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Mungo C, Guliam A, Chinula L, Inturrisi F, Msowoya L, Mkochi T, Jawadu S, de Sanjosé S, Schiffman M, Tang JH, Smith JS. Comparison of the ScreenFire and Xpert HPV assays for the detection of human papillomavirus and cervical precancer among women living with HIV in Malawi. Infect Agent Cancer 2024; 19:24. [PMID: 38760798 PMCID: PMC11100048 DOI: 10.1186/s13027-024-00585-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/03/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND The World Health Organization recommends human papillomavirus (HPV) testing for primary cervical cancer screening, including among women living with HIV (WLWH). Low-and-middle-income countries account for 85% of the cervical cancer burden globally, yet have limited access to HPV-based screening, largely due to cost. This study aims to compare the performance of a rapid, isothermal amplification HPV assay (ScreenFire) to that of the Xpert HPV assay for the detection of HPV and cervical precancer among WLWH in Malawi. METHODS We utilized stored self- and provider-collected specimens from a prospective cohort study of WLWH in Malawi from July 2020 to February 2022. Specimens were tested with both Xpert and ScreenFire HPV assays. The overall and within-channel non-hierarchical agreement between ScreenFire and Xpert was determined for both self- and provider-collected specimens. Hierarchical ScreenFire HPV positivity by channel was compared to Xpert for each histological diagnosis-cervical intraepithelial neoplasia grade 2 or worse (CIN2+) compared to RESULTS 315 matched self- and provider-collected specimens had valid results from both Xpert and ScreenFire testing and were included in analyses, of which 279 and 36 were HPV positive and HPV negative, respectively, on Xpert self-collection. Of the 315, 245 (78%) had normal pathology, 21 CIN1 (7%), 14 CIN2 (4%), and 35 CIN3 (11%). Of the 245 with normal pathology, 213 (87%) and 188 (77%) were HPV-positive on Xpert and ScreenFire self-collected specimens, respectively. Among provider-collected specimens, the assays had 80% agreement on overall HPV positivity (unweighted kappa 0.59, 95% 0.50-0.69). ScreenFire was HPV-positive in 90% of self-collected specimens that were HPV-positive on Xpert. Channel agreement between the assays was high for both self- and provider-collected specimens, but slightly lower for HPV18/45. In hierarchical analysis, ScreenFire demonstrated high concordance with Xpert testing for detecting CIN2+ cases in all channels, missing no HPV 16 or HPV 18/45 positive CIN2+ case that was positive on Xpert, in both self- and provider-collected specimens. CONCLUSION In this study of stored specimens, the ScreenFire HPV assay performed well in the detection of HPV and CIN2+ among WLWH compared to the Xpert HPV assay. If supported by larger validation studies, ScreenFire could be an affordable alternative point-of-care HPV assay for use in LMICs.
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Affiliation(s)
- Chemtai Mungo
- Department of Obstetrics and Gynecology, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA.
| | - Anagha Guliam
- Barnard College of Columbia University, New York City, NY, USA
| | - Lameck Chinula
- Department of Obstetrics and Gynecology, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
- University of North Carolina Project-Malawi, Lilongwe, Malawi
| | - Federica Inturrisi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Lizzie Msowoya
- University of North Carolina Project-Malawi, Lilongwe, Malawi
| | - Tawonga Mkochi
- University of North Carolina Project-Malawi, Lilongwe, Malawi
| | - Siniya Jawadu
- University of North Carolina Project-Malawi, Lilongwe, Malawi
| | - Silvia de Sanjosé
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- ISGlobal, Barcelona, Spain
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Jennifer H Tang
- Department of Obstetrics and Gynecology, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
- University of North Carolina Project-Malawi, Lilongwe, Malawi
| | - Jennifer S Smith
- Gillings School of Global Public Health, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
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Montero-Gómez A. [Diagnosis by isothermal amplification of nucleic acids. Opportunity for community pharmacies]. FARMACEUTICOS COMUNITARIOS 2024; 16:46-53. [PMID: 39156031 PMCID: PMC11328073 DOI: 10.33620/fc.2173-9218.(2024).14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/16/2024] [Indexed: 08/20/2024]
Abstract
This review focuses on describing new commercially available POC-type molecular diagnostic systems that can be easily implemented in community pharmacies and have the potential to expand the portfolio of pharmaceutical services and make a significant contribution to the improvement of public health.Knowledge of new molecular diagnostic techniques other than PCR is relatively unexplored. However, the available options are diverse and have reached sufficient technological maturity for large-scale use. The SARS-CoV-2 pandemic has brought diagnostic tests to market that, in some cases, have been used exclusively in research for decades.Isothermal nucleic acid amplification technology continues to evolve and it is likely that in the coming years we will witness an exponential increase in its use, as well as the development of new improvements that further simplify and reduce the cost of each assay.Furthermore, we cannot ignore the fact that during the COVID-19 pandemic, the public has become accustomed to self-diagnosing through mass distribution channels such as community pharmacies. Which can open the sector to other diseases - such as sexually transmitted diseases or animal health -, food control, water and air contamination (fungi) or the presence of allergens.Knowledge of them is an essential technological surveillance strategy for the pharmaceutical sector.
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Mungo C, Guliam A, Chinula L, Inturrisi F, Msowoya L, Mkochi T, Jawadu S, de Sanjosé S, Schiffman M, Tang JH, Smith JS. Comparison of the ScreenFire and Xpert HPV assays for the detection of human papillomavirus and cervical precancer among women living with HIV in Malawi. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.21.24303142. [PMID: 38617305 PMCID: PMC11014639 DOI: 10.1101/2024.02.21.24303142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Background The World Health Organization (WHO) recommends human papillomavirus (HPV) testing for primary cervical cancer screening, including among women living with HIV (WLWH). Low-and-middle-income countries (LMICs) account for 85% of the cervical cancer burden globally, yet have limited access to HPV-based screening, largely due to cost. This study aims to compare the performance of a rapid, isothermal amplification HPV assay (ScreenFire) to that of the Xpert HPV assay for the detection of HPV and cervical precancer among WLWH in Malawi. Methods We utilized stored self- and provider-collected specimens from a prospective cohort study of WLWH in Malawi from July 2020 to February 2022. Specimens were tested with both Xpert and ScreenFire HPV assays. The overall and within-channel non-hierarchical agreement between ScreenFire and Xpert was determined for both self- and provider-collected specimens. Hierarchical ScreenFire HPV positivity by channel was compared to Xpert for each histological diagnosis - cervical intraepithelial neoplasia grade 2 or worse (CIN2+) compared to Results 315 matched self- and provider-collected specimens had valid results from both Xpert and ScreenFire testing and were included in analyses. Of these, 245 (78%) had normal pathology, 21 CIN1 (7%), 14 CIN2 (4%), and 35 CIN3 (11%). Among provider-collected specimens, the assays had 80% agreement on overall HPV positivity (unweighted kappa 0.59, 95% 0.50-0.69). ScreenFire was HPV-positive in 90% of self-collected specimens that were HPV-positive on Xpert. Channel agreement between the assays was high for both self- and provider-collected specimens, but slightly lower for HPV18/45. In hierarchical analysis, ScreenFire demonstrated high concordance with Xpert testing for detecting CIN2+ cases in all channels, missing no HPV 16 or HPV 18/45 positive CIN2+ case that was positive on Xpert, in both self- and provider-collected specimens. Conclusion In this study of stored specimens, the ScreenFire HPV assay performed well in the detection of HPV and CIN2+ among WLWH compared to the Xpert HPV assay. If supported by larger validation studies, ScreenFire could be an affordable alternative point-of-care HPV assay for use in LMICs.
