HPV Cancer Resources

Helpful Information for Parents, Patients, Partners, and Providers

Helpful Information for Parents, Patients, Partners, and Providers

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The Challenges of Cancer Screening

The focus of the information in the FAQs below is on screening for HPV-caused cancers. Cancer screening in general is a subject that is under active investigation by many different academic investigators and diagnostic companies. While it sounds great to be able to detect cancers at an early stage, the practical outcomes of these efforts are not so clearcut. Sometimes detecting a cancer early does nothing more than give you a longer period to worry and to undergo treatment. That’s because early detection is not, in many cases, helpful in extending survival. Some cancers that are found will not actually be problematic (that is, they grow so slowly that they may not be a threat to your overall health). I recommend that you take a look at this article describing the pluses and minuses of cancer screening. If cancer treatments become more effective over time, it may help shift the balance towards early detection.

Blood Tests That Detect Cancers Create Risks for Those Who Use Them

Let’s focus on HPV-cancer blood tests. Results obtained by testing patient samples for circulating tumor HPV DNA (ctHPV DNA) are now commercially available, but are not yet widely used. Why? The reasons are outlined in this article: Xie, D.X. et al Clinical Uncertainties of Circulating Tumor DNA in Human Papillomavirus–Related Oropharyngeal Squamous Cell Carcinoma in the Absence of National Comprehensive Cancer Network Guidelines. DOI: 10.1200/JCO.22.00264 Journal of Clinical Oncology 2022.

From this article: “At present, ctHPV DNA detection without concurrent clinical or radiographic correlates represents an outcome without actionable implications outside of clinical trials. The magnitude of a positive ctHPV DNA test appears to be associated with disease burden; however, there are no established cutoffs to guide a diagnostic evaluation to a locoregional or distant site, and the clinical significance of ctHPV DNA variation as a continuous variable is unknown. Moreover, the definition of an abnormal test has varied between studies—while one study defined two consecutive abnormal ctHPV DNA tests as criteria for positive, others considered one abnormal test to be positive. Notably, studies to date and commercially available assays have used heterogeneous HPV detection assays; validation is needed, especially of commercially available tests, as methods are expected to influence thresholds of positivity and performance characteristics. Establishing clear definitions of clinically meaningful positivity will be important for physicians and survivors.

Another important consideration in the absence of prospective data is the potential harmful psychological impact of ctHPV DNA on survivors between a positive test and clinical recurrence, and the impact of false positive tests and lead time bias. With better understanding of the kinetics, dynamics, and prognostic value of ctHPV DNA, we will be able to counsel patients on the meaning and significance of their test results when it is used as a method of surveillance.”

Screening for HPV-caused Cancers

Before diving in to the questions below, you might want to read What Cancer Screening Tests Really Tell Us. This information from the National Cancer Institute clearly explains some of the challenges involved, and how misleading some cancer screening statistics can be.

  • 1) Is screening recommended to find HPV-caused cancers?

    Open or Close
    Yes and no. It depends on which HPV-caused cancers we’re talking about:

    Cervical cancer
    For many years, the only screening tests recommended by the U.S. Preventive Services Task Force (USPSTF) for HPV-caused cancers was the Pap test for cervical malignancies. This test has been the gold standard for detecting precancerous cells of the cervix that may develop into cancer. Recently, however, it has been proposed that the Pap test can be replaced by molecular tests that screen for the presence of the HPV virus. The USPSTF issued its latest recommendations in 2018 for cervical cancer screening, which now say that women 30 and older can drop the traditional Pap tests every 3 years in favor of testing for human papillomavirus (HPV) every 5 years, if they choose to.

    Here are the details:
    Women 21-29 should receive a pap test every 3 years to check the cervical lining for abnormal cells.
    Women 30-65 should receive either a pap test every 3 years, an HPV test every 5 years, or a combination of both every 5 years.
    Healthy women younger than 21 most likely don't need any screening.
    Women older than 65 who've had normal testing in recent prior years likely don't need any screening.
    Healthy women who've had a hysterectomy with cervix removal likely do not need screening.

    In July 2020 the American Cancer Society updated their recommendations for screening, changing the suggested start age to 25 when it has previously been 21, along with HPV testing every five years. Those with a cervix should begin regular screenings for cancer at age 25, which moves back the 2012 recommendation of screenings starting at age 21. At the same time, the new guidelines suggest that individuals with a cervix be tested for HPV every five years starting at 25 years of age (the previous guidelines had recommended these tests at age 30 on). The guidelines also recommend HPV testing without an accompanying Pap test as HPV tests are more accurate and can be done less frequently. Not all facilities have made the switch to HPV testing alone and so a standalone Pap test every 3 years or a combination of the tests every 5 years is acceptable for now, the ACS says.

    In July 2021, the World Health Organization recommended that the HPV DNA test replace the Pap smear for cervical cancer screening. According to this article, “the majority of countries in the world (78%), use the pap smear alone or combined with other tests, to screen for cervical cancer, says the WHO. The current testing figures remain low globally. The WHO says that only 35% of women aged 30 to 49 have been screened at least once in their life for cervical cancer.”

    One of the biggest challenges in HPV screening programs is determining whether a woman is infected with a high risk (i.e. likely to cause cancer) HPV strain, a low risk strain, or a combination of strains. This challenge has led researchers to investigate new methods that can easily identify a large number of different strains, be they high or low risk. A paper in 2022 showed that it was possible to identify these different strains using advanced PCR techniques that vary the melting temperature. This technique may eventually come to be widely used.

    Alirezaei, M. et al Discrimination of human papillomavirus genotypes using innovative technique nested-high resolution melting. Scientific Reports volume 12, Article number: 13943 (2022)

    “The long-term safety of a single negative human papillomavirus (HPV) test for cervical cancer screening is unclear. The HPV FOr cerviCAL Cancer Trial (FOCAL) was a randomized trial comparing HPV testing with cytology. The FOCAL-DECADE cohort tracked women who received one HPV test during FOCAL, and were HPV negative, for up to 10 years to identify cervical intraepithelial neoplasia grade 2 or worse (CIN2+) and grade 3 or worse (CIN3+) detected through a provincial screening program. Methods: FOCAL participants who received one HPV test, were negative, and had at least one post-FOCAL cervix screen were included (N = 5,537). We constructed cumulative incidence curves of CIN2+/CIN3+ detection, analyzed cumulative risk of detection at intervals post-HPV test, calculated average incidence rates for detection, and compared hazard across ages.

    Results: Ten years after one negative HPV test, the probability of CIN2+ detection was lower than 1%, with most lesions detected 7 years or later. Average incidence rates of CIN2+/CIN3+ lesions over follow-up were 0.50 [95% confidence interval (CI), 0.31–0.78] and 0.18 (95% CI, 0.07–0.36) per 1,000 person-years, respectively. Hazards were higher for younger ages (nonsignificant trend).

    Conclusions: Among women with a single negative HPV test, long-term risk of CIN2+ detection was low, particularly through 7 years of follow-up; thus, one negative HPV test appears to confer long-term protection from precancerous lesions. Even 10-year risk is sufficiently low to support extended testing intervals in average-risk populations.”

    Gottschlich A, et al. Assessing 10-year safety of a single negative HPV test for cervical cancer screening: Evidence from FOCAL-DECADE cohort. Cancer Epidemiology, Biomarkers & Prevention|November 30, 2020

    There is some evidence that cervical cancer screening tests are being overused. See Wright, J.D. et al Overuse of Cervical Cancer Screening Tests Among Women With Average Risk in the United States From 2013 to 2014. JAMA Netw Open. 2021;4(4):e218373. doi:10.1001/jamanetworkopen.2021.8373 FREE download

    Researchers conducted a detailed review of mRNA testing for HPV in cervical cancer screening tests. These were their findings: “HrHPV RNA testing with APTIMA (the HPV assay) had similar cross-sectional sensitivity for CIN2+ and CIN3+ and slightly higher specificity than DNA tests. Four studies with 4–7 years of follow-up showed heterogeneous safety outcomes. One study with up to 10 years of follow-up showed no differences in cumulative detection of CIN3+ after negative mRNA versus DNA screening. APTIMA could be accepted for primary cervical cancer screening on clinician-collected cervical samples at intervals of around 5 years. APTIMA is less sensitive on self-collected samples than clinician-collected samples.”

