Comparison of the INNO-LiPA and PapType assays for detection of human papillomavirus in archival vulva dysplasia and/or neoplasia tissue biopsy specimens.
ABSTRACT INNO-LiPA and PapType human papillomavirus (HPV) genotyping assays were compared for detection of HPV genotypes on archival vulvar tissue. The INNO-LiPA assay detected 49 HPV-16 infections, compared with 47 detected by the PapType assay. The INNO-LiPA assay detected amplifiable DNA in 59 (91%) biopsy specimens, compared with 57 (88%) specimens for which amplifiable DNA was detected by the PapType assay. The two genotyping assays were highly comparable.
- SourceAvailable from: Chandini Raina Macintyre[Show abstract] [Hide abstract]
ABSTRACT: Objective. We investigate the prevalence of human papillomavirus (HPV) in oesophageal squamous cell carcinoma (OSCC) tissues compared to oesophageal tissue from healthy controls, in an Australian cohort. Methods. We conducted a hospital-based case-control study of 99 patients with OSCC and 100 healthy controls to examine the presence of HPV DNA. Paraffin tissues were tested using the PapType high-risk HPV detection and genotyping kit and with INNO-LiPA HPV Genotyping Extra. The biopsy samples were tested for HPV using a PCR-ELISA method based on the L1 consensus primer set PGMY09-PGMY11. Results. HPV DNA of the oncogenic genotype 16 was detected in 1/99 case specimens, a rate of 1010 per 100,000 (95% CI: 30-5500). All control specimens were negative for HPV. Significantly higher rates of smoking, other aerodigestive cancers, and mortality were seen among cases than controls. A pooled analysis of this study and the only other Australian case-control study found that 9/321 cases and 0/155 controls were positive for HPV. The pooled odds ratio for HPV being a risk factor for OSCC was 9.35 (95% CI: 0.47-190.33). Conclusion. Our results suggest that in this multifactorial cancer HPV may be an additional risk factor; although a larger, better powered study is needed.Journal of oncology. 01/2014; 2014:236482.
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ABSTRACT: Background HR HPV genotypes when assayed collectively, achieve high sensitivity but low specificity for the prediction of CIN2+. Knowledge of the specific genotypes in an infection may facilitate the use of HR HPV detection in routine clinical practice. Objectives To compare the rate of HR HPV detection and the accuracy of CIN2+ prediction between PapType test (Genera Biosystems) and other commercially available HR HPV assays, and to examine the value of full HPV genotyping. Study design. PreservCyt samples from 1099 women referred for abnormal cervical cytology were used. CIN2+ was chosen as the primary end-point but CIN3+ was also evaluated. A hierarchy of HR HPV genotypes was created using PPV and this was used to create 3 groups of genotypes with potentially different management. Results The PapType assay has a specificity of 22.4% and a sensitivity of 94.6% for CIN2+ prediction. Classification into Groups A (HPV33 and HPV16, very highly predictive), B (HPV31, 18, 52, 35, 58, 51 highly predictive) and C (HPV68, 45, 39, 66, 56, 59, intermediate predictive) could double the specificity (44.5%) but only slightly reduce the sensitivity for CIN2+ (91.5%) and CIN3+ (94.0%). Conclusions The PapType assay is a simple, reproducible and effective test for HR HPV detection and genotyping. HPV 33 was found to have a very high PPV and should therefore be managed as for HPV16.Journal of clinical virology: the official publication of the Pan American Society for Clinical Virology 01/2014; · 3.12 Impact Factor
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ABSTRACT: Genetic variation of 49 human papillomavirus (HPV) 6 and 22 HPV11 isolates from recurrent respiratory papillomatosis (RRP) (n = 17), genital warts (n = 43), anal cancer (n = 6) and cervical neoplasia cells (n = 5), was determined by sequencing the long control region (LCR) and the E6 and E7 genes. Comparative analysis of genetic variability was examined to determine whether different disease states resulting from HPV6 or HPV11 infection cluster into distinct variant groups. Sequence variation analysis of HPV6 revealed that isolates cluster into variants within previously described HPV6 lineages, with the majority (65%) clustering to HPV6 sublineage B1 across the three genomic regions examined. Overall 72 HPV6 and 25 HPV11 single nucleotide variations, insertions and deletions were observed within samples examined. In addition, missense alterations were observed in the E6/E7 genes for 6 HPV6 and 5 HPV11 variants. No nucleotide variations were identified in any isolates at the four E2 binding sites for HPV6 or HPV11, nor were any isolates found to be identical to the HPV6 lineage A or HPV11 sublineage A1 reference genomes. Overall, a high degree of sequence conservation was observed between isolates across each of the regions investigated for both HPV6 and HPV11. Genetic variants identified a slight association with HPV6 and anogenital lesions (p = 0.04). This study provides important information on the genetic diversity of circulating HPV 6 and HPV11 variants within the Australian population and supports the observation that the majority of HPV6 isolates cluster to the HPV6 sublineage B1 with anogenital lesions demonstrating an association with this sublineage (p = 0.02). Comparative analysis of Australian isolates for both HPV6 and HPV11 to those from other geographical regions based on the LCR revealed a high degree of sequence similarity throughout the world, confirming previous observations that there are no geographically specific variants for these HPV types.PLoS ONE 01/2013; 8(5):e63892. · 3.73 Impact Factor
JOURNAL OF CLINICAL MICROBIOLOGY, Nov. 2011, p. 3980–3982
Copyright © 2011, American Society for Microbiology. All Rights Reserved.
