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Mishra SK, Nelson CW, Zhu B, Pinheiro M, Lee HJ, Dean M, Burdett L, Yeager M, Mirabello L. Improved detection of low-frequency within-host variants from deep sequencing: A case study with human papillomavirus. Virus Evol 2024; 10:veae013. [PMID: 38455683 PMCID: PMC10919477 DOI: 10.1093/ve/veae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/19/2024] [Accepted: 02/01/2024] [Indexed: 03/09/2024] Open
Abstract
High-coverage sequencing allows the study of variants occurring at low frequencies within samples, but is susceptible to false-positives caused by sequencing error. Ion Torrent has a very low single nucleotide variant (SNV) error rate and has been employed for the majority of human papillomavirus (HPV) whole genome sequences. However, benchmarking of intrahost SNVs (iSNVs) has been challenging, partly due to limitations imposed by the HPV life cycle. We address this problem by deep sequencing three replicates for each of 31 samples of HPV type 18 (HPV18). Errors, defined as iSNVs observed in only one of three replicates, are dominated by C→T (G→A) changes, independently of trinucleotide context. True iSNVs, defined as those observed in all three replicates, instead show a more diverse SNV type distribution, with particularly elevated C→T rates in CCG context (CCG→CTG; CGG→CAG) and C→A rates in ACG context (ACG→AAG; CGT→CTT). Characterization of true iSNVs allowed us to develop two methods for detecting true variants: (1) VCFgenie, a dynamic binomial filtering tool which uses each variant's allele count and coverage instead of fixed frequency cut-offs; and (2) a machine learning binary classifier which trains eXtreme Gradient Boosting models on variant features such as quality and trinucleotide context. Each approach outperforms fixed-cut-off filtering of iSNVs, and performance is enhanced when both are used together. Our results provide improved methods for identifying true iSNVs in within-host applications across sequencing platforms, specifically using HPV18 as a case study.
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Affiliation(s)
- Sambit K Mishra
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, P.O. Box B, Bldg. 430, Frederick, MD 21702, USA
| | - Chase W Nelson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
| | - Maisa Pinheiro
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
| | - Hyo Jung Lee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, P.O. Box B, Bldg. 430, Frederick, MD 21702, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
| | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, P.O. Box B, Bldg. 430, Frederick, MD 21702, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, P.O. Box B, Bldg. 430, Frederick, MD 21702, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
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Gradissimo A, Clarke MA, Xue X, Castle PE, Raine-Bennett TR, Schiffman M, Wentzensen N, Strickler HD, Burk RD. A novel human papillomavirus and host DNA methylation score and detection of cervical adenocarcinoma. J Natl Cancer Inst 2023; 115:1535-1543. [PMID: 37467068 PMCID: PMC10699843 DOI: 10.1093/jnci/djad134] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/09/2023] [Accepted: 07/04/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND The widespread introduction of Pap testing in the 1960s was followed by substantial reductions in the incidence of cervical squamous cell cancer (SCC). However, the incidence of cervical adenocarcinoma (ADC) did not decrease, likely because of low Pap test sensitivity for ADC and adenocarcinoma in situ (AIS). This study assessed a novel human papillomavirus (HPV) and host DNA Methylation Score for AIS and ADC screening. METHODS We measured methylation levels at CpG sites in the L2/L1 open reading frames of HPV16, HPV18, and HPV45-as well as 2 human loci, DCC and HS3ST2. Specifically, we tested exfoliated cervicovaginal cells from women in the HPV Persistence and Progression (PaP) cohort who were positive for 1 of HPV16, 18, or 45, including: 1) 176 with AIS/ADC, 2) 353 with cervical intraepithelial neoplasia-3 (CIN3) or SCC, and 3) controls who either cleared (HPV-Clearers; n = 579) or had persistent HPV16, 18, or 45 infection (HPV-Persisters; n = 292). CpG site-specific methylation percentages were measured using our reported next-generation methods. The Methylation Score was the average methylation percentage across all 35 CpG sites tested. RESULTS Each individual CpG site had higher methylation percentages in exfoliated cervicovaginal cells collected from patients with AIS/ADC, and as well as those with CIN3/SCC, relative to either control group (weakest P = .004). The Methylation Score for AIS/ADC had a sensitivity of 74% and specificity of 89%. The multivariate odds ratio (OR) between the Methylation Score (4th vs 1st quartile) for AIS/ADC was ORq4-q1 = 49.01 (PBenjamini-Hochberg = 4.64E-12), using HPV-Clearers as controls. CIN3/SCC had similar, albeit weaker, associations with the Methylation Score. CONCLUSIONS HPV16/18/45-infected women with Methylation Scores in the highest quartile had very high odds of AIS/ADC, suggesting they may warrant careful histologic evaluation of the cervical transition zone (eg, conization or loop electrosurgical excision procedure [LEEP]).
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Affiliation(s)
- Ana Gradissimo
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Immunology, Memorial Sloan Kettering Cancer Center, Manhattan, NY, USA
| | - Megan A Clarke
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Xiaonan Xue
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Philip E Castle
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Howard D Strickler
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Robert D Burk
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Departments of Microbiology & Immunology, Gynecology & Women’s Health, Albert Einstein College of Medicine, Bronx, NY, USA
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3
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Demarco M, Egemen D, Hyun N, Chen X, Moscicki AB, Cheung L, Carter-Pokras O, Hammer A, Gage JC, Clarke MA, Castle PE, Befano B, Chen J, Dallal C, He X, Desai K, Lorey T, Poitras N, Raine-Bennett TR, Perkins RB, Wentzensen N, Schiffman M. Contribution of Etiologic Cofactors to CIN3+ Risk Among Women With Human Papillomavirus-Positive Screening Test Results. J Low Genit Tract Dis 2022; 26:127-134. [PMID: 35249974 PMCID: PMC8940696 DOI: 10.1097/lgt.0000000000000667] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE The US screening and management guidelines for cervical cancer are based on the absolute risk of precancer estimated from large clinical cohorts and trials. Given the widespread transition toward screening with human papillomavirus (HPV) testing, it is important to assess which additional factors to include in clinical risk assessment to optimize management of HPV-infected women. MATERIALS AND METHODS We analyzed data from HPV-infected women, ages 30-65 years, in the National Cancer Institute-Kaiser Permanente Northern California Persistence and Progression study. We estimated the influence of HPV risk group, cytology result, and selected cofactors on immediate risk of cervical intraepithelial neoplasia grade 3 or higher (CIN 3+) among 16,094 HPV-positive women. Cofactors considered included, age, race/ethnicity, income, smoking, and hormonal contraceptive use. RESULTS Human papillomavirus risk group and cytology test result were strongly correlated with CIN 3+ risk. After considering cytology and HPV risk group, other cofactors (age, race/ethnicity, income, smoking, and hormonal contraceptive use) had minimal impact on CIN 3+ risk and did not change recommended management based on accepted risk thresholds. We had insufficient data to assess the impact of long-duration heavy smoking, parity, history of sexually transmitted infection, or immunosuppression. CONCLUSIONS In our study at the Kaiser Permanente Northern California, the risk of CIN 3+ was determined mainly by HPV risk group and cytology results, with other cofactors having limited impact in adjusted analyses. This supports the use of HPV and cytology results in risk-based management guidelines.
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Affiliation(s)
- Maria Demarco
- Division of Cancer Epidemiology and Genetics and Division of Cancer Prevention, National Cancer Institute, Bethesda, MD
| | - Didem Egemen
- Division of Cancer Epidemiology and Genetics and Division of Cancer Prevention, National Cancer Institute, Bethesda, MD
| | - Noorie Hyun
- Division of Cancer Epidemiology and Genetics and Division of Cancer Prevention, National Cancer Institute, Bethesda, MD
| | - Xiaojian Chen
- Division of Cancer Epidemiology and Genetics and Division of Cancer Prevention, National Cancer Institute, Bethesda, MD
| | | | - Li Cheung
- Division of Cancer Epidemiology and Genetics and Division of Cancer Prevention, National Cancer Institute, Bethesda, MD
| | - Olivia Carter-Pokras
- Division of Cancer Epidemiology and Genetics and Division of Cancer Prevention, National Cancer Institute, Bethesda, MD
| | | | - Julia C. Gage
- Division of Cancer Epidemiology and Genetics and Division of Cancer Prevention, National Cancer Institute, Bethesda, MD
| | - Megan A. Clarke
- Division of Cancer Epidemiology and Genetics and Division of Cancer Prevention, National Cancer Institute, Bethesda, MD
| | - Philip E. Castle
- Division of Cancer Epidemiology and Genetics and Division of Cancer Prevention, National Cancer Institute, Bethesda, MD
| | - Brian Befano
- Division of Cancer Epidemiology and Genetics and Division of Cancer Prevention, National Cancer Institute, Bethesda, MD
| | - Jie Chen
- Division of Cancer Epidemiology and Genetics and Division of Cancer Prevention, National Cancer Institute, Bethesda, MD
| | - Cher Dallal
- Division of Cancer Epidemiology and Genetics and Division of Cancer Prevention, National Cancer Institute, Bethesda, MD
| | - Xin He
- Division of Cancer Epidemiology and Genetics and Division of Cancer Prevention, National Cancer Institute, Bethesda, MD
| | - Kanan Desai
- Division of Cancer Epidemiology and Genetics and Division of Cancer Prevention, National Cancer Institute, Bethesda, MD
| | - Thomas Lorey
- Kaiser Permanente Northern California, San Francisco, CA
| | - Nancy Poitras
- Kaiser Permanente Northern California, San Francisco, CA
| | | | | | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics and Division of Cancer Prevention, National Cancer Institute, Bethesda, MD
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics and Division of Cancer Prevention, National Cancer Institute, Bethesda, MD
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Pinheiro M, Harari A, Schiffman M, Clifford GM, Chen Z, Yeager M, Cullen M, Boland JF, Raine-Bennett T, Steinberg M, Bass S, Xiao Y, Tenet V, Yu K, Zhu B, Burdett L, Turan S, Lorey T, Castle PE, Wentzensen N, Burk RD, Mirabello L. Phylogenomic Analysis of Human Papillomavirus Type 31 and Cervical Carcinogenesis: A Study of 2093 Viral Genomes. Viruses 2021; 13:1948. [PMID: 34696378 PMCID: PMC8540939 DOI: 10.3390/v13101948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/09/2021] [Accepted: 09/21/2021] [Indexed: 12/17/2022] Open
Abstract
Human papillomavirus (HPV) type 31 (HPV31) is closely related to the most carcinogenic type, HPV16, but only accounts for 4% of cervical cancer cases worldwide. Viral genetic and epigenetic variations have been associated with carcinogenesis for other high-risk HPV types, but little is known about HPV31. We sequenced 2093 HPV31 viral whole genomes from two large studies, one from the U.S. and one international. In addition, we investigated CpG methylation in a subset of 175 samples. We evaluated the association of HPV31 lineages/sublineages, single nucleotide polymorphisms (SNPs) and viral methylation with cervical carcinogenesis. HPV31 A/B clade was >1.8-fold more associated with cervical intraepithelial neoplasia grade 3 and cancer (CIN3+) compared to the most common C lineage. Lineage/sublineage distribution varied by race/ethnicity and geographic region. A viral genome-wide association analysis identified SNPs within the A/B clade associated with CIN3+, including H23Y (C626T) (odds ratio = 1.60, confidence intervals = 1.17-2.19) located in the pRb CR2 binding-site within the E7 oncogene. Viral CpG methylation was higher in lineage B, compared to the other lineages, and was most elevated in CIN3+. In conclusion, these data support the increased oncogenicity of the A/B lineages and suggest variation of E7 as a contributing risk factor.
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Affiliation(s)
- Maisa Pinheiro
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.P.); (M.S.); (M.Y.); (M.C.); (J.F.B.); (M.S.); (S.B.); (Y.X.); (K.Y.); (B.Z.); (L.B.); (S.T.); (P.E.C.); (N.W.)
| | - Ariana Harari
- Departments of Pediatrics and Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA;
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.P.); (M.S.); (M.Y.); (M.C.); (J.F.B.); (M.S.); (S.B.); (Y.X.); (K.Y.); (B.Z.); (L.B.); (S.T.); (P.E.C.); (N.W.)
| | - Gary M. Clifford
- Early Detection, Prevention and Infections Branch, International Agency for Research on Cancer (IARC/WHO), 150 cours Albert Thomas, CEDEX 08, 69372 Lyon, France; (G.M.C.); (V.T.)
| | - Zigui Chen
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China;
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.P.); (M.S.); (M.Y.); (M.C.); (J.F.B.); (M.S.); (S.B.); (Y.X.); (K.Y.); (B.Z.); (L.B.); (S.T.); (P.E.C.); (N.W.)
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
| | - Michael Cullen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.P.); (M.S.); (M.Y.); (M.C.); (J.F.B.); (M.S.); (S.B.); (Y.X.); (K.Y.); (B.Z.); (L.B.); (S.T.); (P.E.C.); (N.W.)
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
| | - Joseph F. Boland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.P.); (M.S.); (M.Y.); (M.C.); (J.F.B.); (M.S.); (S.B.); (Y.X.); (K.Y.); (B.Z.); (L.B.); (S.T.); (P.E.C.); (N.W.)
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
| | - Tina Raine-Bennett
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA;
| | - Mia Steinberg
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.P.); (M.S.); (M.Y.); (M.C.); (J.F.B.); (M.S.); (S.B.); (Y.X.); (K.Y.); (B.Z.); (L.B.); (S.T.); (P.E.C.); (N.W.)
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
| | - Sara Bass
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.P.); (M.S.); (M.Y.); (M.C.); (J.F.B.); (M.S.); (S.B.); (Y.X.); (K.Y.); (B.Z.); (L.B.); (S.T.); (P.E.C.); (N.W.)
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
| | - Yanzi Xiao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.P.); (M.S.); (M.Y.); (M.C.); (J.F.B.); (M.S.); (S.B.); (Y.X.); (K.Y.); (B.Z.); (L.B.); (S.T.); (P.E.C.); (N.W.)
| | - Vanessa Tenet
- Early Detection, Prevention and Infections Branch, International Agency for Research on Cancer (IARC/WHO), 150 cours Albert Thomas, CEDEX 08, 69372 Lyon, France; (G.M.C.); (V.T.)
