In-solution Method for Streamlining Next-Generation Genome Sequencing Shown to be Uniform, Reproducible across Many Samples

SANTA CLARA, Calif., Researchers from the Moores University of California San Diego (UCSD) Cancer Center, The Scripps Institute, and Agilent Technologies Inc. (NYSE: A) have shown that “solution enrichment,” followed by next generation sequencing is highly accurate and reproducible, and it can make large scale population studies economically feasible without upfront expenditure for capital equipment.

The researchers sequenced the exons and potential regulatory elements of 622 genes distributed across the genome that are candidate intervals for playing a role in healthy aging. They also included three contiguous genomic intervals containing variants associated with age-related diseases for a total of 3.6Mb using only standard molecular biology equipment and the Agilent SureSelect Target Enrichment System. They were able to call known SNPs with 99.7% accuracy, as well as tens of novel variants, the vast majority of them heterozygotes.

The researchers performed the sequencing on an Illumina Genome Analyzer and used SureSelect capture probes in-solution manufactured by Agilent Technologies for target enrichment. The findings are published in the on-line journal GenomeBiology, and can be accessed at http://genomebiology.com/content/pdf/gb-2009-10-10-r116.pdf

The article states that, in recent years, genome-wide association studies have identified “compelling” associations between more than 350 locations along the human genome and common complex traits. But a much larger number of samples must be analyzed to move beyond statistical associations to pinpoint the exact causes of these traits. The article explains that current methods of DNA sequencing cost too much for such large-scale population studies.

The authors write, “Next-generation sequencing technologies and their increased capacity have made it feasible to efficiently sequence hundreds of megabases of DNA. However, the current costs for sequencing entire human genomes make this approach prohibitively expensive for population studies.”

“SureSelect is a very scalable capture method,” said Olivier Harismendy, Ph.D., project scientist at the Moores UCSD Cancer Center. “It allows you to process multiple samples simultaneously. All you need is already in your lab: a 96-well plate, a magnet and a multichannel pipetter, and here is your high-throughput.”

“The product we tested is very mature and the uniformity of the capture went up when compared to the proof-of concept experiment published earlier this year,” said Kelly Frazer, Ph.D, Professor and Chief, Division of Genome Information Science, Pediatrics. “In the end, this comes out to less sequencing for an increased sensitivity to detect variants. With these experiments, we now understand better the impact of probe design and tiling frequency which are key parameters to improve capture uniformity and SNP calling.”

“We were thinking about improving the economics of very large scale, automated studies from the very first days of SureSelect Target Enrichment, and it’s gratifying to see investigators accomplish this without compromising accuracy or reproducibility,” said co-author Emily LeProust, Ph.D., Agilent R&D Chemistry and Genome Partitioning program manager.

The conclusion is that the solution-hybridization-based method can generate highly uniform coverage of sequence targets that is reproducible across a large number of samples. This means that large-scale population studies using next-generation sequencing could become economically feasible, fueling breakthroughs in health research.

More information about Agilent SureSelect Target Enrichment System is available at www.opengenomics.com/SureSelect.
About Agilent Technologies

Agilent Technologies Inc. (NYSE: A) is the world’s premier measurement company and a technology leader in communications, electronics, life sciences and chemical analysis. The company’s 17,000 employees serve customers in more than 110 countries. Agilent had net revenues of $4.5 billion in fiscal 2009. Information about Agilent is available on the Web at www.agilent.com.

About Moores UCSD Cancer Center

The Moores UCSD Cancer Center is one of the nation’s 40 National Cancer Institute-designated Comprehensive Cancer Centers, combining research, clinical care and community outreach to advance the prevention, treatment and cure of cancer. For more information, visit http://health.ucsd.edu/cancer