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Affiliation(s)
- Chemtai Mungo
- Department of Obstetrics and Gynecology, University of North Carolina-Chapel Hill
| | | | - Lameck Chinula
- Department of Obstetrics and Gynecology, University of North Carolina-Chapel Hill
- University of North Carolina Project-Malawi, Lilongwe, Malawi
| | - Federica Inturrisi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Lizzie Msowoya
- University of North Carolina Project-Malawi, Lilongwe, Malawi
| | - Tawonga Mkochi
- University of North Carolina Project-Malawi, Lilongwe, Malawi
| | - Siniya Jawadu
- University of North Carolina Project-Malawi, Lilongwe, Malawi
| | - Silvia de Sanjosé
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Gillings School of Global Public Health, University of North Carolina-Chapel Hill
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Jennifer H. Tang
- Department of Obstetrics and Gynecology, University of North Carolina-Chapel Hill
- University of North Carolina Project-Malawi, Lilongwe, Malawi
| | - Jennifer S. Smith
- Gillings School of Global Public Health, University of North Carolina-Chapel Hill
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Zhang Y, Zhang W, Du H, Qu X, Chen Y, Wang J, Wu R. A comparative analysis of cycle threshold (Ct) values from Cobas4800 and AmpFire HPV assay for triage of women with positive hrHPV results. BMC Infect Dis 2023; 23:783. [PMID: 37950154 PMCID: PMC10636838 DOI: 10.1186/s12879-023-08737-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND To compare the triage performance of HPV viral loads reflected by cycle threshold values (CtV) from two different HPV testing assays: the PCR based Cobas4800 and the isothermal amplification based AmpFire assay. METHODS We used the data from a sub-study of The Chinese Multi-Center Screening Trial and analyzed the data of the cases positive in both Cobas4800 and AmpFire assays with recorded CtV. Spearman's correlation was applied to analyze the association between CtV from AmpFire and Cobas4800 assays, as well as the correlation between CtV and the histological lesion grades. The 50th percentile of CtV was used as the cutoff to construct triage algorithms for HPV-positive cases. McNemar's test was used to analyze the differences in sensitivity and specificity for detecting CIN2 + and CIN3 + in different triage algorithms. RESULTS Four hundred forty-six HPV positive women who had consistent HPV results from Cobas4800 and AmpFire in terms of the HPV genotype and reported Ct values were included in the analysis. The mean CtV of hrHPV tested by Cobas4800 and AmpFire were linear correlated. Direct association were showed between the severity of cervical lesions and the HPV viral loads reflected by CtV of hrHPV, HPV16, non-16/18 hrHPV and A9 group from both assays. HPV16/18 genotyping combined with low-CtV for non-16/18 hrHPV, especially A9 group, were demonstrated to be satisfactory in the sensitivity and specificity for detecting CIN2 + or CIN3 + . CONCLUSION Ct value represented a good triage marker in both PCR-based and isothermal amplification HPV detection.
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Affiliation(s)
- Yi Zhang
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen Peking University- The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, P. R. China
- Shenzhen Key Laboratory On Technology for Early Diagnosis of Major Gynecologic Diseases, Shenzhen, 518036, P. R. China
| | - Wei Zhang
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen Peking University- The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, P. R. China
- Shenzhen Key Laboratory On Technology for Early Diagnosis of Major Gynecologic Diseases, Shenzhen, 518036, P. R. China
| | - Hui Du
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen Peking University- The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, P. R. China
- Shenzhen Key Laboratory On Technology for Early Diagnosis of Major Gynecologic Diseases, Shenzhen, 518036, P. R. China
| | - Xinfeng Qu
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen Peking University- The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, P. R. China
- Shenzhen Key Laboratory On Technology for Early Diagnosis of Major Gynecologic Diseases, Shenzhen, 518036, P. R. China
| | - Yun Chen
- Peking University Shenzhen Hospital, Shenzhen, China
| | - Jianliu Wang
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China.
| | - Ruifang Wu
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen Peking University- The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, P. R. China.
- Shenzhen Key Laboratory On Technology for Early Diagnosis of Major Gynecologic Diseases, Shenzhen, 518036, P. R. China.
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Moyo S, Ramogola-Masire D, Moraka NO, Tawe L, Noubary F, Motsumi K, Manowe G, Zuze B, Radibe B, Hungwe FTT, Mohammed T, Maphorisa C, Shapiro R, Gaseitsiwe S, Luckett R. Comparison of the AmpFire® Multiplex HPV Assay to the Xpert® HPV Assay for detection of human papillomavirus and cervical disease in women with human immunodeficiency virus: a pragmatic performance evaluation. Infect Agent Cancer 2023; 18:29. [PMID: 37165397 PMCID: PMC10170707 DOI: 10.1186/s13027-023-00504-z] [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: 02/20/2023] [Accepted: 04/14/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Low- and middle-income countries (LMICs) account for nearly 85% of the global cervical cancer burden, yet have the least access to high-performance screening. International guidelines recommend human papillomavirus testing (HPV) as primary screening, yet implementation is inhibited by the cost of HPV testing. Atila AmpFire® HPV Assay (AmpFire) is both affordable and easy to use, and offers individual genotyping. The objective of this study was to compare the performance of the AmpFire HPV assay to the Xpert® HPV assay in detection of both HPV and clinically significant cervical disease. METHODS We utilized stored cervical specimens from a prospective cohort study of women living with human immunodeficiency virus (HIV) in Botswana conducted from May to July 2018. Positive and negative percent agreement was calculated for the AmpFire and Xpert assays, as was detection of high-grade cervical dysplasia. RESULTS 63 stored cervical specimens had detectable DNA after thawing and were included in the analysis. The positive percent agreement was 91.2% (95%CI 76.3-98.1) and negative percent agreement was 79.3% (95% CI 60.3-92.0). Six cases positive by AmpFire but negative by Xpert were HPV genotypes 35, 52 (n = 2), 58, 68, and co-infection with HPV 45 and 68. Both Xpert and AmpFire assays detected HPV in all 10 samples of women who had high-grade cervical dysplasia. CONCLUSIONS The AmpFire HPV assay demonstrated excellent analytic performance in both detection of HPV and clinically significant cervical disease. AmpFire HPV is a promising option to increase access to affordable, type-specific HPV screening for cervical cancer in LMICs.
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Affiliation(s)
- Sikhulile Moyo
- Botswana Harvard Health Partnership, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | | | - Leabaneng Tawe
- Faculty of Medicine, University of Botswana, Gaborone, Botswana
| | - Farzad Noubary
- Department of Health Sciences, Northeastern University, Boston, MA, USA
| | | | | | | | | | - Faith T T Hungwe
- School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Biochemistry and Chemistry, Stockholm University, Stockholm, Sweden
| | | | | | - Roger Shapiro
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Kirstein, 3Rd Floor, 330 Brookline Avenue, Boston, MA, 02215, USA
- Harvard Medical School, Boston, MA, USA
| | - Simani Gaseitsiwe
- Botswana Harvard Health Partnership, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Rebecca Luckett
- Botswana Harvard Health Partnership, Gaborone, Botswana.
