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Dx Focus Jul 8, 2010: Clinical and Regulatory PCR and Nucleic Acid Testing News

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Roche today announced data from its "Addressing the Need for Advanced HPV Diagnostics," or ATHENA, trial in the US to test the ability of its PCR-based genotyping test to identify women with cervical pre-cancer missed by cytological examination with a Pap test.

The trial, which examined more than 47,000 women, demonstrated that one in 10 women age 30 years and older who had a normal Pap test but who tested positive for HPV genotypes 16 and/or 18 with Roche's Cobas 4800 HPV test, had cervical precancer.

Roche said that the data demonstrate the importance of HPV genotyping to increase the accuracy of assessing cervical cancer risk, especially by screening for the two highest risk HPV genotypes; and underscore the limitations of relying upon cytology testing alone in identifying women with cervical pre-cancer.

Researcher Thomas Wright of Columbia University presented the data this week at the International Papillomavirus Conference in Montreal.

"The ATHENA data show that women who are positive for HPV 16 and/or 18 should be directly referred for closer examination of the cervix by colposcopy," Wright said in a statement. "Screening for high-risk HPV genotypes provides important additive information to Pap testing, and screening for the two highest risk types, HPV 16 and 18, should be included to provide predictive information about a woman's risk for having cervical precancer or cancer."

The Roche Cobas 4800 HPV Test is a qualitative in vitro test to detect HPV in patient specimens. The test uses PCR amplification of target DNA and nucleic acid hybridization to detect 14 high-risk HPV types in a single analysis.

Roche launched the test with CE Mark in 2009, and it is currently under review and pending pre-market approval the US Food and Drug Administration. The test is not currently available in the United States.


Cancer molecular diagnostics company Epigenomics said this week that it has launched the Epi proLung BL Reflex Assay in Europe.

Epi proLung determines the methylation status of the SHOX2 gene in bronchial lavage material routinely obtained during the clinical workup of patients suspected to have lung cancer. Studies have shown that increased methylation of SHOX2 indicates the presence of malignant lung disease.

Epi proLung detects SHOX2 methylation status using a plate-based real-time PCR system. It has been validated for use on Life Technologies' Applied Biosystems 7500 Fast Real-Time PCR system.

Epigenomics said that the test provides the opportunity to diagnose more patients with a much higher degree of certainty at the time of first bronchoscopy. Patients with positive test results may then be funneled into accelerated clinical staging and therapy, avoiding delays and potentially reducing costs.

In Germany, about 172,000 bronchoscopies are performed for suspected lung cancer every year, Epigenomics said. To introduce the test, Epigenomics will work with a selected number of pathology institutes at university hospitals with a focus on lung cancer in Germany and Switzerland. These reference centers will include Charité University Hospital Berlin and University Hospital Zurich.

Pathologists and clinicians at these reference centers will provide scientific and medical oversight in the launch phase. Following the successful introduction into these home markets, Epigenomics said it intends to address additional European markets through direct marketing and sales as well as distributors.

Epi proLung is the company's second real-time PCR-based diagnostic test to receive the CE Mark for IVD. In October, the company launched the Epi proColon blood-based test to detect colorectal cancer by determining the methylation of the Septin9 gene in colon and rectal tumors.

The Scan

Gone, But Now Reconstructed SARS-CoV-2 Genomes

In a preprint, a researcher describes his recovery of viral sequences that had been removed from a common database.

Rare Heart Inflammation Warning

The Food and Drug Administration is adding a warning about links between a rare inflammatory heart condition and two SARS-CoV-2 vaccines, Reuters reports.

Sandwich Sampling

The New York Times sent tuna sandwiches for PCR analysis.

Nature Papers Describe Gut Viruses, New Format for Storing Quantitative Genomic Data, More

In Nature this week: catalog of DNA viruses of the human gut microbiome, new dense depth data dump format to store quantitative genomic data, and more.