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Illumina CEO Backs Sequencing for NIPT; Array Revenues Down 2 Percent in Q3

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NEW YORK (GenomeWeb) – Despite a recent study that suggested array-based non-invasive prenatal testing may be an effective alternative to next-generation sequencing-based tests, Illumina appears unconcerned that its customers will switch platforms.

Illumina's NIPT business is based on its sequencing technologies and has been a fast growing part of its business. The firm said this week that its NIPT sales were a key driver behind its service revenues climbing around 70 percent year over year for the third quarter, and CEO Jay Flatley noted on a conference call that Illumina saw 70 percent sequential growth in NIPT samples accessioned.

Illumina has signed up several partners to use its sequencing technology in developing non-invasive prenatal tests, and many competitors in the space, including Sequenom and Natera, base their tests on sequencing as well. But one competitor already selling a sequencing-based NIPT, Ariosa Diagnostics, recently published a paper that demonstrated the utility of array-based NIPT, which has some questioning if arrays can take a bite out of the market.

As reported by BioArray News last month, Ariosa used custom Affymetrix GeneChips on cell-free DNA obtained from 878 women in the study, and found that the array-based approach generated more consistent data in a shorter period of time and at a lower cost than its sequencing-based assay.

Ariosa had launched its Harmony NIPT, which is based on Illumina sequencing, in 2012. But based on the results of its recent study, the firm may be weighing a potential migration of its assay to the array format.

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

But Ariosa's study appears to have had little effect on Illumina's thinking. Asked during the Q&A portion of the firm's third quarter conference call whether Illumina sees a risk of others switching to arrays for NIPT, Flatley replied, "We have done a very close evaluation of how well you can run NIPT on arrays, and we are convinced that you can't achieve the same quality with arrays that you can get on sequencing. That particular customer that switched over was a very minor revenue customer for us, so we don't think it will have any significant impact on our overall revenue forecast."

Flatley further noted Illumina's partnership with Berry Genomics, under which the Chinese genetic testing firm is seeking Chinese Food and Drug Administration approval to run its Bambni non-invasive prenatal test on Illumina's NextSeq 500 platform. He said that partnership "continues to progress well, and we expect the CFDA to approve Berry's submission in the coming quarters."

Array sales slip

Illumina reported that its third quarter microarray revenue was down 2 percent year over year to around $70.3 million, but Flatley said on the call that those sales were above the firm's forecast.

Strength in genotyping services and IVF applications were offset by a decline in the firm's Infinium genotyping sales, Flatley noted. "Importantly, the Infinium business declined less than in prior quarters due to demand from agriculture customers purchasing our iSelect and our bovine arrays," he added.

During the quarter, array sales to ag customers grew 26 percent year over year, he noted, adding, "We continue to project strong interest from this segment."

Flatley also noted that Illumina's array business had won two biobanking and two large consortia deals, "which have improved our outlook for this market over the next year."

"The biobanking business is going to have some resurgence over the next couple of years," he said. "They tend to be projects of reasonably big sizes, tens of thousands to upwards of 100,000 samples. Having said that, the projects tend to use arrays of relatively low complexity, so the price per array continues to fall in the marketplace, [and] that offsets the number of samples by lower pricing."

The firm still anticipates array sales will decline in the mid-teens in the fourth quarter, due to a difficult quarterly comparison, and resulting in a lower to mid-single-digit decline for the full year. "Beyond 2014, we're projecting the array business to be approximately flat," said Flatley.

Overall, Illumina's Q3 revenues increased 35 percent year over year to $480.6 million, driven by its sequencing instruments and consumables. It posted a profit of $93.5 million, or $.63 per share, for the quarter.


For a detailed report on Illumina's Q3 financials, please see this article published by GenomeWeb Daily News.

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