The sexual assault microbiome: Detecting contact when minimal male DNA is present.

1. Statement of the Problem

Sexual assault does not always result in the transfer of detectable levels of DNA.  This is especially true in cases of genital penetration without ejaculation.  It has been estimated up to 60% of rape kits produce insufficient male  DNA. This work addresses the problem of associating perpetrators with sexual assaults when human DNA is missing or insufficient.  Instead DNA from bacterial transfer will be used to determine if sexual contact has occurred.

2. Subjects

DNA will be collected from 30 female volunteers and 40 male volunteers, 20 of which are couples, with Institutional Review Board (IRB) approval.

3. Partnerships

This effort will be performed by Florida International University, The Center for Forensic Science Research and Education, and EZBiome.  The Broward Sheriff’s Office (BSO) will also assist in developing case acceptance protocol. Florida International University will select volunteers, collect samples and perform grant administration. EzBbiome will perform sequencing and initial data analysis.  Statistical analysis and report writing will be performed at EzBiome, FIU, and CSFRE.

4. Research Design and Methods

We plan to analyze the microbiome of 70 individuals in total, including 20 married couples, who will be swabbed before and after sexual contact to investigate the degree of transfer of the male microbiome into the female microbiome and the transfer of the female microbiome to the male following consensual relations. Both vaginal and labial swabs will be collected from females. An additional 20 males and 10 females will be recruited to determine the stability of their genital microbiome over a month-long period.

5. Analysis

Samples will be collected and prepared at FIU.  Extraction and deep sequencing will take place at EzBiome, who will sequence, and perform bioinformatic analysis. Results will be tabulated and statistically analyzed at  EzBiome and FIU with the assistance of CFSFRE and Dr. George Duncan.  Karin Crenshaw of the Broward Sheriff’s Office DNA Laboratory will assist with the development of forensic protocols  with Dr. Duncan, a former manager of that lab.

6. Products, Reports, Data Archiving

A method for connecting sexual assault evidence with suspects using the vaginal and penile microbiome will be delivered.  The method will include protocols for sample collection and analysis, along with a statistical method for assessing transfer and contact.  Manuscripts describing study results including microbiome transfer after contact to individuals and longitudinal studies will be published in peer-reviewed journals. CA/NCF