    Arbyn, M. et al Accuracy and effectiveness of HPV mRNA testing in cervical cancer screening: a systematic review and meta-analysis. The Lancet Oncology DOI:https://doi.org/10.1016/S1470-2045(22)00294-7.

    If you’re interested in the details of these molecular tests for HPV, the Pan American Health Organization has published a review detailing how the tests work in their Summary of Commercially Available HPV Tests, or look at this Powerpoint presentation from Prof. Dr. Elizaveta Padalko from 2015 HPV Diagnosis: Current HPV Tests published by the International Centre for Reproductive Health.

    NOTE: A study in July 2020 from researchers at Quest Diagnostics (NYSE: DGX) and the University of Pittsburgh Medical Center (UPMC) provided new evidence that the HPV screening test is significantly less likely to detect cervical cancer and precancer than cotesting, a method which combines HPV and Pap (Papanicolaou test by liquid based cytology) testing using the same specimen.

    Kaufman, H.W. et al Contributions of Liquid-Based (Papanicolaou) Cytology and Human Papillomavirus Testing in Cotesting for Detection of Cervical Cancer and Precancer in the United States. American Journal of Clinical Pathology, aqaa074, https://doi.org/10.1093/ajcp/aqaa074. FREE download

    Australia has recently changed their cervical cancer screening protocols that allows women to self-collect samples for HPV testing. No need to go to the doctors office to get checked for cervical cancer as part of their National Cervical Cancer Screening Program. You can do this in your own home and then send the sample in for analysis. Click on this link to learn more about their National Cervical Screening Program.

    Researchers at Rice University announced in 2023 the development of an easy, low cost point-of-care DNA test for HPV infections. An inexpensive and easy to use test could make cervical cancer screening more accessible in low- and middle-income countries where the disease kills more than 300,000 women each year. Worldwide, there were 604,000 new cases of cervical cancer in 2020, and 342,000 women died of the disease that year, according to the World Health Organization. About 90% of those cervical cancer deaths occurred in low- and middle-income countries. The DNA testing platform combines two technologies, isothermal DNA amplification and lateral flow detection that can provide results in 45 minutes and requires only two pieces of equipment for doing the test. The test is directed at finding DNA from HPV strains 16 and 18, which are responsible for about 70% of cervical cancer cases. The goal is to add in detection of additional cancer causing strains before the test is released for use, as well as to decrease the time the test takes, and to eliminate issues related to false positives and negatives. The hope is to catch cervical pre-cancers using the test and treating them before they become full blown cervical cancer.

    Kundrod, K.A. et al An integrated isothermal nucleic acid amplification test to detect HPV16 and HPV18 DNA in resource-limited settings. Science Translational Medicine Vol. 15 No. 701 (2023) DOI: 10.1126/scitranslmed.abn4768

    Head and neck cancers

    A 2015 paper in Science Translational Medicine suggests that tumor DNA (somatic mutations or human papillomavirus genes) in the saliva and plasma could be a potentially valuable biomarker for detection of head and neck cancers caused by HPV. Wang Y et al Detection of somatic mutations and HPV in the saliva and plasma of patients with head and neck squamous cell carcinomas Sci Transl Med. 2015 June 24; 7(293): 293ra104. doi:10.1126/scitranslmed.aaa8507.

    Note that at-home HPV screening tests have so far yielded mixed results. Mailing at-home human papillomavirus (HPV) test kits to underscreened women failed to significantly increase the detection or treatment of cervical precancers compared with usual care. Among nearly 20,000 women with a lapse in screening, 12 of those randomized to receive at-home HPV test kits by mail were ultimately found to have cervical precancers compared with eight in the group who were sent reminders for in-clinic Papanicolaou screening, a non-significant difference (relative risk [RR] 1.49, 95% CI 0.61-3.64). No difference was seen for treatment of these precancers, all 12 in the intervention group versus seven in the usual care group (RR 1.70, 95% CI 0.67-4.32).

    Winer, R.L. Effect of Mailed Human Papillomavirus Test Kits vs Usual Care Reminders on Cervical Cancer Screening Uptake, Precancer Detection, and Treatment
    A Randomized Clinical Trial. JAMA Netw Open. 2019;2(11):e1914729. doi:10.1001/jamanetworkopen.2019.14729 FREE DOWNLOAD

    Anal, penile, vaginal, and vulval cancers
    At present, there are no standard screening tests recommended for any of these HPV-caused cancers.
  • 2) What’s the status of screening tests for HPV-caused oral and other cancers?

    Open or Close
    The biggest problem here has been that detecting HPV infections is not the same thing as detecting HPV caused cancers. It’s technically possible to test various other tissues (e.g. the oral cavity, or the anus) to see if one has been infected with a cancer causing strain of HPV. However, it’s very clear that only a very small percentage of people infected with these strains will actually develop cancers (see the Epidemiology of HPV Cancers page). Most won’t because their immune system will successfully fight off the virus, a process that can take months to several years. Because of the expenses involved in testing, and the real dangers of scaring people by telling them they have a cancer causing virus (even though the chances of them actually developing cancer are very low), this type of screening is not generally done.

    Random detection of HPV DNA in an oral/ oropharyngeal swab or saliva sample has no known utility as a screening test, because most patients will clear the infection without long-term consequences, and a positive saliva test is unlikely to direct a clinician to the anatomical site of an early (silent) cancer.

    Reference: Pytynia KB et al Epidemiology of HPV-associated oropharyngeal cancer Oral Oncol. 2014 May ; 50(5): 380–386. doi:10.1016/j.oraloncology.2013.12.019.

    However, there has been a recent advance in this area that is still being clinically validated. This new technique, if fully developed, may enable doctors to readily screen people for HPV-caused oral cancers via a spit test, meaning they could be diagnosed at earlier stages when the cancer is often easier to treat.
    The new procedure simultaneously looks for the presence of both cancer-causing strains of HPV as well as the cancer itself in saliva. It uses a technique known as acoustofluidics to look for specific cancer proteins in exosomes, which are small vesicles made and secreted by many cancer cells. You can read this article which describes the basics of the test, or the original research paper that I’ve listed below:

    Wang, Z. Acoustofluidic Salivary Exosome Isolation: A Liquid Biopsy Compatible Approach for Human Papillomaviruse-Associated Oropharyngeal Cancer Detection. The Journal of Molecular Diagnostics, Vol. 22, No. 1, January 2020 https://doi.org/10.1016/j.jmoldx.2019.08.004 FREE Download

    A different approach using next generation HPV sequencing is being looked at for detecting circulating tumor DNA (ctDNA) in patients being treated for HPV cancers. “Detectable HPV ctDNA at end-of-treatment was associated with inferior PFS with 100% sensitivity and 67% specificity for recurrence. Accurate HPV genotyping was successful from 100% of pretreatment samples. HPV ctDNA fragment sizes were consistently shorter than non–cancer-derived cell-free DNA (cfDNA) fragments, and stereotyped cfDNA fragmentomic patterns were observed across HPV genomes.”

    “Conclusions: HPV-seq is a quantitative method for ctDNA detection that outperforms dPCR and reveals qualitative information about ctDNA.”

    Leung, E. et al HPV Sequencing Facilitates Ultrasensitive Detection of HPV Circulating Tumor DNA. Clinical Cancer Research doi: 10.1158/1078-0432.CCR-19-2384.

    In screening people to see if they have HPV+ cancers, there are two general ways this is done. One uses PCR, a method that detects the presence of HPV DNA, and the other is an immunohistochemistry test that stains cells looking for the presence of the p16 protein, which is considered a marker of HPV driven cancers. A study was done to compare the accuracy of three possible diagnostic test strategies, i.e. (a) hrHPV DNA PCR (DNA), (b) p16(INK4a) immunohistochemistry (IHC) (p16), and (c) the combination of both tests (considering joint DNA and p16 positivity as positivity criterion). These tests were performed on tissue samples from 99 Belgian OPC patients enrolled in the HPV-AHEAD study. Presence of HPV E6*I mRNA (mRNA) was considered as the reference, indicating HPV etiology.

    In looking at the results, measurements include both sensitivity and selectivity. What do these measure?