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.P.); (M.S.); (M.Y.); (M.C.); (J.F.B.); (M.S.); (S.B.); (Y.X.); (K.Y.); (B.Z.); (L.B.); (S.T.); (P.E.C.); (N.W.)
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.P.); (M.S.); (M.Y.); (M.C.); (J.F.B.); (M.S.); (S.B.); (Y.X.); (K.Y.); (B.Z.); (L.B.); (S.T.); (P.E.C.); (N.W.)
| | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.P.); (M.S.); (M.Y.); (M.C.); (J.F.B.); (M.S.); (S.B.); (Y.X.); (K.Y.); (B.Z.); (L.B.); (S.T.); (P.E.C.); (N.W.)
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
| | - Sevilay Turan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.P.); (M.S.); (M.Y.); (M.C.); (J.F.B.); (M.S.); (S.B.); (Y.X.); (K.Y.); (B.Z.); (L.B.); (S.T.); (P.E.C.); (N.W.)
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
| | - Thomas Lorey
- Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA 94710, USA;
| | - Philip E. Castle
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.P.); (M.S.); (M.Y.); (M.C.); (J.F.B.); (M.S.); (S.B.); (Y.X.); (K.Y.); (B.Z.); (L.B.); (S.T.); (P.E.C.); (N.W.)
- Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.P.); (M.S.); (M.Y.); (M.C.); (J.F.B.); (M.S.); (S.B.); (Y.X.); (K.Y.); (B.Z.); (L.B.); (S.T.); (P.E.C.); (N.W.)
| | - Robert D. Burk
- Departments of Pediatrics and Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA;
- Department of Epidemiology & Population Health, and Obstetrics, Gynecology and Women’s Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.P.); (M.S.); (M.Y.); (M.C.); (J.F.B.); (M.S.); (S.B.); (Y.X.); (K.Y.); (B.Z.); (L.B.); (S.T.); (P.E.C.); (N.W.)
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Bee KJ, Gradissimo A, Chen Z, Harari A, Schiffman M, Raine-Bennett T, Castle PE, Clarke M, Wentzensen N, Burk RD. Genetic and Epigenetic Variations of HPV52 in Cervical Precancer. Int J Mol Sci 2021; 22:ijms22126463. [PMID: 34208758 PMCID: PMC8234014 DOI: 10.3390/ijms22126463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/21/2022] Open
Abstract
The goal of this study was to identify human papillomavirus (HPV) type 52 genetic and epigenetic changes associated with high-grade cervical precancer and cancer. Patients were selected from the HPV Persistence and Progression (PaP) cohort, a cervical cancer screening program at Kaiser Permanente Northern California (KPNC). We performed a nested case-control study of 89 HPV52-positive women, including 50 cases with predominantly cervical intraepithelial neoplasia grade 3 (CIN3) and 39 controls without evidence of abnormalities. We conducted methylation analyses using Illumina sequencing and viral whole genome Sanger sequencing. Of the 24 CpG sites examined, increased methylation at CpG site 5615 in HPV52 L1 region was the most significantly associated with CIN3, with a difference in median methylation of 17.9% (odds ratio (OR) = 4.8, 95% confidence interval (CI) = 1.9–11.8) and an area under the curve of 0.73 (AUC; 95% CI = 0.62–0.83). Complete genomic sequencing of HPV52 isolates revealed associations between SNPs present in sublineage C2 and a higher risk of CIN3, with ORs ranging from 2.8 to 3.3. This study identified genetic and epigenetic HPV52 variants associated with high risk for cervical precancer, improving the potential for early diagnosis of cervical neoplasia caused by HPV52.
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Affiliation(s)
- Katharine J. Bee
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (K.J.B.); (A.G.); (Z.C.); (A.H.)
- DBV Technologies, 92120 Montrouge, France
| | - Ana Gradissimo
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (K.J.B.); (A.G.); (Z.C.); (A.H.)
| | - Zigui Chen
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (K.J.B.); (A.G.); (Z.C.); (A.H.)
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ariana Harari
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (K.J.B.); (A.G.); (Z.C.); (A.H.)
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; (M.S.); (P.E.C.); (M.C.); (N.W.)
| | - Tina Raine-Bennett
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA;
| | - Philip E. Castle
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; (M.S.); (P.E.C.); (M.C.); (N.W.)
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA
| | - Megan Clarke
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; (M.S.); (P.E.C.); (M.C.); (N.W.)
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; (M.S.); (P.E.C.); (M.C.); (N.W.)
| | - Robert D. Burk
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (K.J.B.); (A.G.); (Z.C.); (A.H.)
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Microbiology & Immunology, and Obstetrics, Gynecology & Women’s Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Correspondence: ; Tel.: +1-718-430-3720
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Age-related distribution of uncommon HPV genotypes in cervical intraepithelial neoplasia grade 3. Gynecol Oncol 2021; 161:741-747. [PMID: 33795132 DOI: 10.1016/j.ygyno.2021.03.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 03/24/2021] [Indexed: 11/21/2022]
Abstract
AIM Cervical cancer prevention guidelines include Human Papillomavirus (HPV) test, cytology, and HPV-16/18 typing for triage to determine the risk of cervical intraepithelial neoplasia (CIN) grade 3 as the best proxy of cervical cancer risk. In doing that, they do not consider how age can modify the type-specific risk of CIN3. The present study aimed to evaluate the age-related distribution of HPV genotypes affecting the risk-assessment in cervical cancer screening programs: non-screening-type-HPV and non-HPV-16/18 in unvaccinated women with CIN3. METHODS Retrospective multi-institutional study, including HPV genotyped women with CIN3 on cone histology treated between 2014 and 2019. The sample was divided into three categories of age: <30, 30-44, ≥45. HPV genotypes were grouped in non-screening-type-HPV (not-including genotypes 16/18/31/33/35/39/45/51/52/56/58/59/66/68) and non-HPV-16/18. Associations and trends between different age-groups and HPV genotypes were measured. RESULTS 1332 women were analyzed. Non-screening-type-HPV CIN3 were 73 (5.5%). Non-HPV-16/18 were found in 417 participants (31.3%). Women over 45 associated with non-screening-type HPV [odds ratio (OR) = 1.87, 95% confidence interval (CI) 1.07-3.25; p = 0.027]. Non-screening-type-HPV prevalence increased significantly with age (3.9% vs 5.1% vs 9.0%, p = 0.016). Women under 30 showed a lower rate of non-HPV-16/18 (OR = 0.65, 95% CI 0.47-0.89; p = 0.007). There was a positive trend with age of non-HPV-16/18 CIN3 (23.6% vs 32.1% vs 38.0%, p = 0.0004). CONCLUSION The proportion of CIN3 lesions unrelated to genotypes detected by primary screening tests increased with age. This implies that age probably modifies the risk of CIN3 and possibly of cancer associated with HPV types. The risk-based recommendation should take into consideration age to define the management of HPV positive women.
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A proposed new generation of evidence-based microsimulation models to inform global control of cervical cancer. Prev Med 2021; 144:106438. [PMID: 33678235 PMCID: PMC8041229 DOI: 10.1016/j.ypmed.2021.106438] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/15/2021] [Accepted: 01/16/2021] [Indexed: 01/30/2023]
Abstract
Health decision models are the only available tools designed to consider the lifetime natural history of human papillomavirus (HPV) infection and pathogenesis of cervical cancer, and the estimated long-term impact of preventive interventions. Yet health decision modeling results are often considered a lesser form of scientific evidence due to the inherent needs to rely on imperfect data and make numerous assumptions and extrapolations regarding complex processes. We propose a new health decision modeling framework that de-emphasizes cytologic-colposcopic-histologic diagnoses due to their subjectivity and lack of reproducibility, relying instead on HPV type and duration of infection as the major determinants of subsequent transition probabilities. We posit that the new model health states (normal, carcinogenic HPV infection, precancer, cancer) and corollary transitions are universal, but that the probabilities of transitioning between states may vary by population. Evidence for this variability in host response to HPV infections can be inferred from HPV prevalence patterns in different regions across the lifespan, and might be linked to different average population levels of immunologic control of HPV infections. By prioritizing direct estimation of model transition probabilities from longitudinal data (and limiting reliance on model-fitting techniques that may propagate error when applied to multiple transitions), we aim to reduce the number of assumptions for greater transparency and reliability. We propose this new microsimulation model for critique and discussion, hoping to contribute to models that maximally inform efficient strategies towards global cervical cancer elimination.
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Bussani C, Malentacchi F, Andersson KL, Fambrini M, Coco C, Pavone D, Fantappiè G, Turrini I, Dubini V, Petraglia F, Sorbi F. High grade cervical intraepithelial neoplasia positive biopsy: the importance of accurate pre-operative workup. ACTA ACUST UNITED AC 2021; 72:413-419. [PMID: 33410312 DOI: 10.23736/s0026-4784.20.04587-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND In cervical cancer screening programs, women with abnormal cytology and confirmation by biopsy are referred for colposcopy for histological evaluation. METHODS We characterized the presence and the genotype of HPV by Linear Array HPV genotyping assay in cytological samples collected from about 400 women undergoing conization, with reported high CIN grade after biopsy. RESULTS The most prevalent genotype was HPV 16, with an increasing presence depending on the severity of the CIN and with the highest incidence in the 26-35 age range. In the group of younger women (<25) we found the highest percentage of CIN3 (39.3%) and the lowest of CIN1 (17.9%). An increase of CIN1 with increasing age was observed. A different distribution of HPV presence was observed depending on CIN grade (P<0.001): CIN1 HPV negative samples were 46.3%, CIN2: 5.8% and CIN3: 1.4%. Interesting, in the analyzed cohort, we observed the presence of 30% of CIN1. Moreover, within CIN1, 85% of them were associated to negative HPV detection, this observation suggested that the detection of HPV presence may be useful to identify low CIN grade that should be reconsidered for surgical treatment. CONCLUSIONS These findings suggest implementing the protocol for the management of women with high risk precancer lesions, with a further HPV test before surgical treatment. The evaluation of HPV presence and genotype before conization might represent a useful tool in reducing or postpone the conization treatment.
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Affiliation(s)
- Cecilia Bussani
- Department of Experimental, Clinical and Biomedical Sciences, University of Florence, Florence, Italy -
| | - Francesca Malentacchi
- Department of Experimental, Clinical and Biomedical Sciences, University of Florence, Florence, Italy
| | - Karin L Andersson
- Colposcopy Service, Toscana Centro Unit of Local Health, USL 3, Palagi Hospital, Florence, Italy
| | - Massimiliano Fambrini
- Department of Experimental, Clinical and Biomedical Sciences, University of Florence, Florence, Italy
| | - Chiara Coco
- Department of Experimental, Clinical and Biomedical Sciences, University of Florence, Florence, Italy
| | - Dora Pavone
- Department of Experimental, Clinical and Biomedical Sciences, University of Florence, Florence, Italy
| | - Giulia Fantappiè
- Department of Experimental, Clinical and Biomedical Sciences, University of Florence, Florence, Italy
| | - Irene Turrini
- Department of Experimental, Clinical and Biomedical Sciences, University of Florence, Florence, Italy
| | - Valeria Dubini
- Colposcopy Service, Toscana Centro Unit of Local Health, USL 3, Palagi Hospital, Florence, Italy
| | - Felice Petraglia
- Department of Experimental, Clinical and Biomedical Sciences, University of Florence, Florence, Italy
| | - Flavia Sorbi
- Department of Experimental, Clinical and Biomedical Sciences, University of Florence, Florence, Italy
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A Study of Partial Human Papillomavirus Genotyping in Support of the 2019 ASCCP Risk-Based Management Consensus Guidelines. J Low Genit Tract Dis 2020; 24:144-147. [PMID: 32243309 PMCID: PMC7141756 DOI: 10.1097/lgt.0000000000000530] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
INTRODUCTION The 2019 ASCCP Risk-Based Management Consensus Guidelines include recommendations for partial human papillomavirus (HPV) genotyping in management of abnormal cervical cancer screening results. The guidelines are based on matching estimates of cervical intraepithelial neoplasia (CIN) 3+ risk to consensus clinical action thresholds. In support of the guidelines, this analysis addresses the risks predicted by individual identification of HPV 16 and HPV 18. METHODS Risk estimates were drawn from a subset of women in the Kaiser Permanente Northern California screening program, whose residual cervical specimens were HPV typed as part of the HPV Persistence and Progression study. We calculated risk of CIN 3+ to assess how identification of HPV 16, HPV 18, or 12 other "high-risk" HPV types would influence recommended clinical management of new abnormal screening results, taking into account current cytologic results and recent screening history. Immediate and/or 5-year risks of CIN 3+ were matched to clinical actions identified in the guidelines. RESULTS Identification of HPV 16 at the first visit including HPV testing elevated immediate risk of diagnosing CIN 3+ sufficiently to mandate colposcopic referral even when cytology was Negative for Intraepithelial Lesions or Malignancy and to support a preference for treatment of cytologic high-grade squamous intraepithelial lesion. HPV 18 less clearly elevated CIN 3+ risk. CONCLUSIONS Identification of HPV 16 clearly mandated consideration in clinical management of new abnormal screening results. HPV 18 positivity must be considered as a special situation because of established disproportionate risk of invasive cancer. More detailed genotyping and use beyond initial management will be considered in guideline updates.
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2019 ASCCP Risk-Based Management Consensus Guidelines: Methods for Risk Estimation, Recommended Management, and Validation. J Low Genit Tract Dis 2020; 24:90-101. [PMID: 32243306 PMCID: PMC7147416 DOI: 10.1097/lgt.0000000000000528] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Supplemental digital content is available in the text. Objective To manage cervical screening abnormalities, the 2019 ASCCP management consensus guidelines will recommend clinical action on the basis of risk of cervical precancer and cancer. This article details the methods used to estimate risk, to determine the risk-based management, and to validate that the risk-based recommendations are of general use in different settings. Methods Based on 1.5 million patients undergoing triennial cervical screening by cotesting at the Kaiser Permanente Northern California from 2003 to 2017, we estimated risk profiles for different clinical scenarios and combinations of past and current human papillomavirus and cytology test results. We validated the recommended management by comparing with the estimated risks in several external data sources. Results Risk and management tables are presented separately by Egemen et al.1 and Demarco et al.2 Risk-based management derived from the Kaiser Permanente Northern California largely agreed with the management implied from the estimated risks of the other data sources. Conclusions The new risk-based guidelines present management of abnormal cervical screening results. By describing the steps used to develop these guidelines, the methods presented in this article can provide a basis for future extensions of the risk-based guidelines.
