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BBSRC Review Targets Challenges of Next-gen Sequencing

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – A leading UK research funding agency has found that next-generation DNA sequencing technologies are being integrated across the biosciences, but new partnerships and bioinformatics tools are needed to keep pace with their advance.

The Biotechnology and Biological Sciences Research Council in a new report states that affordable NGS tools have become "efficient and commonly used" and are "democratizing" high-throughput sequencing, but the opportunities the new sequencers offer do present challenges, particularly for data and facilities resources.

The BBSRC report said that the spread of next-gen sequencing will enable R&D advances that will benefit a broad array of areas, such as personalized treatments and diagnostics, food security, and drug and biopharmaceutical development.

"We have reached the stage where, in many cases, genome sequencing can be viewed as a tool rather than as a project in itself. It is useful right across biology, and has huge potential to contribute to global issues that require solutions based on excellent bioscience research, such as food security, biofuels, and healthy aging," University of Cambridge Professor Ottoline Leyser, who chaired the review, said in a statement today.

Leyser said the review of BBSRC's UK research enterprises has found that at the current time the supply of access to next-gen sequencing has been enough to meet demand for the new tools, but that is not guaranteed in the future.

"The review suggests that having a small number of centralized resources, such as The Genome Analysis Centre, enables us to meet demand with a great degree of flexibility — we can expand only as much as we need to at any one time in response to the needs of the whole community. But some smaller, specialized local provision is also likely to be important," Leyser added.

The BBSRC report found that NGS "raises a number of funding issues" for BBSRC, particularly because the shifting costs of equipment makes it "difficult to determine 'the right time to buy.'"

BBSRC also found that the NGS data production pipeline is "at an early stage of development," and that the associated costs may be affecting the way experiments are structured.

In addition, the report said there is a shortage of suitable software for assembling NGS data, particularly in areas such as metagenomics, and the massive amounts of data generated by these systems is presenting challenges for storage and data transfer. "There is a major gap in NGS data analysis and data interpretation, which is exacerbated by a lack of capacity in computational genomics and bioinformatics," the report warns.

The report proposed a dozen recommendations for BBSRC to consider including encouraging partnerships between NGS tool manufacturers and sequencing facilities; supporting 'taster sessions' and pilot projects to enable the roll-out of new tools in key areas; promoting knowledge sharing between academic researchers and industry and government stakeholders; continued monitoring of the availability of NGS tools and how they are being used; funding research to develop sequence assembly algorithms; and trying to ensure that the bioscience community's needs for NGS data storage, interrogation, and transfer are met.

"It is also clear that training researchers in mathematics and computing so that they are able to work easily with large datasets from day one of their careers is becoming an essential part of maintaining the UK's capability in bioscience research," Leyser said.

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