- Faculty of Medicine, University of Botswana, Gaborone, Botswana.
- Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Kirstein, 3Rd Floor, 330 Brookline Avenue, Boston, MA, 02215, USA.
- Harvard Medical School, Boston, MA, USA.
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Kanyabwisha F, Kim HY, Shi Q, Murenzi G, Tuyisenge P, Kubwimana G, Munyaneza A, Murangwa A, Turizigiye O, Da Costa M, Nsengiyumva B, Chen X, Mutesa L, Anastos KM, Palefsky JM. Comparison of AmpFire and MY09/11 assays for HPV genotyping in anogenital specimen of Rwandan men who have sex with men. Heliyon 2023; 9:e16016. [PMID: 37305475 PMCID: PMC10256914 DOI: 10.1016/j.heliyon.2023.e16016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction The AmpFire HPV genotyping Assay (Atila Biosystems, Mountain View, CA, USA) is a new test for which there are few data regarding its analytic performance and reliability. Using anal and penile swab specimens from a cohort study of men who have sex with men (MSM) in Rwanda, we compared high-risk HPV (hrHPV) detection by AmpFire done at two laboratories, one at University of California San Francisco (UCSF) and the other Rwanda Military Hospital, and well-validated MY09/11-based assay done at UCSF. Methods Anal and penile specimens collected from 338 MSM from March 2016 to September 2016 were tested for high-risk HPV genotypes (hrHPV) by MY09/11, AmpFire UCSF and AmpFire RMH. Cohen's kappa coefficient was used to test for reproducibility. Results The hrHPV positivity by MY09/11 and AmpFire UCSF was 13% and 20.7% (k = 0.73) for anal specimens and was 26.3% and 32.6% (k = 0.67) for penile specimens. Specifically, good reproducibility was for types 16 and 18 (k = 0.69 and k = 0.71) for anal specimens and (k = 0.50 and k = 0.72) for penile specimens. The hrHPV positivity by AmpFire at UCSF and RMH was 20.7% for both laboratories (k = 0.87) for anal specimens and was 34.9% and 31.9% (k = 0.89) for penile specimens. Specifically, excellent reproducibility was for types 16 and 18 for anal specimens (k = 0.80 and k = 1.00) and penile specimens (k = 0.85 and k = 0.91). Conclusion Results show that MY09/11 and AmpFire assays have good reproducibility while the AmpFire UCSF and RMH assays have excellent reproducibility. These results show that AmpFire is a promising HPV genotyping test.
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Affiliation(s)
- Faustin Kanyabwisha
- Rwanda Military Hospital (RMH), KK 80 St, Kigali, Rwanda
- Research for Development (RD Rwanda), KG11 Ave Promise House Building 3rd Floor, Kigali City, Gasabo, Rwanda
- School of Health Sciences, College of Medicine and Health Sciences, University of Rwanda, KK 737 St, Kigali, Rwanda
| | - Hae-Young Kim
- Department of Public Health, New York Medical College, Valhalla, NY, USA
| | - Qiuhu Shi
- Department of Public Health, New York Medical College, Valhalla, NY, USA
| | - Gad Murenzi
- Rwanda Military Hospital (RMH), KK 80 St, Kigali, Rwanda
- Research for Development (RD Rwanda), KG11 Ave Promise House Building 3rd Floor, Kigali City, Gasabo, Rwanda
| | - Patrick Tuyisenge
- Rwanda Military Hospital (RMH), KK 80 St, Kigali, Rwanda
- Research for Development (RD Rwanda), KG11 Ave Promise House Building 3rd Floor, Kigali City, Gasabo, Rwanda
| | - Gallican Kubwimana
- Rwanda Military Hospital (RMH), KK 80 St, Kigali, Rwanda
- Research for Development (RD Rwanda), KG11 Ave Promise House Building 3rd Floor, Kigali City, Gasabo, Rwanda
| | - Athanase Munyaneza
- Rwanda Military Hospital (RMH), KK 80 St, Kigali, Rwanda
- Research for Development (RD Rwanda), KG11 Ave Promise House Building 3rd Floor, Kigali City, Gasabo, Rwanda
| | | | | | - Maria Da Costa
- Department of Infectious Diseases, University of California, San Francisco, USA
| | | | - Xin Chen
- Atila Biosystems Inc, 740 Sierra Vista Ave, Mountain View, CA, 94043, USA
| | - Leon Mutesa
- Rwanda Military Hospital (RMH), KK 80 St, Kigali, Rwanda
- Research for Development (RD Rwanda), KG11 Ave Promise House Building 3rd Floor, Kigali City, Gasabo, Rwanda
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, KK 737 St, Kigali, Rwanda
| | - Kathryn M. Anastos
- Division of General Internal Medicine, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY, 10467, USA
| | - Joel M. Palefsky
- Department of Infectious Diseases, University of California, San Francisco, USA
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Sammouri J, Wong MC, Lynn EJ, El Alam MB, Lo DK, Lin D, Harris TH, Karpinets TV, Court K, Napravnik TC, Wu X, Zhang J, Klopp AH, Ajami NJ, Colbert LE. Serial Genotyping of the Human Papillomavirus in Cervical Cancer: An Insight Into Virome Dynamics During Chemoradiation Therapy. Int J Radiat Oncol Biol Phys 2023:S0360-3016(23)00163-3. [PMID: 36801350 DOI: 10.1016/j.ijrobp.2023.02.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/19/2023] [Accepted: 02/07/2023] [Indexed: 02/18/2023]
Abstract
PURPOSE Human papillomavirus (HPV) is the primary driver of cervical cancer. Although studies in other malignancies correlated peripheral blood DNA clearance with favorable outcomes, research on the prognostic value of HPV clearance in gynecologic cancers using intratumoral HPV is scarce. We aimed to quantify the intratumoral HPV virome in patients undergoing chemoradiation therapy (CRT) and associate this with clinical characteristics and outcomes. METHODS AND MATERIALS This prospective study enrolled 79 patients with stage IB-IVB cervical cancer undergoing definitive CRT. Cervical tumor swabs collected at baseline and week 5 (end of intensity modulated radiation therapy) were sent for shotgun metagenome sequencing and processed via VirMAP, a viral genome sequencing and identification tool for all known HPV types. The data were categorized into HPV groups (16, 18, high risk [HR], and low risk [LR]). We used independent t tests and Wilcoxon signed-rank to compare continuous variables and χ2 and Fisher exact tests to compare categorical variables. Kaplan-Meier survival modeling was performed with log-rank testing. HPV genotyping was verified using quantitative polymerase chain reaction to validate VirMAP results using receiver operating characteristic curve and Cohen's kappa. RESULTS At baseline, 42%, 12%, 25%, and 16% of patients were positive for HPV 16, HPV 18, HPV HR, and HPV LR, respectively, and 8% were HPV negative. HPV type was associated with insurance status and CRT response. Patients with HPV 16+ and other HPV HR+ tumors were significantly more likely to have a complete response to CRT versus patients with HPV 18 and HPV LR/HPV-negative tumors. Overall HPV viral loads predominantly decreased throughout CRT, except for HPV LR viral load. CONCLUSIONS Rarer, less well-studied HPV types in cervical tumors are clinically significant. HPV 18 and HPV LR/negative tumors are associated with poor CRT response. This feasibility study provides a framework for a larger study of intratumoral HPV profiling to predict outcomes in patients with cervical cancer.