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11
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Demarco M, Hyun N, Carter-Pokras O, Raine-Bennett TR, Cheung L, Chen X, Hammer A, Campos N, Kinney W, Gage JC, Befano B, Perkins RB, He X, Dallal C, Chen J, Poitras N, Mayrand MH, Coutlee F, Burk RD, Lorey T, Castle PE, Wentzensen N, Schiffman M. A study of type-specific HPV natural history and implications for contemporary cervical cancer screening programs. EClinicalMedicine 2020; 22:100293. [PMID: 32510043 PMCID: PMC7264956 DOI: 10.1016/j.eclinm.2020.100293] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/11/2020] [Accepted: 02/11/2020] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND HPV testing is replacing cytology for cervical cancer screening because of greater sensitivity and superior reassurance following negative tests for the dozen HPV genotypes that cause cervical cancer. Management of women testing positive is unresolved. The need for identification of individual HPV genotypes for clinical use is debated. Also, it is unclear how long to observe persistent infections when precancer is not initially found. METHODS In the longitudinal NCI-Kaiser Permanente Northern California Persistence and Progression (PaP) Study, we observed the clinical outcomes (clearance, progression to CIN3+, or persistence without progression) of 11,573 HPV-positive women aged 30-65 yielding 14,158 type-specific infections. FINDINGS Risks of CIN3+ progression differed substantially by type, with HPV16 conveying uniquely elevated risk (26% of infections with seven-year CIN3+ risk of 22%). The other carcinogenic HPV types fell into 3 distinct seven-year CIN3+ risk groups: HPV18, 45 (13% of infections, risks >5%, with known elevated cancer risk); HPV31, 33, 35, 52, 58 (39%, risks >5%); and HPV39, 51, 56, 59, 68 (23%, risks <5%). In the absence of progression, HPV clearance rates were similar by type, with 80% of infections no longer detected within three years; persistence to seven years without progression was uncommon. The predictive value of abnormal cytology was most evident for prevalent CIN3+, but less evident in follow-up. A woman's age did not modify risk; rather it was the duration of persistence that was important. INTERPRETATION HPV type and persistence are the major predictors of progression to CIN3+; at a minimum, distinguishing HPV16 is clinically important. Dividing the other HPV types into three risk-groups is worth considering.
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Key Words
- AGC, Atypical glandular cells
- AIS, Adenocarcinoma in-situ
- ASC-H+, Atypical squamous cells - cannot exclude HSIL
- ASC-US, Atypical squamous cells of undetermined significance
- BD, Becton Dickinson
- CIN, Cervical intraepithelial neoplasia
- HC2, Hybrid Capture 2
- HPV genotype
- HPV outcome, Clearance
- HPV, human papillomavirus
- KPNC, Kaiser Permanente Northern California
- LSIL, Low-grade squamous intraepithelial lesion
- NCI, National Cancer Institute
- NILM, Negative for intraepithelial lesion or malignancy
- PCR, Polymerase chain reaction
- PaP, Persistence and Progression
- Persistence
- Progression
- STM, Specimen transport medium
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Affiliation(s)
- Maria Demarco
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, United States
- University of Maryland School of Public Health, College Park, MD, United States
| | - Noorie Hyun
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, United States
- Division of Biostatistics, Institute of Health and Equity, Medical College of Wisconsin, Milwaukee, WI, United States
| | | | - Tina R. Raine-Bennett
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, United States
| | - Li Cheung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, United States
| | - Xiaojian Chen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, United States
| | - Anne Hammer
- Department of Obstetrics and Gynecology, Aarhus University Hospital, Denmark
- Department of Clinical Medicine, Aarhus University, Denmark
| | - Nicole Campos
- Center for Health Decision Science, Department of Health Policy and Management, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Walter Kinney
- Regional Laboratory, Kaiser Permanente Northern California, Berkeley, CA, United States
| | - Julia C. Gage
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, United States
| | - Brian Befano
- Information Management Services Inc., Calverton, MD, United States
| | - Rebecca B. Perkins
- Department of Obstetrics and Gynecology, Boston Medical Center/Boston University School of Medicine, Boston, MA, United States
| | - Xin He
- University of Maryland School of Public Health, College Park, MD, United States
| | - Cher Dallal
- University of Maryland School of Public Health, College Park, MD, United States
| | - Jie Chen
- University of Maryland School of Public Health, College Park, MD, United States
| | - Nancy Poitras
- Regional Laboratory, Kaiser Permanente Northern California, Berkeley, CA, United States
| | - Marie-Helene Mayrand
- Department of Obstetrics and Gynecology, Université de Montréal and Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montreal, Canada
- Department of Social and Preventive Medicine, Université de Montréal and Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montreal, Canada
| | - Francois Coutlee
- Department of Microbiology, Université de Montréal and CRCHUM, Montreal, Canada
| | - Robert D. Burk
- Albert Einstein College of Medicine, Bronx, NY, United States
| | - Thomas Lorey
- Regional Laboratory, Kaiser Permanente Northern California, Berkeley, CA, United States
| | | | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, United States
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, United States
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12
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Malentacchi F, Bussani C, Pavone D, Anderson KL, Fambrini M, Cocco C, Fantappiè G, Pieralli A, Dubini V, Petraglia F, Sorbi F. HPV genotype distribution and age correlation in a selected Italian population undergoing conization. ACTA ACUST UNITED AC 2020; 72:1-11. [DOI: 10.23736/s0026-4784.20.04506-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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13
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Zhu B, Xiao Y, Yeager M, Clifford G, Wentzensen N, Cullen M, Boland JF, Bass S, Steinberg MK, Raine-Bennett T, Lee D, Burk RD, Pinheiro M, Song L, Dean M, Nelson CW, Burdett L, Yu K, Roberson D, Lorey T, Franceschi S, Castle PE, Walker J, Zuna R, Schiffman M, Mirabello L. Mutations in the HPV16 genome induced by APOBEC3 are associated with viral clearance. Nat Commun 2020; 11:886. [PMID: 32060290 PMCID: PMC7021686 DOI: 10.1038/s41467-020-14730-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 01/28/2020] [Indexed: 12/24/2022] Open
Abstract
HPV16 causes half of cervical cancers worldwide; for unknown reasons, most infections resolve within two years. Here, we analyze the viral genomes of 5,328 HPV16-positive case-control samples to investigate mutational signatures and the role of human APOBEC3-induced mutations in viral clearance and cervical carcinogenesis. We identify four de novo mutational signatures, one of which matches the COSMIC APOBEC-associated signature 2. The viral genomes of the precancer/cancer cases are less likely to contain within-host somatic HPV16 APOBEC3-induced mutations (Fisher's exact test, P = 6.2 x 10-14), and have a 30% lower nonsynonymous APOBEC3 mutation burden compared to controls. We replicate the low prevalence of HPV16 APOBEC3-induced mutations in 1,749 additional cases. APOBEC3 mutations also historically contribute to the evolution of HPV16 lineages. We demonstrate that cervical infections with a greater burden of somatic HPV16 APOBEC3-induced mutations are more likely to be benign or subsequently clear, suggesting they may reduce persistence, and thus progression, within the host.
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Affiliation(s)
- Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Yanzi Xiao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Gary Clifford
- Infections and Cancer Epidemiology Group, International Agency for Research on Cancer, 150 Cours Albert Thomas, 69372, Lyon, Cedex 08, France
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Michael Cullen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Joseph F Boland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sara Bass
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Mia K Steinberg
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Tina Raine-Bennett
- Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - DongHyuk Lee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Robert D Burk
- Departments of Pediatrics, Microbiology and Immunology, and Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Maisa Pinheiro
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Chase W Nelson
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - David Roberson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Thomas Lorey
- Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA, USA
| | | | - Philip E Castle
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Joan Walker
- University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Rosemary Zuna
- University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.
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Age-Related Changes in the Fraction of Cervical Intraepithelial Neoplasia Grade 3 Related to HPV Genotypes Included in the Nonavalent Vaccine. JOURNAL OF ONCOLOGY 2019; 2019:7137891. [PMID: 31781217 PMCID: PMC6875331 DOI: 10.1155/2019/7137891] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 08/21/2019] [Accepted: 10/22/2019] [Indexed: 11/25/2022]
Abstract
Objective The prevalence of some human papillomavirus (HPV) genotypes has been shown to change with age. So, also the distribution of HPV genotypes included in the nonavalent vaccine may not be the same at all ages, and this could mean that vaccine protection against cervical cancer may be affected by age. The present study aimed to evaluate whether there are age-related changes in the fraction of high-grade cervical intraepithelial neoplasia (CIN) attributable to HPV genotypes included in the nonavalent vaccine. Methods Two hundred four consecutive women undergoing conization with a histological diagnosis of CIN3 were retrospectively analyzed. All included women had a preconization HPV genotyping (HPV Sign® Genotyping Test). The women were divided into three groups according to age: <35, 35–44, and ≥45 years of age. Based on HPV genotypes detected in cervical lesions, the age-related changes in the expected vaccine protection were evaluated by the Cochran–Armitage test for trend. Results The fraction of CIN3 attributable to HPV genotypes included in the nonavalent vaccine showed a significant negative trend with increasing age, with potential vaccine protection of 82% after the age of 45 (p=0.006). The rate of HPV-16 and HPV-33, included in the vaccine, showed a negative trend with age (p=0.047 and p=0.044, respectively). Among HPV genotypes not covered by the vaccine, the rate of non-high-risk HPVs (genotypes: 53-54-70-73-82-85-87) showed a significant positive trend with increasing age (p=0.018). Conclusions Although the fraction of CIN3 attributable to genotypes included in the nonavalent HPV vaccine was high even after age 45, older women appeared to be more at risk of high-grade CIN related to HPV genotypes not included in the vaccine. Interestingly, older women showed a higher rate of precancerous cervical lesions associated with non-high-risk HPV. The present findings seem to raise the question about the management of cervical pathology at a later age in a future postvaccination era.
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Bonde J, Bottari F, Parvu V, Pedersen H, Yanson K, Iacobone AD, Kodsi S, Landoni F, Vaughan L, Ejegod DM, Sandri MT. Bayesian analysis of baseline risk of CIN2 and ≥CIN3 by HPV genotype in a European referral cohort. Int J Cancer 2019; 145:1033-1041. [PMID: 30895602 PMCID: PMC6617734 DOI: 10.1002/ijc.32291] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/24/2019] [Accepted: 02/25/2019] [Indexed: 12/16/2022]
Abstract
Whereas HPV16 and HPV18 have been the focus in current risk-based cervical cancer screening algorithms using HPV genotype information, mounting evidence suggests that oncogenic HPV types such as HPV31, 33, 52 and 58 pose a ≥CIN3 risk equivalent to or greater than that of HPV18, and the combined risk of HPV31 and HPV33 rivals even HPV16 in women above 30 years of age. Here, we evaluate the baseline risk of CIN2 and CIN3 by genotype in a colposcopy referral population from Denmark and Italy. In total, 655 women were enrolled upon a referral to colposcopy after a positive screening sample. All samples were HPV analyzed using Onclarity HPV assay with extended genotyping and combined with the histology outcomes, a Bayesian probability modeling was used to determine the risk per genotype assessed. The combined data for this referral population showed that the ≥CIN2 risk of HPV16 was 69.1%, HPV31 at 63.3%, HPV33/58 at 52.7%, HPV18 at 46.6% and HPV52 at 40.8%. For ≥CIN3, the risks were 44.3%, 38.5%, 36.8%, 30.9% and 16.8% for HPV16, HPV31, HPV18, HPV33/58 and HPV52, respectively, indicating that the baseline risk of disease arising from HPV16 is, not surprisingly, the highest among the oncogenic HPV genotypes. We find that the HPV genotype-specific ≥CIN2 and ≥CIN3 risk-patterns are so distinct that, for example, 35/39/68 and 56/59/66 should be considered only for low intensive follow-up, thereby proposing active use of this information in triage strategies for screening HPV-positive women.
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Affiliation(s)
- Jesper Bonde
- Molecular Pathology Laboratory, Department of Pathology, Copenhagen University, Hvidovre Hospital, Hvidovre, Denmark
| | - Fabio Bottari
- Laboratory Medicine Division, European Institute of Oncology, Milan, Italy
| | | | - Helle Pedersen
- Molecular Pathology Laboratory, Department of Pathology, Copenhagen University, Hvidovre Hospital, Hvidovre, Denmark
| | | | - Anna D Iacobone
- Preventive Gynecology Unit, European Institute of Oncology, Milan, Italy
| | - Salma Kodsi
- Becton Dickinson and Company, Sparks, MD, USA
| | - Fabio Landoni
- Department of Medicine and Surgery, University of Milan Bicocca, Milan, Italy
| | | | - Ditte M Ejegod
- Molecular Pathology Laboratory, Department of Pathology, Copenhagen University, Hvidovre Hospital, Hvidovre, Denmark
| | - Maria T Sandri
- Laboratorio Analisi Cliniche, Humanitas Research Hospital, Milan, Italy
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16
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Dovey de la Cour C, Guleria S, Nygård M, Trygvadóttir L, Sigurdsson K, Liaw KL, Hortlund M, Lagheden C, Hansen BT, Munk C, Dillner J, Kjaer SK. Human papillomavirus types in cervical high-grade lesions or cancer among Nordic women-Potential for prevention. Cancer Med 2019; 8:839-849. [PMID: 30632704 PMCID: PMC6382723 DOI: 10.1002/cam4.1961] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 12/11/2018] [Accepted: 12/16/2018] [Indexed: 12/29/2022] Open
Abstract
It is valuable to establish a population‐based prevaccination baseline distribution of human papillomavirus (HPV) types among women with high‐grade cervical intraepithelial neoplasia (CIN) grade 2 or 3 and cervical cancer in order to assess the potential impact of HPV vaccination. In four countries (Denmark, Norway, Sweden, and Iceland), we collected consecutive series of cervical cancers (n = 639) and high‐grade precancerous cervical lesions (n = 1240) during 2004‐2006 before implementation of HPV vaccination and subjected the specimens to standardized HPV genotyping. The HPV prevalence was 82.7% (95% confidence interval [CI] 79.0‐86.4) in CIN2, 91.6% (95% CI 89.7‐93.5) in CIN3, and 86.4% (95% CI 83.7‐89.1) in cervical cancer. The most common HPV types in CIN2/3 were HPV16 (CIN2: 35.9%, 95% CI 31.2‐40.6; CIN3: 50.2%, 95% CI 46.8‐53.6) and HPV31 (CIN2: 10.9%, 95% CI 7.8‐13.9; CIN3: 12.1%, 95% CI 9.9‐14.3), while HPV16 and HPV18 were the most frequent types in cervical cancer (48.8%, 95% CI 44.9‐52.7 and 15.3%, 95% CI 12.5‐18.1, respectively). The prevalence of HPV16/18 decreased with increasing age at diagnosis in both CIN2/3 and cervical cancer (P < 0.0001). Elimination of HPV16/18 by vaccination is predicted to prevent 42% (95% CI 37.0‐46.7) of CIN2, 57% (95% CI 53.8‐60.5) of CIN3 and 64% (95% CI 60.3‐67.7) of cervical cancer. Prevention of the five additional HPV types HPV31/33/45/52/58 would increase the protection to 68% (95% CI 63.0‐72.2) in CIN2, 85% (95% CI 82.4‐87.2) in CIN3 and 80% (95% CI 77.0‐83.2) in cervical cancer. This study provides large‐scale and representative baselines for assessing and evaluating the population‐based preventive impact of HPV vaccination.
