Applied Biosystems Genomic Analysis Platform Fuels New Era of Life-Sciences Research

Business Wire,  May 6, 2008  

• E-mail
• Print
• Link

At the Cold Spring Harbor Laboratory meeting this week, Dr. Edwards will present data of whole-genome methylation profiles of a panel of tumors and matched normal controls that show, for the first time, in a whole genome context, the differences in methylation patterns between normal and tumor breast tissue. Based on this data, Dr. Edwards will describe a new role for methylation in cancer, where methylation changes in particular regions of cancer genomes may reflect a cellular defense system that kills cancerous cells.

"Using the SOLiD System, we have interrogated the methylation status of more than 500 million CpG sites, which far exceeds the sum total of methylation data previously available," said Dr. Bestor. "The DNA data quality of runs from the platform that included the new performance enhancements has been excellent."

SOLiD System Enhancements Set New Levels of Performance and Ease-of-Use for Genomic Analysis

Applied Biosystems this week is making available new upgrades to chemistry and software that will double throughput, simplify workflows and decrease system run times. These enhancements will be a part of all future shipments of the SOLiD System. These enhancements will also be made available to existing customers through local service and support teams located around the world.

With these new enhancements, the SOLiD System can consistently generate more than 6 billion bases of sequence data per run, which doubles throughput levels compared to when the system became commercially available just six months ago. This level of throughput maintains the SOLiD System as the highest throughput genomic analysis system available today. The SOLiD System is expected to scale further, as it has already demonstrated more than 10 billion bases per run at some customer locations, and up to 17 billion bases at Applied Biosystems' research and development facilities.

In addition to the number of bases sequenced per run, throughput can also be measured by the number of sequence tags that a genetic analysis system can generate for quantitative applications, such as gene expression profiling, identification of transcription factor binding sites, and serial analysis of gene expression (SAGE). Sequence tags, derived from short pieces of mRNA transcripts, are used for sequencing-based quantitative gene expression techniques. These techniques, such as SAGE, are used to rapidly identify differences in genome-wide patterns of gene expression, which could be associated with disease, regulatory cell networks or cell differentiation. With the upgrades to software and chemistry announced today, the SOLiD System now generates up to 240 million sequence tags per run. This increase in throughput of sequence tags is expected to further reduce the cost of conducting sequencing-based gene expression applications.

Upgrades to chemistry and software have also resulted in improvements to sample preparation methods. These improvements are expected to result in simplified workflows, with less DNA sample now being required for use in DNA sequencing and RNA analysis applications. The number of manual pipetting steps researchers need to perform when preparing samples used in emulsion PCR have also been reduced. A smaller emulsion device, an optimized emulsion PCR protocol, and software upgrades have significantly shortened run times for both fragment and mate-pair library runs. Another result is higher quality data for most sequencing reactions, including more even representation of bases across the entire sequence composition range - GC content - of the genome.