Tsiodras et al. BMC Cancer 2010, 10:53 http://www.biomedcentral.com/1471-2407/10/53 and PCR in our study is the fact that GP5+/GP6+ pri- mers may actually miss some cases deleted in the L1 region of the virus. In addition, some of the samples exhibiting discordance may have infection with HPV types such as HPV 42, 44 or 68 not amplified by the used primers, but still detectable by the HC2 cocktails. Moreover, HC2 probe B cocktail can react with phylo- genetically related HPV types not represented in the probe such as HPV 67, CP 6108, and CP8061. Finally, the prevalence of latent infection differs across studies, depending upon demographic parameters; this may also affect the sensitivity and specificity of the two tests. Our results confirm the higher prevalence of HPV infection in women with abnormal cytology, in concor- dance with most studies so far published, that have observed that the increase in HPV prevalence is related to the increasing grade of squamous intraepithelial lesions [22-26]. Rates of HPV detection in samples with normal cytology vary widely in the literature in women with normal cytology and range from 4.9% to 30.4% for the HC2 assay and from 3 to 34.3% for PCR testing [18,19,21,25,27]. This wide range is explained by the dif- ferent nature of participating populations in such stu- dies, and by technical evolutions in the diagnostic tests used[21,28]. The higher analytical sensitivity of PCR explains the higher detection rates compared to HC2 in samples with low-grade cytological and no histological abnormalities and may be suggestive of the presence of latent HPV infection requiring a molecular test with higher analytical sensitivity. Similar to other observations, both hybrid capture and PCR HPV DNA testing showed a strong correlation with the diagnosis of CIN lesions or squamous cell car- cinoma [23,29]. The extremely high negative predictive values of both molecular tests underlie their importance in screening for high grade lesions and are in concor- dance with previous publications[18]. In high grade cytological and histological lesions, HPV detection rates appeared to be a little higher with PCR than with HC2 testing; for example HC2 did not identify high risk viruses in seven instances of CIN2+ histological lesions, in which cases PCR was positive. However positive and negative likelihood ratios were similar for positive HC2 (any result) or PCR - HPV positive testing (any result) both for CIN2+ or for CIN3+ histology. Actually, HC2 had a better PLR while PCR had a better NLR in both histological categories. This means that with a positive HC2 there was a greater likelihood of disease (≥ CIN2) than with PCR, while with a negative HPV PCR there was a lesser likelihood of disease (≥ CIN2) than with HC2. Nevertheless, in essence both tests gave similar results. Likelihood ratios can be used to calculate the odds of post test probabilities if multiplied by the odds of the prevalence of the disease. For example, a patient Page 6 of 8 in our study had a post test probability of disease (CIN2 +) of only 5.1% (using the Bayes nomogram) if she had a negative HC2 test (according to our study she had a pre-test probability of 20.4% of having a positive test). Similarly a negative PCR for high risk types 16, 18, 31 and 33 has a post test probability of disease (CIN2+) of 1.93% (Table 4). The limitation of a population that is not systematically screened, but is consecutively enrolled for deriving this data is of course recognized. However, both molecular HPV tests did not outperform cytology that had comparable if not better results, especially if the HSIL+ cytological lesion cutoff point was used. In our study all HSIL lesions by cytology were either CIN 2 or CIN 3 by histology and all cytological diagnoses of invasive carcinomas were subsequently confirmed by histology. Possible explanations for this observation include the following: a) the experience of all doctors involved; b) the increased alertness of both the referring gynecologist and the cytopathologist examining the slides; c) the fact that the Department of Cytopathology is accredited and therefore undergoes continuous quality assessment/quality control evaluation. Although none of the patients with normal cytology and an HPV infection had a biopsy proven lesion higher than CIN 1 in our study, these women should not be considered false-positive but as having a real risk for progression to abnormal cytological findings and cervi- cal neoplasia [30-33]. It is known that development of precancerous lesions may shortly follow infection with HPV, despite the belief that long-term infection is a pre- requisite for such an event [34]. Thus, these women should be prospectively followed by their gynecologist and submitted to cytology and other testing, as appro- priate[35,36]. The use of HPV testing has been recom- mended for women with ASCUS[37] and it has been shown that approximately one third of women with HSIL are subsequently identified from an initial ASCUS diagnosis [25]. These women, after positive HPV DNA testing should be referred for colposcopy[38]; our study underlines this argument, since one woman with ASCUS, had a single infection with HPV type 16 and biopsy disclosed squamous cell carcinoma. Nowadays, in the revised Bethesda 2001 classification system this case would probably be diagnosed as ASC-H. A molecular technique, more sensitive and specific than HC2 may be more appropriate for such patients. The current observations further confirm the associa- tion of high risk HPV types with cytological detection of HSIL or invasive carcinoma but also with histologically confirmed premalignant or malignant lesions [39-41]. All cases of CIN 2, CIN 3 or carcinomas harbored single or multiple HPV high risk oncogenic type infections. In our study single infections with HPV types 16 or 18 in cases of invasive carcinoma were strong evidence for