Polymerase chain reaction detection of Y-chromosome sequences in vaginal fluid of women accessing a sexually transmitted disease clinic

Sex Transm Dis. 2006 Jan;33(1):22-5. doi: 10.1097/01.olq.0000194600.83825.81.


Background: Reporting bias and validity estimation of self-reports in clinical settings is a major problem in sexual behavior research.

Objective: The objective of this study was to determine if a newly described biomarker tool helps clarify sensitivity issues related to condom use self-report.

Methods: A polymerase chain reaction (PCR) assay to detect Y-chromosome (Yc) fragments was used to assess detectability and longevity of YcDNA in vaginal swabs collected from 141 women seeking care for sexually transmitted disease (STD)-related symptoms or as a reported sexual contact to STD. Data analyzed were collected in 1992 to 1994 as part of the Transmission, Acquisition, and Condom Use study. Archived vaginal swab samples were selected from women who in the accompanying survey reported their last intercourse in the previous 14 days. Survey data about partners, sexual behaviors, and self-reported condom use in the previous month was also retrieved.

Results: Overall, 137 (97.2%) vaginal samples had usable PCR assay results; 90 (65.7%) had detectable YcDNA content. Linear regression showed that number of days since last sexual intercourse was a significant predictor of YcDNA concentration. PCR results were compared with self-reported condom use. Of the women, 67 (47.5%) women reported no condom use in the last 14 days, and 36 (25.5%) women reported using condoms consistently. Although YcDNA was detected in the swabs of both condom reporting groups, mean DNA content was significantly lower among the consistent condom users.

Conclusion: The YcPCR assay can detect DNA in a clinical sample of women for up to two weeks. This assay may be useful as a qualitative adjunct to behavioral studies to further understanding of sexual behavior reporting in women.

Publication types

  • Evaluation Study
  • Research Support, N.I.H., Extramural

MeSH terms

  • Adult
  • Ambulatory Care Facilities*
  • Biomarkers / analysis
  • Chromosomes, Human, Y / chemistry*
  • Chromosomes, Human, Y / genetics
  • Condoms / statistics & numerical data
  • DNA / analysis
  • Female
  • Humans
  • Male
  • Polymerase Chain Reaction / methods*
  • Sexual Behavior
  • Sexually Transmitted Diseases / prevention & control*
  • Specimen Handling / methods
  • Vagina / chemistry*


  • Biomarkers
  • DNA