Our analytical framework allows estimation of HGAIN cases attributable to individual HPV genotypes in the context of multiple concurrent HPV infections, which are very common among HIV-infected MSM. Our results suggest that licensed and investigational HPV prophylactic vaccines have the potential to prevent a substantial proportion of HGAIN cases in this population.

The cobas human papillomavirus (HPV) test (cobas) was recently approved by the U.S. Food and Drug Administration (FDA) and identifies HPV16 and HPV18 separately as well as detecting a pool of 11 HR-HPV genotypes (HPV31, -33, -35, -39, -45, -51, -52, -56, -58, -59, -68) and also HPV66. We compared cobas, Linear Array (LA), and Hybrid Capture 2 (HC2) assays for detection of carcinogenic HPV DNA, and cobas and LA for detection of HPV16 and HPV18 DNA, among the first 1,852 women enrolled in the HPV Persistence and Progression Cohort (PaP Cohort) study. Specimens were tested by all 3 assays 1 year after an HC2-positive result. In 1,824 specimens with cobas results, cobas had an 85.9% agreement with HC2 and 91.0% agreement with LA for carcinogenic HPV detection. When results between cobas and HC2 disagreed, cobas tended to call more women HPV positive (P < 0.01). Categorizing cobas and LA results hierarchically according to cancer risk (HPV16, HPV18, other carcinogenic HPV genotypes, or carcinogen negative), there was a 90% agreement for all categories of HPV (n ‫؍‬ 1,824). We found good agreement between the two U.S. FDA-approved HPV tests, with discrepancies between the two assays due to specific characteristics of the individual assays. Additional studies are needed to compare HC2 and cobas for detecting and predicting CIN3 to understand the clinical implications of the discrepant test results between the two tests. In the United States, testing for a pool of high-risk genotypes of the human papillomavirus (HR-HPV) is currently used as an adjunct to cervical cytology for general screening. There are data supporting the individual detection of the two most carcinogenic genotypes, HPV16 and HPV18, which might be clinically useful for differentiating HPV-positive, cytology-negative women at higher and lower cancer risk (3, 7). The cobas HPV test (cobas; Roche Molecular Systems, Pleasanton, CA) was recently approved by the U.S. Food and Drug Administration (FDA) and identifies HPV16 and HPV18 separately as well as detecting a pool of 11 HR-HPV genotypes (HPV31,) and also HPV66. The test has been validated in some initial studies (1, 13), and we sought to further add to the literature by assessing the interassay agreement between cobas and two other well-validated HPV DNA assays using samples collected in specimen transport medium (STM) (Qiagen, Gaithersburg, MD).Specifically, we compared cobas to (i) Linear Array (LA) (Roche Molecular Systems), an HPV genotyping assay that, while not approved by the FDA, is widely used for research (4,5,11,14) and is CE marked for use in Europe, and (ii) the FDA-approved Hybrid Capture 2 assay (HC2) (Qiagen Corporation, Gaithersburg, MD), which targets the 13 HR-HPV genotypes and cross-reacts with HPV66 (as well as a few other possibly carcinogenic or low-risk types) (2). MATERIALS AND METHODSTo enrich the study population for HPV positivity, this study was nested within the HPV Persistence and Progression Cohort (PaP Cohort) study (9). Kaiser Permanente Northern California (KPNC) rout...