    From Wikipedia:
    If the goal of the test is to identify everyone who has a condition, the number of false negatives should be low, which requires high sensitivity. That is, people who have the condition should be highly likely to be identified as such by the test. This is especially important when the consequence of failing to treat the condition are serious and/or the treatment is very effective and has minimal side effects.

    If the goal of the test is to accurately identify people who do not have the condition, the number of false positives should be very low, which requires a high specificity. That is, people who do not have the condition should be highly likely to be excluded by the test. This is especially important when people who are identified as having a condition may be subjected to more testing, expense, stigma, anxiety, etc.”

    Results: “Ninety-nine OPC patients were included, for which the positivity rates were 36.4%, 34.0% and 28.9% for DNA, p16 and mRNA, respectively. Ninety-five OPC patients had valid test results for all three tests (DNA, p16 and mRNA). Using mRNA status as the reference, DNA testing showed 100% (28/28) sensitivity, and 92.5% (62/67) specificity for the detection of HPV-driven cancer. p16 was 96.4% (27/28) sensitive and equally specific (92.5%; 62/67). The sensitivity and specificity of combined p16 + DNA testing was 96.4% (27/28) and 97.0% (65/67), respectively. In this series, p16 alone and combined p16 + DNA missed 1 in 28 HPV driven cancers, but p16 alone misclassified 5 in 67 non-HPV driven as positive, whereas combined testing would misclassify only 2 in 67.

    Single hrHPV DNA PCR and p16(INK4a) IHC are highly sensitive but less specific than using combined testing to diagnose HPV-driven OPC patients. Disease prognostication can be encouraged based on this combined test result.

    Simoens, C. et al Accuracy of high-risk HPV DNA PCR, p16(INK4a) immunohistochemistry or the combination of both to diagnose HPV-driven oropharyngeal cancer. BMC Infectious Diseases 22, article 676 (2022). FREE download

    A more recent trend is to have dental offices screen patient for visible signs of oral cancer, which is not a bad idea. Tumors caught this way could then be treated in a standard way. However, the fact that your dentist might not find anything doesn’t mean that you don’t have an oral tumor. It could be hidden in your throat past what your dentist can observe. Tonsillar HPV tumors start out in the tonsillar crypts, which are deeply buried at the back of the throat and are not visible in the mouth at an early stage. If you’re going to the dentist, they should really be vigilant in looking for oral cancers, whether those caused by HPV, or caused by something else.

    You can read what the US Preventative Services Task Force has to say about oral cancer screening (i.e. the pros and cons) here. Here’s a short version of their conclusions:
    In the current recommendation, the USPSTF found inadequate evidence that the oral screening examination accurately detects oral cancer. It also found inadequate evidence that screening for oral cancer and treatment of screen-detected oral cancer improves morbidity or mortality. The evidence for screening for oral cancer remains insufficient; therefore, the USPSTF is unable to make a recommendation in favor of or against screening.

    There are no frequently used screening tests for cancers of the penis, vagina, vulva, or anus.

    Having said that, a study has been launched to look at the efficacy of screening for anal cancer. The idea is to test the theory that screening with anal smears can detect precancers and thus reduce cancers. This will be a government-funded clinical trial called ANCHOR. When these precancerous lesions are found in the women and men in the trial, they are randomly assigned to have the lesions either treated or monitored every six months. Both groups are being followed for five years. The trial is limited to people known to be at very high risk of anal cancer, such as those infected with HIV, the AIDS virus. That virus compromises their immune systems, so they are prone to HPV infection. One study found more than a quarter of HIV-positive women had severe anal precancers. Another group that doctors recommend screening for anal cancer are women who have had organ transplant recipients and who take immune-suppressing drugs to prevent organ rejection.

    To learn more about screening for anal cancer, check out Pos,icki, A-B et al. Screening for Anal Cancer in Women. J Low Genit Tract Dis. 2015 July ; 19(3 0 1): S26–S41. doi:10.1097/LGT.0000000000000117. This paper is available as a FREE download.


    An interesting and promising paper was published in 2020 that illustrates the basis of a new blood test that can be used to look for recurrence of HPV-oropharyngeal cancers in patients following treatment. It can distinguish between merely being HPV+ from having HPV+ tumor present.This could be a big advance in surveillance screening if it proves out in the marketplace with much greater numbers of patients. The technology underlying the research has been licensed from the University of North Carolina to Naveris, which has designed and validated NavDx®, a laboratory developed test for cancer-associated HPV detection. NavDx® identifies minute fragments of tumor-modified viral HPV DNA, which is distinct from native viral HPV DNA. The company recently began providing the test through its CLIA laboratory to leading head and neck oncology treatment centers for patients with HPV-caused oropharyngeal cancers. No patients who did NOT have circulating HPV DNA in their blood had a cancer recurrence, while a number of those that had HPV fragments in their blood did develop a recurrence within a few months. These blood based screening tests may supplant both PET scans and scoping out the oropharynx at some future point.

    I wonder if it could also be used in an initial HPV cancer detection screen (and extend to other cancers beyond oropharyngeal). For now, claims are limited to tracking recurrence of HPV-caused oropharyngeal cancers.

    Chera, B.S. et al Plasma Circulating Tumor HPV DNA for the Surveillance of Cancer Recurrence in HPV-Associated Oropharyngeal Cancer. DOI: 10.1200/JCO.19.02444 Journal of Clinical Oncology. FREE download.


    A similar approach to the one above is being developed by scientists at the U. of Michigan. The assay is based on PCR and uses a blood sample to monitor those with cancers caused by either HPV strains 16 or 18. The authors envision this test being used in place of patient scans to track how well patients are doing following their treatments i.e. is the tumor shrinking, or has it disappeared. They “found that longitudinal changes HPV16 ctDNA correlate with treatment response and that ctDNA responses are observed earlier than conventional imaging (average 70 days, range: 35–166). With additional validation in multi-site studies, this assay may enable early identification of treatment failure, allowing patients to be directed promptly toward clinical trials or alternative therapies.”

    Haring, C.T. et al. Human papilloma virus circulating tumor DNA assay predicts treatment response in recurrent/metastatic head and neck squamous cell carcinoma. Oncotarget Oncotarget. 2021; 12:1214-1229. doi.org/10.18632/oncotarget.27992 FREE download

    In yet another approach, serial sampling of saliva for the presence of HPV-16 showed a rising level in a patient over a three year period. This led to the discovery of an asymptomatic small tonsil tumor that was removed via surgery. More clinical trials would need to be done to see if serial oral saliva sampling with associated rising virus levels is indicative of the formation of oral HPV driven cancer.

    Kai Dun Tang, K. D. et al. An Occult HPV-Driven Oropharyngeal Squamous Cell Carcinoma Discovered Through a Saliva Test. Frontiers in Oncology, 2020; 10 DOI: 10.3389/fonc.2020.00408


    Another screening test in the works looks promising for detecting HPV16 positive cancers, whether oropharyngeal or anal cancer. This study aims to assess the clinical performance of a newly developed HPV16-L1 DRH1 epitope-specific serological assay. It measures the levels of a particular antibodies directed against the L1 protein of HPV16. “The DRH1-competitive-serological-assay showed a sensitivity of 95% (95% CI, 77.2 99.9%) for HPV16-driven HNSCC, and 90% (95% CI, 55.5 99.7%) for HPV16-induced anal cancer in HIV-positives. Overall diagnostic specificity was 99.46% for men and 99.29% for women ! 30 years. After vaccination, anti- body level increased from average 364 ng/ml to 37,500 ng/ml. During post-therapy-monitoring, HNSCC patients showing an antibody decrease in the range of 30 100% lived disease free over a period of up to 26 months. The increase of antibodies from 2750 to 12,000 ng/ml mirrored recurrent disease. We can also show that the L1-capsidprotein is expressed in HPV16-DNA positive tumor-tissue. Interpretation: HPV16-L1 DRH1 epitope-specific antibodies are linked to HPV16-induced malignant disease. As post-treatment biomarker, the assay allows independent post-therapy monitoring as well as early diagnosis of tumor recurrence. An AUC of 0.96 indicates high sensitivity and specificity for early detection of HPV16-induced disease.”

    This assay is only specific at present for disease caused by the HPV16 strain, but not those caused by other HPV strains. This test has been commercialized in Germany by Abviris, as described in the section below on Commercial screening tests.

