Analyzing Thousands of DNA and Protein Samples per Day – Automatically

In genomics and proteomics, the number of samples to be analyzed can quickly grow to the hundreds, thousands and even tens of thousands. This growth is driven by factors such as the increasing complexity of sample mixtures, the number of mutations to examine and the number of targets to analyze.

For researchers, the challenge lies in rapidly transforming large data sets into knowledge and insight. In DNA and protein analysis, the most promising solutions provide greater automation, higher throughput, better quality data and powerful data analysis tools.

Replacing tedious slab-gel analysis

The traditional approach has been slab-gel analysis via methods such as agarose gel and SDS-PAGE. These methods have significant limitations: time-consuming sample preparation, limited resolution and quantitative accuracy, subjective analysis, and poor reproducibility of results.

Today, microfluidics provide a digital alternative that is automated, accurate and reproducible. In 1999, the Agilent 2100 bioanalyzer was one of the first products to utilize microfluidic technology. Since its introduction, the Agilent bioanalyzer has become a well-established solution, garnering over 1,200 literature references and driving the sale of more than 1 million of the associated DNA, RNA, protein and cell LabChips.

The bioanalyzer's success follows from its capabilities and performance. It integrates sample handling, separation, staining, detection and data analysis into a single platform and, for some types of protein analysis, provides a 20-fold reduction in total turnaround time versus standard gel electrophoresis.

Addressing the entire workflow

To enable greater throughput, Agilent has developed the 5100 Automated Lab-on-a-Chip Platform (ALP), a self-contained laboratory in a benchtop-sized instrument. By integrating analytical instrumentation, complete automation and a relational database in a single system, the 5100 ALP delivers better reproducibility and greater accuracy while handling more data in one step than slab-gel techniques.

Agilent offers two versions of the 5100 ALP: a standard system for DNA analysis and an extended system that can perform both DNA and protein analysis. Both versions provide three important capabilities that enhance throughput:

The Agilent 5100 ALP is a self-contained laboratory in a benchtop-sized instrument

• Automated and unattended sample handling. Loading samples automatically from standard well-plate formats (96 or 384) saves the time and effort of pipetting samples into gel wells. On-chip electrophoresis separation is much faster than SDS-PAGE and also provides wider dynamic range, higher resolution and greater reproducibility.
   
• Fast and reliable sample analysis. Eliminating manual data entry saves time and reduces errors. What's more, the system's normalized digital results can be reliably reproduced and compared—independent of operator, time or location. The system uses internal standards and standardized assays: the DNA 1000 HT-4 Kit is for analysis of PCR or multiplexed (mPCR) fragments, and the Protein 200 HT-2 Kit is for sizing and quantitation analysis of proteins.
   
• Reproducible and customizable data analysis. Linking the analytical system directly to an integrated Oracle^® database enables efficient handling and analysis of large data sets and makes customized data mining and sample comparisons fast and simple.

Exploring possible applications

There are hundreds of potential applications for the high throughput capabilities of the 5100 ALP. These range from QC of the DNA libraries used in cancer studies to analysis of proteins and protein fractions in purification processes. Other possible applications include gene expression screening via RT-PCR analysis, verification of PCR fragments and determination of concentration before costly sequencing runs, and analysis of mPCR products in GMO testing and pathogen detection.

By expanding on the capabilities of the 2100 bioanalyzer, the 5100 ALP allows for unattended analysis of thousands of DNA or protein samples per day. Every aspect of the system has been planned to help organize the entire workflow and achieve high quality final results when dealing with today's large data sets and high throughput projects.

For more information

To learn more about the Agilent 5100 ALP, please visit the product page and view the online demos. For additional information about Agilent chemical analysis products and resources, please visit the Life Sciences/Chemical Analysis main page.

Oracle is a U.S. registered trademark of Oracle Corporation, Redwood City, California.