Results from a prototype real-time PCR assay that separately detected human papillomavirus genotype 16 (HPV16), HPV18, and 12 other carcinogenic HPV genotypes in aggregate (cobas 4800 HPV test) and results from a PCR assay that detects 37 HPV genotypes individually (Linear Array) were compared using a convenience sample of cervical specimens (n ‫؍‬ 531). The percentage of total agreement between the two assays was 94.7% (95% confidence interval, 92.5 to 96.5%). The Linear Array test was more likely than cobas 4800 HPV test to test positive for the 12 other carcinogenic HPV genotypes among women without evidence of cervical disease (P ‫؍‬ 0.004).Persistent cervical infections by approximately 15 carcinogenic human papillomavirus (HPV) genotypes cause cervical cancer and its immediate precursor lesions (17,22,27). DNA testing for carcinogenic HPV has proven itself to be more sensitive, albeit slightly less specific, for the detection of cervical intraepithelial neoplasia lesion grade 2 (CIN2) and more severe lesions (CIN2ϩ) (1,10,11,15,18,19). Carcinogenic HPV DNA testing of cervical samples has been introduced as an adjunct to cervical cytology into primary cervical cancer screening in the United States (20,26), and the International Agency for Research on Cancer has endorsed its use as a stand-alone option in primary cervical cancer screening (14).The introduction of carcinogenic HPV DNA testing with cervical cytology as a primary screening modality creates a clinical dilemma-the management of carcinogenic HPV DNA-positive, cytology-negative women (4), who remain at a low but significant risk of CIN2ϩ. One solution for identifying women at risk for CIN2ϩ in this subgroup is the separate detection of HPV genotype 16 (HPV16) and HPV18, the most carcinogenic HPV genotypes, referring HPV16-or HPV18-positive women immediately to colposcopy and following up with HPV16-and HPV18-negative women after a year (13,26). While the first generation of clinical HPV tests pooled all carcinogenic HPV genotypes and did not include separate HPV genotyping, at least for HPV16 and HPV18, most of the next generation of clinical tests will offer at least HPV16 and HPV18 genotyping. The utility of full HPV genotyping is less certain (2), as it has been shown that repeatedly testing positive for any carcinogenic HPV is a good proxy for HPV genotypespecific persistence, especially in women aged 30 years and older (7).One of the next-generation tests, the cobas 4800 HPV test, detects a pool of 12 carcinogenic HPV genotypes in aggregate, with concurrent, separate detection of HPV16 and HPV18. We conducted the first evaluation of the cobas 4800 HPV test and compared the results to previously reported results (8) generated by a now well-validated Linear Array HPV genotyping test (5, 6, 9, 12) and to cervical diagnoses.We acquired a convenience sample of 552 anonymized residual PreservCyt (PC; Hologic) specimens, after cytologic interpretation and the histologic diagnosis had been rendered, with human subject research approvals as previously ...

We evaluated a commercialized PCR assay, Linear Array, that detects 37 human papillomavirus (HPV) genotypes, using a sample of liquid cytology specimens (n ‫؍‬ 534). We found a strong association of an increasing level of HPV risk (HPV type 16 [HPV16] > HPV18 > other carcinogenic types > noncarcinogenic types > negative specimens) with increasing severities of cytologic interpretations (P Trend < 0.0005) and histologic diagnoses (P Trend < 0.0005).Carcinogenic human papillomavirus (HPV) testing has now been approved in the United States as an adjunct to cytology for triage of equivocal cytology at all ages and for general screening for women of Ն30 years old (15). Several studies have now shown that detection of specific carcinogenic HPV types, especially HPV type 16 (HPV16) and HPV18, may be useful in differentiating carcinogenic HPV-positive women at greater and lower risk of having or developing precancer, cervical intraepithelial neoplasia grade 3 (CIN3), or cancer (CIN3ϩ) (1,2,8). Identifying women with persistent carcinogenic HPV infection may also be clinically useful (9). Together, these data support a role for HPV genotyping in cervical cancer screening.Commercial HPV genotyping assays are currently under development. We evaluated one assay, Linear Array (LA; Roche Molecular Systems, Alameda, CA), a PCR-based genotyping assay that detects 37 HPV genotypes which is a commercialized version of the line blot assay (13). MATERIALS AND METHODSCervical specimens and data. We acquired blinded residual