    Weiland, T., et al. DRH1: a novel blood-based HPV tumour marker. EBioMedicine 56 (2020) 102804. https://doi.org/10.1016/j.ebiom.2020.102804 FREE download

    Commercial Screening Tests for HPV-caused Cancers

    There are several such tests. Please read what I said at the very top of this page under The Challenges of Cancer Screening to get an idea about why these tests are not widely used yet.

    Naveris sells the NavDx blood test that detects HPV-associated cancers by quantifying fragments of tumor-specific DNA shed by cancer cells into the blood. It measures the number of tumor-tissue modified HPV virus (TTMV) particles in plasma cell-free DNA by digital droplet PCR. The company claims that NavDx distinguishes TTMV from other, non-cancer associated sources of HPV DNA.
    The test (available in the US) can be used:
    Pretreatment to provide a baseline measure of TTMV levels, as well as identify the correct tumor-associated HPV strain.
    During treatment to monitor TTMV levels as a measure of treatment effectiveness.
    Post treatment surveillance to identify patients who would benefit from imaging following a positive test, or provide peace of mind with a negative result.

    The test claims to offer >95% sensitivity for recurrence detection, and >99% probability of being recurrence free if TTMV remain undetectable after treatment.

    Expanding on their blood based test, Naveris has developed a similar saliva based test. The goal here is to hopefully use this saliva based test to detect early stage HPV oropharyngeal cancers. It it less invasive than a blood test, but produces similar results, according to the company.

    The utility of this test was compared with current post-treatment surveillance practices (physical examinations and imaging). This retrospective clinical case series included 1,076 consecutive patients across 108 U.S. sites who were ≥ 3 months post-treatment for HPV-driven OPSCC and who had one or more TTMV-HPV DNA tests (NavDx, Naveris Laboratories) obtained during surveillance between February 6, 2020, and June 29, 2021. Test results were compared with subsequent clinical evaluations.
    Results: “Circulating TTMV-HPV DNA was positive in 80 of 1,076 (7.4%) patients, with follow-up available on all. At first positive surveillance testing, 21 of 80 (26%) patients had known recurrence while 59 of 80 (74%) patients were not known to have recurrent disease. Among these 59 patients, 55 (93%) subsequently had a confirmed recurrence, 2 patients had clinically suspicious lesions, and 2 had clinically “no evidence of disease” (NED) at last follow-up. To date, the overall positive predictive value of TTMV-HPV DNA testing for recurrent disease is 95% (N = 76/80). In addition, the point-in-time negative predictive value is 95% (N = 1,198/1,256).”
    Berger, B.M. et al Detection of Occult Recurrence Using Circulating Tumor Tissue Modified Viral HPV DNA among Patients Treated for HPV-Driven Oropharyngeal Carcinoma. Clinical Cancer Research, Translational Cancer Mechanisms and Therapy June 08 2022 https://doi.org/10.1158/1078-0432.CCR-22-0562

    You can read more about this paper in this story from Physicians Weekly from Nov. 2022.

    Levels of TTMV can vary widely in patients who test positive. Research has been done to try and figure out what factors contribute to the TTMV score generated. Clinical N stage was the strongest predictor of detecting TTMV HPV DNA in circulation. A majority of patients with undetectable TTMV HPV DNA also had clinical stage N0 illness. he prevalence and score of TTMV HPV DNA also rose with increasing clinical nodal stage, biggest lymph node diameter, and nodal maximum standardized uptake value on positron emission tomography/computed tomography. In multivariate analysis, TTMV HPV DNA score was substantially related to clinical nodal stage and nodal maximal standardized uptake value. For more info, see Rettig, E.M. et al “Association of Pretreatment Circulating Tumor Tissue–Modified Viral HPV DNA With Clinicopathologic Factors in HPV-Positive Oropharyngeal Cancer,” JAMA Otolaryngol Head Neck Surg. 2022;148(12):1120-1130. doi:10.1001/jamaoto.2022.3282

    Keep in mind that the ability to diagnose a recurrence at an earlier date does not mean that will lead to increased survival. It only means the cancer is found earlier. Separate studies would have to be done to determine if there is a survival benefit.

    Another study using the NavDx test was published in July 2023, along with a separate commentary:

    Ferrandino, R.M. et al Performance of Liquid Biopsy for Diagnosis and Surveillance of Human Papillomavirus–Associated Oropharyngeal Cancer. JAMA Otolaryngol Head Neck Surg. Published online July 9, 2023. doi:10.1001/jamaoto.2023.1937 (FREE download).

    Miriam N. Lango Circulating Human Papillomavirus Tumor DNA—Ready for Prime Time? JAMA Otolaryngol Head Neck Surg. Published online July 9, 2023. doi:10.1001/jamaoto.2023.1938 (FREE download)

    The bottom line from this study, as explained in the commentary, is that the NavDx test may be valuable at some point for diagnosing HPV+ cancers, and for surveillance after treatment. At present, though, the test still has some limitations that preclude it's widespread use at the moment. It's not clear what a testing schedule should look like after treatment, and it's also not clear if earlier detection of a recurrence is associated with a longer survival time. The test has more value if it is positive (indicates a true positive) but the sensitivity for finding true negatives is closer to 90%, meaning about one out of ten patients will be told they are negative when in fact they are positive. The other issue is that a positive result doesn't identify the location of the tumor. The conclusion from the Ferrandino study concluded, "This cohort study demonstrated that when evaluated in a clinical setting, the TTMV-HPV DNA assay demonstrated 100% specificity in both diagnosis and surveillance. However, the sensitivity was 91.5% for the diagnosis cohort and 88.4% for the surveillance cohort, signifying that nearly 1 in 10 negative tests among patients with HPV-associated OPSCC was a false negative."

    Can using the NavDx test be cost effective?
    One analysis suggests that's the case. The total cost of five years of post treatment surveillance using CT scans and back of throat scopes was estimated to cost the medical system $69K.
    Substituting the NavDx test for CT scans reduced the cost down to about $40K.
    "Of the p16+ OPSCC patients (n = 214), 23 had confirmed recurrence (11%). Standard work-flow model determined 72 imaging studies and 2198 physical examinations with FL were needed to detect one recurrence. Potential individual patient cost reduction during surveillance was 42%."
    Lin, M.G. et al Novel HPV Associated Oropharyngeal Squamous Cell Carcinoma Surveillance DNA Assay Cost Analysis. Laryngoscope (2023) FREE download. https://doi.org/10.1002/lary.30701


    Abviris sells the Prevo-Check blood test for the early detection of cancers caused by HPV16 cancers. The test is based on competitive immunoassay in form of a rapid test for the qualitative detection of DRH1 antibody equivalents by means of the antibody clone DRH1. This antibody is directed against a protein which is produced only by cells in which HPV16 has actively affected the cell division. This means that the antibody is only present if a sub clinical HPV16 infection has progressed to a cancer pre-stage or carcinoma.

    The test claims a clinical specificity > 99%, and a clinical sensitivity of 95%. This test is NOT available in the US, but is available in Germany.

    Sysmex Inostics has developed the SafeSEQ cfHPV-DNA Test (HPV-SEQ) that detects cell-free HPV DNA (cfHPV-DNA) across a broad dynamic range, enabling high-resolution monitoring for patients with HPV+ OPSCC, a type of head and neck cancer. accurately quantifying circulating HPV 16 and HPV 18 DNA in patients with HPV-related cancers. However, as of May 2023, there is virtually no info about the test on their website, and it is not ready to be used by patients.


    QIAGEN announced a collaboration in Nov. 2020 with BioNTech on a companion diagnostics development for HPV-associated squamous cell carcinoma of the head and neck. They plan to develop a tissue-based therascreen® test covering a panel of HPV genotypes, paired with investigational treatment BNT113, to identify patients whose cancers are caused by HPV infections. The assay will detect the presence of HPV genotypes and will be developed on QIAGEN´s RGQ MDx platform, a member of the QIAsymphony family of products. QIAGEN plans to expand the panel for use across HPV-driven cancers such as cervical cancer and other cancers, in order to provide a universal HPV companion diagnostic (CDx) for QIAGEN’s pharmaceutical partners.

    Another interesting screening test for both oral cancer and oropharyngeal cancer are saliva tests being developed by Viome. In May 2021, Viome “announced its proprietary mRNA analysis technology combined with its next-generation AI platform has been designated a Breakthrough Device by The Food and Drug Administration (FDA) for early detection of oral cancer and throat cancer.”