Vol. 49, No. 11
Comparison of the INNO-LiPA and PapType Assays for Detection
of Human Papillomavirus in Archival Vulva Dysplasia and/or
Neoplasia Tissue Biopsy Specimens?
Sarah E. Tan,1,2,3* Suzanne M. Garland,1,2,3,4Alice R. Rumbold,5,6and Sepehr N. Tabrizi1,2,3,4
Department of Microbiology and Infectious Diseases, The Royal Women’s Hospital, Melbourne, Victoria, Australia1;
Department of Obstetrics and Gynaecology, The University of Melbourne, Melbourne, Victoria, Australia2;
WHO HPV LabNet Regional Reference Laboratory—Western Pacific Region, Melbourne, Victoria,
Australia3; Murdoch Children’s Research Institute, Melbourne, Victoria, Australia4;
Menzies School of Health Research, Darwin, Northern Territory, Australia5; and
Discipline of Obstetrics and Gynaecology, The University of
Adelaide, Adelaide, South Australia, Australia6
Received 15 March 2011/Returned for modification 16 June 2011/Accepted 6 September 2011
INNO-LiPA and PapType human papillomavirus (HPV) genotyping assays were compared for detection of
HPV genotypes on archival vulvar tissue. The INNO-LiPA assay detected 49 HPV-16 infections, compared with
47 detected by the PapType assay. The INNO-LiPA assay detected amplifiable DNA in 59 (91%) biopsy
specimens, compared with 57 (88%) specimens for which amplifiable DNA was detected by the PapType assay.
The two genotyping assays were highly comparable.
Human papillomavirus (HPV) is involved in the etiology of
a number of human mucosal cancers, particularly those of the
anogenital region (2, 15). With the recent introduction and
further development of HPV prophylactic vaccines (5, 8), ep-
idemiological studies are needed to determine the prevalence
of HPV genotypes present in HPV-related cancer and precan-
cerous lesions. This requires evaluation of HPV retrospectively
by using archival tissues. Challenges often arise when examin-
ing HPV genotypes in paraffin-embedded tissues. DNA can
degrade due to extensive or inappropriate storage conditions,
resulting in cross-linking, fragmentation, and chemical modi-
fication, which can affect the detection by PCR (1, 4, 7).
This study compared two commercially available HPV
genotyping detection kits, the INNO-LiPA HPV Genotyp-
ing Extra (INNO-LiPA) (Innogenetics, Ghent, Belgium)
(14) and PapType high-risk (HR) HPV detection and geno-
typing (PapType) (Genera Biosystems, Melbourne, Victo-
ria, Australia) kits, to amplify and detect HPV genotypes in
archival vulvar tissue.
The INNO-LiPA assay uses SPF10 primers to amplify a
region of the HPV L1 gene and detects 28 anogenital HPV
genotypes, including 12 HR HPVs, 1 probable HR HPV, 7
possible HR HPVs, and 8 low-risk types (9). In addition to
having an internal control, the INNO-LiPA assay also had two
HPV internal controls (both 65-bp products from the L1 re-
gion). This assay uses conventional PCR and reverse line blot
hybridization for the detection of controls and HPV genotypes.