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Affiliation(s)
| | - Sonia Guleria
- Unit of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Mari Nygård
- Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Laufey Trygvadóttir
- Icelandic Cancer Registry, Icelandic Cancer Society, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Kristjan Sigurdsson
- Icelandic Cancer Registry, Icelandic Cancer Society, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | | | - Maria Hortlund
- Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Camilla Lagheden
- Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Bo T Hansen
- Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Christian Munk
- Unit of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Joakim Dillner
- Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Susanne K Kjaer
- Unit of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark.,Department of Obstetrics and Gynecology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
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Chen Z, DeSalle R, Schiffman M, Herrero R, Wood CE, Ruiz JC, Clifford GM, Chan PKS, Burk RD. Niche adaptation and viral transmission of human papillomaviruses from archaic hominins to modern humans. PLoS Pathog 2018; 14:e1007352. [PMID: 30383862 PMCID: PMC6211759 DOI: 10.1371/journal.ppat.1007352] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 09/22/2018] [Indexed: 02/07/2023] Open
Abstract
Recent discoveries on the origins of modern humans from multiple archaic hominin populations and the diversity of human papillomaviruses (HPVs) suggest a complex scenario of virus-host evolution. To evaluate the origin of HPV pathogenesis, we estimated the phylogeny, timing, and dispersal of HPV16 variants using a Bayesian Markov Chain Monte Carlo framework. To increase precision, we identified and characterized non-human primate papillomaviruses from New and Old World monkeys to set molecular clock models. We demonstrate specific host niche adaptation of primate papillomaviruses with subsequent coevolution with their primate hosts for at least 40 million years. Analyses of 212 HPV16 complete genomes and 3582 partial sequences estimated ancient divergence of HPV16 variants (between A and BCD lineages) from their most recent common ancestors around half a million years ago, roughly coinciding with the timing of the split between archaic Neanderthals and modern Homo sapiens, and nearly three times longer than divergence times of modern Homo sapiens. HPV16 A lineage variants were significantly underrepresented in present African populations, whereas the A sublineages were highly prevalent in European (A1-3) and Asian (A4) populations, indicative of viral sexual transmission from Neanderthals to modern non-African humans through multiple interbreeding events in the past 80 thousand years. Remarkably, the human leukocyte antigen B*07:02 and C*07:02 alleles associated with increased risk in cervix cancer represent introgressed regions from Neanderthals in present-day Eurasians. The archaic hominin-host-switch model was also supported by other HPV variants. Niche adaptation and virus-host codivergence appear to influence the pathogenesis of papillomaviruses.
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Affiliation(s)
- Zigui Chen
- Departments of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Rob DeSalle
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY, United States of America
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, United States of America
| | - Rolando Herrero
- International Agency for Research on Cancer, World Health Organization, Lyon, France
- Proyecto Epidemiológico Guanacaste, Fundación INCIENSA, San José, Costa Rica
| | - Charles E. Wood
- Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC, United States of America
| | - Julio C. Ruiz
- Department of Veterinary Sciences, The University of Texas MD Anderson Cancer Center, Bastrop, Texas, United States of America
| | - Gary M. Clifford
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Paul K. S. Chan
- Departments of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Robert D. Burk
- Departments of Pediatrics, Microbiology and Immunology; Epidemiology and Population Health; Obstetrics, Gynecology and Woman’s Health, Albert Einstein College of Medicine, Bronx, NY, United States of America
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Abstract
Objective To inform impending postcolposcopy guidelines, this analysis examined the subsequent risk of CIN 3+ among women with a grade lower than CIN 2 (< CIN 2) colposcopy results, taking into account the referring results that brought them to colposcopy and cotest results postcolposcopy. Methods We analyzed 107,005 women from 25 to 65 years old, recommended for colposcopy at Kaiser Permanente Northern California. We estimated absolute risks of CIN 3+ among women: (1) recommended for colposcopy (precolposcopy), (2) following colposcopy and with histology results < CIN 2 (postcolposcopy), and (3) with cotest results 12 months after a < CIN 2 colposcopy (return cotest). Results After colposcopy showing < CIN 2 (n = 69,790; 87% of the women at colposcopy), the 1-year risk of CIN 3+ was 1.2%, compared with 6.3% at the time of colposcopy recommendation. Negative cotest results 1 year after colposcopy identified a large group (37.1%) of women whose risk of CIN 3+ (i.e., <0.2% at 3 years after postcolposcopy cotest) was comparable with women with normal cytology in the screening population. These risks are consistent with current guidelines recommending repeat cotesting 12 months after colposcopy < CIN 2 and a 3-year return for women with a negative postcolposcopy cotest. Conclusions Most women are at low risk of subsequent CIN 3+ after a colposcopy showing < CIN 2, especially those who are human papillomavirus–negative postcolposcopy, consistent with current management guidelines for repeat testing intervals. Before the finalizing the upcoming guidelines, we will consider additional rounds of postcolposcopy cotesting.
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19
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Cervical cancer screening and subsequent procedures in women under the age of 25 years between 2007 and 2013 in France: a nationwide French healthcare database study. Eur J Cancer Prev 2018; 27:479-485. [DOI: 10.1097/cej.0000000000000360] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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20
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Validation of a Human Papillomavirus (HPV) DNA Cervical Screening Test That Provides Expanded HPV Typing. J Clin Microbiol 2018; 56:JCM.01910-17. [PMID: 29491018 DOI: 10.1128/jcm.01910-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 02/26/2018] [Indexed: 12/14/2022] Open
Abstract
As cervical cancer screening shifts from cytology to human papillomavirus (HPV) testing, a major question is the clinical value of identifying individual HPV types. We aimed to validate Onclarity (Becton Dickinson Diagnostics, Sparks, MD), a nine-channel HPV test recently approved by the FDA, by assessing (i) the association of Onclarity types/channels with precancer/cancer; (ii) HPV type/channel agreement between the results of Onclarity and cobas (Roche Molecular Systems, Pleasanton, CA), another FDA-approved test; and (iii) Onclarity typing for all types/channels compared to typing results from a research assay (linear array [LA]; Roche). We compared Onclarity to histopathology, cobas, and LA. We tested a stratified random sample (n = 9,701) of discarded routine clinical specimens that had tested positive by Hybrid Capture 2 (HC2; Qiagen, Germantown, MD). A subset had already been tested by cobas and LA (n = 1,965). Cervical histopathology was ascertained from electronic health records. Hierarchical Onclarity channels showed a significant linear association with histological severity. Onclarity and cobas had excellent agreement on partial typing of HPV16, HPV18, and the other 12 types as a pool (sample-weighted kappa value of 0.83); cobas was slightly more sensitive for HPV18 and slightly less sensitive for the pooled high-risk types. Typing by Onclarity showed excellent agreement with types and groups of types identified by LA (kappa values from 0.80 for HPV39/68/35 to 0.97 for HPV16). Onclarity typing results corresponded well to histopathology and to an already validated HPV DNA test and could provide additional clinical typing if such discrimination is determined to be clinically desirable.
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21
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Clarke MA, Gradissimo A, Schiffman M, Lam J, Sollecito CC, Fetterman B, Lorey T, Poitras N, Raine-Bennett TR, Castle PE, Wentzensen N, Burk RD. Human Papillomavirus DNA Methylation as a Biomarker for Cervical Precancer: Consistency across 12 Genotypes and Potential Impact on Management of HPV-Positive Women. Clin Cancer Res 2018; 24:2194-2202. [PMID: 29420222 DOI: 10.1158/1078-0432.ccr-17-3251] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/28/2017] [Accepted: 01/29/2018] [Indexed: 11/16/2022]
Abstract
Purpose: Human papillomavirus (HPV) DNA methylation testing is a promising triage option for women testing HPV positive during cervical cancer screening. However, the extent to which methylation indicates precancer for all 12 carcinogenic HPV types has not been evaluated.Experimental Design: In this nested case-control study, we tested up to 30 cases of precancer [cervical intraepithelial neoplasia grade 3 (CIN3)/adenocarcinoma in situ (AIS)] and 30 normal controls for each carcinogenic type (single infections with 16/18/31/33/35/39/45/51/52/56/58/59). Next-generation bisulfite sequencing was performed on CpG sites within the L1 and L2 genes. We calculated differences in methylation, ORs, and AUC. Using a fixed sensitivity of 80%, we evaluated the specificity and the risk of CIN3/AIS for best performing CpG sites, and compared the performance of an explorative multi-type methylation assay with current triage strategies.Results: Methylation was positively associated with CIN3/AIS across all 12 types. AUCs for the top sites ranged from 0.71 (HPV51 and HPV56) to 0.86 (HPV18). A combined 12-type methylation assay had the highest Youden index (0.46), compared with cytology (0.31) and a 5-type methylation assay, including only previously described types (0.26). The 12-type methylation assay had higher sensitivity (80% vs. 76.6%) and lower test positivity compared with cytology (38.5% vs. 48.7%). The risk of CIN3/AIS was highest for methylation positives and lowest for cytology or HPV16/18 positives.Conclusions: HPV DNA methylation is a general phenomenon marking the transition from HPV infection to precancer for all 12 carcinogenic types. Development of a combined multitype methylation assay may serve as a triage test for HPV-positive women. Clin Cancer Res; 24(9); 2194-202. ©2018 AACR.
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Affiliation(s)
- Megan A Clarke
- Division of Cancer Epidemiology and Genetics, NCI, Rockville, MD, USA.
| | - Ana Gradissimo
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, NCI, Rockville, MD, USA
| | - Jessica Lam
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York
| | | | - Barbara Fetterman
- Regional Laboratory, The Permanente Medical Group, Oakland, California
| | - Thomas Lorey
- Regional Laboratory, The Permanente Medical Group, Oakland, California
| | - Nancy Poitras
- Regional Laboratory, The Permanente Medical Group, Oakland, California
| | | | - Philip E Castle
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, New York
| | | | - Robert D Burk
- Departments of Epidemiology and Population Health, Microbiology and Immunology, and Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, New York
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22
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Mirabello L, Yeager M, Yu K, Clifford GM, Xiao Y, Zhu B, Cullen M, Boland JF, Wentzensen N, Nelson CW, Raine-Bennett T, Chen Z, Bass S, Song L, Yang Q, Steinberg M, Burdett L, Dean M, Roberson D, Mitchell J, Lorey T, Franceschi S, Castle PE, Walker J, Zuna R, Kreimer AR, Beachler DC, Hildesheim A, Gonzalez P, Porras C, Burk RD, Schiffman M. HPV16 E7 Genetic Conservation Is Critical to Carcinogenesis. Cell 2017; 170:1164-1174.e6. [PMID: 28886384 PMCID: PMC5674785 DOI: 10.1016/j.cell.2017.08.001] [Citation(s) in RCA: 183] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/05/2017] [Accepted: 08/01/2017] [Indexed: 12/29/2022]
Abstract
Although most cervical human papillomavirus type 16 (HPV16) infections become undetectable within 1-2 years, persistent HPV16 causes half of all cervical cancers. We used a novel HPV whole-genome sequencing technique to evaluate an exceptionally large collection of 5,570 HPV16-infected case-control samples to determine whether viral genetic variation influences risk of cervical precancer and cancer. We observed thousands of unique HPV16 genomes; very few women shared the identical HPV16 sequence, which should stimulate a careful re-evaluation of the clinical implications of HPV mutation rates, transmission, clearance, and persistence. In case-control analyses, HPV16 in the controls had significantly more amino acid changing variants throughout the genome. Strikingly, E7 was devoid of variants in precancers/cancers compared to higher levels in the controls; we confirmed this in cancers from around the world. Strict conservation of the 98 amino acids of E7, which disrupts Rb function, is critical for HPV16 carcinogenesis, presenting a highly specific target for etiologic and therapeutic research.
