1. A new sequencing-based women’s health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis
- Author
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Adam Caughey, Katia Soto-Liebe, Felipe Melis-Arcos, Juan Cristobal Jimenez, Raul Pino, Harold Nuñez, Amanda Morton, José M. Pérez-Donoso, Audrey D. Goddard, Pamela A. Nieto, Nathaniel A. Walton, Sarah Gupta, Zachary Apte, Eduardo H. Morales, Elisabeth M. Bik, Victor Alegria-Mera, Juan A. Ugalde, Kira Harman, Juan Pablo Cárdenas, Paulo C. Covarrubias, Juan Pablo Bustamante, Francisco J. Ossandon, Graham Gass, Ignacio Varas, Luis E. Leon, Sara W. Bird, Cristian Bravo, Daniel Almonacid, Kwasi Addae, Eduardo Olivares, Donna Marie B. Hongo, Nicolás Órdenes-Aenishanslins, Denisse Bravo, Richard Phan, Patricia Vera-Wolf, Jessica Richman, Camila F. Navas, and Laurens Kraal
- Subjects
Cervical cancer ,Hpv types ,Immunology ,medicine ,Vaginal microbiome ,Dna test ,Microbiome ,Hpv detection ,Biology ,medicine.disease ,Genotyping ,Self sampling - Abstract
The composition of the vaginal microbiome, including both the presence of pathogens involved in sexually transmitted infections (STI) as well as commensal microbiota, has been shown to have important associations for a woman’s reproductive and general health. Currently, healthcare providers cannot offer comprehensive vaginal microbiome screening, but are limited to the detection of individual pathogens, such as high-risk human papillomavirus (hrHPV), the predominant cause of cervical cancer. There is no single test on the market that combines HPV, STI, and microbiome screening. Here, we describe a novel inclusive women’s health assay that combines self-sampling with sequencing-based HPV detection and genotyping, vaginal microbiome analysis, and STI-associated pathogen detection. The assay includes genotyping and detection of 14 hrHPV types, 5 low-risk HPV types (lrHPV), as well as the relative abundance of 32 bacterial taxa of clinical importance, includingLactobacillus,Sneathia,Gardnerella, and 4 pathogens involved in STI, with high sensitivity, specificity, and reproducibility. For each of these taxa, healthy ranges were determined in a group of 50 self-reported healthy women. The hrHPV portion of the test was evaluated against the Digene High-Risk HPV HC2 DNA test with vaginal samples obtained from 185 women. Results were concordant for 181/185 of the samples (overall agreement of 97.83%, Cohen’s kappa = 0.93), with sensitivity and specificity values of 94.74% and 98.64%, respectively. Two discrepancies were caused by the Digene assay’s known cross-reactivity with low-risk HPV types, while two additional samples were found to contain hrHPV not detected by Digene. This novel assay could be used to complement conventional cervical cancer screening, because its self-sampling format can expand access among women who would otherwise not participate, and because of its additional information about the composition of the vaginal microbiome and the presence of pathogens.
- Published
- 2017
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