The PapType HPV genotyping test directs the amplification
of a region of the HPV L1 gene and allows for the identifica-
tion of 12 HR genotypes, 1 probable HR HPV, 1 possible HR
HPV, and 2 low-risk genotypes (9). A conventional PCR prod-
uct is hybridized to the HPV type-specific probes bound to
labeled silica microspheres, and binding events are read by
Biopsy specimens stored as formalin-fixed paraffin-embed-
ded tissue were obtained from 65 histologically diagnosed
cases of high-grade vulvar intraepithelial neoplasia (VIN-2/3)
(n ? 59) and invasive vulvar cancer (n ? 6), with patients
between 18 and 50 years of age at diagnosis.
Seven-micrometer sections were processed for histological
analysis by using a sandwich sectioning method (5). Outer
sections were stained with hematoxylin and eosin to confirm
the initial histological diagnosis, while the three inner sections
remained unstained for DNA extraction and HPV detection
(5). To minimize cross-contamination, the microtome blade
was changed and the microtome surface was cleaned with
xylene after sectioning of each sample. Regular changing of
gloves was performed between each sample, and the sectioning
of HPV-negative tissue specimens (negative control) was car-
ried out in a random order to ensure no DNA carryover. One
section was deparaffinized and DNA extracted as previously
described (12). For the INNO-LiPA assay, typing strips were
visually interpreted according to the manufacturer’s instruc-
Comparison of INNO-LiPA and PapType assays for prepa-
ration, amplification, and detection of HPV genotypes in ar-
chival vulvar tissue is shown in Table 1. Comparison of the
amplification efficiencies of internal controls and the abilities
to detect single-HPV-genotype infections is shown in Table 2.
Agreement in detection of HPV genotypes was determined by
Cohen’s kappa statistics, which are a measure of agreement
which is in excess of that due to chance. Due to the cross-
reactivity of the probes in the INNO-LiPA test, coinfection
with other HPV genotypes cannot be ruled out, and hence,
coinfection has been noted.
* Corresponding author. Mailing address: Department of Microbi-
ology and Infectious Diseases, The Royal Women’s Hospital, Locked
Bag 300, Parkville, Victoria 3052, Australia. Phone: (61-3) 8345-3678.
Fax: (61-3) 8345-2225. E-mail: email@example.com.
?Published ahead of print on 21 September 2011.
demonstrated that the PapType assay takes half the amount of
hands-on time of the INNO-LiPA assay. The PapType assay
produces computer-generated results, whereas the INNO-LiPA
assay requires manual reading of line blot strips. Amplification of
the respective internal controls demonstrated that 22% (n ? 13)
were successfully amplified using the INNO-LiPA assay, com-
pared with 31% (n ? 20) amplified with the PapType assay (P ?
and detected in 56% (n ? 18) and 71% (n ? 46) for HPV control
1 and HPV control 2, respectively. There was almost perfect
agreement between assays in the detection of HPV-16 (? value ?
0.959) (P ? 0.84) and perfect agreement for the detection of
HPV-33 (? value ? 1.000), although the sample size was small for
the latter comparison (n ? 9). All biopsy specimens that were
internal control negative/HPV negative by the INNO-LiPA kit
(n ? 7) were also identified as internal control negative/HPV
negative by the PapType kit. Two cases were recorded as discor-
dant; both cases were HPV-16 positive using the INNO-LiPA
The INNO-LiPA assay detected 4 multiple-HPV-genotype infec-
tions (16 and 33, 16 and 33, 16 and 52, and 16 and 39), compared
with the PapType assay detecting 2 multiple-HPV-genotype in-
fections (16 and 33 and 16 and 39).
This study has shown that there is very good agreement
between the INNO-LiPA and PapType assays for the detection
of single infections, namely, HPV-16 and HPV-33, the only two
genotypes detected. This is in accordance with HPV-16 being
the most prevalent HPV genotype detected in high-grade VIN
and vulvar cancers, followed by HPV-33 (3, 10). HPV-18 was
not detected in any biopsy specimens in this study; this is in
accordance with other studies (11, 13), and this may be due to
a difference between HPV genotypes and tropisms for vulvar
epithelium. The PapType assay takes less hands-on time than
the INNO-LiPA assay, and classification of HPV genotype-
positive bands on the INNO-LiPA strip is subjective to inter-
pretation and may take additional time to complete, whereas
the PapType assay produces computer-generated results.