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Affiliation(s)
| | - Matthew C Wong
- Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | | | | | | | - Tatiana V Karpinets
- Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | - Xiaogang Wu
- Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianhua Zhang
- Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Nadim J Ajami
- Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
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Gomez Cherey JF, Payalef SN, Fleider L, Reyes AP, Maldonado VA, Losada MO, Chen X, Cardinal LH, Wang Y, Tatti SA, Perazzi BE. Microbiota unbalance in relation to high-risk human papillomavirus cervical infection. Int J Gynecol Cancer 2023; 33:482-488. [PMID: 36604120 DOI: 10.1136/ijgc-2022-003760] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
OBJECTIVES To assess vaginal dysfunction using basic vaginal states and the presence of lactobacillary microbiota in patients with human papillomavirus (HPV) infection with no squamous intra-epithelial lesions (SIL), with low-grade squamous intra-epithelial lesions (L-SIL), and with high-grade squamous intra-epithelial lesions (H-SIL) or squamous cell carcinoma compared with a control group (HPV-negative); to establish the prevalence of bacterial vaginosis, candidiasis, and trichomoniasis in the different age groups; and to characterize the species of lactobacilli according to the type of lesion. METHODS A cross-sectional study was carried out of patients who underwent clinical examination and collection of vaginal fornixes to study basic vaginal states and culture. Species identification of lactobacilli was performed by mass spectrometry. The results were analyzed using the χ2 and Fisher's tests; p<0.05 was considered significant. High-risk viral types were determined using a multiplex real-time polymerase chain reaction test. RESULTS A total of 741 patients were analyzed and divided into three age groups: Group 1 aged 18-24 years (n=138), Group 2 aged 25-50 years (n=456), and Group 3 aged >50 years (n=147). All groups were further divided into an HPV-negative (control) group and an HPV-positive group without lesions, with L-SIL, or with H-SIL/squamous cell carcinoma. The prevalence of unbalanced basic vaginal states in patients with H-SIL/squamous cell carcinoma was 72.7% (p=0.03) in Group 1, 53.1% (p=0.05) in Group 2, and no cases of unbalance were detected in Group 3. The prevalence of bacterial vaginosis in women with H-SIL/squamous cell carcinoma in Group 1 was 54.5% and in Group 2 was 43.7%. Patients with H-SIL/squamous cell carcinoma had a prevalence of 21.4% of Lactobacillus crispatus, 42.9% of L. jensenii, and 14.3% of L. iners. CONCLUSIONS A greater unbalance of vaginal microbiota was observed in patients with SIL, especially in those with H-SIL/squamous cell carcinoma. In this group, an increase in L. jensenii and L. iners compared with control was found. L. crispatus had a similar prevalence to the control group. It is important to characterize the lactobacilli species since the unbalance alters the vaginal microenvironment and acts as a co-factor in the persistence of HPV infection.
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Affiliation(s)
- Juan Facundo Gomez Cherey
- Programa de Diagnóstico, Terapéutica y Vacunación del Tracto Genital Inferior, Universidad de Buenos Aires Facultad de Medicina, Ciudad Autónoma de Buenos Aires, Argentina
| | - Sandra Noemi Payalef
- Departamento de Bioquímica Clínica - Laboratorio de Bacteriología Clínica, Universidad de Buenos Aires Facultad de Farmacia y Bioquimica, Ciudad Autónoma de Buenos Aires, Argentina.,Instituto de Fisiopatología y Bioquímica Clínica (INFIBIOC), Universidad de Buenos Aires Facultad de Farmacia y Bioquimica, Buenos Aires, Argentina
| | - Laura Fleider
- Programa de Diagnóstico, Terapéutica y Vacunación del Tracto Genital Inferior, Universidad de Buenos Aires Facultad de Medicina, Ciudad Autónoma de Buenos Aires, Argentina
| | - Ana Paula Reyes
- Departamento de Bioquímica Clínica - Laboratorio de Bacteriología Clínica, Universidad de Buenos Aires Facultad de Farmacia y Bioquimica, Ciudad Autónoma de Buenos Aires, Argentina.,Instituto de Fisiopatología y Bioquímica Clínica (INFIBIOC), Universidad de Buenos Aires Facultad de Farmacia y Bioquimica, Buenos Aires, Argentina
| | - Verónica Andrea Maldonado
- Programa de Diagnóstico, Terapéutica y Vacunación del Tracto Genital Inferior, Universidad de Buenos Aires Facultad de Medicina, Ciudad Autónoma de Buenos Aires, Argentina
| | - Mirta Olga Losada
- Departamento de Bioquímica Clínica - Laboratorio de Bacteriología Clínica, Universidad de Buenos Aires Facultad de Farmacia y Bioquimica, Ciudad Autónoma de Buenos Aires, Argentina.,Instituto de Fisiopatología y Bioquímica Clínica (INFIBIOC), Universidad de Buenos Aires Facultad de Farmacia y Bioquimica, Buenos Aires, Argentina
| | - Xin Chen
- Atila BioSystems, Mountain View, California, USA
| | - Lucia Helena Cardinal
- Departamento de Patología, Universidad de Buenos Aires Facultad de Medicina, Ciudad Autónoma de Buenos Aires, Argentina
| | | | - Silvio Alejandro Tatti
- Programa de Diagnóstico, Terapéutica y Vacunación del Tracto Genital Inferior, Universidad de Buenos Aires Facultad de Medicina, Ciudad Autónoma de Buenos Aires, Argentina
| | - Beatriz Elizabeth Perazzi
- Departamento de Bioquímica Clínica - Laboratorio de Bacteriología Clínica, Universidad de Buenos Aires Facultad de Farmacia y Bioquimica, Ciudad Autónoma de Buenos Aires, Argentina.,Instituto de Fisiopatología y Bioquímica Clínica (INFIBIOC), Universidad de Buenos Aires Facultad de Farmacia y Bioquimica, Buenos Aires, Argentina
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9
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Murangwa A, Desai KT, Gage JC, Murenzi G, Tuyisenge P, Kanyabwisha F, Musafili A, Kubwimana G, Mutesa L, Anastos K, Kim HY, Castle PE. Agreement between Xpert and AmpFire tests for high-risk human papillomavirus among HIV-positive women in Rwanda. Afr J Lab Med 2022; 11:1827. [PMID: 36353194 PMCID: PMC9639372 DOI: 10.4102/ajlm.v11i1.1827] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 05/26/2022] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND High-risk human papillomavirus (hrHPV) may cause more than 99% of cervical cancers worldwide. Little is known about performance differences in tests for hrHPV. OBJECTIVE This study analysed agreement for detection of hrHPV between the established, clinically validated Xpert HPV assay and the novel isothermal amplification-based AmpFire HPV genotyping assay. METHODS This study was nested in a larger project on cervical cancer screening among approximately 5000 women living with HIV in Kigali, Rwanda. This sub-study included 298 participants who underwent initial screening for cervical cancer using the Xpert HPV assay and visual inspection with acetic acid in 2017 and tested positive by either or both. Participants were rescreened using colposcopy, and cervical samples were collected between June 2018 and June 2019. Samples were then tested for HPV using the Xpert HPV assay and AmpFire HPV genotyping assay. Agreement between results from both tests was analysed using an exact version of McNemar test and chi-square test. RESULTS Overall agreement and kappa value for detection of hrHPV by Xpert and AmpFire were 89% and 0.77 (95% confidence interval: 0.70-0.85). AmpFire was marginally more likely to diagnose hrHPV-positive than Xpert (p = 0.05), due primarily to the extra positivity for HPV16 (p < 0.001). CONCLUSION Overall, there was good to excellent agreement between the Xpert and AmpFire when testing hrHPV types among women living with HIV. AmpFire was more likely to test extra cases of HPV16, the most carcinogenic HPV type, but the clinical meaning of detecting additional HPV16 infections remains unknown.
