Amy after her PhD defense, holding a congratulatory gift from QIAGEN
Our Young Investigator series allows us to acknowledge rising scientists in the forensic field. We hope that they inspire you with their story, as they are our future!
Dr. Amy S. Holmes recently graduated from the Sam Houston State University, Huntsville, TX where she received her PhD. Her research focused on exploring solutions to the problem of sub-optimal disaster victim identification (DVI) methods for processing large numbers of decomposing human remains for DNA typing. In addition, her research involved optimizing protocols for in-field sample collection, room-temperature storage, and faster processing of DNA samples from decomposing human tissues. Let’s follow her story!
Tell us about your background and how you became interested in forensic science?
I was 15 years old when Hurricane Katrina came through my hometown just 30 minutes north of New Orleans. I was attending a private art school there, which was damaged by the hurricane, and I was never able to return. Three months later when I did return to my hometown, I had a lot of free time due to the loss of my extracurricular activity and strict curfews implemented by the city. At the same time, my interests in forensic science sparked as I became increasingly aware of the pervasiveness of crime in my area, and I started diving into the forensic television shows and crime thriller books. When I was pursuing my Masters in Forensic Science, I was presented with a research project investigating faster DNA-based methods for identifying victims of mass disasters and I am thrilled to be able to give back to my beloved community.
Can you provide a summary of your project?
Mass disasters such as hurricanes, tsunamis, wars, and terrorism events often result in large numbers of casualties. One of the most important considerations following a mass disaster is victim identification. However, recovery and identification efforts are sometimes complicated by harsh environmental conditions, limited facilities, loss of electricity and refrigeration. If remains cannot be stored or identified quickly, the body decomposes and the DNA in those tissues degrades and fragments making DNA typing more difficult. In addition, quick victim identification is also a goal for DVI operational teams as they attempt to bring closure to the victim’s families, and assist government agencies that must account for the deceased. As a result, the demand for a rapid turnaround time is often stressed; however, due to the overwhelmingly large number of samples requiring processing, this may not be feasible. Significant rate-limiting steps in the STR typing workflow are DNA extraction (approx. 3–4 hours), DNA quantification (1–2 hours), and standard PCR amplification (approx. 2–3 hours). My project investigated the effectiveness of various quick, in-field methods for collecting DNA from decomposing human remains. In addition, several DNA preservation, purification, and amplification strategies were tested in order to facilitate faster and more direct DNA-based identification processes for cases such as mass disasters or rural casework. Overall, our results indicate that sufficient DNA can be collected and preserved at ambient temperature using some of the methods tested, provided that DNA is not already severely degraded before collection.
Please describe a typical day for you in the lab.
As a PhD student and academic researcher, there is no typical day in the lab. Some days I would have class and I would spend a lot of time preparing presentations, writing papers, or studying for exams. Other days, I could get into the lab and focus on my own research, designing experiments to test variables or troubleshooting issues that I or other researchers are experiencing. Experiences such as rescuing instruments in a flooding building to amplifying twelve 96-well plates on the same instrument in a single day have prepared me for real life situations. I also spend a lot of time training and mentoring junior researchers so they too can be successful with their own independent research projects.
What do you find most interesting about your project? Have you seen any surprising results?
What I loved most about my PhD research project was the opportunity to collaborate with the Applied Anatomical Research Center here at SHSU, several leading scientists from across the world, and forensic industry partners such as QIAGEN. I am highly appreciative of our QIAGEN representatives for their amazing support throughout my research project, providing me with products and solutions for my very challenging samples. One of my most interesting results was with samples that I processed via direct PCR with the Investigator 24plex GO! Kit. These samples produced comparable STR results to the traditional DNA analysis workflow with the Investigator 24plex QS Kit in a fraction of the time and without the need to quantify and normalize DNA template for amplification.
What are the benefits of your research?
The combination of quick and simple in-field sample collection methods, DNA preservation, and more rapid or direct sample processing has tremendous potential for forensic application and ultimately criminal justice investigation. This work also demonstrates the potential for improved STR profiling success and reduced time and cost for forensic analyses compared with current DVI practices for DNA identification.
What are the major challenges you face with regards to sample collection, STR processing and data analysis?
At Sam Houston State University, we have a willed body donation center (Applied Anatomical Research Center, AARC) where I encounter a wide range of samples; from fresh and high-quality samples to highly decomposed, degraded, and low template DNA samples. In addition, I store these tissues in chemical preservatives that contain high concentrations of PCR inhibitors in order to adequately preserve the DNA, which in turn poses a challenge during downstream analysis. My research investigated direct PCR (skipping DNA extraction) and/or rapid purification (<30 minutes) with these difficult samples. Therefore, the utility of quality indicators in the Investigator Quantiplex Pro and the Investigator 24plex kits have been a tremendous tool for identifying, and then troubleshooting issues with highly degraded and inhibited samples.
Which QIAGEN products do you use and what do you like about the products?
In our lab, we have many QIAGEN instruments and fully employ a wide range of QIAGEN chemistry. We have the QIAcube and the EZ1 Advanced XL for use with the Investigator DNA extraction kits. I also routinely use the Investigator Quantiplex Pro Kit, and the Investigator 24plex QS and GO! Kits. We have found the quality indicators in Quantiplex Pro to be indicative of the DNA integrity of our challenging samples, and quite predictive of downstream STR success. I also personally love having the Quantiplex Pro data analysis tool handy on my personal computer for data analysis, and I cannot rave enough about the quality sensors in the Investigator 24plex kits. Having the quality sensors in my STR profiles has saved me tons of time troubleshooting issues especially with my direct PCR samples, such as DNA degradation versus PCR inhibition versus complete PCR failure due to a power outage. We are also currently securing a QIAgility and Rotor-Gene Q for our lab, and I am looking forward to using these in my future work.
Outside of forensic science, what are your hobbies?
I have always been interested in the arts but my passions lie with pencil drawings and getting messy with paints. I also love to craft and build anything with my carpenter husband. Another hobby of mine is rescuing dogs and cats in need, especially puppies and kittens that are sick or without their mothers. My co-workers especially love it when I bring them to work for puppy/kitten therapy! I also love spending time outdoors, fishing, and gardening.
Discover more about Amy’s research in our new application note.