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Affiliation(s)
- Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Gary M Clifford
- Infections and Cancer Epidemiology Group, International Agency for Research on Cancer 150, Cours Albert Thomas, 69372 Lyon Cedex 08, France
| | - Yanzi Xiao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Michael Cullen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Joseph F Boland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Chase W Nelson
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York City, NY, USA
| | - Tina Raine-Bennett
- Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Zigui Chen
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Sara Bass
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Qi Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Mia Steinberg
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - David Roberson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Jason Mitchell
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Thomas Lorey
- Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Silvia Franceschi
- Infections and Cancer Epidemiology Group, International Agency for Research on Cancer 150, Cours Albert Thomas, 69372 Lyon Cedex 08, France
| | - Philip E Castle
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Joan Walker
- University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Rosemary Zuna
- University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Aimée R Kreimer
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Daniel C Beachler
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; HealthCore Inc., Safety and Epidemiology, Wilmington, DE, USA
| | - Allan Hildesheim
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Paula Gonzalez
- Agencia Costarricense de Investigaciones Biomédicas (ACIB), former Proyecto Epidemiológico Guanacaste, Fundación INCIENSA, Guanacaste, Costa Rica
| | - Carolina Porras
- Agencia Costarricense de Investigaciones Biomédicas (ACIB), former Proyecto Epidemiológico Guanacaste, Fundación INCIENSA, Guanacaste, Costa Rica
| | - Robert D Burk
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA; Departments of Pediatrics, Microbiology and Immunology, and Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
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Enderle I, Le Baccon FA, Pinsard M, Joueidi Y, Lavoué V, Levêque J, Nyangoh Timoh K. [Pap Smear after 65 years]. ACTA ACUST UNITED AC 2017; 45:478-485. [PMID: 28864050 DOI: 10.1016/j.gofs.2017.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 07/18/2017] [Indexed: 12/01/2022]
Abstract
The French recommendations (in favor of stopping cervical cancer screening by cervico-uterine smear from 65 years of age) are logical in the context of organized screening; however, it is not yet generalized in France. The proportion of invasive cervical cancer in the oldest patients is high and these cancers are more evolved and have a more pejorative prognosis. The prevalent infection with high-risk HPV virus remains important in elderly patients: if the HPV infection does not appear to be more risky in the elderly, HPV-induced lesions appear to be more evolving. Unfortunately, pap smear coverage rates are low in the most advanced age groups. Patients without adequate follow-up are exposed to invasive cancer after age 65: all studies insist on the protective effect of two or more normal pap smears between 50 and 65 years that would allow to stop screening. Recent publications in Europe insist, however, on the value of continuing screening beyond the age of 65 in populations that live longer. For the clinician, in France, patients who could benefit from systematic FCU after age 65 could be those: (1) who request it, (2) who have an HPV history, (3) who have not had more than 3 consecutive normal pap smears or (4) who have an associated pathogenic condition. The place of the HPV test deserves to be considered: because of its very high negative predictive value, it could be performed as an exit test or as an alternative test to the pap smear.
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Affiliation(s)
- I Enderle
- Département de gynécologie obstétrique et reproduction humaine, CHU Anne-de-Bretagne, 16, boulevard de Bulgarie BP 90347, 35203 Rennes cedex 2, France
| | - F-A Le Baccon
- Département de gynécologie obstétrique et reproduction humaine, CHU Anne-de-Bretagne, 16, boulevard de Bulgarie BP 90347, 35203 Rennes cedex 2, France
| | - M Pinsard
- Département de gynécologie obstétrique et reproduction humaine, CHU Anne-de-Bretagne, 16, boulevard de Bulgarie BP 90347, 35203 Rennes cedex 2, France
| | - Y Joueidi
- Département de gynécologie obstétrique et reproduction humaine, CHU Anne-de-Bretagne, 16, boulevard de Bulgarie BP 90347, 35203 Rennes cedex 2, France
| | - V Lavoué
- Département de gynécologie obstétrique et reproduction humaine, CHU Anne-de-Bretagne, 16, boulevard de Bulgarie BP 90347, 35203 Rennes cedex 2, France
| | - J Levêque
- Département de gynécologie obstétrique et reproduction humaine, CHU Anne-de-Bretagne, 16, boulevard de Bulgarie BP 90347, 35203 Rennes cedex 2, France.
| | - K Nyangoh Timoh
- Département de gynécologie obstétrique et reproduction humaine, CHU Anne-de-Bretagne, 16, boulevard de Bulgarie BP 90347, 35203 Rennes cedex 2, France
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24
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Sundström K, Herweijer E, Sparén P, Ploner A. Reply to Ryser et al. Int J Cancer 2017; 141:416-418. [DOI: 10.1002/ijc.30757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 04/05/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Karin Sundström
- Department of Laboratory Medicine; Karolinska Institutet; Stockholm Sweden
| | - Eva Herweijer
- Department of Medical Epidemiology and Biostatistics; Karolinska Institutet; Stockholm Sweden
| | - Pär Sparén
- Department of Medical Epidemiology and Biostatistics; Karolinska Institutet; Stockholm Sweden
| | - Alexander Ploner
- Department of Medical Epidemiology and Biostatistics; Karolinska Institutet; Stockholm Sweden
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25
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Giannella L, Fodero C, Boselli F, Rubino T, Mfuta K, Prandi S. Age-related changes in pre- and post-conization HPV genotype distribution among women with high-grade cervical intraepithelial neoplasia. Int J Gynaecol Obstet 2017; 137:72-77. [PMID: 28129439 DOI: 10.1002/ijgo.12106] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 12/12/2016] [Accepted: 01/24/2017] [Indexed: 11/05/2022]
Abstract
OBJECTIVE To assess the effect of age on pre- and post-conization HPV genotype distribution. METHODS The present retrospective observational study included consecutive women with high-grade cervical intraepithelial neoplasia who underwent conization at the Cervical Cancer Screening Centre of Reggio Emilia, Italy, and University Hospital of Modena, Italy, between February 1, 2012, and October 31, 2014. Pre-conization and 6-month post-conization HPV genotyping results were compared between four age groups (<30, 30-39, 40-49, and ≥50 years) and age-related changes in the HPV genotypes present were evaluated. RESULTS There were 162 patients included. The lowest occurrence of pre-conization high-risk and probable high-risk HPV genotypes was observed among patients aged at least 50 years when compared with younger patients (P=0.017). Conversely, women aged at least 50 years exhibited the highest level of post-conization high-risk and probable high-risk HPV genotypes (P=0.043). Additionally, an increasing incidence of recording identical pre- and post-conization HPV genotypes was associated with increasing age (P=0.024), as was increasing post-treatment recurrence of cervical intraepithelial neoplasia grade 2+ (P=0.030). CONCLUSION The presence of high-risk and probable high-risk HPV genotypes was lowest among older patients before conization and was highest among these patients post-conization; post-treatment HPV clearance decreased with age and increasing age could be a risk factor for post-conization recurrence.
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Affiliation(s)
- Luca Giannella
- Local Health Authority of Reggio Emilia, Division of Obstetrics and Gynecology, Cesare Magati Hospital, Scandiano, Italy.,Cervical Cancer Screening Centre, IRCCS-Arcispedale Santa Maria Nuova, Reggio Emilia, Italy
| | - Cristina Fodero
- Cervical Cancer Screening Centre, IRCCS-Arcispedale Santa Maria Nuova, Reggio Emilia, Italy
| | - Fausto Boselli
- Mother-Infant Department, Institute of Obstetrics and Gynecology, University of Modena and Reggio Emilia, Modena, Italy
| | - Teresa Rubino
- Cervical Cancer Screening Centre, IRCCS-Arcispedale Santa Maria Nuova, Reggio Emilia, Italy
| | - Kabala Mfuta
- Local Health Authority of Reggio Emilia, Division of Obstetrics and Gynecology, Cesare Magati Hospital, Scandiano, Italy.,Cervical Cancer Screening Centre, IRCCS-Arcispedale Santa Maria Nuova, Reggio Emilia, Italy
| | - Sonia Prandi
- Cervical Cancer Screening Centre, IRCCS-Arcispedale Santa Maria Nuova, Reggio Emilia, Italy
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Mirabello L, Yeager M, Cullen M, Boland JF, Chen Z, Wentzensen N, Zhang X, Yu K, Yang Q, Mitchell J, Roberson D, Bass S, Xiao Y, Burdett L, Raine-Bennett T, Lorey T, Castle PE, Burk RD, Schiffman M. HPV16 Sublineage Associations With Histology-Specific Cancer Risk Using HPV Whole-Genome Sequences in 3200 Women. J Natl Cancer Inst 2016; 108:djw100. [PMID: 27130930 PMCID: PMC5939630 DOI: 10.1093/jnci/djw100] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 01/19/2016] [Accepted: 02/24/2016] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND HPV16 is a common sexually transmitted infection although few infections lead to cervical precancer/cancer; we cannot distinguish nor mechanistically explain why only certain infections progress. HPV16 can be classified into four main evolutionary-derived variant lineages (A, B, C, D) that have been previously suggested to have varying disease risks. METHODS We used a high-throughput HPV16 whole-genome sequencing assay to investigate variant lineage risk among 3215 HPV16-infected women. Using sublineages A1/A2 as the reference, we assessed all variant lineage associations with infection outcome over three or more years of follow-up: 1107 control subjects ( RESULTS A4 sublineage was associated with an increased risk of cancer, specifically adenocarcinoma (OR = 9.81, 95% CI = 2.02 to 47.69, P = 4.7x10(-03)). Lineage B had a lower risk of CIN3 (OR = 0.51, 95% CI = 0. 28 to 0.91, P = 02) while lineage C showed increased risk (OR = 2.06, 95% CI = 1.09 to 3.89, P = 03). D2/D3 sublineages were strongly associated with an increased risk of CIN3 and cancer, particularly D2 (OR for cancer = 28.48, 95% CI = 9.27 to 87.55, P = 5.0x10(-09)). D2 had the strongest increased risk of glandular lesions, AIS (OR = 29.22, 95% CI = 8.94 to 95.51, P = 2.3x10(-08)), and adenocarcinomas (OR = 137.34, 95% CI = 37.21 to 506.88, P = 1.5x10(-13)). Moreover, the risk of precancer and cancer for specific variant lineages varied by a women's race/ethnicity; those women whose race/ethnicity matched that of the infecting HPV16 variant had an increased risk of CIN3 + (P < 001). CONCLUSIONS Specific HPV16 variant sublineages strongly influence risk of histologic types of precancer and cancer, and viral genetic variation may help explain its unique carcinogenic properties.
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Affiliation(s)
- Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Michael Cullen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Joseph F Boland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Zigui Chen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Xijun Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Qi Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Jason Mitchell
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - David Roberson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Sara Bass
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Yanzi Xiao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Tina Raine-Bennett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Thomas Lorey
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Philip E Castle
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Robert D Burk
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
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Schiffman M, Hyun N, Raine-Bennett TR, Katki H, Fetterman B, Gage JC, Cheung LC, Befano B, Poitras N, Lorey T, Castle PE, Wentzensen N. A cohort study of cervical screening using partial HPV typing and cytology triage. Int J Cancer 2016; 139:2606-15. [DOI: 10.1002/ijc.30375] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 07/01/2016] [Accepted: 07/15/2016] [Indexed: 01/10/2023]
Affiliation(s)
- Mark Schiffman
- National Cancer Institute Division of Cancer Epidemiology and Genetics; Rockville MD
| | - Noorie Hyun
- National Cancer Institute Division of Cancer Epidemiology and Genetics; Rockville MD
| | | | - Hormuzd Katki
- National Cancer Institute Division of Cancer Epidemiology and Genetics; Rockville MD
| | - Barbara Fetterman
- Kaiser Permanente Northern California Regional Laboratory; Berkeley CA
| | - Julia C. Gage
- National Cancer Institute Division of Cancer Epidemiology and Genetics; Rockville MD
| | | | | | - Nancy Poitras
- Kaiser Permanente Northern California Regional Laboratory; Berkeley CA
| | - Thomas Lorey
- Kaiser Permanente Northern California Regional Laboratory; Berkeley CA
| | - Philip E. Castle
- Department of Epidemiology and Population Health; Albert Einstein College of Medicine; Bronx NY
| | - Nicolas Wentzensen
- National Cancer Institute Division of Cancer Epidemiology and Genetics; Rockville MD
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Hammer A, Rositch A, Qeadan F, Gravitt PE, Blaakaer J. Age-specific prevalence of HPV16/18 genotypes in cervical cancer: A systematic review and meta-analysis. Int J Cancer 2016; 138:2795-803. [DOI: 10.1002/ijc.29959] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/29/2015] [Accepted: 11/25/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Anne Hammer
- Department of Obstetrics and Gynecology; Aarhus University Hospital; Aarhus Denmark
- Department of Clinical Medicine; Aarhus University; Aarhus Denmark
| | - Anne Rositch
- Johns Hopkins Bloomberg School of Public Health; MD
| | - Fares Qeadan
- Department of Internal Medicine; University of New Mexico Health Sciences Center; NM
| | - Patti E Gravitt
- Department of Pathology; University of New Mexico Health Sciences Center; NM
| | - Jan Blaakaer
- Department of Obstetrics and Gynecology; Aarhus University Hospital; Aarhus Denmark
- Department of Clinical Medicine; Aarhus University; Aarhus Denmark
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Brotherton JM, Malloy M, Budd AC, Saville M, Drennan KT, Gertig DM. Effectiveness of less than three doses of quadrivalent human papillomavirus vaccine against cervical intraepithelial neoplasia when administered using a standard dose spacing schedule: Observational cohort of young women in Australia. PAPILLOMAVIRUS RESEARCH 2015. [PMCID: PMC5891730 DOI: 10.1016/j.pvr.2015.05.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Background Optimised two-dose human papillomavirus (HPV) vaccine schedules are now endorsed for young adolescents by the World Health Organization. Limited data are available about effectiveness of <3 doses using a standard dose schedule. Methods Deterministic data linkage was undertaken between the Victorian Cervical Cytology Registry and National HPV Vaccination Program Register to determine quadrivalent HPV vaccination status and incidence of cervical pathology among vaccine eligible women (aged 26 years or younger in 2007) screened in Victoria, Australia between April 2007 and December 2011. Proportional hazards regression was used to estimate hazard ratios (HR) adjusted for age, socioeconomic status and area of residence. Women were stratified into those vaccinated before or after first screen. Results Any number of doses (1, 2 or 3) were associated with lower rates of high grade and low grade cytology diagnoses as long as doses were given before screening commencement (one dose HR high grade 0.44 (95% CI 0.32–0.59), one dose low grade 0.48 (95% CI 0.40–0.58); two doses HR high grade 0.63 (95% CI 0.50–0.80), HR low grade 0.52 (95% CI 0.44–0.61); three doses HR high grade 0.53 (95% CI 0.47–0.60), HR low grade 0.73 (95% CI 0.68–0.78)). Three doses of vaccine, but not fewer, were associated with reduced risk of high grade histologically confirmed abnormality in this cohort, regardless of whether vaccination occurred before or after screening (HR before 0.71 (95% CI 0.64–0.80), HR after 0.87 (95% CI 0.82–0.93)). Secondary analyses censoring end points occurring within 1, 6, 12, or 24 months of final vaccine dose suggested an increasing effect of partial vaccination courses over time. Conclusion Our data suggest that less than three doses of quadrivalent HPV vaccine provides some protection against cervical intraepithelial neoplasia, even when measured within 5 years in a population including those who were sexually active at the time of vaccination.