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Affiliation(s)
| | - Kanan T. Desai
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, United States
| | - Julia C. Gage
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, United States
| | | | | | | | - Aimable Musafili
- Department of Paediatrics and Child Health, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Gallican Kubwimana
- Rwanda Military Hospital, Kigali, Rwanda
- Research for Development (RD Rwanda), Kigali, Rwanda
| | - Leon Mutesa
- Research for Development (RD Rwanda), Kigali, Rwanda
- Centre for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Kathryn Anastos
- Departments of Medicine and Epidemiology & Population Health, Albert Einstein College of Medicine and Montefiore Health Systems, Bronx, New York, United States
| | - Hae-Young Kim
- Department of Public Health, New York Medical College, Valhalla, New York, United States
| | - Philip E. Castle
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, United States
- Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, Rockville, Maryland, United States
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10
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Desai KT, Adepiti CA, Schiffman M, Egemen D, Gage JC, Wentzensen N, de Sanjose S, Burk RD, Ajenifuja KO. Redesign of a rapid, low-cost HPV typing assay to support risk-based cervical screening and management. Int J Cancer 2022; 151:1142-1149. [PMID: 35666530 PMCID: PMC9378567 DOI: 10.1002/ijc.34151] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/21/2022] [Accepted: 05/18/2022] [Indexed: 11/24/2022]
Abstract
Accelerated cervical cancer control will require widespread human papillomavirus (HPV) vaccination and screening. For screening, sensitive HPV testing with an option of self-collection is increasingly desirable. HPV typing predicts risk of precancer/cancer, which could be useful in management, but most current typing assays are expensive and/or complicated. An existing 15-type isothermal amplification assay (AmpFire, Atila Biosystems, USA) was redesigned as a 13-type assay (ScreenFire) for public health use. The redesigned assay groups HPV types into four channels with differential cervical cancer risk: (a) HPV16, (b) HPV18/45, (c) HPV31/33/35/52/58 and (d) HPV39/51/56/59/68. Since the assay will be most useful in resource-limited settings, we chose a stratified random sample of 453 provider-collected samples from a population-based screening study in rural Nigeria that had been initially tested with MY09-MY11-based PCR with oligonucleotide hybridization genotyping. Frozen residual specimens were masked and retested at Atila Biosystems. Agreement on positivity between ScreenFire and prior PCR testing was very high for each of the channels. When we simulated intended use, that is, a hierarchical result in order of clinical importance of the type groups (HPV16 > 18/45 > 31/33/35/52/58 > 39/51/56/59/68), the weighted kappa for ScreenFire vs PCR was 0.90 (95% CI: 0.86-0.93). The ScreenFire assay is mobile, relatively simple, rapid (results within 20-60 minutes) and agrees well with reference testing particularly for the HPV types of greatest carcinogenic risk. If confirmed, ScreenFire or similar isothermal amplification assays could be useful as part of risk-based screening and management.
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Affiliation(s)
- Kanan T. Desai
- Clinical Epidemiology Unit, Clinical Genetic Branch, Division of Cancer Epidemiology and GeneticsNational Cancer InstituteRockvilleMarylandUSA
| | - Clement A. Adepiti
- Department of Obstetrics, Gynecology, and PerinatologyThe Obafemi Awolowo UniversityIle‐IfeOsun StateNigeria
| | - Mark Schiffman
- Clinical Epidemiology Unit, Clinical Genetic Branch, Division of Cancer Epidemiology and GeneticsNational Cancer InstituteRockvilleMarylandUSA
| | - Didem Egemen
- Clinical Epidemiology Unit, Clinical Genetic Branch, Division of Cancer Epidemiology and GeneticsNational Cancer InstituteRockvilleMarylandUSA
| | - Julia C. Gage
- Clinical Epidemiology Unit, Clinical Genetic Branch, Division of Cancer Epidemiology and GeneticsNational Cancer InstituteRockvilleMarylandUSA
| | - Nicolas Wentzensen
- Clinical Epidemiology Unit, Clinical Genetic Branch, Division of Cancer Epidemiology and GeneticsNational Cancer InstituteRockvilleMarylandUSA
| | - Silvia de Sanjose
- Clinical Epidemiology Unit, Clinical Genetic Branch, Division of Cancer Epidemiology and GeneticsNational Cancer InstituteRockvilleMarylandUSA
- ISGlobalBarcelonaSpain
| | - Robert D. Burk
- Albert Einstein Cancer CenterAlbert Einstein College of MedicineNew YorkNew YorkUSA
| | - Kayode O. Ajenifuja
- Department of Obstetrics, Gynecology, and PerinatologyThe Obafemi Awolowo UniversityIle‐IfeOsun StateNigeria
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11
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Murenzi G, Shumbusho F, Hansen N, Munyaneza A, Gage JC, Muhoza B, Kanyabwisha F, Pierz A, Tuyisenge P, Anastos K, Castle PE. Long-term human papillomavirus vaccination effectiveness and immunity in Rwandan women living with and without HIV: a study protocol. BMJ Open 2022; 12:e061650. [PMID: 36008069 PMCID: PMC9422845 DOI: 10.1136/bmjopen-2022-061650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
INTRODUCTION Prophylactic human papillomavirus (HPV) vaccines have been shown to be highly effective in protecting women against cervical infections, high-grade abnormalities and cancer caused by the targeted HPV types. However, the evidence for their effectiveness in women living with HIV (WLWH) is less clear. METHODS WLWH and HIV-negative women who likely did (birth cohorts 1996 and later) and WLWH and HIV(-) negative who likely did not (birth cohorts before 1996) receive HPV vaccination (n=3028; 757 participants for each of the four groups). Between groups, we will compare cervicovaginal, anal and oral prevalent and 6-12 month persistent HPV6/11/16/18 infections as measured using a modified AmpFire HPV genotyping assay that tests for 15 high-risk or intermediate-risk HPV genotypes, HPV6 and HPV11. We will also compare the HPV immune response in HPV-vaccinated WLWH to HPV-vaccinated HIV-negative women using an anti-HPV16 and anti-HPV18 ELISA. Vaccination status will be confirmed through national vaccination records. ANALYSIS We will calculate point prevalence and prevalence of 6-12 month persisting infections by individual HPV-type specific infections and groups of infections for each anatomic site and for each group of women. Results will be stratified by age at vaccination, age at enrolment and the number of doses (3 vs 2) as well as other factors possibly associated with HPV prevalence. Differences in endpoints between groups, overall and between subgroups, will be tested for statistical significance (p<0.05) using Fisher's exact or Pearson χ2 test. Differences in geometric mean titres and seropositivity will be tested for statistical significance using the Mann-Whitney and Fisher's exact tests, respectively. ETHICS AND DISSEMINATION The study was approved by the Albert Einstein College of Medicine Institutional Review Board and the Rwanda National Ethics Committee. Results will be disseminated through publication in peer-reviewed journals.
