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Polymerase Chain Reaction Detection of Y Chromosome Sequences in Vaginal Fluid: Preliminary Studies of a Potential Biomarker for Sexual Behavior

Zenilman, Jonathan M. MD* †; Yuenger, Jeffrey*; Galai, Noya; Turner, Charles F. PhDDagger; §; Rogers, Susan M. PhDDagger; ∥

Sexually Transmitted Diseases: February 2005 - Volume 32 - Issue 2 - p 90-94
doi: 10.1097/01.olq.0000149668.08740.91

Background: Self-reported measures of sexual behavior are subject to nontrivial reporting biases.

Objective: The objective of this study was to develop a behavioral biomarker of recent sexual activity among females that is inexpensive, easily administered, and can be used in low sexually transmitted disease prevalence populations.

Methods: We developed a polymerase chain reaction (PCR) assay to detect Y chromosome (Yc) fragments. The Yc primers were developed against a 200-basepair (bp) microsatellite repeat sequence, which is unique to the male genome. A standard PCR technique was used. Assay sensitivity was determined quantitatively using donated semen samples. To assess longevity of detectability, we recruited female subjects in monogamous relationships. Seventeen subjects had unprotected intercourse followed by 3 weeks of abstinence from vaginal intercourse. Self-administered vaginal swabs (SAVS) were collected every other day. In addition to the swabs, subjects kept daily sexual diaries. Swabs were processed by semiquantitative PCR, and Yc decay curves were determined for each subject. The half-life of Yc in vaginal fluid was calculated on the collection of individual decay curves by a random-effects regression model approach.

Results: The sensitivity of our Yc-PCR assay was determined to be 5 copies of Yc. In the longevity studies, Yc was detectable in SAVS up to 15 postcoital days (PCD). Mean Yc DNA concentration in SAVS eluate followed an exponential decay pattern for each subject. Mean concentrations were 66.7 ng/mL at PCD-1, 20.6 ng/mL at PCD-7, and 4.5 ng/mL at PCD-15. The estimated half-life for Yc clearance was 3.83 days.

Conclusion: The swab-based Yc-DNA PCR assay can detect coitus in women for a 2-week retrospective period. This can be used to validate sexual behavior-reporting and condom use in women and promises to be a useful tool in sexual behavior research.

From the *Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland; the †Department of Epidemiology, Johns Hopkins University School of Public Health, Baltimore, Maryland; the ‡Program in Health and Behavior Measurement, Research Triangle Institute, Washington, DC; §City University of New York, Queens College and the Graduate Center, New York, NY; and the ∥Department of Maternal and Child Health, School of Public Health, University of North Carolina, Chapel Hill, North Carolina

This work was supported by NIH grants AI-46181 and HD-43674 to 01. Bonnie Cooper assisted in the specimen collection, Corlina McNeil Solis, and Julie Giles performed the laboratory analyses, and Robin Pollini assisted in data management. Authors at Johns Hopkins University conducted the phase 1 determination of assay sensitivities independently. The phase 2 clinical characterization of assay performance in sexually active women was conducted as a collaboration of Johns Hopkins University and RTI authors.

Correspondence: Jonathan M. Zenilman, MD, Division of Infectious Diseases, Johns Hopkins Bayview Medical Center, 4940 Eastern Ave., Baltimore, MD 21224. E-mail:

Received for publication May 6, 2004, and accepted September 7, 2004.

© Copyright 2005 American Sexually Transmitted Diseases Association