July 23, 2018 by Dale Yuzuki
At 18% growth compounded annually, you’ll need to double your productivity every four years
Market research is a strange animal. This industry depends upon the opinion of those they follow (namely customers of companies they track) to determine new trends and growth opportunities, and within the diagnostics business there are plenty of market research companies to keep track of a large $65+ billion-dollar worldwide market.
Within the next-generation sequencing-based NGS market for routine analysis of clinical samples, the current estimates in sample volumes (and dollar volumes) range between 15% and 22%, depending on the source. And if you do some calculations, an 18% annual increase means a clinical laboratory needs to double its throughput in only 4 years.
Can a laboratory double its throughput in four years without hiring more people and buying more instrumentation? Will the overflowing number of samples simply be outsourced to service providers?
Selecting enrichment a key choice in the clinical NGS workflow
One key consideration for next-generation sequencing in a clinical setting is the sequencing enrichment technology chosen. Two methods are currently in wide usage: hybridization-based and multiplex PCR-based. In brief, a hybridization-based method has an important advantage in its scalability: whole-exome methods primarily use this method, as well as target regions that are in the several-hundred kilobases large range. Disadvantages include long procedure times (typically three days to a full week), and a relatively higher amount of DNA needed for input (on the order of 50 ng and higher).
For PCR-based methods, its important advantage is in its specificity (on-target enrichment), as well as its shorter time for sequencing library preparation. Another advantage is its low input (on the order of 10 ng or less). Disadvantages for PCR include complexity of assay design.
In your choosing what technology to use for NGS target enrichment, hands-on time and overall workflow time, from DNA sample to sequencer-ready library, are important and useful metrics to use in comparing methods.
Naturally assay performance has multiple measurements that can be hard to compare across platforms. One important measurement is % of target covered at a given percentage of the average. For example, say you are enriching for two genes, BRCA1 and BRCA2, a target of 17 kb. At 500x average coverage, what percent of the 17 kb is covered at least 20% of 500x, or 100x? This measurement is what percentage of the target is 20% of the mean coverage, and the closer to 100% the better.
Automation is an option to increase throughput
Liquid handling automation is often seen as a method to increase both laboratory throughput while simultaneously reducing human error. A common challenge however is how ‘automate-able’ a given NGS library protocol is to begin with. Something that may seem simple for a laboratory technician (dispensing an enzyme for example into a master mix then adding samples) on an individual strip-tube can incur unexpected complications when placing this procedure within a liquid handler. For example, not only may that enzyme mix need to be kept on ice or cooled down, but the enzyme mix may be very viscous and difficult to pipette accurately.
Nonetheless automation is an attractive option for increasing throughput, and should be part of any laboratory’s plans for increasing productivity.
Can technology come to the rescue?
Pillar Biosciences has developed a new technology for overlapping multiplex PCR called SLIMamp, that can dramatically streamline the NGS enrichment workflow, accompanied by very high on-target mapping rates, and is easily automated. The workflow, from DNA sample to sequencer-ready library, can be completed in less than eight hours with minimal hands-on time. Coupled with Pillar’s PiVAT (Pillar Variant Analysis Toolkit) software, Pillar’s standard or custom panels should be considered for any laboratory looking for an efficient and economical NGS enrichment solution.
For more information about any of our standard or custom panels please feel free to contact us by email, and be sure to ask for a sample to test in your own laboratory.