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Thermo Fisher Hopes New Array Will Help Labs Expand Carrier Screening

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NEW YORK (GenomeWeb) – Thermo Fisher Scientific has announced a new microarray-based assay for pan-ethnic carrier testing, which will be available to customers beginning next month.

The panel, called CarrierScan, is designed to cover more than 6,000 genomic variants across 600 inherited disease genes, consolidating content that Thermo Fisher said can otherwise require the use of multiple different tests and tools or even outsourcing certain tests to other labs.

The assay runs on Thermo Fisher's Applied Biosystems GeneTitan Multi-Channel processing instrument, and labs have the choice of manual or automated sample preparation. Users can also opt to customize the assay if there is a particular area of need that is not covered, or that is covered insufficiently.

The new assay is for research use only, not for clinical patient testing. But as with many RUO materials, testing labs can integrate it into laboratory-developed tests and seek certification under CLIA to use those tests in their clinical and commercial testing of patients.

Gene by Gene is one of those labs. Doron Behar, the company's chief science officer, discussed the firm's work helping Thermo Fisher develop the new panel, as well as its expectations for using it in its own business going forward.

Thermo Fisher said that the content of the panel is based on empirical selection of probes and biological verification of the most common variants. It includes bi-allelic and multi-allelic single nucleotide variants, as well as indels and copy number variations in challenging regions like highly orthologous genes and pseudogenes.

"The development process was very long and careful … over about a year and a half," Behar said, from initial curation of the panel to developing it for Thermo Fisher's array technology.

While the panel doesn't cover every relevant disease area — for example, alternative technologies are needed for fragile X carrier testing — it incorporates as many targets as possible that are clinically valid and applicable to the microarray format, he said.

Carrier screening has been undergoing a shift toward more comprehensive methods over the last several years — driven by increasing ethnic diversity, coupled with advances in understanding of the genetic contributions to disease.

A few years ago, at the cusp of this shift, a number of professional societies — including the American College of Medical Genetics and Genomics, the American College of Obstetricians and Gynecologists, and the Maternal Society for Maternal-Fetal Medicine — issued a joint statement on expanded carrier screening tests.

But at the time, the societies did not endorse or make any specific recommendations for the use of comprehensive carrier screens.

This year, however, ACOG has taken a much more definitive step, issuing a committee opinion this month that recognizes expanded carrier screening as an acceptable strategy, and specifically recommends the use of testing that can be offered and discussed during family planning consistently from patient to patient and regardless of ethnicity.

More specifically, the ACOG opinion concludes that pan-ethnic, expanded, or ethnic-specific carrier screening strategies are all acceptable. Each provider should decide on a strategy to offer consistently to their patients. But, if a patient wants a different test — for example, a more comprehensive one — doctors should make that available to her after counseling on its limitations, benefits, and alternatives.

Describing its new CarrierScan this week, Thermo Fisher called it the market's first pan-ethnic assay of its kind. However other comprehensive tests — many employing next-gen sequencing — have been increasingly used over the last several years.

For example, Good Start Genetics has shared data in past years evaluating the clinical effectiveness of its NGS pan-ethnic carrier screening test, GoodStart Select, showing that it could detect carriers who would have been missed by other technologies.

Counsyl also converted its genoptying-based carrier screen product to NGS in 2015, and published a study last year showing that its own comprehensive approach would likely identify individuals who carry disease-associated alleles and would not have been screened if following the standard recommendations at the time.

Other labs, like New Jersey-based Recombine, have adopted strategies using both array-based genotyping and NGS. In Recombine's case, the company utilizes custom Illumina genotyping chips.

Thermo Fisher's new CarrierScan stands out from these examples not only because it covers an even greater number of genes than many companies have reported, but also because it is an assay product that labs can incorporate into their own facility, without the need to send out samples for testing by an outside firm like Good Start, Counsyl, or others.

"The ability to integrate expanded carrier research in a laboratory setting with a single, automated microarray platform, instead of outsourcing it, can help molecular research laboratories reduce time to results and remain competitive," Thermo Fisher said.

Behar also argued that while NGS-based carrier testing has blossomed over the last several years, there are aspects of arrays that make them more appropriate to the carrier screening setting in his opinion, namely the avoidance of detecting or reporting variants of unknown significance.

"We are trying to be as accurate and as regulated as we can for the healthcare provider," he said. "To do that, we need to have a list, that no matter how long it is or how comprehensive, it is still finite and we can be confident about the pathogenicity about every included variant."

The new Thermo Fisher assay, he argued, allows for a dramatic boost to detection rates, with minimal risk to couples and providers from potential VUS.

Providers of NGS-based carrier tests however continue to argue for the superiority of their approaches, and continue to collect interesting data.

For example, a mathematical modeling study published last year by Good Start suggested that despite the higher cost of NGS, sequencing-based carrier screening may actually be more cost effective than genotyping technologies.

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