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Affiliation(s)
- Gad Murenzi
- Einstein-Rwanda Research and Capacity Building Program, Rwanda Military Hospital, Kigali, Rwanda
- Einstein-Rwanda Research and Capacity Building Program, Research for Development (RD Rwanda), Kigali, Rwanda
| | - Fabienne Shumbusho
- Einstein-Rwanda Research and Capacity Building Program, Rwanda Military Hospital, Kigali, Rwanda
- Einstein-Rwanda Research and Capacity Building Program, Research for Development (RD Rwanda), Kigali, Rwanda
| | - Natasha Hansen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Athanase Munyaneza
- Einstein-Rwanda Research and Capacity Building Program, Rwanda Military Hospital, Kigali, Rwanda
- Einstein-Rwanda Research and Capacity Building Program, Research for Development (RD Rwanda), Kigali, Rwanda
| | - Julia C Gage
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Benjamin Muhoza
- Einstein-Rwanda Research and Capacity Building Program, Rwanda Military Hospital, Kigali, Rwanda
- Einstein-Rwanda Research and Capacity Building Program, Research for Development (RD Rwanda), Kigali, Rwanda
| | - Faustin Kanyabwisha
- Einstein-Rwanda Research and Capacity Building Program, Rwanda Military Hospital, Kigali, Rwanda
- Einstein-Rwanda Research and Capacity Building Program, Research for Development (RD Rwanda), Kigali, Rwanda
| | - Amanda Pierz
- Department of Community Health and Health Sciences, CUNY Graduate School of Public Health and Health Policy, New York, New York, USA
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Patrick Tuyisenge
- Einstein-Rwanda Research and Capacity Building Program, Rwanda Military Hospital, Kigali, Rwanda
- Einstein-Rwanda Research and Capacity Building Program, Research for Development (RD Rwanda), Kigali, Rwanda
| | - Kathryn Anastos
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, USA
| | - Philip E Castle
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
- Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland, USA
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12
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Alirezaei M, Mosawi SH, Afgar A, Zarean M, Movahhed TK, Abbasi V, Fotouhi-Ardakani R. Discrimination of human papillomavirus genotypes using innovative technique nested-high resolution melting. Sci Rep 2022; 12:13943. [PMID: 35977949 PMCID: PMC9382607 DOI: 10.1038/s41598-022-14730-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 06/13/2022] [Indexed: 11/09/2022] Open
Abstract
The prompt detection of human papillomavirus and discrimination of its genotypes by combining conventional methods in new molecular laboratories is essential to achieve the global call of eliminating cervical cancer. After predicting the melting temperature of an approximately 221 bp region of the L1 gene from different HPV genotypes by bioinformatics software, an innovative technique based on the nested- high resolution melting was designed with three approaches and using conventional PCR, qPCR, and diagnostic standards. HPV-positive samples identified by microarray along with diagnostic standards were evaluated by qPCR-HRM and discordant results were subjected to sequencing and analyzed in silico using reference types. In addition to screening for human papillomavirus, nested-qPCR-HRM is one of the modified HRM techniques which can discriminate some genotypes, including 6, 16, 18, 52, 59, 68 and 89. Despite the differences in diagnostic capabilities among HRM, microarray and sequencing, a number of similarities between HRM, and sequencing were diagnostically identified as the gold standard method. However, the bioinformatics analysis and melting temperature studies of the selected region in different HPV genotypes showed that it could be predicted. With numerous HPV genotypes and significant genetic diversity among them, determining the virus genotype is important. Therefore, our goal in this design was to use the specific molecular techniques with several specific primers to increase sensitivity and specificity for discriminating a wide range of HPV genotypes. This approach led to new findings to evaluate the ability of different approaches and procedures in accordance with bioinformatics.
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Affiliation(s)
- Melika Alirezaei
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, 3736175513, Iran
| | | | - Ali Afgar
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran
| | - Mehdi Zarean
- Department of Parasitology and Mycology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Tahereh Komeili Movahhed
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, 3736175513, Iran
| | - Vajiheh Abbasi
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, 3736175513, Iran
| | - Reza Fotouhi-Ardakani
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, 3736175513, Iran. .,Department of Medical Biotechnology, School of Medicine, Qom University of Medical Sciences, Qom, Iran.
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13
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Vanderbilt CM, Bowman AS, Middha S, Petrova-Drus K, Tang YW, Chen X, Wang Y, Chang J, Rekhtman N, Busam KJ, Gupta S, Hameed M, Arcila ME, Ladanyi M, Berger MF, Dogan S, Zehir A. Defining Novel DNA Virus-Tumor Associations and Genomic Correlates Using Prospective Clinical Tumor/Normal Matched Sequencing Data. J Mol Diagn 2022; 24:515-528. [PMID: 35331965 PMCID: PMC9127461 DOI: 10.1016/j.jmoldx.2022.01.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/27/2021] [Accepted: 01/31/2022] [Indexed: 12/11/2022] Open
Abstract
This study is the largest analysis of DNA viruses in solid tumors with associated genomics. To achieve this, a novel method for discovery of DNA viruses from matched tumor/normal next-generation sequencing samples was developed and validated. This method performed comparably to reference methods for the detection of high-risk (HR) human papilloma virus (HPV) (area under the receiver operating characteristic curve = 0.953). After virus identification in 48,148 consecutives samples from 42,846 unique patients, novel virus tumor associations were established by segregating tumor types to determine whether each DNA virus was enriched in each of the tumor types compared with the remaining cohort. All firmly established solid tumor-virus associations (eg, HR HPV in cervical cancer) were confirmed, and the novel associations discovered included: human herpes virus 6 in neuroblastoma, human herpes virus 7 in esophagogastric cancer, and HPV42 in digital papillary adenocarcinoma. These associations were confirmed in an independent validation cohort. HR HPV- and Epstein-Barr virus-associated tumors showed newly discovered genomic associations, including a lower tumor mutation burden. The study demonstrated the ability to study the role of DNA viruses in human cancer from clinical genomics data and established the largest cohort that can be utilized as a validation set for future discovery efforts.
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Affiliation(s)
- Chad M Vanderbilt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Anita S Bowman
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sumit Middha
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kseniya Petrova-Drus
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yi-Wei Tang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Xin Chen
- Atila Biosystems Inc., Mountain View, California
| | | | - Jason Chang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Natasha Rekhtman
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Klaus J Busam
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sounak Gupta
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Meera Hameed
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Berger
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Snjezana Dogan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Zehir
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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14
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Paytubi S, Taberna M, Mena M, Quirós B, Gomà M, Alemany L, Bosch FX, Pavón MÁ. The Isothermal Amplification AmpFire Assay for Human Papillomavirus (HPV) Detection and Genotyping in Formalin-Fixed, Paraffin-Embedded Oropharyngeal Cancer Samples. J Mol Diagn 2021; 24:79-87. [PMID: 34801703 DOI: 10.1016/j.jmoldx.2021.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/12/2021] [Accepted: 10/13/2021] [Indexed: 12/01/2022] Open
Abstract
Human papillomavirus (HPV)-related oropharyngeal squamous cell carcinomas (OPSCCs) represent a distinct clinical entity compared with HPV-negative tumors with particular regard to treatment response and survival outcome. The aim of this study was to assess the AmpFire Multiplex HR-HPV tests, for the detection and genotyping of 15 high-risk (HR) HPV types in formalin-fixed, paraffin-embedded (FFPE) samples and identify HPV-driven OPSCC. DNA from 160 OPSCC FFPE specimens plus 23 samples from other head and neck primary sites was tested. Results were compared with those obtained using Linear Array HPV-DNA Genotyping Test. Linear Array and AmpFire Multiplex HR-HPV tests showed, for all samples and specifically for OPSCCs, an overall concordance agreement of 98.9% and 99.4% and a Cohen κ coefficient of 0.972 and 0.984, respectively. A concordance of 100% for HPV16 and HPV18 was observed. The overall agreement between p16INK4a overexpression and HPV detection by the AmpFire Multiplex HR-HPV assay in 145 OPSCC samples was 93.8%, with a Cohen κ coefficient of 0.848. The AmpFire HPV Tests are simple assays for detection and genotyping of HPV-DNA in OPSCC FFPE samples and can be easily implemented in the clinical practice setting for HPV-DNA detection.