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Cullen M, Boland JF, Schiffman M, Zhang X, Wentzensen N, Yang Q, Chen Z, Yu K, Mitchell J, Roberson D, Bass S, Burdette L, Machado M, Ravichandran S, Luke B, Machiela MJ, Andersen M, Osentoski M, Laptewicz M, Wacholder S, Feldman A, Raine-Bennett T, Lorey T, Castle PE, Yeager M, Burk RD, Mirabello L. Deep sequencing of HPV16 genomes: A new high-throughput tool for exploring the carcinogenicity and natural history of HPV16 infection. PAPILLOMAVIRUS RESEARCH (AMSTERDAM, NETHERLANDS) 2015; 1:3-11. [PMID: 26645052 PMCID: PMC4669577 DOI: 10.1016/j.pvr.2015.05.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 05/27/2015] [Indexed: 11/27/2022]
Abstract
For unknown reasons, there is huge variability in risk conferred by different HPV types and, remarkably, strong differences even between closely related variant lineages within each type. HPV16 is a uniquely powerful carcinogenic type, causing approximately half of cervical cancer and most other HPV-related cancers. To permit the large-scale study of HPV genome variability and precancer/cancer, starting with HPV16 and cervical cancer, we developed a high-throughput next-generation sequencing (NGS) whole-genome method. We designed a custom HPV16 AmpliSeq™ panel that generated 47 overlapping amplicons covering 99% of the genome sequenced on the Ion Torrent Proton platform. After validating with Sanger, the current "gold standard" of sequencing, in 89 specimens with concordance of 99.9%, we used our NGS method and custom annotation pipeline to sequence 796 HPV16-positive exfoliated cervical cell specimens. The median completion rate per sample was 98.0%. Our method enabled us to discover novel SNPs, large contiguous deletions suggestive of viral integration (OR of 27.3, 95% CI 3.3-222, P=0.002), and the sensitive detection of variant lineage coinfections. This method represents an innovative high-throughput, ultra-deep coverage technique for HPV genomic sequencing, which, in turn, enables the investigation of the role of genetic variation in HPV epidemiology and carcinogenesis.
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Affiliation(s)
- Michael Cullen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Joseph F. Boland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Xijun Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Qi Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Zigui Chen
- Department of Epidemiology and Population Health, At Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Jason Mitchell
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - David Roberson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Sara Bass
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Laurie Burdette
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Moara Machado
- Department de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Sarangan Ravichandran
- Frederick National Laboratory for Cancer Research, Simulation, Analysis and Mathematical Modeling Group Advanced Biomedical Computing Center, Frederick, MD, USA
| | - Brian Luke
- Frederick National Laboratory for Cancer Research, Simulation, Analysis and Mathematical Modeling Group Advanced Biomedical Computing Center, Frederick, MD, USA
| | - Mitchell J. Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Mark Andersen
- Thermo Fisher Scientific (Formerly Life Technologies), Carlsbad, CA, USA
| | - Matt Osentoski
- Thermo Fisher Scientific (Formerly Life Technologies), Carlsbad, CA, USA
| | - Michael Laptewicz
- Thermo Fisher Scientific (Formerly Life Technologies), Carlsbad, CA, USA
| | - Sholom Wacholder
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Ashlie Feldman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Tina Raine-Bennett
- Regional Laboratory and Women’s Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Thomas Lorey
- Regional Laboratory and Women’s Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Philip E. Castle
- Department of Epidemiology and Population Health, At Albert Einstein College of Medicine, Bronx, NY, USA
- Global Coalition Against Cervical Cancer, Arlington, VA, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Robert D. Burk
- Department of Epidemiology and Population Health, At Albert Einstein College of Medicine, Bronx, NY, USA
- Division of Gynecologic Oncology, Department of Obstetrics & Gynecology and Women’s Health, at Albert Einstein College of Medicine, Bronx, NY, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
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Krishnan K, Thomas A. Correlation of cervical cytology with high-risk HPV molecular diagnosis, genotypes, and histopathology-A four year study from the UAE. Diagn Cytopathol 2015; 44:91-7. [DOI: 10.1002/dc.23391] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Revised: 09/01/2015] [Accepted: 11/09/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Kavita Krishnan
- Specialist Anatomic Pathology; Premier Diagnostic Center (Prime Healthcare Group); Dubai UAE
| | - Antony Thomas
- Specialist Pathologist and Laboratory Director; Premier Diagnostic Center (Prime Healthcare Group); Dubai UAE
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Hammer A, Mejlgaard E, Gravitt P, Høgdall E, Christiansen P, Steiniche T, Blaakaer J. HPV genotype distribution in older Danish women undergoing surgery due to cervical cancer. Acta Obstet Gynecol Scand 2015; 94:1262-8. [DOI: 10.1111/aogs.12731] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 08/10/2015] [Indexed: 12/19/2022]
Affiliation(s)
- Anne Hammer
- Department of Obstetrics and Gynecology; Aarhus University Hospital; Aarhus Denmark
- Department of Clinical Medicine; Aarhus University; Aarhus Denmark
| | - Else Mejlgaard
- Department of Pathology; Aarhus University Hospital; Aarhus Denmark
| | - Patti Gravitt
- Department of Pathology; University of New Mexico; Albuquerque NM USA
| | - Estrid Høgdall
- Department of Pathology; Copenhagen University Hospital; Herlev Denmark
| | | | - Torben Steiniche
- Department of Clinical Medicine; Aarhus University; Aarhus Denmark
- Department of Pathology; Aarhus University Hospital; Aarhus Denmark
| | - Jan Blaakaer
- Department of Obstetrics and Gynecology; Aarhus University Hospital; Aarhus Denmark
- Department of Clinical Medicine; Aarhus University; Aarhus Denmark
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Schiffman M, Boyle S, Raine-Bennett T, Katki HA, Gage JC, Wentzensen N, Kornegay JR, Apple R, Aldrich C, Erlich HA, Tam T, Befano B, Burk RD, Castle PE. The Role of Human Papillomavirus Genotyping in Cervical Cancer Screening: A Large-Scale Evaluation of the cobas HPV Test. Cancer Epidemiol Biomarkers Prev 2015; 24:1304-10. [PMID: 26088703 PMCID: PMC4560647 DOI: 10.1158/1055-9965.epi-14-1353] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 04/15/2015] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The cobas HPV Test ("cobas"; Roche Molecular Systems) detects HPV16 and HPV18 individually, and a pool of 12 other high-risk (HR) HPV types. The test is approved for (i) atypical squamous cells of undetermined significance (ASC-US) triage to determine need for colposcopy, (ii) combined screening with cytology ("cotesting"), and (iii) primary HPV screening. METHODS To assess the possible value of HPV16/18 typing, >17,000 specimens from a longitudinal cohort study of initially HPV-positive women (HC2, Qiagen) were retested with cobas. To study accuracy, cobas genotyping results were compared with those of an established method, the Linear Array HPV Genotyping Test (LA, Roche Molecular Systems). Clinical value of the typing strategy was evaluated by linking the cobas results (supplemented by other available typing results) to 3-year cumulative risks of CIN3+. RESULTS Grouped hierarchically (HPV16, else HPV18, else other HR types, else negative), the κ statistic for agreement between cobas and LA was 0.86 [95% confidence interval (CI), 0.86-0.87]. In all three scenarios, HPV16-positive women were at much higher 3-year risk of CIN3+ than HPV16-negative women: women ages 21 and older with ASC-US (14.5%; 95% CI, 13.5%-15.5% vs. 3.5%; 95% CI, 3.3-3.6); women ages 30 years and older that were HPV-positive cytology-negative (10.3%; 95% CI, 9.6-11.1 vs. 2.3%; 95% CI, 2.2-2.4); and all women 25 years and older that were HPV-positive (18.5%; 95% CI, 17.8-19.2 vs. 4.3%; 95% CI, 4.2-4.4). CONCLUSION The cobas and LA results show excellent agreement. The data support HPV16 typing. IMPACT HPV16 typing is useful in the management of HPV-positive/cytology-negative women in cotesting, of all HPV-positive women in primary HPV testing, and perhaps in the management of HPV-positive women with ASC-US. Cancer Epidemiol Biomarkers Prev; 24(9); 1304-10.
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Affiliation(s)
| | - Sean Boyle
- Roche Molecular Systems, Pleasanton, California
| | | | | | | | | | | | | | | | | | - Thanh Tam
- Roche Molecular Systems, Pleasanton, California
| | - Brian Befano
- Information Management Services, Calverton, Maryland
| | - Robert D Burk
- Albert Einstein College of Medicine, The Bronx, New York
| | - Philip E Castle
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, The Bronx, New York. Global Coalition Against Cervical Cancer, Arlington, Virginia
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The Influence of Human Papillomavirus Genotypes on Visual Screening and Diagnosis of Cervical Precancer and Cancer. J Low Genit Tract Dis 2015; 19:220-3. [DOI: 10.1097/lgt.0000000000000088] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Giannella L, Fodero C, Boselli F, Mfuta K, Rubino T, Prandi S. Age-related changes in the diagnostic assessment of women with severe cervical lesions. Climacteric 2015; 18:617-23. [PMID: 25603323 DOI: 10.3109/13697137.2015.1005592] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVES To evaluate the effect of age on the diagnostic assessment of women with severe cervical intraepithelial neoplasia (CIN). METHODS This retrospective observational study included 338 consecutive women with a diagnosis of CIN3 on cone specimen. Patients were divided into three groups according to age: < 35 years (Group A), 35-49 years (Group B), and ≥ 50 years (Group C). Clinical and colposcopic variables were compared, and human papillomavirus (HPV) genotype distribution was measured. RESULTS The most common HPV genotype was HPV-16 (63.65%), followed by HPV-33 (7%), HPV-18 (6.2%), and HPV-31 (5.4%). The rate of the following high-grade lesion predictors was lower in Group C than in Groups A and B: HPV-16 infections (55.9% vs. 75% vs. 70.9%, respectively, p = 0.022); high-grade colposcopic impression (29.4% vs. 51.8% vs. 51.7%, respectively, p < 0.0001); and high-grade cytological changes (30.9% vs. 56.2% vs. 45.4%, respectively, p = 0.025). An endocervical lesion location was more frequent in Group C than in Groups A and B (55.6% vs. 6.8% vs. 11.8%, respectively, p < 0.0001). CONCLUSION Women aged 50 years and older with CIN3 showed a significant reduction of high-grade lesion predictors along with physiological confounding cervical changes (transformation zone type 3 and endocervical lesion location). The diagnostic work-up of cervical lesions in older women should provide their potential consideration as a special population.
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Affiliation(s)
- L Giannella
- * Local Health Authority of Reggio Emilia, Division of Obstetrics and Gynecology, Cesare Magati Hospital , Scandiano , Italy
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Mirabello L, Frimer M, Harari A, McAndrew T, Smith B, Chen Z, Wentzensen N, Wacholder S, Castle PE, Raine-Bennett T, Schiffman M, Burk RD. HPV16 methyl-haplotypes determined by a novel next-generation sequencing method are associated with cervical precancer. Int J Cancer 2015; 136:E146-53. [PMID: 25081507 PMCID: PMC4262737 DOI: 10.1002/ijc.29119] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 07/03/2014] [Indexed: 01/02/2023]
Abstract
We have developed and evaluated a next-generation bisulfite sequencing (NGS) assay to distinguish HPV16 cervical precancer (CIN2-3; N=59) from HPV16-positive transient infections (N=40). Cervical DNA was isolated and treated with bisulfite and HPV16 methylation was quantified by (i) amplification with barcoded primers and massively parallel single molecule sequencing and (ii) site-specific pyrosequencing. Assays were evaluated for agreement using intraclass correlation coefficients (ICC). Odds ratios (OR) for high methylation vs. low methylation were calculated. Single site pyrosequencing and NGS data were correlated (ICC=0.61) and both indicated hypermethylation was associated with precancer (ORs of 2-37). Concordant NGS and pyrosequencing results yieled ORs that were stronger when compared with using either assay separately. Within the L1 region, the ORs for CIN2-3 were 14.3 and 22.4 using pyrosequencing and NGS assays, respectively; when both methods agreed the OR was 153. NGS assays provide methylation haplotypes, termed methyl-haplotypes from single molecule reads: cases had increased methyl-haplotypes with ≥1 methylated CpG site(s) per fragment compared with controls, particularly in L1 (p=3.0×10(-8)). The maximum discrimination of cases from controls for a L1 methyl-haplotype had an AUC of 0.89 corresponding to a sensitivity of 92.5% and a specificity of 73.1%. The strengthening of the OR when the two assays were concordant suggests the true association of CpG methylation with precancer is stronger than with either assay. As cervical cancer prevention moves to DNA testing methods, DNA based biomarkers, such as HPV methylation could serve as a reflex strategy to identify women at high risk for cervix cancer.
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Affiliation(s)
- Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD
| | - Marina Frimer
- Division of Gynecologic Oncology, Department of Obstetrics & Gynecology and Women’s Health, at Albert Einstein College of Medicine, Bronx, NY
| | - Ariana Harari
- Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY
| | - Thomas McAndrew
- Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY
| | - Benjamin Smith
- Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY
| | - Zigui Chen
- Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD
| | - Sholom Wacholder
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD
| | | | - Tina Raine-Bennett
- Women’s Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD
| | - Robert D. Burk
- Division of Gynecologic Oncology, Department of Obstetrics & Gynecology and Women’s Health, at Albert Einstein College of Medicine, Bronx, NY
- Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY
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Hariri S, Unger ER, Schafer S, Niccolai LM, Park IU, Bloch KC, Bennett NM, Steinau M, Johnson ML, Markowitz LE. HPV type attribution in high-grade cervical lesions: assessing the potential benefits of vaccines in a population-based evaluation in the United States. Cancer Epidemiol Biomarkers Prev 2014; 24:393-9. [PMID: 25416715 DOI: 10.1158/1055-9965.epi-14-0649] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Two currently available vaccines targeting human papillomavirus (HPV) types 16 and 18 could prevent 70% of cervical cancers and 50% of high-grade cervical lesions. Next-generation vaccines against additional types, such as a candidate 9-valent vaccine against HPV6/11/16/18/31/33/45/52/58, could further reduce HPV-associated disease burden. METHODS HPV was typed in archived tissues from women ages 21 to 39 years residing in five catchment areas in the United States with cervical intraepithelial neoplasia 2/3 and adenocarcinoma in situ (CIN2+) using L1 consensus PCR and type-specific hybridization. Type attribution was estimated using weights to account for lesions with multiple types detected. RESULTS From 2008 to 2011, 5,498 of 6,306 (87.2%) specimens obtained from 8,469 women with CIN2+ had valid typing results; HPV DNA was detected in 97.3%. Overall, 50.1% of lesions were attributable to HPV16/18, ranging from 50.3% to 52.4% among those ages 21 to 34 years, and significantly declined in 35 to 39 year-olds (43.5%). HPV16/18 attribution was higher in non-Hispanic whites (56.4%) versus racial/ethnic minorities (range, 41.8%-45.9%; P < 0.001). HPV31/33/45/52/58 attribution was 25.0% overall and increased with age (P < 0.001). A higher proportion of CIN2+ was attributable to HPV31/33/45/52/58 in non-Hispanic black (29.9%), Hispanic (29.2%), and Asian (33.1%) women compared with non-Hispanic whites (22.8%; P < 0.001). CONCLUSIONS Overall, 75% of lesions were attributable to 7 oncogenic HPV types: 50% to HPV16/18 and 25% to HPV31/33/45/52/58. HPV16/18 had the largest attributable fraction in CIN2+ across all subpopulations, although to a lesser extent in older women and racial/ethnic minorities. IMPACT Vaccines targeting additional oncogenic HPV types could prevent more high-grade cervical lesions, especially among racial/ethnic minorities.
