Study shows Sequenom's MALDI-TOF platform finds high-risk HPV missed by standard DNA test

JULY 28, 2009--A new study shows that a widely used DNA test for human papillomavirus (HPV)--known to cause cervical cancer in women--produced a significant percentage of potential false negatives. By contrast, MALDI-TOF/PCR-MS technology detected the high-risk HPV in nearly half of the false-negative subjects. Further work to define clinically meaningful HPV thresholds is needed, but the finding is being called "an important advance in the early detection of cervical cancer."

JULY 28, 2009--A study by the University of Michigan (Ann Arbor, MI) shows that a widely used DNA test for human papillomavirus (HPV)--known to cause cervical cancer in women--produced a significant percentage of potential false negatives. As many as 15% of the women in the study determined (using the most common test for HPV DNA) to be negative for HPV in the cervix may actually be infected at clinically relevant viral loads, the report concluded. By contrast, polymerase chain reaction and mass spectroscopy (PCR-MS) technology detected the high-risk HPV in nearly half (46.7%) of the false-negative subjects.

The study, titled, Development and Evaluation of a PCR and Mass Spectroscopy-based (PCR-MS) Method for Quantitative, Type-specific Detection of Human Papillomavirus, will be published in the September 2009 edition of the Journal of Virological Methods. The assay used in the study is exclusively licensed by Sequenom Inc. (San Diego, CA; NASDAQ:SQNM).

"We found that nearly half of the 75 women who had been called HPV-negative by the HC2 test had detectable levels of HPV DNA by the PCR-MS method," said Divya Patel, PhD, MPH, of the University of Michigan, one of the study investigators, and lead author of the paper. "More importantly, because the PCR-MS method also measures the quantity of HPV relative to the number of human cells in the sample, or 'viral load,' we determined that about 15% of these samples had HPV loads comparable to the HPV loads found in women called HPV-positive by the HC2 test. While further work to define clinically meaningful HPV detection thresholds is required, our results suggest that a type-specific, quantitative PCR-MS based test may be an important advance in the early detection of cervical cancer."

Approximately 9,000 American women are diagnosed with cervical cancer each year despite regular cervical screening.

Study methodology:
--199 cervical scrapings from women who had been routinely screened for
HPV DNA using the Hybrid Capture 2 (HC2) test (the standard of care in many countries and the most widely used clinical HPV test), and 77 tissue samples taken from tumors in confirmed cervical cancer patients were analyzed using a prototype assay developed by the late Dr. David Kurnit at the University of Michigan (subsequently, the assay has been exclusively licensed by Sequenom and known as the AttoSense HPV assay).

--Using Sequenom's proprietary MassARRAY system, which couples standard polymerase chain reaction (PCR) techniques with mass spectrometry (PCR-MS), study samples were simultaneously screened, genotyped and quantified for each of 13 HPV genotypes highly associated with cervical cancer.

Results summary:
--Nearly half (46.7%) of the 75 cervical scraping samples that were negative for high-risk HPV by the HC2 test were positive by PCR-MS, and approximately 15% of these samples contained a higher viral load than the clinically validated cut-off of the HC2 test.

--Eighteen (14.5%) of 124 cervical scraping samples that were positive by HC2 for high-risk HPV were negative by PCR-MS. In all these cases, degenerate DNA sequencing failed to detect any of the 13 high-risk HPV types included in the HC2 test, reflecting false positive results in the HC2 test.

"This is another example of how the precision of PCR-MS can be applied to solve important medical and scientific problems," said Charles Cantor, PhD, chief scientific officer of Sequenom. "Showing exceptional analytical performance in a proof-of-concept study is a significant step in designing an assay with great clinical performance. The hybridization techniques used today, simply cannot match the state-of-the-art analytical performance found with PCR-MS.

"We are very excited about the future prospects for the AttoSense HPV test, particularly the potential to close the last major gap in screening for cervical cancer and thus possibly saving thousands of lives," Dr. Cantor continued. "We are moving forward to utilize the capabilities of our MassARRAY platform to improve this test further, as having an assay that shows great standalone potential as well as the possibility of combining with other tests for HPV could play a key role in HPV genotyping. We believe that the AttoSense HPV test could be an important addition to our growing women's health portfolio and is another example of our commitment to improving the health of women around the world."

For more information see Sequenom's website.

Posted by Barbara G. Goode, barbarag@pennwell.com, for BioOptics World.

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