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Affiliation(s)
- Sonia Paytubi
- Cancer Epidemiology Research Program, Catalan Institute of Oncology, IDIBELL, ONCOBELL, Barcelona, Spain.
| | - Miren Taberna
- Medical Oncology Department, Catalan Institute of Oncology, IDIBELL, ONCOBELL, Barcelona, Spain
| | - Marisa Mena
- Cancer Epidemiology Research Program, Catalan Institute of Oncology, IDIBELL, ONCOBELL, Barcelona, Spain; Centro de Investigación Biomédica en Red: Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain
| | - Beatriz Quirós
- Cancer Epidemiology Research Program, Catalan Institute of Oncology, IDIBELL, ONCOBELL, Barcelona, Spain; Centro de Investigación Biomédica en Red: Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain
| | - Montserrat Gomà
- Department of Pathology, Hospital Universitari Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Laia Alemany
- Cancer Epidemiology Research Program, Catalan Institute of Oncology, IDIBELL, ONCOBELL, Barcelona, Spain; Centro de Investigación Biomédica en Red: Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain
| | - Francesc X Bosch
- Cancer Epidemiology Research Program, Catalan Institute of Oncology, IDIBELL, ONCOBELL, Barcelona, Spain; Centro de Investigación Biomédica en Red: Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain; Universitat Oberta de Catalunya, Barcelona, Spain
| | - Miguel Á Pavón
- Cancer Epidemiology Research Program, Catalan Institute of Oncology, IDIBELL, ONCOBELL, Barcelona, Spain; Centro de Investigación Biomédica en Red: Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain.
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15
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Patient Satisfaction With Human Papillomavirus Self-Sampling in a Cohort of Ethnically Diverse and Rural Women in Yunnan Province, China. J Low Genit Tract Dis 2021; 24:349-352. [PMID: 32796262 PMCID: PMC7515469 DOI: 10.1097/lgt.0000000000000560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Rural Yunnan Province is one of the most ethnically, culturally, and religiously diverse regions in China. The majority of its women have never been screened for cervical cancer. It is not known whether women would feel comfortable and ultimately even prefer using a human papillomavirus (HPV) self-swabbing method.
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16
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Abstract
Men who have sex with men (MSM) have a high prevalence of anal and penile human papillomavirus (HPV) infections with MSM living with HIV (MSMLH) bearing the highest rates. Data on anogenital high-risk HPV (hrHPV) among MSM in Rwanda and the associated risk factors are scant.
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17
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Yang Z, Francisco J, Reese AS, Spriggs DR, Im H, Castro CM. Addressing cervical cancer screening disparities through advances in artificial intelligence and nanotechnologies for cellular profiling. BIOPHYSICS REVIEWS 2021; 2:011303. [PMID: 33842926 PMCID: PMC8015256 DOI: 10.1063/5.0043089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
Almost all cases of cervical cancer are caused by the human papilloma virus (HPV). Detection of pre-cancerous cervical changes provides a window of opportunity for cure of an otherwise lethal disease when metastatic. With a greater understanding of the biology and natural course of high-risk HPV infections, screening methods have shifted beyond subjective Pap smears toward more sophisticated and objective tactics. This has led to a substantial growth in the breadth and depth of HPV-based cervical cancer screening tests, especially in developed countries without constrained resources. Many low- and middle-income countries (LMICs) have less access to advanced laboratories and healthcare resources, so new point-of-care (POC) technologies have been developed to provide test results in real time, improve the efficiency of techniques, and increase screening adoption. In this Review, we will discuss how novel decentralized screening technologies and computational strategies improve upon traditional methods and how their realized promise could further democratize cervical cancer screening and promote greater disease prevention.
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Affiliation(s)
| | | | - Alexandra S. Reese
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - David R. Spriggs
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Hyungsoon Im
- Authors to whom all correspondence should be addressed: and
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18
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Connors KA, Abbott S, Jair K, Daniels J, Lintner M, Klein D, Wimpleberg A, Jordan JA. Cross comparison of AmpFire HPV genotyping assay and Roche human papillomavirus (HPV) linear array for HPV genotyping of anal swab samples. J Virol Methods 2021; 292:114113. [PMID: 33652016 DOI: 10.1016/j.jviromet.2021.114113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 11/26/2022]
Abstract
Although anal cancers represent just 0.5 % of all new cancer cases in U.S., rates have increased markedly, with highest rates in HIV-infected MSM. American Cancer Society estimates there will be ∼9090 new cases and ∼1420 deaths in 2021. We compared Roche Linear Array HPV Genotyping (Roche) and AmpFire HPV Genotyping (AmpFire) assays for concordance and agreement to detect 15 hr-HPV types from 151 anal specimens. Within run precision of AmpFire was assessed on 50 anal specimens. Specimens with Roche Combo-positive and HPV33, HPV35 and/or HPV58-positive results were further tested using HPV52-specific TaqMan assay. AmpFire generated valid results on 149/151 (98.7 %) specimens; 135/149 (90.6 %) and 134/149 (89.9 %) had detectable HR-HPV DNA by AmpFire or Roche, respectively. Overall concordance was 89.8 % (2007/2235, κ = 0.65). HPV16 showed highest overall concordance at 93.3 % (139/149, κ = 0.84). HPV68 had lowest overall concordance at 77.2 % (115/149, κ = 0.28). Kappa values were interpreted as being moderate or good for all other HR-HPV types. Within run precision generated 744/750 concordant results; R2 value = 0.97 (p < 0.0001) (Mantel Test). In conclusion, AmpFire and Roche demonstrated good inter-assay agreement for detecting most HR-HPV types from anal samples, with AmpFire detecting a broader range of HPV68 subtypes and detecting HPV52 without the need for confirmatory testing.
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Affiliation(s)
- Kaleigh A Connors
- Department of Epidemiology, School of Public Health, The George Washington University, Washington, DC, USA
| | | | - Kamwing Jair
- Department of Epidemiology, School of Public Health, The George Washington University, Washington, DC, USA
| | - Jason Daniels
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Madison Lintner
- Department of Epidemiology, School of Public Health, The George Washington University, Washington, DC, USA
| | | | | | - Jeanne A Jordan
- Department of Epidemiology, School of Public Health, The George Washington University, Washington, DC, USA.
