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The Staying Power of Chromosomal Microarray Analysis: Innovations on the Horizon Will Future Proof Tried and True Technology

Purple, blue, yellow, green and grey dots on a yellow background representing a microarray.
Credit: Pete Linforth / Pixabay
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Genetic research labs are under constant pressure to increase their throughput while bringing down costs. Even though emerging new technologies can help labs expand their analysis capabilities, it’s possible for labs to increase productivity with their current installed equipment base as existing technologies evolve to meet their needs. For example, chromosomal microarray analysis (CMA) is considered the gold standard for cytogenetic analysis, providing critical insight into potentially significant variants of interest and faster results with no batching requirements than other methods. While this technology is certainly tried and true, its utility will only continue to grow with innovations such as faster turnaround times, improved coverage and automated data analysis greatly improving efficiency and productivity for busy, high-volume genetic research labs.


CMA delivers faster turnaround times while reducing sample requirements

With an ongoing shortage of trained lab professionals, labs are looking for solutions to improve efficiency to keep up with the growing demand for genetic analysis without increasing headcount. In addition, as the use of non-invasive prenatal testing (NIPT) and other early screening methods expands into low-risk pregnancies, there is an increased demand for prenatal confirmatory analysis with CMA. Moreover, for labs doing prenatal testing, time is always of the essence.

In response to these pressures, there are two ways labs can increase efficiency and productivity. The first option is to invest in additional lab equipment, which is expensive and takes up precious bench space. The second option is to increase turnaround time with advanced assays that can be run using their existing installed equipment. Given the options, accelerating time to results without new equipment is the obvious choice, which is why the R&D team at Thermo Fisher Scientific has been focused on developing a faster CMA workflow. Turnaround times as short as two days will enable labs to increase productivity up to 100% and get answers faster for their customers while also improving efficiency and profitability.

It's also important to note that efforts to improve lab efficiency and productivity can be negated when labs have to deal with insufficient or low-quality sample inputs, which can lead to failed runs. Our team also reduced the input sample requirements so labs can get reliable, reproducible results from as little as 100 ng input DNA – up to 50% less than what’s required with other CMA workflows – even when samples aren’t high quality.


CMA provides coverage of up to 99.9% of clinically relevant genes

The goal of genetic analysis is to get an answer as quickly as possible without the need for subsequent tests; therefore, a single test with all the relevant content based on current clinical knowledge is ideal. CMA has always been known for its comprehensive coverage of the genome. The beauty of the technology platform is that it is easy to update as our understanding of disease continues to grow and gene databases are updated. Today’s microarrays include more content than ever before, covering up to 99.9% of clinically relevant genes. In addition, current arrays also include an expanded reference model, providing labs with reliable, reproducible results with just one sample – no need for a reference run – despite variability in sample handling, sample types, etc.

The type of microarray platform you’re using also affects the ability to customize content. Using a photolithographic method, as opposed to a bead-based method, ensures reproducibility in content and results. This is because photolithographic technology synthesizes all probes on the array at once, rather than synthesizing probes individually and then mixing them together to create a large batch from which to pull samples that are not guaranteed to be representative of the whole.


With automated interpretation, labs get the answers they need faster

Ultimately, lab directors don’t care about the exact nature of copy number changes but rather what is relevant about those changes. There can be all kinds of “silent” copy number changes that show no phenotypic effect. To rule out these silent changes and look at what’s important, that’s where interpretation comes in.

At the end of the day, lab directors need to understand the clinical impact of the identified copy number changes. We have collaborated with Genoox to enable lab directors to directly upload the CytoScan data and align copy number changes to the ACMG 5-tier classification system with links to clinical evidence.

Interpretation has historically been a bottleneck for labs. Traditionally, it took hours of manual research poring over databases to find associations. Today, labs can streamline data analysis with automated software solutions that can help quickly guide them to the areas they need to explore so they can offer clinical judgment on results faster.  


While innovation is happening across the genetic analysis spectrum, microarray technology will remain an important tool for genetic research labs

The number of population-scale genetic research projects being led around the world grows by the day, while simultaneously, broader use of next-generation sequencing (NGS) is driving new discoveries.  As we combine new discoveries with population-scale studies to clinical utility, microarrays become the tool of choice for fast, accessible, cost-effective and reliable genetic analysis that can scale from a single sample to a large population.

At Thermo Fisher, our focus is on providing customers with the right solution; most customers aren’t focused on the tool, instead they focus on providing high-quality data and interpretation. Our team has worked with NGS, PCR, mass spectrometry, microfluidics and microarrays. Being able to understand the advantages and limitations of the different tools enables our R&D teams to learn from and build on each other’s shared expertise and insights so our instruments have the same reliability and familiar user experience our customers have come to know and love.

We are investing across the entire spectrum of genetic analysis solutions and see a strong future for microarray technology. Microarrays currently in development may offer faster turnaround times, improved coverage and automated interpretation. How can we provide deeper insights into even more rare alleles? Are there opportunities to expand our sample input types? How can we improve sample prep? CMA remains an important tool for labs, and the innovations underway today will ensure CMA has staying power in the future.

About the author: 

Robert Balog is senior director of R&D at Thermo Fisher Scientific. He has worked across the spectrum of in vitro diagnostics, from R&D through regulatory approval. He began his career building genomic tools and instruments for the Human Genome Project. With a PhD in biomedical engineering and an MBA from the University of California, Berkely Haas School of Business, he brings strong technical expertise and market development experience to his role leading R&D for Thermo Fisher’s microarray platform.