The discrepant results that were observed in this study may
be due to the amount of DNA added in each assay. The
INNO-LiPA assay requires 10 ?l, compared to 5 ?l for the
PapType assay, resulting in an initially higher concentration of
DNA in the PCR: HPV genotypes not detected may have been
present in low copy numbers (6). A number of specimens were
HPV genotype positive though negative for the respective in-
ternal control. This may be due to amplicon size of the internal
controls relative to HPV genotypes, as fragmentation and deg-
radation of DNA is often encountered with archival tissue, and
generation of larger amplicons is often difficult with archival
tissue (1, 12). In the small number of samples, the INNO-LiPA
assay detected 4 cases with multiple HPV types, whereas the
PapType assay detected 2 samples with multiple types; how-
ever, the two assays detected similar genotypes. Comparison of
the abilities of the two assays to detect multiple HPV infections
would need to be verified in a larger study.
In conclusion, the INNO-LiPA and PapType assays are com-
parable HPV genotyping tests when applied to vulvar archival
paraffin-embedded tissue for the detection of HPV genotypes.
The INNO-LiPA assay is able to detect a greater number of
low-risk HPV genotypes and employs a smaller amplicon; the
PapType assay has an automated result output and less
hands-on time. Both assays are efficient genotyping tests and
have contrasting benefits for future epidemiological studies in
relation to the detection of single and multiple HPV infections.
S.E.T. was supported by The Royal Women’s Hospital Post Grad-
uate Degree Scholarship from The Royal Women’s Hospital and the
Women’s Centre for Infectious Diseases, The Royal Women’s Hospi-
tal, Melbourne, Australia. A.R.R. is supported by the Jean B. Reid
Fellowship from the University of Adelaide Medical Endowment
We thank Tania Tabone for help in critical reading of this article.
Genera Biosystems provided PapType high-risk HPV detection and
S.M.G. and S.N.T. were previously members of the clinical devel-
opment advisory board at Genera Biosystems; however, this advisory
TABLE 2. Comparison of single infections detected using
INNO-LiPA and PapType HPV genotyping assays in
65 biopsy specimens from patients with high-grade
vulva dysplasia or vulva cancer
No. (%) of specimens with detection result
IC positive/HPV genotype negative
IC negative/HPV gentoype positive
HPV control 1d,e
HPV control 2d
IC and HPV negative
Total HPV genotypes detected58 56
aIC, internal control.
bAssessable indicates either positive for IC or an HPV genotype.
cEither MLC-1 positive by PapType or HLA-DPB1 positive by INNO-LiPA.
This parameter had a P value of 0.22.
dDetected by the INNO LiPA HPV genotyping test only.
eP ? 0.84.
fWe were unable to rule out coinfection with HPV-52 and -54.
TABLE 1. Comparison of INNO-LiPA and PapType kits for
preparation, amplification and detection of HPV genotypes
in 16 archival vulvar tissue biopsy specimens
ParameterINNO-LiPA kit PapType kit
Amount of DNA in
270-bp region of the
288-bp region of the alkali
myosin light chain
140-150 (depending on
Detection time (min)
Presentation of results
Reverse line blot assayFlow cytometry
Manual reading of line
blot strip (?1-2 min
VOL. 49, 2011NOTES 3981
board has ceased to exist. S.M.G. has received advisory board fees and
grant support from CSL Biotherapies and GlaxoSmithKline (GSK),
lecture fees from Merck, GSK, and Sanofi Pasteur, and funding
(through her employing institution) to conduct HPV vaccine studies
for Merck, Sharp and Dohme (MSD) and GSK and is a member of the
Merck Global Advisory Board and the Merck Scientific Advisory Com-
mittee for HPV. This relates to work outside this study. S.E.T. is the
recipient of a GSK Australian Postgraduate Support Grant for work
outside this study. CSL has provided funding to the authorship group
to support a workshop on genetic susceptibility to vulvar cancer.
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3982 NOTESJ. CLIN. MICROBIOL.