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19
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Nunez-Bajo E, Silva Pinto Collins A, Kasimatis M, Cotur Y, Asfour T, Tanriverdi U, Grell M, Kaisti M, Senesi G, Stevenson K, Güder F. Disposable silicon-based all-in-one micro-qPCR for rapid on-site detection of pathogens. Nat Commun 2020; 11:6176. [PMID: 33268779 PMCID: PMC7710731 DOI: 10.1038/s41467-020-19911-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/29/2020] [Indexed: 12/15/2022] Open
Abstract
Rapid screening and low-cost diagnosis play a crucial role in choosing the correct course of intervention when dealing with highly infectious pathogens. This is especially important if the disease-causing agent has no effective treatment, such as the novel coronavirus SARS-CoV-2, and shows no or similar symptoms to other common infections. Here, we report a disposable silicon-based integrated Point-of-Need transducer (TriSilix) for real-time quantitative detection of pathogen-specific sequences of nucleic acids. TriSilix can be produced at wafer-scale in a standard laboratory (37 chips of 10 × 10 × 0.65 mm in size can be produced in 7 h, costing ~0.35 USD per device). We are able to quantitatively detect a 563 bp fragment of genomic DNA of Mycobacterium avium subspecies paratuberculosis through real-time PCR with a limit-of-detection of 20 fg, equivalent to a single bacterium, at the 35th cycle. Using TriSilix, we also detect the cDNA from SARS-CoV-2 (1 pg) with high specificity against SARS-CoV (2003).
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Affiliation(s)
| | | | - Michael Kasimatis
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Yasin Cotur
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Tarek Asfour
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Ugur Tanriverdi
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Max Grell
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Matti Kaisti
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
- Department of Future Technologies, University of Turku, 20500, Turku, Finland
| | - Guglielmo Senesi
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Karen Stevenson
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, Scotland, EH26 0PZ, UK
| | - Firat Güder
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
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20
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Zhang W, Du H, Huang X, Wang C, Duan X, Liu Y, Shi B, Zhang W, Qu X, Wei L, Schiffman M, Belinson JL, Wu R. Evaluation of an isothermal amplification HPV detection assay for primary cervical cancer screening. Infect Agent Cancer 2020; 15:65. [PMID: 33110442 PMCID: PMC7583687 DOI: 10.1186/s13027-020-00328-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/25/2020] [Indexed: 12/12/2022] Open
Abstract
Objective The aim of this research was to evaluate independently the performance of a new isothermal amplification assay for cervical cancer screening compared to two previously validated PCR-based assays and histologic endpoints. Methods This is a sub-study from the Chinese multi-center screening trial (CHIMUST). The self-collected and clinician-collected specimens stored in PreservCyt at − 4 °C from 6042 women with complete data were tested with the AmpFire assay. These specimens had been previously tested with Cobas and SeqHPV assays. In the primary study all patients with an abnormal test were referred to colposcopy where all had directed and/or random biopsies plus ECC. No additional patients were called back based on the AmpFire results. Results 6042/6619 women had complete data (mean age 44.1). There were 57 cases of CIN 2, 35 cases of CIN 3 and 2 cancers. The sensitivity for CIN2+ and CIN3+ were similar among the three assays (both direct and self-collected). For the specificities in all categories (CIN2+/CIN3+ and self and direct collection), isothermal amplification assay was either equal to or more specific than Cobas but consistently less specific than SeqHPV. Conclusion The AmpFire HPV assay showed similar sensitivity to Cobas and SeqHPV for CIN2+ and CIN3+ on both self and clinician-collections (P>0.05), with good specificity. The speed, low cost, and simplicity of this assay will make it particularly suited for low and middle resource settings. Its accuracy with self-collection makes it applicable for mass screening programs.
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Affiliation(s)
- Wei Zhang
- Peking University Shenzhen Hospital, Shenzhen, 518036 P. R. China.,Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecological diseases, Shenzhen, P. R. China
| | - Hui Du
- Peking University Shenzhen Hospital, Shenzhen, 518036 P. R. China.,Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecological diseases, Shenzhen, P. R. China
| | - Xia Huang
- Peking University Shenzhen Hospital, Shenzhen, 518036 P. R. China.,Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecological diseases, Shenzhen, P. R. China
| | - Chun Wang
- Peking University Shenzhen Hospital, Shenzhen, 518036 P. R. China.,Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecological diseases, Shenzhen, P. R. China
| | - Xianzhi Duan
- Capital Medical University Beijing Tongren Hospital, Beijing, P. R. China
| | - Yan Liu
- Fudan University Huanshan Hospital, Shanghai, P. R. China
| | - Bin Shi
- The second Hospital of Hebei Medical University, Shijiazhuang, P. R. China
| | - Wei Zhang
- Wuhan University Zhongnan Hospital, Wuhan, P. R. China
| | - Xinfeng Qu
- Expert in Three Engineering Office, Shenzhen Maternal of Peking University Shenzhen Hospital, Shenzhen, 518036 China
| | - Lihui Wei
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, P. R. China
| | - M Schiffman
- National Cancer Institute, Division of Epidemiology and Genetics, Bethesda, USA
| | - J L Belinson
- Women's Health Institute, Cleveland Clinic, Cleveland, OH USA.,PPreventive Oncology International, Inc., Shaker Heights, USA
| | - Ruifang Wu
- Peking University Shenzhen Hospital, Shenzhen, 518036 P. R. China.,Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecological diseases, Shenzhen, P. R. China
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21
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Evaluation of Liquid Versus Dry Specimen Transport With a Newly Validated Isothermal Amplification High-Risk Human Papillomavirus Assay. J Low Genit Tract Dis 2020; 24:243-246. [PMID: 32569253 DOI: 10.1097/lgt.0000000000000546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
OBJECTIVE The aim of the study was to determine whether the proportion of positive high-risk human papillomavirus (HR-HPV) tests in endocervical specimens transported dry differs from paired specimens transported in liquid media. METHODS Five hundred women aged of 30 to 55 years were recruited, Shanxi Bethune Hospital, China. Two samples were collected from the endocervix per patient, one placed into empty vial, the other into a liquid transport solution. All samples were analyzed by AmpFire HR-HPV assay. RESULTS Total 1,000 samples collected from 500 patients were analyzed by the AmpFire HR-HPV assay. The total invalid rate was 0.2% (2/1,000). The proportion of endocervical samples testing positive for HR-HPV transported dry (42.2%, 210/498 [95% CI = 37.8%-46.6%]) was similar to the proportion of paired endocervical samples testing positive transported in liquid media (40.4%, 201/498 [95% CI = 36.0%-44.8%], p = .18 [McNemar test]). That the 2 transport methods are likely measuring the same positive (and negative) specimens is suggested by the finding that κ value for the correlation of positive HR-HPV in endocervical specimens transported dry with those transported in liquid media was 0.86 (95% CI = 0.81-0.90). CONCLUSIONS Endocervical specimens transported dry have similar proportion of positive HR-HPV tests as those transported in liquid media. Dry brush transport of endocervical samples paired with the special characteristics of AmpFire HR-HPV may become an important addition to population based cervical cancer screening.
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22
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Jang D, Shah A, Arias M, Ratnam S, Smieja M, Chen X, Wang Y, Speicher DJ, Chernesky M. Performance of AmpFire HPV assay on neck cervical lymph node aspirate and oropharyngeal samples. J Virol Methods 2020; 279:113840. [DOI: 10.1016/j.jviromet.2020.113840] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/20/2020] [Accepted: 02/22/2020] [Indexed: 11/24/2022]
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