Bringing FISH Into the 21st Century
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Today’s cytogenetic laboratories are being challenged to optimize reagent and labor costs as well as reduce assay times by using more efficient technologies. To address this need, BioDot – a global leader in high-throughput ultra-low volume dispensing systems – is working to develop the next generation of cytogenetics by revamping fluorescence in situ hybridization (FISH), a key molecular cytogenetic technique.
Technology Networks recently spoke with Brian Kirk, BioDot’s vice president of business development, to learn more about FISH, its advantages and applications. In this interview, Brian also highlights how new technology is tackling some of the limitations of classical FISH to bring the technique into the 21st century.
Anna MacDonald (AM): Can you provide an overview of FISH and some of the applications it is used for?
Brian Kirk (BK): Cytogenetic analyses of samples are used to identify chromosomal abnormalities for the detection and research of genetic disorders, hematological diseases and cancer. Fluorescence in situ hybridization, specifically, is a tried and tested cytogenetics technique for visualizing and mapping genetic material in a cell. FISH uses fluorescent probes to target specific DNA sequences to detect known genetic alterations via standard laboratory methodologies. With FISH, scientists can detect genetic abnormalities including deletions, duplications or translocations. It can also perform chromosome “painting,” which uses multiple fluorophores to detect
AM: Why is the technique such a popular diagnostic tool?
BK: FISH is highly specific and accurate and can be used with a variety of protocol options and sample types, including blood, bone marrow, and solid tumors. Because FISH is a staple of so many cytogenetics labs, there is plenty of existing expertise already present in the lab, a robust supply chain for the required reagents and established workflows already in place. The use of FISH in solid tumors is particularly beneficial as it preserves the integrity of the tissue. Replacing FISH with new technologies, like next generation sequencing (NGS), can be an expensive and complex task that involves introducing new workflows and hiring bioinformaticians who can analyze large quantities of data. Additionally, many of these emerging technologies have more complex protocols with longer turnaround times, while FISH can be performed with a relatively short turnaround time. These hurdles are prohibitive for many labs while FISH remains the gold standard of cytogenetics that continues to be improved upon.
AM: What are some of the limitations traditionally associated with the technique?
BK: FISH has traditionally involved a manual, hands-on approach to process and analyze samples. DNA FISH probes are rather expensive reagents, particularly when using supplier recommended volumes of reagent per slide. Many labs are looking for opportunities to automate this process to increase throughput improving productivity, quality and cost-effectiveness, while using less probe per sample for additional savings. However, new technology is available to address these challenges cementing FISH as the gold standard for cytogenetic testing and benefiting disease research for years to come.
AM: How is new technology revamping the technique and helping to overcome these issues?
BK: The latest in FISH technology introduces standardization, automation and miniaturization to increase efficiency and throughput while reducing cost for the laboratory.
At BioDot, we have developed a more efficient, multiplexed platform for FISH. Using non-contact and quantitative fluid dispensing technology to miniaturize and automate slide preparation, we’re able to dispense nanoliters of fluid onto glass slides with increased precision, faster and without the need for user oversight. It enables highly reproducible assays to be multiplexed with eight individual hybridization areas per slide. This addresses many of the inefficiencies of classical FISH by enabling reliable testing of much smaller sample sizes, reducing the volume of expensive fluorescent probes required from 10 microliters per test to just 0.5 microliters per sample and generating fewer pieces of glass to process and analyze. The reduction in probe use results in significant savings for labs, since probe use makes up the highest cost of FISH.
This improved FISH methodology can be used to process various matrices, diluting or concentrating samples automatically prior to printing them onto the slides, enabling a greater degree of standardization. The increased reproducibility enables reliable automation of analyses, using an automated fluorescence microscope to further reduce turnaround times. A built-in barcode reader means that each sample is carefully tracked throughout processing, making sample management a lot easier and far more efficient. This vendor-independent approach has been validated for most of the common FISH probe suppliers with a wide range of different probe sets. Clinical diagnostic labs have already begun adopting this transformation, which we’ve dubbed Cytogenetics 2.0.
AM: What can we expect in the future for cytogenetics? How big a role will alternative technologies such as NGS play?
BK: Laboratory diagnostic procedures are rarely singular applications but rather complementary studies that provide for a complete picture of the patient’s condition. While alternative methodologies like NGS are certainly valuable diagnostic tools, FISH remains a gold standard for diagnostics due to the ease of use and the ability to perform same day studies from sample receipt to result. Automation of FISH with reduced probe volumes and less hands-on time will contribute to the ongoing expansion of FISH testing in the clinical and research laboratory, ultimately driving better patient outcomes.
Brian Kirk was speaking to Anna MacDonald, Science Writer for Technology Networks.