    Viome's proprietary technology and AI platform is a first-of-its-kind screening tool for oral cancer and throat cancer, two life-threatening diseases that are traditionally diagnosed manually by a primary care clinician by visual or tactile senses in a subjective way, often going undiscovered. Making saliva the new liquid biopsy, Viome analyzes samples for the presence of Oral Squamous Cell Carcinoma (OSCC) and Oropharyngeal Cancer (OPC). Viome has employed unique mRNA analysis technology and breakthrough machine learning techniques to accurately discover the interactions between microbial activities and human gene expression in the progression of these cancers.”

    Guruduth Banavar et al. The salivary metatranscriptome as an accurate diagnostic indicator of oral cancer, (2020). DOI: 10.21203/rs.3.rs-55052/v1

    From the abstract: “Despite advances in cancer treatment, the five-year mortality rate for oral cancers (OC) is 40%, mainly due to the lack of early diagnostics. To advance early diagnostics for high-risk and average-risk populations, we developed and evaluated machine-learning (ML) classifiers using metatranscriptomic data from saliva samples (n=433) collected from oral premalignant disorders (OPMD), OC patients (n=71) and normal controls (n=171). Our diagnostic classifiers yielded a receiver operating characteristics (ROC) area under the curve (AUC) up to 0.9, sensitivity up to 83% (92.3% for stage 1 cancer) and specificity up to 97.9%. Our metatranscriptomic signature incorporates both taxonomic and functional microbiome features, and reveals a number of previously known and novel taxa and functional pathways associated with OC. For the first time, we demonstrate the potential clinical utility of an AI/ML model for diagnosing OC early, opening a new era of non-invasive diagnostics, enabling early intervention and improved patient outcomes.”
  • 3) Should I be screened to see if I’ve been infected by HPV?

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    This would not only be difficult to do, it wouldn’t be terribly helpful in most cases. It’s possible to detect the virus using tissue swabs combined with molecular diagnostics, but you would need to test a number of tissues (for example, women would need to have their mouths, vulva, vagina, rectum, and cervixes tested). If you test negative, it’s possible that the swabbing could have missed a small area where the infection has taken hold. If you test positive, especially for one of the more common cancer causing strains (e.g. 16 and 18), then you are still highly unlikely to develop an HPV caused cancer (see the question and answer below). Being told that you are carrying a cancer causing virus can have significant negative psychological effects on people, even though in most instances these infections will not develop into cancer.

    It’s for these reasons that screening tests are focused on checking for cancer, not merely for the presence of the virus. The one exception is cervical cancer screening, as explained in the answer to the first question above.

  • 4) If you’re HPV positive, does that mean you will develop cancer?

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    Not at all. In fact, the vast majority of people who are infected will never show any signs of the infection at all. Their immune systems will fight and eventually eliminate the virus. Consider that the number of people in the US infected with HPV is estimated to be about 79 million, with 14 million more infected every year. High-risk genital HPV infections affect about 25 percent of men and 20 percent of women. The prevalence of any type of oral HPV infection among adults ages 18-69 in 2011-2014 was about 7 percent, while the prevalence of high-risk oral HPV infection was 4 percent.

    Now lets do some calculations.With 79 million people infected, about 20 million men and about 16 million women will have the high risk genital HPV infections. But the number of men who were diagnosed with any HPV associated cancers in 2015 was 18,939 (less than 0.1%), and the number of women diagnosed with any HPV-associated cancer that same year was 24,432 (about 0.15%). This means that less than 1 in a thousand infected men, and less than 2 in a thousand infected women, will be diagnosed with an HPV genital cancer each year.

    That’s the risk each year. What about cumulative lifetime risk (since we live many, many years)? For individuals not vaccinated against HPV (remember, vaccinated people are protected), the cumulative risk of developing an HPV-associated cancer was 1.4% in white women, and about 0.98% in white men. Thus, about 1 in 71 white women will develop one of these cancers, and about 1 in 100 white men will. If we focus just on cervical cancer, the estimated lifetime risk for developing cervical cancer is only 0.68%, or about 1 in 147 women.

    Howlader, et al SEER cancer statistics review, 1975-2009 (vintage 2009 populations). National Cancer Institute, https://seer.cancer.gov/archive/csr/1975_2009_pops09/.

    This data has also been broken down by various ethnic/racial groups (white, Asian, hispanic, and black). Here are some of the findings:

    The prevalence of oral high risk HPV strains was lower in Asians than other groups.

    The prevalence of high-risk oral HPV was higher among men than women in all race and Hispanic groups, although the difference was not significant among non-Hispanic Asian adults.

    The prevalence of any genital HPV was lowest among non-Hispanic Asian adults and highest among non-Hispanic black adults.
  • 5) How are HPV-caused cancers discovered? What are the symptoms?

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    These cancers are generally found once symptoms present themselves, except for cervical cancer, where abnormal cells (that have not yet become cancer) are often first detected by the Pap smear (or now, by swabs that look for the presence of HPV DNA or RNA). Details about the rational for using HPV testing in place of the Pap test can be found here.

    Cancers caused by HPV are found in a variety of tissues. These include the cervix, vagina, and vulva in women, the penis in men, and the oral cavity and anus in both men and women. Samples of tissue are generally removed and then tested using a variety of molecular techniques to determine if the tissue contains the HPV virus, and, if so, what strain of the virus it is. Knowing if a cancer is positive or negative for HPV can make a significant difference in choosing treatment options and in calculating the potential outcomes for the patient following treatment. This is because the virus actually plays a primary role in the process by which the normal cells are transformed into cancer cells.

    Here are some of the symptoms of oral cavity and oropharyngeal cancer:
    - A sore in the mouth that doesn't heal (common).
    - Pain in the mouth that doesn’t go away (also very common).
    - A lump or thickening in the cheek.
    - A white or red patch on the gums, tongue, tonsil, or lining of the mouth.
    - A sore throat or a feeling that something is caught in the throat that doesn’t go away.
    - Trouble chewing or swallowing.
    - Trouble moving the jaw or tongue.
    - Numbness of the tongue or other area of the mouth.
    - Swelling of the jaw that causes dentures to fit poorly or become uncomfortable.
    - Loosening of the teeth or pain around the teeth or jaw.
    - Voice changes.
    - A lump or mass in the neck (most common, see below).
    - Weight loss.
    - Constant bad breath.

    The most common symptom (for people who are later diagnosed with an HPV-caused cancer) that brings them to the doctor’s office are lumps in the neck.These lumps are caused by the migration of cancer cells from the oropharynx into the lymph nodes located there.

    Here are some of the symptoms of anal cancers:
    - Rectal bleeding.
    - Rectal itching.
    - A lump or mass at the anal opening.
    - Pain or a feeling of fullness in the anal area.
    - Narrowing of stool or other changes in bowel movements.
    - Abnormal discharge from the anus.
    - Swollen lymph nodes in the anal or groin areas.

    Screening for anal cancer is done using DARE (digital and rectal examination).

    Here are some of the symptoms of vaginal cancer:
    - Unusual vaginal bleeding, for example, after intercourse or after menopause.
    - Watery vaginal discharge.
    - A lump or mass in your vagina.
    - Painful urination.
    - Frequent urination.
    - Constipation.
    - Pelvic pain.

    Here are some of the symptoms of vulvar cancer:
    - An area on the vulva that looks different from normal – it could be lighter or darker than the normal skin around it, or look red or pink.
    - A bump or lump, which could be red, pink, or white and could have a wart-like or raw surface or feel rough or thick.
    - Thickening of the skin of the vulva.
    - Itching.
    - Pain or burning.
    - Bleeding or discharge not related to the normal menstrual period.
    - An open sore (especially if it lasts for a month or more).

    Here are some of the symptoms of cervical cancer:
    - Abnormal vaginal bleeding, such as bleeding after vaginal sex, bleeding after menopause, bleeding and spotting between periods, and having (menstrual) periods that are longer or heavier than usual. Bleeding after douching or after a pelvic exam may also occur.
    - An unusual discharge from the vagina − the discharge may contain some blood and may occur between your periods or after menopause.
    - Pain during sex.