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Affiliation(s)
- Susan Hariri
- Division of STD Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia.
| | - Elizabeth R Unger
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Sean Schafer
- HIV/STD/TB Program, Center for Public Health Practice, Oregon Public Health Division, Portland, Oregon
| | - Linda M Niccolai
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut
| | - Ina U Park
- California Department of Public Health, STD Control Branch, Richmond, California
| | - Karen C Bloch
- Departments of Medicine and Health Policy, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Nancy M Bennett
- Center for Community Health and Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York
| | - Martin Steinau
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Michelle L Johnson
- Division of STD Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Lauri E Markowitz
- Division of STD Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
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Prevalence of human papillomavirus types in invasive cervical cancers from 7 US cancer registries before vaccine introduction. J Low Genit Tract Dis 2014; 18:182-9. [PMID: 24477171 DOI: 10.1097/lgt.0b013e3182a577c7] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
OBJECTIVE We conducted a baseline study of human papillomavirus (HPV) type prevalence in invasive cervical cancers (ICCs) using data from 7 cancer registries (CRs) in the United States. Cases were diagnosed between 1994 and 2005 before the implementation of the HPV vaccines. MATERIALS AND METHODS Cancer registries from Florida, Kentucky, Louisiana, Michigan, Hawaii, Iowa, and Los Angeles, California identified eligible ICC cases and obtained sections from representative blocks of archived tumor specimens for DNA extraction. All extracts were assayed by linear array and, if inadequate or HPV negative, retested with INNO-LiPA Genotype test. Clinical and demographic factors were obtained from the CRs and merged with the HPV typing data to analyze factors associated with different types and with HPV negativity. RESULTS A total of 777 ICCs were included in this analysis, with broad geographic, age, and race distribution. Overall, HPV was detected in 91% of cases, including 51% HPV-16, 16% HPV-18 (HPV-16-negative), and 24% other oncogenic and rare types. After HPV-16 and -18, the most common types were 45, 33, 31, 35, and 52. Older age and nonsquamous histology were associated with HPV-negative typing. CONCLUSIONS This study provides baseline prevaccine HPV types for postvaccine ICC surveillance in the future. HPV-16 and/or -18 were found in 67% of ICCs, indicating the potential for vaccines to prevent a significant number of cervical cancers.
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Joste NE, Ronnett BM, Hunt WC, Pearse A, Langsfeld E, Leete T, Jaramillo M, Stoler MH, Castle PE, Wheeler CM. Human papillomavirus genotype-specific prevalence across the continuum of cervical neoplasia and cancer. Cancer Epidemiol Biomarkers Prev 2014; 24:230-40. [PMID: 25363635 DOI: 10.1158/1055-9965.epi-14-0775] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The New Mexico HPV Pap Registry was established to measure the impact of cervical cancer prevention strategies in the United States. Before widespread human papillomavirus (HPV) vaccine implementation, we established the baseline prevalence for a broad spectrum of HPV genotypes across the continuum of cervical intraepithelial neoplasia (CIN) and cancer. METHODS A population-based sample of 6,272 tissue specimens was tested for 37 HPV genotypes. The number of specimens tested within each diagnostic category was: 541 negative, 1,411 CIN grade 1 (CIN1), 2,226 CIN grade 2 (CIN2), and 2,094 CIN grade 3 (CIN3) or greater. Age-specific HPV prevalence was estimated within categories for HPV genotypes targeted by HPV vaccines. RESULTS The combined prevalence of HPV genotypes included in the quadrivalent and nonavalent vaccines increased from 15.3% and 29.3% in CIN1 to 58.4% and 83.7% in CIN3, respectively. Prevalence of HPV types included in both vaccines tended to decrease with increasing age for CIN1, CIN2, CIN3, and squamous cell carcinoma (SCC), most notably for CIN3 and SCC. The six most common HPV types in descending order of prevalence were HPV-16, -31, -52, -58, -33, and -39 for CIN3 and HPV-16, -18, -31, -45, -52, and -33 for invasive cancers. CONCLUSIONS Health economic modeling of HPV vaccine impact should consider age-specific differences in HPV prevalence. IMPACT Population-based HPV prevalence in CIN is not well described, but is requisite for longitudinal assessment of vaccine impact and to understand the effectiveness and performance of various cervical screening strategies in vaccinated and unvaccinated women.
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Affiliation(s)
- Nancy E Joste
- Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico. New Mexico HPV Pap Registry Steering Committee (see acknowledgements for the list of collaborative members)
| | - Brigitte M Ronnett
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - William C Hunt
- Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico. New Mexico HPV Pap Registry Steering Committee (see acknowledgements for the list of collaborative members)
| | - Amanda Pearse
- Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Erika Langsfeld
- Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Thomas Leete
- Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - MaryAnn Jaramillo
- Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico. New Mexico HPV Pap Registry Steering Committee (see acknowledgements for the list of collaborative members)
| | - Mark H Stoler
- New Mexico HPV Pap Registry Steering Committee (see acknowledgements for the list of collaborative members). Department of Pathology, University of Virginia, Charlottesville, Virginia
| | - Philip E Castle
- New Mexico HPV Pap Registry Steering Committee (see acknowledgements for the list of collaborative members). Global Cancer Initiative, Chestertown, Maryland
| | - Cosette M Wheeler
- Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico. New Mexico HPV Pap Registry Steering Committee (see acknowledgements for the list of collaborative members). Department of Obstetrics and Gynecology, House of Prevention Epidemiology (HOPE), University of New Mexico Health Sciences Center, Albuquerque, New Mexico.
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A study of genotyping for management of human papillomavirus-positive, cytology-negative cervical screening results. J Clin Microbiol 2014; 53:52-9. [PMID: 25339396 DOI: 10.1128/jcm.02116-14] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The effective management of women with human papillomavirus (HPV)-positive, cytology-negative results is critical to the introduction of HPV testing into cervical screening. HPV typing has been recommended for colposcopy triage, but it is not clear which combinations of high-risk HPV types provide clinically useful information. This study included 18,810 women with Hybrid Capture 2 (HC2)-positive, cytology-negative results and who were age ≥30 years from Kaiser Permanente Northern California. The median follow-up was 475 days (interquartile range [IQR], 0 to 1,077 days; maximum, 2,217 days). The baseline specimens from 482 cases of cervical intraepithelial neoplasia grade 3 or cancer (CIN3+) and 3,517 random HC2-positive noncases were genotyped using 2 PCR-based methods. Using the case-control sampling fractions, the 3-year cumulative risks of CIN3+ were calculated for each individual high-risk HPV type. The 3-year cumulative risk of CIN3+ among all women with HC2-positive, cytology-negative results was 4.6%. HPV16 status conferred the greatest type-specific risk stratification; women with HC2-positive/HPV16-positive results had a 10.6% risk of CIN3+, while women with HC-2 positive/HPV16-negative results had a much lower risk of 2.4%. The next most informative HPV types and their risks in HPV-positive women were HPV33 (5.9%) and HPV18 (5.9%). With regard to the etiologic fraction, 20 of 71 cases of cervical adenocarcinoma in situ (AIS) and adenocarcinoma in the cohort were positive for HPV18. HPV16 genotyping provides risk stratification useful for guiding clinical management; the risk among HPV16-positive women clearly exceeds the U.S. consensus risk threshold for immediate colposcopy referral. HPV18 is of particular interest because of its association with difficult-to-detect glandular lesions. There is a less clear clinical value of distinguishing the other high-risk HPV types.
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Wheeler CM, Hunt WC, Cuzick J, Langsfeld E, Robertson M, Castle PE. The influence of type-specific human papillomavirus infections on the detection of cervical precancer and cancer: A population-based study of opportunistic cervical screening in the United States. Int J Cancer 2014; 135:624-34. [PMID: 24226935 PMCID: PMC4020996 DOI: 10.1002/ijc.28605] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 11/05/2013] [Accepted: 11/07/2013] [Indexed: 11/11/2022]
Abstract
There are limited data on the prospective risks of detecting cervical precancer and cancer in United States (US) populations specifically where the delivery of opportunistic cervical screening takes place outside managed care and in the absence of organized national programs. Such data will inform the management of women with positive screening results before and after widespread human papillomavirus (HPV) vaccination and establishes a baseline preceding recent changes in US cervical cancer screening guidelines. Using data reported to the statewide passive surveillance systems of the New Mexico HPV Pap Registry, we measured the 3-year HPV type-specific cumulative incidence of cervical intraepithelial neoplasia grade 2 or more severe (CIN2+) and grade 3 or more severe (CIN3+) detected during real-world health care delivery across a diversity of organizations, payers, clinical settings, providers and patients. A stratified sample of 47,541 cervical cytology specimens from a screening population of 379,000 women underwent HPV genotyping. Three-year risks for different combinations of cytologic interpretation and HPV risk group ranged from <1% (for several combinations) to approximately 70% for CIN2+ and 55% for CIN3+ in women with high-grade (HSIL) cytology and HPV16 infection. A substantial proportion of CIN2+ (35.7%) and CIN3+ (30.9%) were diagnosed following negative cytology, of which 62.3 and 78.2%, respectively, were high-risk HPV positive. HPV16 had the greatest 3-year risks (10.9% for CIN2+,8.0% for CIN3+) followed by HPV33, HPV31, and HPV18. Positive results for high-risk HPV, especially HPV16, the severity of cytologic interpretation, and age contribute independently to the risks of CIN2+ and CIN3+.
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Affiliation(s)
- Cosette M Wheeler
- Department of Pathology, University of New Mexico Health Sciences Center, House of Prevention Epidemiology (HOPE)Albuquerque, NM
- Department of Obstetrics and Gynecology, University of New Mexico Health Sciences Center, House of Prevention Epidemiology (HOPE)Albuquerque, NM
| | - William C Hunt
- Department of Pathology, University of New Mexico Health Sciences Center, House of Prevention Epidemiology (HOPE)Albuquerque, NM
- Department of Obstetrics and Gynecology, University of New Mexico Health Sciences Center, House of Prevention Epidemiology (HOPE)Albuquerque, NM
| | - Jack Cuzick
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Queen Mary University of LondonLondon, United Kingdom
| | - Erika Langsfeld
- Department of Pathology, University of New Mexico Health Sciences Center, House of Prevention Epidemiology (HOPE)Albuquerque, NM
- Department of Obstetrics and Gynecology, University of New Mexico Health Sciences Center, House of Prevention Epidemiology (HOPE)Albuquerque, NM
| | - Michael Robertson
- Department of Pathology, University of New Mexico Health Sciences Center, House of Prevention Epidemiology (HOPE)Albuquerque, NM
- Department of Obstetrics and Gynecology, University of New Mexico Health Sciences Center, House of Prevention Epidemiology (HOPE)Albuquerque, NM
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Cuzick J, Ho L, Terry G, Kleeman M, Giddings M, Austin J, Cadman L, Ashdown-Barr L, Costa MJ, Szarewski A. Individual detection of 14 high risk human papilloma virus genotypes by the PapType test for the prediction of high grade cervical lesions. J Clin Virol 2014; 60:44-9. [PMID: 24630483 PMCID: PMC4012136 DOI: 10.1016/j.jcv.2014.02.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 02/01/2014] [Accepted: 02/04/2014] [Indexed: 01/07/2023]
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.
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Affiliation(s)
- Jack Cuzick
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London EC1M 6BQ, UK.
| | - Linda Ho
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London EC1M 6BQ, UK
| | - George Terry
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London EC1M 6BQ, UK
| | - Michelle Kleeman
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London EC1M 6BQ, UK
| | - Michael Giddings
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London EC1M 6BQ, UK
| | - Janet Austin
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London EC1M 6BQ, UK
| | - Louise Cadman
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London EC1M 6BQ, UK
| | - Lesley Ashdown-Barr
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London EC1M 6BQ, UK
| | - Maria J Costa
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London EC1M 6BQ, UK
| | - Anne Szarewski
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London EC1M 6BQ, UK
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Molecular epidemiology of human papillomavirus infections in cervical samples from cuban women older than 30 years. J Low Genit Tract Dis 2013; 18:210-7. [PMID: 24270200 DOI: 10.1097/lgt.0b013e3182a7bb89] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE This study aimed to provide information about the molecular epidemiology of human papillomavirus (HPV) in a group of Cuban women. MATERIALS AND METHODS DNA from cervical samples was analyzed using a quantitative real-time polymerase chain reaction (PCR), which detects 6 of the clinically most relevant high-risk HPV types. Furthermore, end point PCR and sequencing were performed. Three hundred twenty-two women (211 with positive and 111 with negative cytologic results) aged between 30 and 69 years were enrolled. Risk factors associated with HPV infections and premalignant lesions were also investigated. RESULTS HPV DNA was detected in 76.1% (245/322) of the studied population, and 34 different genotypes were found. There was an association between HPV infection and low educational level, history of oral contraceptives, menopausal stage, as well as cigarette and/or alcohol consumption. Besides, in a multivariate analysis, previous positive Pap test result and positive colposcopy finding were both predictor variables for HPV infections and for premalignant lesions. Human papillomavirus infection was found in 94.3% of women (199/211) with positive cytologic result and in 41.4% (46/111) of those with negative results, being more likely that the first group was infected with any HPV (odds ratio = 23.43; 95% CI = 11.70-46.92; p = .000). The most common genotypes were HPV types 16, 18, 31, 58, 33, and 45. All the cases with HPV positive findings had at least 1 high-risk HPV genotype. CONCLUSIONS This is the first report of the molecular epidemiology of HPV in Cuban women, based on results from a DNA sequence and quantitative PCR. Most individuals were infected with high-risk HPV types. These findings support the inclusion of HPV vaccine in Cuba.
