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HPV Genotyping Test From GeneFirst Performs Well in Evaluation, Aims to Report All High-Risk Types

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NEW YORK (GenomeWeb) – GeneFirst has wrapped up a performance evaluation which found the firm's single-tube, multiplex genotyping assay for human papillomaviruses (HPV), the Papilloplex, to have a high level of agreement with four other assays.

Infection with HPV is the primary cause of cervical cancer, leading to an estimated 270,000 deaths worldwide per year. Screening for HPV nucleic acids is now recommended as part of a "co-testing" strategy along with a Pap test, with at least one test — Roche's Cobas HPV assay — approved in the US to be used alone as a primary screening method.

The GeneFirst HPV test evaluation, which was presented last month at the European Congress of Clinical Microbiology and Infectious Diseases, was performed in collaboration with the Scottish HPV Archive, Edinburgh, an arm of the Scottish HPV Investigators Network, or SHINE, and funded by a UK Technology Strategy Board grant, Devarshi Kapadia, GeneFirst's sales and marketing manager, told GenomeWeb in an interview.

The Scottish HPV Archive provided 500 samples that were enriched for cervical cancers, and performed the evaluation using HPV tests and platforms in their labs, including the Qiagen Digene Hybrid Capture 2 HPV DNA Test (HC2), Abbott Molecular's RealTime High Risk HPV, as well as a research-use only test from DiaMex called the Optiplex HPV Genotyping kit and Roche's Linear Array HPV Genotyping Test.

The HC2 test targets a number of HPV strains but does not report out genotypes. Abbott's test is the one comparator to the GeneFirst assay that is real-time PCR, but it only reports genotype if the strain is a member of the two families most strongly associated with cervical cancer, the 16 or 18 strains. The Roche and DiaMex assays, meanwhile, report on genotype but also require post-PCR hybridization.

"This is where we come in with our strengths," Kapadia said. "Everything happens in a single closed tube, and because it is highly multiplexed we can differentiate all 14 high-risk genotypes in a single reaction."

In the evaluation, the overall proportional agreement between the GeneFirst and the HC2 test was 90 percent, while for the Optiplex, Abbott, and Roche tests, proportional agreement was 94, 95, and 96 percent, respectively. Type-specific concordance was also high with all four assays.

GeneFirst will now focus on obtaining CE marking for the test, and Kapadia noted the type-specific capabilities may make it particularly useful for epidemiological applications.

While the firm plans to sell into the European market, there is currently no consensus on the benefit of extensive genotyping and current National Health Service screening looks for "yes or no" HPV detection, Kapadia said.

As such, for GeneFirst, "a research-use kit is also going to be one of the target markets, where actually epidemiologists are doing more genotyping more prevalence studies," he said, adding, "But I think within two to three years, genotyping will be the industry norm."

The firm also has a collaboration with Fosun Pharmaceuticals and Diagnostics, a firm with offices in China, and, "once the CE marking completes, they are going to focus in China with the same genotyping kit as well."

Reporting only genotypes of HPV 16/18 and "other" may also not be a great long-term strategy for other firms, considering that 16/18 are the types covered by the HPV vaccine. Kapadia suggested testing for the remaining dozen high-risk HPV types, which now account for 30 percent of all cervical cancers, will become even more important in the future.

"Different genotypes have different prevalence and different actions, it's complex science, so we would like to propose genotyping for all types and then deciding what the algorithm is going to be on who to treat and who not treat."

The core technology of the Papilloplex test is called multiplex probe amplification, or MPA. For each target there is a dual-labelled target-hybridizing oligonucleotide and an oligo that is partially complementary to it. Probes labelled with the same fluorescence dye can be distinguished because probes themselves, independent of target, have different melting temperatures. If a target is present, its corresponding probe is consumed during PCR amplification. Comparing melting profiles of the probes reveals which probe is consumed, and this in turn indicates which target is present in a sample.

GeneFirst has also developed a new way to make the test quantitative by using a specially designed reference control. This method has been patented by the firm's CEO, Guoliang Fu, Kapadia said. 

Besides the MPA technology-based Papilloplex, GeneFirst also has additional applications in development based on other core technologies. The firm's polymerase chain displacement reaction (PCDR) is designed using a special polymerase called SP, as previously described by GenomeWeb.

The firm's multiplex mutation detection PCR, or MMD-PCR, is being used to prepare cancer mutation detection kits detecting multiple mutations within cancer genes such as KRAS, BRAF, and EGFR in a simple and sensitive way.

GeneFirst has also developed a tagged bidirectional sequencing method called TBD-Seq that reduces the high error rate normally found in next-generation sequencing by using specialized, patented strategies, Kapadia said.

Differentiation in the HPV market

GeneFirst will be competing with about 300 other molecular diagnostic tests for HPV, Kapadia said.

This may play to the firm's advantage, Kapadia said, because there is no consensus in the best way to test for HPV. The circumstance may also be better for patients, because it is adapted to local needs and resources. 

One primary strategy for GeneFirst to gain market share is to validate its test on a number of instruments. It is currently demonstrated on Thermo Fisher Scientific's ABI 7500 for the CE marking, but the firm is working to show it can be used on other platforms so that customers will not have to make any additional capital investments after purchasing the test.

The company is also developing collaborations with academia and is exploring alternative samples as a way to differentiate itself.

GeneFirst is working with a device manufacturer called Novosanis, and with Alex Vorsters at the University of Antwerp to evaluate first-void urine as a testing specimen type. Urine was shown in one recent meta-analysis to have good accuracy in the detection of cervical HPV.

The firm is also hoping to have its test included in an upcoming Valgent study comparing HPV assays, and anticipates working with university researchers on HPV prevalence studies in different resource settings.

GeneFirst is also pursuing self-collected, or patient-collected samples as a potential differentiator. One study recently showed that this method could be effective when used on an HPV test from Cepheid, as reported by GenomeWeb.

Connecting with collaborators in industry and academia is key, and GeneFirst is accomplishing this by focusing on the most important HPV-related conferences globally. The firm recently presented at ECCMID, and will be presenting validation data on the alternative sample types at the European Research Organization on Genital Infection and Neoplasia, or Eurogin 2016.

In terms of self-collection, Kapadia said there are currently mixed views on the potential benefits, but that in a developed-world market it may actually be even more readily used due to a higher education level of women there.

Finally, the quantitative aspect of the test may provide some differentiation.

"One of the important visions for us is to go closer to personalized medicine, and combining genotyping and quantitation is hopefully going to give more accurate answers based on an individual person," Kapadia said. 

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