    Here are some of the symptoms of penile cancer:
    - An area of skin becoming thicker.
    - Changes in the skin color.
    - A lump.
    - An ulcer (sore) that might bleed.
    - A reddish, velvety rash under the foreskin.
    - Small, crusty bumps.
    - Flat, bluish-brown growths.
    - Smelly discharge (fluid) or bleeding under the foreskin.
  • 6) How do they determine if a head and neck cancer tumor is positive for HPV?

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    There are updated guidelines that were published in Sept. 2018 by the American Society of Clinical Oncology (ASCO). They are:

    - HPV tumor status should be determined for newly diagnosed oropharyngeal squamous cell carcinomas.
    - HPV tumor status testing may be performed by surrogate marker p16 immunohistochemistry either on the primary tumor or from cervical nodal metastases only if an oropharyngeal primary tumor is present.
    - The threshold for positivity is at least 70% nuclear and cytoplasmic expression with at least moderate to strong intensity.
    - Additional confirmatory testing may be done at the discretion of the pathologist or treating clinician.
    - Pathologists should not routinely determine HPV tumor status in non-squamous carcinomas of the oropharynx or non-oropharyngeal squamous cell carcinomas of the head and neck.
    - When there is uncertainty of histologic type or whether a poorly differentiated oropharyngeal tumor is non-squamous, HPV tumor status testing may be warranted and at the discretion of the pathologist or treating clinician.

    Additional information is available from ASCO.
  • 7) What’s the link between failure to find oropharyngeal tumors via screening programs, and “cancers of unknown origin” aka “cancers of unknown primary (CUP)”?

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    The most common symptom that leads patients with HPV-caused oral cancers to visit their doctors is a lump in the neck. This lump may be caused by the growth of cancer cells in the lymph nodes in the neck. It can also be caused by other things that are NOT cancer. The lump will often be biopsied by doing a fine needle aspirate, which can reveal if cancer cells are actually present, and if they are HPV positive or not. The finding of a lump will lead your doctor to look for the place where a cancer might have actually started (again, if it is cancer) before it spread to the lymph nodes. Common places to look would be the tonsils, base of the tongue, and back of the throat. Sometimes, however, no source of the cancer can be readily found in these locations, in which case the tumor may be classified as being of unknown origin. About 3 to 5 percent of head and neck cancers are classified as cancers of unknown origin. To learn more about cancers of unknown origin, look at this page on the website of Beyond Five - The Face of Head and Neck Cancer.

    As to what percentage of these “cancers with unknown origins” are actually HPV positive, well, that answer is complicated. Results have varied in a number of different studies for reasons explained in the paper listed below. Here’s an important observation: as with other oropharyngeal cancers, having a cancer of unknown origin that is HPV positive is generally associated with a better outcome (i.e. it responds better to treatment) than those that are HPV negative.

    Reference: Sivars et al Human Papillomavirus as a Diagnostic and Prognostic Tool in Cancer of Unknown Primary in the Head and Neck Region Anticancer Research 36: 487-494 (2016) FREE ARTICLE

    Here’s a review on the basic issues of identifying the origins of CUP:
    Kato, S. Cancer of Unknown Primary in the Molecular Era.Trends in Cancer Volume 7, issue 5, p465-477, 2021. DOI:https://doi.org/10.1016/j.trecan.2020.11.002 FREE ARTICLE
  • 8) Does HPV play a role in the development of cervical “pre-cancers”?

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    Yes. Changes to cells in the cervix caused by the virus may be classified as pre-cancerous, and may lead to outright cervical cancer over time. These changes to the cervix can be detected early, leading to treatment that prevents the development of cervical cancer. Keep in mind that most women who have abnormal cervical screening test results do NOT have cervical cancer.

    Details can be found on the Understanding Cervical Changes: Next Steps After an Abnormal Screening Test page of the National Cancer Institute website.

    A number of studies have been conducted to determine if at-home HPV tests may be useful for cervical cancer prevention. These studies are designed specifically for screening of women who, for a variety of reasons, have difficulty visiting their doctors to be tested for cervical pre-cancers. Programs have been tested in Norway, Sweden, the Netherlands, and in the US. The study in the US found that 78% of the women used the testing kits they were sent, and that 12.4% of women who swabbed their vaginas (close to the cervix) were found to harbor high risk (i.e. cancer causing strains) of HPV. This percentage is nearly the same as what is observed in doctors offices. These women were informed that they should visit their doctors for follow up care.
    You can read about this study here, or look at the original paper: Des Marias et al
    Home Self-Collection by Mail to Test for Human Papillomavirus and Sexually Transmitted Infections. Obstetrics and Gynecology Nov. 5, 2018.

    The presence or absence of HPV is predictive of the future development of higher grade cervical pre-cancers as well as cervical cancer. The HPV FOr cerviCAL Cancer Trial (FOCAL) was a randomized trial comparing HPV testing to cytology. The FOCAL-DECADE cohort tracked women who received one HPV test during FOCAL, and were HPV negative, for up to 10 years to identify cervical intraepithelial neoplasia grade 2 or worse (CIN2+) and grade 3 or worse (CIN3+) detected through a provincial (British Columbia, Canada) screening program.

    “Conclusions:Among women with a single negative HPV test, long-term risk of CIN2+ detection was low, particularly through seven years of follow-up; thus, one negative HPV test appears to confer long-term protection from precancerous lesions. Even 10-year risk is sufficiently low to support extended testing intervals in average-risk populations. Impact:Our findings support the safety of screening policies using HPV testing alone at five-year or longer intervals.”

    Gottschlich, A, et al. Assessing 10-year safety of a single negative HPV test for cervical cancer screening: Evidence from FOCAL-DECADE cohort. Cancer Epidemiology, Biomarkers & Prevention, doi: 10.1158/1055-9965.EPI-20-1177

    The strain of HPV that you are infected with can make a difference in how your cancer progresses. Efforts are underway to understand how this works by doing DNA sequencing of the virus in clinical samples. This program is known as HPVDeepSeq. This has led to an understanding that there are six different “classes” of HPV infections. Still to be determined is if knowing the exact details about the infection will lead to differences in treatments or outcomes. It’s a complex subject, and the answers to these questions are simply not known yet.
    A rapid approach to profiling the HPV virome for multiple applications in discovery and therapeutics.
  • 9) Is there a blood test that can be used to screen head and neck cancer patients and determine if they are likely to have a recurrence?

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    I don’t know of any such test on the market, but there is one in development from researchers at the University of North Carolina Lineberger Comprehensive Cancer Center. It’s designed to measure HPV fragments that have been released into the blood by dead or dying cancer cells. It can distinguish these HPV fragments from HPV that may be present from an active infection. The test is being developed as an alternative way of following patients after their treatments have concluded. If it works, it may enable doctors to begin treatment earlier for tumors that were not eradicated on previous treatments. It would also save money on fiberoptic exams and CT scans, which would enable these patients to be spared excess radiation exposure. Since the test is measuring HPV fragments, it would not be appropriate for patients who have head and neck cancers that are HPV negative. In theory this test could also work on other HPV positive cancers such as cervical and anal cancers.

    Investigators from the University of North Carolina Lineberger Comprehensive Cancer Center prospectively evaluated a ctHPV-DNA liquid biopsy in 115 patients who had completed definitive chemoradiotherapy for HPV-positive OPSCC. Each patient had PET/CT imaging 3 months after finishing treatment. Investigators tested patients for ctHPV-DNA at 6- to 9-month intervals.

    During a median follow-up of 23 months, 28 patients tested positive for ctHPV-DNA, including 16 patients who had two consecutive positive tests. Also during follow-up, 15 patients developed biopsy-proven recurrence of OPSCC; all 15 had two consecutive positive tests for ctHPV-DNA. The median time from ctHPV-DNA positivity to recurrence was 3.9 months.

    Consecutive positive tests had a positive predictive value of 94%. The previous report from the study showed that a negative test had a negative predictive value of 100%. The test very well could have value in the management of patients with other types of HPV-related cancers. Investigators have already examined the rate of ctHPV-DNA clearance as a biomarker for response to treatment and a possible decision-making tool for treatment de-escalation.

    The testing technology has been licensed to Naveris for commercial development, and multiple medical centers have already partnered with the company to conduct studies across a variety of HPV-related diseases.

    Details can be found at HPV blood test shows promise for tracking head and neck cancer after treatment.

