Genetic testing: Clinical labs face challenges in oligo management

Feb. 21, 2017

From simple reagents to the most advanced diagnostic platforms, clinical labs need the highest-quality materials to ensure optimal results from every genetic test they run. Oligonucleotides (oligos) are an excellent example: these easily overlooked products are the building blocks for many steps in the testing workflow and have a direct effect on the quality of results generated.

Oligos are essential for development of new clinical genetic tests, target enrichment in panel tests, primers for qPCR-based tests, and barcoding samples to enable multiplexing. Clinical labs are major users of these DNA snippets, but they encounter a series of challenges when it comes to choosing optimal products while simultaneously keeping costs in check. The best synthetic DNA has a very low error rate, high coupling efficiency, and excellent reproducibility, but it can be difficult to find all of these attributes in one product.

Indeed, the quality required for oligos has never been higher. Thanks to next generation sequencing (NGS) applications, users need extremely low mutation rates and high purity levels—levels that were not even considered possible a decade ago. With the sensitivity of NGS-based testing, though, these are now routine requirements to consider an assay reliable and robust. Nascent fields such as single-cell analysis and circulating cell-free DNA monitoring will only intensify the need for higher-quality oligos.

Perhaps the biggest problem labs face in managing their oligo usage is that most synthesis providers deliver much larger volumes of DNA than their workflows require. This forces labs to pay for a lot of DNA that they will never use, needlessly increasing the cost of running each test and making it that much harder for lab managers to maximize cost-efficiency. Why do the vendors provide excessive volumes of DNA? The problem stems from technical limitations in the DNA synthesis process. After decades of progress in miniaturizing reactions and other technology improvements that have reduced the scale of oligo production, conventional synthesis methods have hit a wall. Further reductions in the minimum quantity that may be ordered require a completely different approach to synthesis.

Here, we consider the major challenges faced by clinical labs right now in optimizing their oligo-related workflows to generate high-quality results in a cost-efficient manner.

Current challenges

Test development. Clinical labs are continually expanding their test menus, and this often requires designing new laboratory-developed tests (LDTs). These assays, typically developed when there is no good commercially available test for a certain disease or condition, are particularly important for diagnosing rare diseases. Developing them usually involves designing and validating primers to capture the desired genomic region for testing. It’s an iterative process, during which lab members design primers, order them, test their performance, and then tweak the design and begin the process again.

During this phase of development, ordering oligos can quickly add up to a very large bill. Each oligo shipment—even at the minimum volumes available from most synthesis providers—includes enough DNA to run an assay thousands of times. Because so little DNA is needed to test the performance of each primer pair, the vast majority of oligos purchased are never used. If labs could order only the quantity necessary for evaluating primers, they could dramatically reduce costs for test development and use the savings to design even more LDTs to meet the needs of a broader patient community.

Barcode complexity. With the explosion of NGS-based clinical tests, many labs have embraced pooling samples to reduce costs. Running a whole sequencing lane for one sample might be cost-prohibitive, especially considering insurance reimbursement guidelines, but running a dozen samples in a single lane makes NGS-based testing much more feasible. The key element for enabling this is barcoding, or attaching identifying oligos to each sample prior to pooling so that data gathered later can be associated with the right patient.

Unfortunately, any problems with the oligos—including unexpected cross-talk between them—can put all of the results at risk by making it impossible to link specific sequences back to the samples they came from. This can occur in many ways: barcodes that contain overlapping sequence; inadvertently attaching the wrong barcode to a sample; contamination between wells that mixes two barcodes into one sample; or barcodes with such similar sequences that a small error in oligo production makes two or more appear the same. While it is not possible to eliminate these risks completely, the use of advanced design protocols can help clinical labs develop a series of barcodes that are far less likely to lead to the kind of cross-talk that might conflate patient results.

Finding the right supplier while keeping costs in check. When it comes to ordering oligos, clinical labs face a variety of pressures that tend to drive up cost. They must use a service provider that meets all FDA manufacturing criteria for clinical use, which increases production costs due to documentation and other requirements for certification. They may also need very quick turnaround times for urgent patient situations, which can subject their orders to premium pricing. Another problem is finding a service provider that can meet the wide-ranging demands of a clinical lab, from small-scale oligo orders for test development to large-scale orders for assays that are run multiple times a day—not to mention one that offers customized delivery formats, such as ready-to-use oligo formulations or pools in specific tubes or plates. One of the primary concerns for any lab is lot-to-lot consistency of the primers, barcodes, and other oligos they need. For all these reasons, selecting the right supplier is a high-stakes decision that affects cost, quality, data reliability, and speed of testing.

Opportunities ahead

The rise of genetic testing has put increased pressure on clinical labs to deliver medically actionable results without breaking budgets, but many labs continually operate at a financial loss. Oligo expenses represent a significant proportion of genetic test costs; reducing them is therefore an important opportunity to help labs achieve break-even operations.

A new synthesis technology based on a different engineering approach has now made it possible to produce much smaller volumes of DNA while maintaining the high quality and efficiency required by users in clinical labs. Being able to order oligos in the quantity needed would help labs reduce costs, launch more tests, and pool more patient samples. These lower-yield, clinical-grade oligos could allow labs to better serve the medical and patient communities while reining in costs to ensure their own continued operations.

Philipp Wenter serves as Vice President of Manufacturing and R&D for Eurofins Genomics, where he oversaw the recent launch of a new small-scale oligo synthesis technology.