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Easier Hybridization for Microarrays

Tue, 03/26/2013 - 2:09pm
Mike May, PhD

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SciGene’s hybridization cassette holds 1–4 slides. It also consists of only two pieces to simplify assembly. (Source: SciGene)Microarrays started as research tools and now often appear in clinical applications. To survey some of the hybridization systems available for this technology, we talked with experts from Agilent, SciGene, and Tecan.

Several experts point out the ongoing growth in the use of microarrays. For example, Jim Stanchfield, PhD, president of SciGene, says, “Chromosome microarray analysis, or CMA, is growing in clinical applications. This includes growth in testing for pre- and postnatal genetic defects and cancer.”

Also, Corinna Nunn, Agilent product manager for gene expression, says, “For gene-expression profiling, microarrays continue to be the technology of choice for researchers looking to run many samples cost effectively for many genes.”

Moreover, the approach to using microarrays keeps evolving. “From our customers,” says Sirak Kifle, PhD, sales development specialist detection at Tecan, “we see increasing use of protein applications.”

Clinical uses of microarrays also keep spreading. Anniek DeWitte, Agilent product manager for comparative genomic hybridization (CGH) and next generation sequencing software, says, “Oligo microarrays have revolutionized the field of cytogenetics. The main benefit of using arrays is that they are more powerful, because the technology is high-resolution and can detect smaller duplications and deletions, which were previously missed by karyotyping or other traditional techniques.” She adds, “Recently we launched a new CGH labeling kit with improved quality of labeling and hybridization and containing all the reagents needed for CGH sample preparation including reference DNA. The sample preparation can be performed manually or on the Bravo Automated Liquid Handling Platform.”

As microarrays continue to move into the clinic and other new applications, researchers want to perform the hybridization step easier and faster.

 

Increasing Throughput

SciGene’s Mai Tai Hybridization system works with microarrays from Agilent, Oxford Gene Technology, and BlueGnome. The microarrays are held in a cassette for 1–4 slides. A rotating oven is used in the hybridization step with a rotator that holds up to 8 cassettes for a maximum of 32 slides per run. “Our cassette includes just two pieces,” says Stanchfield. “So the assembly is easy.”

For microarrays “temperature regulation is critical,” Stanchfield says. “So we use convection heating. We heat the side walls, and the heat radiates so there are no hot or cold spots.” He adds, “The microarrays all get the same hybridization temperature. It’s regulated to +/–0.2 degrees.”

In cases where researchers want to spot their own microarrays and use cover slips, SciGene offers its Hybex Microarray Incubation System. “It includes a chamber that has two removable slide racks that each hold four slides,” Stanchfield says. After hybridization, the racks clip together with a handle for manual washing using a water bath insert for the Hybex heating unit.”

Other companies also make hybridization systems for improving throughout. For example, the HYB Microarray Hybridization System from Digilab comes in a version that can simultaneously hybridize up to a dozen microarrays. In addition, the TrayMix S4 Hybridization Station from Arrayit reduces hybridization time by as much as 90 percent, according to company literature.

 

Advancing Automation

“Our HS Promicroarray hybridization systems eliminate some of the handling time,” says Kifle at Tecan. These systems come in two versions: the HS 4800 Pro and the HS 400 Pro. The 400 holds 1–4 microarrays, and the 4800 holds 12–48.

“One of the best features of the HS Prohybridization stations is that the whole hybridization process is fully automated, from sample injection to nitrogen drying, and because of that all the conditions are very standardized,” Kifle says, That automation supports a range of protocols. For example, the user can chose from six different agitation modes depending on hybridization buffer viscosity.

This platform also improves accuracy. For example, Kifle says, “It can be difficult to inject samples without bubbles, so we developed our Active Bubble Suppression, or ABS, system.” The sample is homogenously distributed over the slide by an active mixing process during hybridization, which guarantees a bubble-free incubation. He adds, “Due to the improved kinetic behavior with agitation compared to static hybridization, a maximum yield in specificity, sensitivity and reproducibility of the results is achieved.”

These systems provide other conveniences. For example, the user can load six buffers. In addition, both systems include on-slide nitrogen drying procedure (OSND) that results in a low and uniform background, and the slides can be scanned immediately without further drying procedures.

Kifle says that academic researchers make up most of the users of the HS Pro microarray hybridization systems. He adds that the systems are also being used by biotechnology companies and in clinical settings.

As microarrays extend into clinical applications and other arenas, users require advances in hybridization. Today’s market gives users a range of choices.

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