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Ariosa Study Finds Arrays Deliver 'More Accurate' NIPT Results than NGS in Shorter Time

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NEW YORK (GenomeWeb) – Ariosa Diagnostics has developed a new microarray-based method for carrying out its Harmony Non-Invasive Prenatal Test that it believes offers significant advantages over its existing, next-generation sequencing-based approach.

The San Jose, Calif.-based company compared its sequencing-based assay with a new protocol run using custom Affymetrix GeneChips on cell-free DNA obtained from 878 women. According to the company, the array-based approach generated more consistent data in a shorter period of time and at a lower cost than its sequencing-based assay. The results of the comparison study are discussed in a new paper in the journal Fetal Diagnosis and Therapy.

Ariosa CEO Ken Song told BioArray News in a phone interview this week that the firm's new microarray-based approach is a "big technological breakthrough" for non-invasive prenatal testing. And while he would not comment on whether Ariosa would move to offering Harmony exclusively on the microarray platform, he did hint that the company is weighing such a move.

"I would say that if you have a better technology, it behooves one to have a plan to implement it," Song said. He also noted that offering a less expensive test could help Ariosa reach more customers. "Our vision since the beginning was to provide access to as many women as possible around the world," Song said. "And cost does matter."

All major NIPT players, from Verinata Health to Sequenom to Natera, offer next-generation sequencing-based tests. And while some researchers, notably at Baylor College of Medicine, have striven to create a robust, array-based NIPT protocol, none have been confident enough in its performance to introduce it for routine clinical purposes.

Song credited Ariosa's Digital Analysis of Selected Regions, or DANSR, assay, with allowing the firm to move beyond sequencing.

"Up until now, people thought of sequencing as the only read out for NIPT," Song said. "But there are certain designs to the DANSR assay that allow us to use multiple platforms and not be limited to one modality."

In Song's words, sequencing is a "great research tool" that has "been propelled toward being thought of as a clinical diagnostic platform." At the same time, he said that the technology is "inherently complex" and is often more suitable as a discovery platform. "Once you have found what you are looking for, you are better off going toward a more stable technology, and arrays fall into that group," he said.

In the recent comparison study, Ariosa's scientists used custom, 100,000-marker arrays printed in Affymetrix's Axiom-384HT multiwell format, which enables users to run 384 samples at the same time. While the Santa Clara, Calif.-based microarray vendor initially designed the Axiom-384HT with the high sample volume agricultural biotechnology market in mind, Song said that the platform "really suits our needs for throughput and technology performance."

He said that Ariosa decided to use Affymetrix products in part because of this high-sample-volume option, and because the custom array "marries well with DANSR."

Ariosa was established in 2008 and launched Harmony in 2012 based on Illumina sequencing. The test can be run on maternal plasma obtained from women who are 10 weeks into pregnancy to assess the risk of Trisomy 21, Down syndrome, in the fetus. According to Ariosa, the test is available in about 90 countries and has been used to guide care in 300,000 pregnancies worldwide.

The company has not been immune from litigation in the competitive NIPT market though. In April, Illumina sued Ariosa, alleging that Ariosa's test infringes on the San Diego vendor's IP. Ariosa is also facing an IP infringement suit brought by Verinata Health, an Illumina-owned company.

According to Song, it is the firm's DANSR assay, which permits the targeted selection of chromosomes of interest for analysis, and its Fetal-Fraction Optimized Risk of Trisomy Evaluation, or FORTE, data analysis algorithm, that comprise the core of the Harmony test. FORTE is used to determine trisomy risk, assay variability across samples, and compute fetal fraction variability within samples.

In its comparison study, Ariosa used the custom Affymetrix chips and sequencing to generate data from the DANSR products. The results of the study were unambiguous. As the authors wrote in the paper, "NIPT using microarrays provided faster and more accurate cfDNA measurements than sequencing." Assay variability, as a measure of variance of chromosomal cfDNA counts, was lower for microarrays than for sequencing. And analysis time using microarrays was faster – 7.5 hours using microarrays versus 56 hours using sequencing.

Additionally, the company reported that fetal fraction precision was improved 1.6-fold by assaying more polymorphic sites with microarrays, and that arrays correctly classified all trisomy and nontrisomy cases. "NIPT using microarrays delivers more accurate cfDNA analysis than next-generation sequencing and can be performed in less time," the authors concluded.

"Microarrays are faster and cheaper than sequencing, and the data quality is better," said Song of the study's results. "The data speaks for itself."

Affymetrix seems to agree with Song's sentiment. Kim Caple, vice president of global clinical strategic marketing at the company, told BioArray News that the new study "demonstrates microarrays have simpler workflow, provide faster turnaround time, and provide equivalent or better performance" than next-generation sequencing.

"For certain applications, microarrays continue to be a better choice than NGS," Caple said.

Since the paper went online, Song said that Ariosa has received "overwhelmingly positive feedback." He called the successful development of Ariosa's array-based approach a "huge advance for the field." At the same time, he said that moving to an array platform from next-generation sequencing was not unusual in the clinical diagnostics arena.

"If you look at how people developed other tests, they went from Sanger sequencing to next-generation sequencing, or from Taqman assays to quantitative PCR," Song said. "There are multiple tools out there. It just takes work to validate them."

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