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Vrdoljak-Mozetič D, Krašević M, Verša Ostojić D, Štemberger-Papić S, Rubeša-Mihaljević R, Bubonja-Šonje M. HPV16 genotype, p16/Ki-67 dual staining and koilocytic morphology as potential predictors of the clinical outcome for cervical low-grade squamous intraepithelial lesions. Cytopathology 2013; 26:10-8. [DOI: 10.1111/cyt.12121] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2013] [Indexed: 12/11/2022]
Affiliation(s)
| | - M. Krašević
- Department of Pathology; University of Rijeka; Rijeka Croatia
| | - D. Verša Ostojić
- Department of Clinical Cytology; University of Rijeka; Rijeka Croatia
| | | | | | - M. Bubonja-Šonje
- Department of Clinical Microbiology; Clinical Hospital Centre Rijeka; Faculty of Medicine; University of Rijeka; Rijeka Croatia
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Carcinogenic HPV prevalence and age-specific type distribution in 40,382 women with normal cervical cytology, ASCUS/LSIL, HSIL, or cervical cancer: what is the potential for prevention? Cancer Causes Control 2013; 25:179-89. [DOI: 10.1007/s10552-013-0320-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 11/04/2013] [Indexed: 11/26/2022]
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Bernard E, Pons-Salort M, Favre M, Heard I, Delarocque-Astagneau E, Guillemot D, Thiébaut ACM. Comparing human papillomavirus prevalences in women with normal cytology or invasive cervical cancer to rank genotypes according to their oncogenic potential: a meta-analysis of observational studies. BMC Infect Dis 2013; 13:373. [PMID: 23941096 PMCID: PMC3751808 DOI: 10.1186/1471-2334-13-373] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 08/08/2013] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Mucosal human papillomavirus (HPV) infection is a necessary cause of cervical cancer. Vaccine and non-vaccine genotype prevalences may change after vaccine introduction. Therefore, it appears essential to rank HPV genotypes according to their oncogenic potential for invasive cervical cancer, independently of their respective prevalences. METHODS We performed meta-analyses of published observational studies and estimated pooled odds ratios with random-effects models for 32 HPV genotypes, using HPV-16 as the reference. RESULTS Twenty-seven studies yielded 9,252 HPV-infected women: 2,902 diagnosed with invasive cervical cancer and 6,350 with normal cytology. Expressed as (odds ratio [95% confidence interval]), HPV-18 (0.63 [0.51, 0.78]) ranked closest to HPV-16, while other genotypes showed continuously decreasing relative oncogenic potentials: HPV-45 (0.35 [0.22, 0.55]), HPV-69 (0.28 [0.09, 0.92]), HPV-58 (0.24 [0.15, 0.38]), HPV-31 (0.22 [0.14, 0.35]), HPV-33 (0.22 [0.12, 0.38]), HPV-34 (0.21 [0.06, 0.80]), HPV-67 (0.21 [0.06, 0.67]), HPV-39 (0.17 [0.09, 0.30]), HPV-59 (0.17 [0.09, 0.31]), HPV-73 (0.16 [0.06, 0.41]), and HPV-52 (0.16 [0.11, 0.23]). CONCLUSIONS Our results support the markedly higher oncogenic potentials of HPV-16 and -18, followed by HPV-31, -33, -39, -45, -52, -58 and -59, and highlight the need for further investigation of HPV-34, -67, -69 and -73. Overall, these findings could have important implications for the prevention of cervical cancer.
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Affiliation(s)
- Erik Bernard
- Institut Pasteur, Unité de Pharmaco-Épidémiologie et Maladies Infectieuses, 25-28 rue du Dr Roux, 75724 Paris Cedex 15 France
- INSERM, U657, 25-28 rue du Dr Roux, 75724 Paris Cedex 15 France
- Univ Versailles–St-Quentin-en-Yvelines, EA 4499, UFR des Sciences de la Santé Simone Veil, 2 avenue de la Source de la Bièvre, 78180 Montigny Le Bretonneux France
| | - Margarita Pons-Salort
- Institut Pasteur, Unité de Pharmaco-Épidémiologie et Maladies Infectieuses, 25-28 rue du Dr Roux, 75724 Paris Cedex 15 France
- INSERM, U657, 25-28 rue du Dr Roux, 75724 Paris Cedex 15 France
- UPMC Univ Paris 06, Cellule Pasteur UPMC, 25-28 rue du Dr Roux, 75724 Paris Cedex 15 France
| | - Michel Favre
- Institut Pasteur, Centre National de Référence des HPV, 25-28 rue du Dr Roux, 75724 Paris Cedex 15 France
- Institut Pasteur, Genetics, Papillomavirus and Human Cancer Unit, 25-28 rue du Dr Roux, 75724 Paris Cedex 15 France
| | - Isabelle Heard
- Institut Pasteur, Centre National de Référence des HPV, 25-28 rue du Dr Roux, 75724 Paris Cedex 15 France
- UPMC Univ Paris 06, UMRS 943, Groupe Hospitalier Pitié–Salpêtrière, 91-105 boulevard de l’Hôpital, 75013 Paris, France
- INSERM, U943, Groupe Hospitalier Pitié–Salpêtrière, 91-105 boulevard de l’Hôpital, 75013 Paris, France
| | - Elisabeth Delarocque-Astagneau
- Institut Pasteur, Unité de Pharmaco-Épidémiologie et Maladies Infectieuses, 25-28 rue du Dr Roux, 75724 Paris Cedex 15 France
- INSERM, U657, 25-28 rue du Dr Roux, 75724 Paris Cedex 15 France
- Univ Versailles–St-Quentin-en-Yvelines, EA 4499, UFR des Sciences de la Santé Simone Veil, 2 avenue de la Source de la Bièvre, 78180 Montigny Le Bretonneux France
| | - Didier Guillemot
- Institut Pasteur, Unité de Pharmaco-Épidémiologie et Maladies Infectieuses, 25-28 rue du Dr Roux, 75724 Paris Cedex 15 France
- INSERM, U657, 25-28 rue du Dr Roux, 75724 Paris Cedex 15 France
- Univ Versailles–St-Quentin-en-Yvelines, EA 4499, UFR des Sciences de la Santé Simone Veil, 2 avenue de la Source de la Bièvre, 78180 Montigny Le Bretonneux France
- AP–HP, Hôpital Raymond Poincaré, 104 boulevard Raymond Poincaré, 92380 Garches, France
| | - Anne CM Thiébaut
- Institut Pasteur, Unité de Pharmaco-Épidémiologie et Maladies Infectieuses, 25-28 rue du Dr Roux, 75724 Paris Cedex 15 France
- INSERM, U657, 25-28 rue du Dr Roux, 75724 Paris Cedex 15 France
- Univ Versailles–St-Quentin-en-Yvelines, EA 4499, UFR des Sciences de la Santé Simone Veil, 2 avenue de la Source de la Bièvre, 78180 Montigny Le Bretonneux France
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Vujosević D, Vuksanović V, Poljak M, Jokmanović N. Human papillomavirus genotype spectrum in studied group of Montenegrin women. ACTA MEDICA (HRADEC KRALOVE) 2013; 55:130-2. [PMID: 23297521 DOI: 10.14712/18059694.2015.50] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The risk of high-grade lesions and carcinoma is known to correlate with specific high-risk HPV genotypes. The distribution of HPV types varies between countries and little is known about HPV distribution in our country. Therefore, the purpose of this study was to determine the range and frequency of HPV genotypes in studied group of women in Montenegro. HPV genotypes were determined using the method of enzyme restriction of PCR products amplified with group-specific primers MY09/MY11 and restricted with seven different restriction endonucleases. Out of the total number of women HPV infection was found in 1/5 of participants (20%). Genotyping performed in HPV DNA positive women shows that the HPV genotype 16 is dominant and present in more than 1/3 of the participants (36.8%). The second most frequent HPV infection is with HPV genotype 58 and it is found in 10.5% of participants. HPV 31 and HPV 6 infections are present in 7.9% of women, while infections with other genotypes were demonstrated individually by 2.6%. Multiple HPV infection was demonstrated in 18.4% and they are dominant in younger women (aged 25 to 30 years).
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Affiliation(s)
- Danijela Vujosević
- Center for Medical Microbiology, Institute of Public Health, Podgorica, Montenegro.
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Wentzensen N, Sun C, Ghosh A, Kinney W, Mirabello L, Wacholder S, Shaber R, LaMere B, Clarke M, Lorincz AT, Castle PE, Schiffman M, Burk RD. Methylation of HPV18, HPV31, and HPV45 genomes and cervical intraepithelial neoplasia grade 3. J Natl Cancer Inst 2012; 104:1738-49. [PMID: 23093560 DOI: 10.1093/jnci/djs425] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Persistent infections with carcinogenic human papillomavirus (HPV) types are the necessary cause of cervical cancer. We recently demonstrated that the HPV16 genome is strongly methylated in cervical precancer compared with transient infections. However, the extent of methylation in other HPV types and its role in progression to cancer is poorly understood. METHODS We analyzed whole-genome methylation patterns of the three next most carcinogenic HPV genotypes: HPV31 (closely related to HPV16), and two other closely related types, HPV18 and HPV45. DNA was extracted from cervical cytology specimens from 92 women with precancer and 96 women infected with HPV31, HPV18, or HPV45, but who had no cytological or histological abnormalities. After bisulfite modification, genome-wide pyrosequencing was performed covering 80-106 sites. We calculated differences in median methylation, odds ratios, areas under the curve, and Spearman rank correlation coefficients for methylation levels between different sites. All statistical tests were two-sided. RESULTS For all three HPV types, we observed strongly elevated methylation levels at multiple CpG sites in the E2, L2, and L1 regions among women with cervical intraepithelial neoplasia grade 3 compared with women with transient infections. We observed high correlation of methylation patterns between phylogenetically related types. The highest areas under the curve were 0.81 for HPV31, 0.85 for HPV18, and 0.98 for HPV45. Differential methylation patterns in cervical intraepithelial neoplasia grade 3 patients with multiple infections suggest that methylation can clarify which of the infections is causal. CONCLUSIONS Carcinogenic HPV DNA methylation indicates transforming HPV infections. Our findings show that methylation of carcinogenic HPV types is a general phenomenon that warrants development of diagnostic assays.
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Affiliation(s)
- Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 6120 Executive Blvd, Room 5024, Rockville, MD 20852-7234, USA.
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Brotherton JML, Tabrizi SN, Garland SM. Does HPV type 16 or 18 prevalence in cervical intraepithelial neoplasia grade 3 lesions vary by age? An important issue for postvaccination surveillance. Future Microbiol 2012; 7:193-9. [PMID: 22324989 DOI: 10.2217/fmb.11.161] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
AIM We used existing data to investigate whether prevalence of HPV16/18 in cervical intraepithelial neoplasia 3 (CIN3) varies by age, in order to determine whether age specific baseline data is required as the prevaccination comparator for type-specific surveillance following HPV vaccination programs. MATERIALS & METHODS We analyzed available Australian HPV typing data from 317 cervical smears from women with concurrent CIN3 on biopsy and conducted a review and analysis of the international literature. RESULTS Among 317 women with CIN3, HPV16 was detected in 70% of those 16-25 years old, 59% of 26-35-year-olds and 48% of >36-year-olds (p = 0.025). This association took the form of a trend with decreasing HPV16 prevalence with increasing age (p = 0.007). That HPV16 is commoner in younger women with high-grade cervical lesions was consistent with all but one study of 18 identified in the literature. CONCLUSION In screened populations, younger women with CIN3 are more likely to have HPV16 detected. To make valid pre- and post-vaccination comparisons, surveillance specimens for HPV typing should be both age stratified and lesion specific.
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Affiliation(s)
- Julia M L Brotherton
- Regional WHO Human Papillomavirus Laboratory Network, Department of Microbiology & Infectious Diseases, The Royal Women's Hospital, Locked Bag 300, Parkville, Victoria 3052, Australia.
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Baandrup L, Munk C, Andersen KK, Junge J, Iftner T, Kjær SK. HPV16 is associated with younger age in women with cervical intraepithelial neoplasia grade 2 and 3. Gynecol Oncol 2011; 124:281-5. [PMID: 22036987 DOI: 10.1016/j.ygyno.2011.10.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 10/18/2011] [Accepted: 10/19/2011] [Indexed: 11/28/2022]
Abstract
OBJECTIVE To evaluate if women with HPV16 positive CIN2 and CIN3 are diagnosed at a younger age. METHODS We conducted a population-based cohort study including more than 40,000 women having a liquid based cervical cytology sample taken as part of routine screening. HPV analysis was performed using Hybrid Capture 2 and LiPAv2. The study population was linked to the Danish Pathology Data Bank to retrieve information on subsequent cervical histology. We included HR HPV positive CIN2/3 samples, comprising 173 CIN2 and 467 CIN3 lesions. Due to a high number of multiple concurrent HPV infections, the causative HPV type was assigned to a hierarchically group. RESULTS In CIN3, the estimated proportion of lesions positive for HPV16 was 68.1% among women aged 20 years and decreased to 38.9% among women aged 50 years. A decrease in HPV16 positivity with increasing age was also observed in CIN2. In a multinomial logistic regression analysis, young age was strongly associated with HPV16 positivity in CIN3 lesions (OR=0.46 per 10 year increase in age, 95% CI: 0.32-0.65). The proportion of HPV16 and/or 18 positive lesions among women diagnosed with CIN2 and CIN3 below 30 years of age was 44% and 75%, respectively. CONCLUSIONS HPV16 positivity was significantly associated with younger age at diagnosis of CIN3. In a population vaccinated against HPV16 and 18, we will experience a shift to older ages in cervical precancerous lesions. These findings may imply that cervical cancer screening programs could start at an older age in HPV vaccinated populations.
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Affiliation(s)
- L Baandrup
- Department of Virus, Hormones and Cancer, Institute of Cancer Epidemiology, Danish Cancer Society, Copenhagen, Denmark
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