PreservCyt specimens, after cytologic interpretation had been rendered, from 125 women with normal cytology, 125 women with atypical squamous cell (ASC) cytology, 125 women with low-grade squamous intraepithelial lesion (LSIL) cytology, and 165 women with high-grade squamous intraepithelial lesion (HSIL) cytology or worse (ՆHSIL) from the Medical University of South Carolina. The institutional review board (IRB) of the Medical University of South Carolina approved the study, and the use of these specimens was deemed exempt from review by the NCI IRB. We subsequently excluded 12 specimens called ՆHSIL because of conditions unrelated to cervical abnormalities (e.g., endometrial carcinoma histopathology).In addition to the original histologic diagnosis, each case underwent a pathology review to ascertain the histologic diagnosis. Importantly, six cases originally called CIN2-3 and one case called CIN3 were reclassified as CIN2, and eight cases originally called CIN2-3 and one case called CIN2 were reclassified as CIN3. Also, two cases called CIN2 and two cases called CIN1-2 were reclassified as CIN1. We were not able to retrieve histology results for four women.To supplement the number of specimens from women with severe disease, the University of Arizona supplied 12 blinded specimens from women attending colposcopy, 10 of whom were diagnosed with CIN3 (including carcinoma in situ) and 2 of whom were diagnosed with cancer. Specimens were collected under an IRB-approved protocol, and their use was deemed exempt from ...

f Anal human papillomavirus (HPV) infections are common, and the incidence of anal cancer is high in HIV-infected men who have sex with men (MSM). To evaluate the performance of HPV assays in anal samples, we compared the cobas HPV test (cobas) to the Roche Linear Array HPV genotyping assay (LA) and cytology in HIV-infected MSM. Cytology and cobas and LA HPV testing were conducted for 342 subjects. We calculated agreement between the HPV assays and the clinical performance of HPV testing and HPV genotyping alone and in combination with anal cytology. We observed high agreement between cobas and LA, with cobas more likely than LA to show positive results for HPV16, HPV18, and other carcinogenic types. Specimens testing positive in cobas but not in LA were more likely to be positive for other markers of HPV-related disease compared to those testing negative in both assays, suggesting that at least some of these were true positives for HPV. cobas and LA showed high sensitivities but low specificities for the detection of anal intraepithelial neoplasia grade 2/3 (AIN2/3) in this population (100% sensitivity and 26% specificity for cobas versus 98.4% sensitivity and 28.9% specificity for LA). A combination of anal cytology and HPV genotyping provided the highest accuracy for detecting anal precancer. A higher HPV load was associated with a higher risk of AIN2/3 with HPV16 (P trend < 0.001), HPV18 (P trend ‫؍‬ 0.07), and other carcinogenic types (P trend < 0.001). We demonstrate that cobas can be used for HPV detection in anal cytology specimens. Additional tests are necessary to identify men at the highest risk of anal cancer among those infected with high-risk HPV.T he incidence of anal cancer is low in the general population but high among well-defined populations, such as women with a history of cervical precancer and men who have sex with men (MSM), particularly HIV-infected MSM, in whom the incidence is up to 80-fold higher than that in the general population (1, 2). A large proportion of anal cancer is caused by anal infections with carcinogenic human papillomavirus (HPV) (3), with approximately 80% to 85% caused by HPV16 or HPV18 (4, 5). Recent studies suggest that the epidemiology and biology of anal precancer are similar to those of cervical precancers. For example, a history of multiple anal sex partners is associated with a higher risk of anal HPV infection, and smoking is associated with an increased risk of anal precancer (6). Likewise, several well-characterized biomarkers for cervical cancer, such as HPV genotyping, HPV mRNA detection, and p16INK4a /Ki-67 immunocytochemistry, show similar clinical performance characteristics for the detection of anal precancer compared to those for cervical precancer (7).The high prevalence of anal cancer in high-risk populations, particularly HIV-infected MSM, and the similarity in natural histories between anal and cervical disease suggest that, similar to the successful cervical cancer screening model, the detection and treatment of anal precancer may prevent progre...