Genome Atlas research consortium leveraged the rich TCGA dataset to identify subtypes of glioblastoma based on gene expression and genomic alterations. Laura MacConnaill of Dana-Farber Cancer described OncoMap, a customized genotyping array for “actionable” somatic mutations – ones that confer sensitivity or resistance to cancer drugs. UCLA’s Stan Nelson recounted (again) the sequencing of a well-studied glioblastoma cell line on Life Technologies’ SOLiD platform. A collaborative effort between Harvard, Dana-Farber, and the Broad Institute used mass spectometry genotyping (Sequenom?) to genotype 240,000 sites in 1,000 human tumors.
It was an interesting article overall, and left me with the feeling that (as NCI’s Stephen Chanock was quoted) we are living in a golden age of cancer research.
News Briefs in the Sequencing World
There were some interesting non-cancer tidbits in the issue as well. From the news briefs, I learned that Stephen Lombardi left his position as president of Helicos BioSciences, another discouraging sign for the struggling single-molecule-sequencing company. Pacific Biosystems, meanwhile, announced the ten early-access customers of the Single Molecule Real Time (SMRT) sequencers: WashU, Broad, Baylor, CSHL, JGI, UW, Monsanto, NCI, OICR, and Stanford. RainDance Technologies and Life Technologies announced an agreement to co-market the RDT 1000 enrichment kit with the ABI SOLiD sequencer.
Computing Demands of NGS Data
An article on high-performance computing discussed the challenges of managing next-generation sequencing data. Among the interviewees were David Dooling of WashU and PolITigenomics fame, David Jaffe of the Broad, and Michael Brudno of the University of Toronto. It seems that most genome centers, like ours, are building pipelines from a combination of freely-available and internally developed tools for NGS analysis. The ever-increasing flood of data demands efficiency and automation wherever possible. “We take a holistic approach,” says Dooling. “Find out the areas of ambiguity that are problematic and understand them as best we can.”
In the face of the NGS data deluge, there’s not much time to look back.