HPV-RNA Seq: a powerful diagnostic technique for cervical cancer?

Written by Caitlin Killen

A newly developed test, involving RNA sequencing (RNA-seq), could improve the diagnosis of cervical cancer by determining viral strain and detecting precancerous markers.

In a report published by The Journal of Molecular Diagnostics, researchers led by the Pasteur Institute (Paris, France) have described a novel two-pronged strategy for assessing the risk of cervical cancer in women who have tested positive for human papillomavirus (HPV).

In 99% of cases, cervical cancer is caused by HPV. There are over 200 strains of HPV with differing cancer-causing risk, the ability to distinguish the strain of HPV offers a significant advantage when predicting the probability of cancer development.

“HPV RNA-Seq is a unique test that combines the advantages of molecular assays (HPV typing) and cervical cytology (cell phenotyping).”

“We have developed HPV RNA-Seq, a novel in vitro molecular diagnostics procedure for the detection of high-risk HPV infection and the identification of patients with high-grade squamous intraepithelial lesions, which is a precancerous stage of the cervix. HPV RNA-Seq is a unique test that combines the advantages of molecular assays (HPV typing) and cervical cytology (cell phenotyping),” commented lead investigator Marc Eloit.

HPV RNA-Seq utilizes reverse transcription PCR as well as next-generation sequencing. This combination ensures the quantification of small amounts of RNA, providing insight into the expression of HPV genes, as well as determining the exact strains of HPV present via next-generation sequencing.

The team utilized HPV RNA-Seq to analyze samples from 55 patients with precancerous cervical lesions. The test had the ability to determine the type of HPV infection present by testing a panel of 16 high-risk HPVs. The sensitivity and results were comparable to a commonly used HPV diagnostic kit; HPV RNA-Seq had the additional benefit of being able to detect multiple HPV infections.

The test was able to detect whether HPV was present in 97.3% of cases, as well as having a negative predictive value of 93.8%. It was also demonstrated that HPV RNA-Seq had a greater positive predictive power than cytological analysis. Sensitivity is vital for cervical diagnostic tests, to ensure no unnecessary procedures are performed.

“Effective cervical cancer screening requires high sensitivity and negative predictive value for high-risk HPV infection since women with a negative HPV test are usually tested again only after several years,” explained Eloit.

It is hoped that HPV RNA-Seq will decrease the need for invasive biopsy procedures. The team anticipates that as technology improves over time, they will have the ability to run samples simultaneously, allowing the cost to lower to as little as $10 –$20 per test. It is also thought that the test could be utilized in anal cancer and head and neck cancers, which are also associated with HPV.