    Chera BS, et al Plasma circulating tumor HPV DNA for the surveillance of cancer recurrence in HPV-associated oropharyngeal cancer. J Clin Oncol 2020; DOI: 10.1200/JCO.19.0244. FREE download

    A completely different blood test is being developed for the detection of ALL cancer types. Researchers have shown that the test has a 0.7% false positive rate for cancer detection, meaning that less than 1% of people would be wrongly identified as having cancer. The test was able to predict the tissue in which the cancer originated in 96% of samples, and it was accurate in 93%.

    Cancer cells shed DNA into the blood, and this contributes to what is known as cell-free DNA (cfDNA). However, as the cfDNA can come from other types of cells as well, it can be difficult to pinpoint cfDNA that comes from the tumors. The blood test reported in this study analyses chemical changes to the DNA called "methylation" that usually control gene expression. Abnormal methylation patterns and the resulting changes in gene expression can contribute to tumor growth, so these signals in cfDNA have the potential to detect and localisz cancer. The blood test targets approximately one million of the 30 million methylation sites in the human genome. A machine learning algorithm was used to predict the presence of cancer and the type of cancer based on the patterns of methylation in the cfDNA. The algorithm was trained using a methylation database of cancer and non-cancer signals in cfDNA and is owned by the company involved in this research, GRAIL, Inc. (California, USA).

    Senior author of the paper listed below, Dr Michael Seiden (MD, PhD), President of US Oncology (Texas, USA), said: “Our earlier research showed that the methylation approach outperformed both whole genome and targeted sequencing in the detection of multiple deadly cancer types across all clinical stages, and in identifying the tissue of origin. It also allowed us to identify the most informative regions of the genome, which are now targeted by the refined methylation test that is reported in this paper.”

    In the part of the Circulating Cell-free Genome Atlas (CCGA) study reported below, blood samples from 6,689 participants with previously untreated cancer (2482 patients) and without cancer (4207 patients) from North America were divided into a training set and a validation set. Of these, results from 4316 participants were available for analysis: 3052 in the training set (1531 with cancer, 1521 without cancer) and 1264 in the validation set (654 with cancer and 610 without cancer). Over 50 types of cancer were included.

    The machine learning classifier analyzed blood samples from the participants to identify methylation changes and to classify the samples as cancer or non-cancer, and to identify the tissue of origin. The classifier’s ability to correctly identify when cancer was present (the true positive rate) was also consistent between the two sets. In 12 types of cancer that are often the most deadly (anal, bladder, bowel, esophageal, stomach, head and neck, liver and bile duct, lung, ovarian and pancreatic cancers, lymphoma, and cancers of white blood cells such as multiple myeloma), the true positive rate was 67.3% across clinical stages I, II and III. These 12 cancers account for about 63% of cancer deaths each year in the USA and, at present, there is no way of screening for the majority of them before symptoms show. The true positive rate was 43.9% for all cancer types in the study across the three clinical stages.

    Detection improved with each cancer stage. In the 12 pre-specified cancers, the true positive rate was 39% in stage I, 69% in stage II, 83% in stage III and 92% in stage IV. In all of more than 50 cancer types, the corresponding rates were 18%, 43%, 81% and 93%, respectively.

    The test was also consistent between the training and validation sets in its ability to identify the tissue where cancer had originated, with an accuracy of 93% in the validation set.

    A strength of the CCGA study is that it includes more than 15,000 participants from 142 clinics in North America, ensuring results are generalizable to a diverse population. Ongoing studies are assessing the test’s performance in even broader populations. Limitations include: all the participants with cancer had already been diagnosed with cancer (e.g. via screening or patients presenting with symptoms); the study was not designed to establish the test’s impact on death from cancer or other causes; at the time of this analysis, not all patients had been followed for a year, which is needed to ensure their non-cancer status was accurate; and some inaccuracy occurred in the detection of the tissue of origin for cancers that are driven by the human papilloma virus (HPV), such as cancers of the cervix, anus, and head and neck – this information is being used to improve the test’s performance.

    M.C. Liu et al. (2020) Sensitive and specific multi-cancer detection and localization using methylation signatures in cell-free DNA, Annals of Oncology. DOI: https://doi.org/10.1016/j.annonc.2020.02.011 FREE download

    Associated ClinicalTrials.gov numbers: NCT03085888, NCT03934866, NCT04241796.
  • 10) What’s the story on efforts to develop a new types of screening test for cervical cancer that’s not solely based on either cytology (like the Pap test) or on HPV status, but is instead based on DNA sequencing, PCR, or epigenomics i.e. a measure of DNA methylation? Do these new tests in development look promising?

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    A number of different approaches are being looked at that may have advantages over currently available tests.

    Here is an interesting development that may lead to a less expensive and more accurate test than a combination of standard Pap smears with HPV testing. The idea is to look for a “signature” methylation pattern in the DNA of cells scraped from the cervix that indicates the presence of cervical precancers that are likely to develop into outright cancers. Pap smears can detect only about half of cervical precancers, and HPV tests only determine if a cancer causing form of the virus is present, not whether or not it will cause cancer. The new test, called 5S, should be cheaper if it proves out than existing tests, and require fewer visits to the clinic. That’s because it detects a greater proportion of high-grade disease with a high short-term risk of cervical cancer during an initial screen than the other approaches.

    Here’s the paper:
    Cook et al Evaluation of a validated methylation triage signature for human papillomavirus positive women in the HPV FOCAL cervical cancer screening trial. Int. J. Cancer: 9999, 1–9 (2018) (FREE DOWNLOAD).

    Another new test is HPV-RNA Seq, which is being looked at as an alternative to biopsy for screening for cervical precancers. As the authors stated, “"HPV RNA-Seq is a unique test that combines the advantages of molecular assays (HPV typing) and cervical cytology (cell phenotyping).” The team utilized HPV RNA-Seq to analyze samples from 55 patients with precancerous cervical lesions in a proof of concept study. 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.

    Here’s the paper:
    Perot, P. et al Broad-Range Papillomavirus Transcriptome as a Biomarker of Papillomavirus-Associated Cervical High-Grade Cytology. J Mol Diagn 2019, 21: 768e781; https://doi.org/10.1016/j.jmoldx.2019.04.010. (FREE DOWNLOAD)
  • 11) What was learned from a study in which people were screened for oral cancers? Isn’t it easy to find cancer this way?

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    While it would seem that cancer screening programs should be easy to run, in practice they turn out to be more problematic than most people would think. In one study, otolaryngologists (doctors who specialize in head and neck diseases) were asked to screen individuals who came to a free community clinic. 761 people were screened by being asked about symptoms (medical history) as well as being given a physical exam. Amazingly, 47% of the people (356) screened had one or more symptoms that could be indicative of oral cancer. The most frequent symptoms were hoarseness and difficulty swallowing. It was suspected that 41 of these 356 people actually had cancer. Despite being told this, 22 never returned for a follow up visit. Twelve individuals had a negative workup, and seven were actually confirmed to have either pre-malignant changes or cancer. Four cases of squamous cell carcinoma were found in this group. Interestingly, these four were in the vocal folds, the supra glottis, or the pharyngeal wall.

    The data illustrates the problem with screening programs. Most oral cancer screenings are done by dentists, but in this report it was otolaryngologists who did the study. Lots of people had one or more cancer symptoms, but many people never returned for follow up care. While many people had broad cancer symptoms, in the end less than 1 in 100 people actually had cancer. And only one of those four cancers might have been seen in a screen by dentists.

    Shuman et al Demographics and Efficacy of Head and Neck Cancer Screening. Otolaryngol Head Neck Surg. 2010 September ; 143(3): . doi:10.1016/j.otohns.2010.05.029.

    While cancer screening programs in general sound good, the results do not always meet up with expectations. In a recent review, looking at breast, colon, prostate, and lung cancer screening programs, the percentage of deaths prevented by the screen ranged from 9 to 27 percent (that is, the screen failed to prevent 73 to 91 percent of the deaths). Often glossed over is the harms that the screening programs can inflict, including radiation exposure, colon puncturing, infections following prostate cancer biopsies, and worries inflicted by false positive results.

    Kim et al Cancer screening: A modest proposal for prevention. Cleveland Clinic J. Medicine 86, (3), 2019. doi:10.3949/ccjm.86a.18092
  • 12) I hear there’s a new imaging system being tested in clinical trials for detecting head and neck cancers during surgery. What’s the story?

