Recent years have seen an accelerated growth in sequencing capacity, whilst sequencing costs have plummeted. As a result, powerful techniques and assays based on DNA sequencing (ChIP-Seq, RNA-Seq, genome resequencing, etc.) have been developed that are invaluable additions to the experimental toolkit of biologists and clinicians. However, while becoming increasingly affordable, these new methods require substantial computational infrastructure and expertise that are not available, currently, in most experimental research groups. Indeed, the complexities of post-sequencing analyses and the personnel needed are often underestimated. This mismatch between increased data production techniques on the one hand and increased complexity of analysis on the other have created an analysis and interpretation bottle-neck.
The interpretation bottle-neck
The substantial computational tasks lying downstream of next-generation technologies can be divided into three phases:
Production: harvesting and warehousing the data sets;
Contextualisation: assembling and mapping reads; and
Interpretation: addressing biological or medical hypotheses.
The first two phases are covered well by the significant investments made into new sequencing technologies by scientific bodies in the UK (new MRC sequencing hubs, TGAC, Sanger Institute), private companies and international centres (for instance, the Beijing Genomics Institute). However, there has previously been a critical shortfall in capacity and skills to translate the data into biological and medical progress.
CGAT employs and trains a pool of post-doctoral researchers. These researchers provide assistance to UK-based research groups that are planning to use or are already using next-generation sequencing data. Assistance is provided only on a collaborative basis and is focused on gleaning important biological conclusions from large data sets. The result is high-quality research culminating in high-profile publications under a joint first-authorship model.
UK research groups benefit from CGAT via its expertise in computational genomics, the computational infrastructure and a dedicated post-doctoral researcher. Collaborators contribute sequence data sets and their unique knowledge of their specific research area. More information on analysis.
Post-doctoral trainees in the CGAT group benefit from in-house training, but also the biological insights of collaborators. Working on a variety of projects, trainees accumulate expertise in genome sequencing-related fields, as well as high profile publications.