Cost-Effective DNA Analyzers for Increased Quality and Productivity in Sequencing and Genetic Analysis

In the past decade, advancements in DNA analysis technologies have had an enormous impact on the progress of life science research and have fueled the genomics revolution. From the genome assembly of the Severe Acute Respiratory Syndrome (SARS) virus to HapMap construction, DNA analysis continues to be a vital technical approach for advancing life science research. However, the cost of genetic analysis has historically limited both the number of sites with DNA analyzers and the scope of DNA analysis projects. The latest generation of powerful capillary electrophoresis (CE) DNA analyzers are capable of reducing genetic analysis project costs by 50% or more compared with previous technologies, while offering greater data quality, enhanced laboratory productivity, and greater flexibility.

The latest generation of CE instruments, specifically the 48-capillary 3730 DNA analyzer and 96-capillary 3730xl DNA analyzer (Applied Biosystems, Foster City, CA), offer a much higher level of performance than previous-generation DNA analyzers, and expand the range of possible applications for the technology. The 3730 series platform combines industry-standard reagents, advanced sample tracking, and automation with innovative optics and capillary design. The enhanced optical design provides a higher signal-to-noise ratio and a more uniform signal profile across the array. This design, combined with a POP-7™ polymer, enables longer read lengths and improved color balance for handling fragment analysis samples. Automation features include an integrated plate stacker, internal bar-code reader, and on-board polymer delivery pump (PDP) for highly reliable, unattended operation for up to 48 hr.

Novel assay designs, coupled with instrument advancements and new software, have expanded the versatility of DNA analysis instruments for the next generation of genomic research. In addition to de novo sequencing and fragment analysis, examples of new applications for use on the systems include medical sequencing, or resequencing, and genotyping to identify genetic polymorphisms of predictive significance.

CE has remained the gold standard technology for DNA analysis by providing high data quality, application and read-length flexibility, and project cost savings. As a result, the latest generation of CE instruments from Applied Biosystems are routinely used by institutions worldwide, including academic research laboratories, core and service laboratories, large genome centers, and biotechnology and pharmaceutical companies.

 Genome Sequencing Center at Washington University

The Genome Sequencing Center at the Washington University School of Medicine (St. Louis, MO) was a major contributor to the Human Genome Project and is an internationally esteemed research institution. According to Dr. Elaine Mardis, Associate Professor in Genetics and Director of Technology Development, the Genome Sequencing Center used ABI PRISM® 3700 DNA analyzers (Applied Biosystems) for the bulk of the sequencing work on the human and mouse genomes, but has since moved most of its work to the 3730xl DNA analyzers.

According to Dr. Mardis, because the 3730xl systems are much more productive than previous-generation 3700 CE instruments, the Center needs fewer of them, and also requires fewer technicians and reagents. The Center has begun using the instrument exclusively for its genome sequencing projects because of the substantial cost savings that it provides.

Over the years, the Genome Sequencing Center has continually invested in advanced technology in order to reduce costs while meeting increasing demand. The Center recently used the analyzer to sequence the chimpanzee and chicken genomes, and work is currently under way on two species of Drosophila, the planarian worm, and three additional species of Caenorhabditis (roundworm).

One of the strongest advantages of the instrument is reduced reagent usage from the previous-generation instruments, which substantially reduces sequencing costs. Further, increased automation has contributed to significant increases in reliability and productivity for users of the analyzer. The instrument can be set up to run for two or three days without human intervention. The Center has purchased more 3730xl analyzers, and the number of technicians required for sequencing has been substantially reduced, even as its throughput has significantly risen. Taking into account the reduced reagents, personnel, and maintenance required by the machine and its longer read lengths, costs have dropped by greater than 50% per read.

Washington University Core Laboratory

The Washington University Protein and Nucleic Acid Chemistry Laboratory (PNACL) uses the 48-capillary 3730 DNA analyzer for the majority of sequencing projects. This organization functions as an academic core laboratory, providing services on a fee basis to researchers at the Washington University School of Medicine and undergraduate campus as well as from other universities and biotechnology companies. Like most core laboratories, the PNACL processes a greater variety of samples and sample concentrations prepared under a myriad of different methods, and appreciates the benefits of a high-throughput instrument capable of accurately and easily tracking and processing every sample type with high sensitivity, minimal failures, and little or no drop-off in data quality.

Mr. Timothy Lehnhoff, Laboratory Manager for PNACL, explained that one of the key features that attracted the laboratory to the 3730 DNA analyzer is that one plate of sequencing and another plate of genotyping can be set up to run one right after another, automatically. The laboratory is achieving 99% accuracy on fragments of 800–900 base pairs with the analyzer, a level that was previously reached only on fragments below 600 bp on the Applied Biosystems 3100 genetic analyzer. Reducing the number of sequence reactions that need to be rerun significantly lowers the cost per sample. For example, the laboratory can now usually sequence a 1000-base insert forward and reverse with full overlap in two, at the most three, sequence reactions. Most of the laboratory’s customers are operating on NIH grants at reduced levels of funding, and therefore a reduction in sequencing costs is most welcome.

The laboratory’s growth has occurred mainly in genotyping in recent years as researchers begin to apply the human genome to the practical work of identifying alleles and mutations. The much faster throughput of the instrument has made it possible to offer price reductions, particularly to users who bring the laboratory higher volumes of work, such as 96 samples in a 96-well plate. The 3730 analyzer also has made it possible to reduce normal turnaround time for up to 50 samples from 48 hr to 24, which helps improve the laboratory’s competitive position.

The instrument also provides substantial cost savings over the instruments previously used at the laboratory, because its integrated autosampler automatically loads all 48 samples simultaneously, substantially reducing the time required for loading and injection of samples. The higher data quality and sensitivity of the instrument provide additional cost savings by supplying longer read lengths across a variety of sample concentrations.

The fact that the Washington University Core Laboratory uses the 3730 DNA analyzer while the Genome Sequencing Center uses a 3730xl analyzer highlights the potential different advantages of the two units. The 96-capillary 3730xl analyzer is designed for high-throughput sequencing, large-volume projects, or for those who need the flexibility to offer services for a high volume of samples. The 48-capillary 3730 analyzer is intended for users in a high-throughput setting who have slightly lower throughput needs than provided by the 96-capillary system, and who appreciate the value of a somewhat lower-priced system, but still wish to invest in the benefits of the latest high-throughput technology.