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    The device, called the Otis Wide Field OCT (by Perimeter Medical Imaging), is an ultra-high resolution imaging system that can image tumor specimens in real time during surgery, allowing surgeons to remove all of the cancerous tissue during one procedure, rather than waiting for traditional pathology results to come in afterward, which can often lead to additional procedures. Patients who are participating in the trial agree to have their tumors placed in the system for imaging, which is then compared to the standard pathology evaluation.

    The technology is already being used in ophthalmology, cardiology and dermatology. The current clinical trial will determine if it is, or is not, useful in the setting of head and neck cancers.

    According to the company’s website:
    “The OTIS platform has the potential to make a significant positive impact as an adjunct tool in multiple clinical areas that rely on tissue visualization and assessment such as excised tissue assessment, biopsy assessment, tissue viability assessment for transplantation and tissue triaging selection for genomic-molecular studies and bio-banking.

    High-resolution subsurface image volumes of intact excised tissue

    Automated full specimen scanning

    Intra-operative, real-time results

    Orientation representation

    Non-destructive analysis (preserves entire sample for pathology)

    Interdisciplinary clinical use”

  • 13) Is persistent detection of oral HPV DNA after completion of primary therapy associated with recurrence and survival among patients with HPV-positive oral or oropharyngeal cancer?

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    Yes. In a cohort study of 396 patients, HPV DNA that was identical in type to that found in the tumor was detectable in oral rinses at diagnosis in 80% of patients with HPV-positive oropharyngeal cancer. In a subset of patients with HPV-positive tumors — about 14 percent — the prevalence of oral HPV DNA didn't decline with treatment. Persistent detection of this HPV DNA after completion of primary therapy was significantly associated with an increased risk of cancer recurrence and death. Two-year overall survival was significantly lower among the HPV-positive patients with persistent detection of tumor-type HPV after therapy than among those without detectable tumor-type DNA after therapy (68% vs 95%), as was recurrence-free survival (55% vs 88%). One shortcoming of the study was that the typical follow-up time of about 2 years may have underestimated associations between HPV persistence and cancer recurrence.

    Fakhry, C. et al Association of Oral Human Papillomavirus DNA Persistence With Cancer Progression After Primary Treatment for Oral Cavity and Oropharyngeal Squamous Cell Carcinoma. JAMA Oncol. (2019). doi:10.1001/jamaoncol.2019.0439
  • 14) Might it be possible someday to screen women at risk for developing cervical cancer by simply looking for HPV DNA in their urine, thereby eliminating the need for Pap screens and cervical HPV testing?

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    Maybe. A study was done to optimize conditions for detecting evidence of cancer causing strains of HPV (HR-HPV) in urine; to determine the concordance for HR-HPV detection in matched urine, vaginal and cervical samples; to compare the sensitivity of HPV testing for the detection of CIN2+ in matched samples; and to determine the overall acceptability of urine testing for cervical screening. Initial results looked promising, but would need to be replicated in a much larger study. The urine needed to have preservative added to protect the HPV DNA from degradation.

    Sargent, A et al Cross-sectional study of HPV testing in self-sampled urine and comparison with matched vaginal and cervical samples in women attending colposcopy for the management of abnormal cervical screening. BMJ Open 2019;9:e025388. doi:10.1136/bmjopen-2018-025388. FREE online paper

    Here’s another article that also suggests that urine (in this case first-void urine) may be useful in screen women for cervical cancer.

    Van Keer, S et al. High risk HPV testing in first-void urine for cervical cancer screening: a clinical accurate alternative compared to cervical samples. HPV World World 178 (2021). FREE online paper.
  • 15) Given that so many men (and women) have oral HPV infections and don’t know it, are there any clinical trials being done to identify these people using blood tests?

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    Yes. The overall prevalence of oral HPV infections in men in the U.S. to thought to be upwards of 11 million—much higher than previously believed. At MD Anderson Cancer Center, investigators have launched the HOUSTON study, an acronym for “HPV-related Oropharyngeal and Uncommon Cancers Screening Trial of Men.” They are looking to recruit 5,000 men ages 50 to 64 years to provide blood and saliva samples for serologic HPV testing and oral HPV testing, respectively. Those who are found to have a positive antibody test will be asked to participate in a second phase of the study, which includes an intensive screening program run through MD Anderson’s oral pre-cancer clinic. The hope is that this study will reveal that serological HPV antibody testing is an effective screening tool for HPV-related cancer in men, and hope this becomes the oral equivalent to a pap smear. You can read more about this here.

    This clinical trial is based on studies done by Dr. Karen Anderson at Arizona State University. She has developed a serologic test that predicts extremely well the risk for HPV-related oropharyngeal cancer.” Her group has been able to show that serum antibodies to HPV early proteins, which are rare in the general population, are markers for oropharyngeal cancer. Specifically, they found that those who had antibodies to certain HPV antigens have a greater than 450-fold higher risk of oropharyngeal cancer compared with those who do not have the antibodies. You can read more about how this screening test is done here.

    Anderson KS, et al. Serum Antibodies to the HPV16 Proteome As Biomarkers For Head and Neck Cancer. Brit. J. Cancer 2011 June;104(12): 1896-905. PMID: 21654689. PMCID: PMC3111202. doi:10.1038/bjc.2011.171 FREE paper.

    Given that the incidence of HPV+ oropharyngeal cancers is also increasing in women as well, a blood test for these cancers should also be applicable for women.

  • 16) Are there any screening tests being looked at that can tell if HPV+ oropharyngeal cancer patients have either responded to their treatments, or that have potential to tell which patients may either (1) be eligible for dose de-escalation treatments, or (2) are unlikely to respond to standard chemo-radiation treatments?

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    Such a screening test is indeed being looked at. It measures HPV+ cancer cells that are circulating in the blood, so it’s a blood based test. The HPV (actually, the DNA that is the core of the virus) is measured by a technique known as droplet‐based digital PCR (ddPCR). Here are the results from an early study conducted in Paris, France. Forty‐seven (71%) patients showed a positive pre‐therapeutic HPV ctDNA at time of diagnosis. Interestingly, the quantity of HPV16 ctDNA at baseline, as assessed by ddPCR, was significantly correlated with the T/N/M status or OPSCC stages according to the 2018 new staging criteria for High Risk human papillomavirus (HR HPV) related OPSCC from American Joint Committee on Cancer (AJCC). Moreover, all recurrences and the majority (83%) of death reported events occurred in patients with positive HPV16 ctDNA at baseline. Finally, when post‐treatment blood samples were available (n=6), the kinetic of pre‐/post‐treatment HPV16 ctDNA was clearly associated with treatment success or failure.

    Veyer, D. et al. HPV circulating tumoral DNA quantification by droplet‐based digital PCR: a promising predictive and prognostic biomarker for HPV‐associated oropharyngeal cancers. International J. of Cancer 2019.

    In a similar vein, another group is looking at variations in how HPV functions in oral cancer cells to determine which patients will, and which ones won’t, respond to standard chemo-radiation treatment protocols. The idea is based on the fact that about 15% of HPV+ oral cancer patients do NOT respond very well to the standard treatments, and if one could identify these patients in advance, they could be diverted into other treatment approaches. According to these researchers, they have “developed a prognostic biomarker signature for identifcation of this subgroup of HPV+ OPSCC and validated it in independent cohorts of oropharyngeal and cervical carcinomas. These findings could translate to improved patient stratification for treatment deintensification and new therapeutic approaches for treatment-resistant HPV-related cancer.”

    Gleber-Netto, F.O. et al Variations in HPV function are associated with survival in squamous cell carcinoma. JCI Insight. 2019;4(1):e124762. https://doi.org/10.1172/jci. insight.124762.
  • 17) How many different strains of HPV can be measured in a single test?

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    I’m not sure what the record is, but I did come across this paper describing Type-Seq, which the authors describe as a high throughput way of measuring as many as 51 strains of HPV in a single biological specimen.

    Wagner, S. et al. Evaluation of TypeSeq, a Novel High- Throughput, Low-Cost, Next-Generation Sequencing-Based Assay for Detection of 51 Human Papillomavirus Genotypes. Journal of Infectious Diseases. 2019:220 (15 November).