Applied Biosystems announces software development initiative for next-generation sequencing

Applied Biosystems, an Applera Corporation business, announced today an initiative to support life scientists and independent software vendors (ISVs) in the development and potential commercialisation of bioinformatics applications for next-generation DNA sequencing platforms. As part of this initiative, the company is expanding its Software Development Community to include sample data sets, data file formats and data conversion tools for its SOLiD System, one of the life science industry’s most advanced ultra-high throughput, next-generation sequencing platforms. Applied Biosystems is the first manufacturer of next-generation instrument systems to make these tools available to the bioinformatics community. In doing so, it is directly addressing the industry-wide challenges associated with analysing and managing the vast amounts of research data generated by this ultra-high throughput technology.

Applied Biosystems expects this initiative to drive innovation and speed up the development of new tools that will enable researchers to find more answers faster and more cost effectively, thereby helping life scientists to realise the full potential of next-generation sequencing. The promise of next-generation sequencing technology is to broaden the applications of genomic information in medical research and health care, reduce the cost of DNA sequencing without sacrificing quality, and enable discoveries that may revolutionise the practice of medicine.

Recently, more than 40 researchers from 30 leading academic and commercial institutions convened at Applied Biosystems’ headquarters in Foster City, California, to provide input and share best practices with each other on their respective next-generation sequencing software development initiatives. Among the participants were scientists from the Christian-Albrechts-University in Kiel, Germany, who expressed interest in developing software applications to better understand genetic variations that may correlate with chronic inflammatory diseases, including lupus, scleroderma and dermatomyositis.

“The promise that next-generation genetic analysis technologies will generate better data, faster, and at a lower cost will only be realised when there are sufficient software applications that allow researchers to analyse these data,” said Michael Wittig, a bioinformatician at the Institute for Clinical Molecular Biology in Kiel. “Applied Biosystems’ willingness to provide access to tools and reference data sets is helping us to more rapidly develop the software applications that are necessary to advance our work in understanding genetic variation.”

The Joint Genome Institute (JGI) is an Applied Biosystems early-access collaborator that provides contract sequencing services and develops computational and bioinformatic tools for data management and mining. JGI serves approximately 500 scientists working on a broad range of sequencing projects and provides many of the software applications that they rely on to analyse the data JGI generates on their behalf.

“We are not only interested in the quality of the data each platform generates, but equally important is how willing each vendor is to collaborate with the research community to provide the necessary tools and resources for developing the required software applications,” said Darren Platt, PhD, head of informatics at JGI. “Applied Biosystems has been very forthcoming in sharing information about the SOLiD System platform. We anticipate that this level of assistance will enable us to rapidly develop the software applications our laboratories need to accelerate next-generation research projects.”

As part of this program, Applied Biosystems has dedicated resources to create and support a community of bioinformatics experts that it expects will advance application development in the many research areas supported by the SOLiD System platform. These include, but are not limited to, whole genome sequencing; chromatin immunoprecipitation (ChIP); microbial sequencing; gene expression; microRNA discovery; digital karyotyping; epigenetic profiling; and detection of rare genetic variants. Applications such as these have been identified by prospective customers as being important to driving the early adoption of next-generation sequencing.

“Collaboration with our early-access customers and bioinformatics experts has given us ample opportunity to clearly define what is required to help them to successfully develop the software applications that will ensure their success in conducting next-generation sequencing projects,” said Kimberlee S Caple, vice president and general manager for Applied Biosystems’ next-generation sequencing business unit. “Application-specific software is crucial in building the bridge from the quality data generated by the SOLiD System to new insights that will advance biomedical research by broadening the use of genomic information.”

The SOLiD System, based on sequencing by oligonucleotide ligation and detection, is Applied Biosystems’ next-generation system for ultra-high throughput DNA analysis. Unlike polymerase sequencing approaches, the SOLiD System uses a proprietary technology called stepwise ligation, which generates high quality data for applications such as whole genome sequencing, medical sequencing, genotyping, gene expression and small RNA discovery. Currently in use by early-access customers, the SOLiD System will be commercially available beginning in October.