Donna-Lee Martin on MPS and allele frequency
Donna talks about using MPS analysis of sequence-based data to improve the discriminatory power of DNA evidence
November 13, 2020
The new Investigator blog shines a personal spotlight on young scientists and graduate students as they talk about the exciting early stages of a career in human identification and forensics. The passion and commitment revealed in their stories are an inspiration to all in our community.
This new Investigator blog introduces Donna-Lee Martin, an M.Sc. student at the University of Cape Town. Donna’ current work on analyzing massively parallel sequencing (MPS) data involves establishing sequence-based allele frequency for the South African population while investigating how the MPS workflow can be improved.
1. Tell us about your background and how you became interested in forensic science?
I am a young, aspiring forensic scientist, born and bred in Cape Town, South Africa and I am currently completing my Master's degree in Biomedical Forensic Sciences at the University of Cape Town. The reason I became interested in forensic science has to be the 13-year old me watching Abby on NCIS! There is a certain level of CSI-coolness linked to being a female crime-solver, right?
Although the "CSI effect" may have sparked my interest, it is the Human Innocence Project that sparked my passion. As a scientist, I want to be meticulous, ethical and accurate, but as a human being, I want to be compassionate, caring and genuine. I would like to combine these traits and skills in order to help those who have been wrongly convicted of crimes, and, hopefully, use advanced DNA techniques to help me to do so!
2. Can you provide a summary of the project you are working on?
My project involves analyzing massively parallel sequencing (MPS) data from four South African populations that has been processed using the MiSeq FGx workflow. I will be performing a preliminary analysis of interpretation thresholds and investigating how the workflow can be improved. MPS data will be assessed in terms of concordance with traditional STR profiling methods. Most importantly, my project involves the analysis of sequencing data to establish the first sequence-based allele frequency for the South African population. The use of sequence-based data for forensic DNA profiling will improve the discriminatory power of DNA evidence when used in court.
3. Please describe your typical day in the lab.
My typical day in the lab would involve preparing my experiments for the day and laboratory maintenance. A day in the lab also involves getting hungry 10 minutes into loading the master mix (mistakes were made) and, of course, taking coffee breaks while waiting for PCR results (vital). Although much time is spent in the lab, most of my time is spent analyzing results (fun!).
4. What do you find most interesting about your project? Have you seen any surprising results?
The most interesting results from my project are not findings, but processes that were used to obtain those findings. As MPS data is extensive to analyze, I had to come up with ways to analyze data in the most effective and efficient way as possible. Some interesting results involve the different nomenclature systems used to name sequence data and how different they are from each other. This strengthens the motivation for establishing a standard nomenclature system for all laboratories making use of sequence data in forensic genetics.
5. What are the benefits of your project?
My project will benefit the forensic science community by contributing to sequence-based allele frequency data that is currently lacking around the globe. Using sequence-based data has the advantage of being more accurate, more sensitive and providing a higher discriminatory power when using DNA evidence in criminal court.
6. What are the major challenges faced while working on your project and how do you overcome them?
Some of the major challenges I faced while working on my project was the ability and skill required to process large amounts of sequence data. Using this kind of data in forensics is somewhat new and software programs that allow you to process this kind of data automatically are hard to come across. The project also gives normal people (like me) the opportunity to create easier and more accurate ways of processing sequence data.
7. Which QIAGEN products do you use and what do you like about the products?
Some of the samples used in the MPS population study were previously profiled using the QIAGEN Investigator 24plex GO! Kit. The Investigator STR GO! Lysis Buffer was also used to prepare lysates prior to sequencing. I enjoyed working with these kits as they were easy to use.
8. Outside of forensic science, what are your hobbies?
My hobbies, when I am not devoting my life to my thesis, involve spending time with my family, exploring my own city (COVID-19 and student budget permitting) and animating!