Young Investigator Catarina Xavier on DNA phenotyping
The Young Investigator Community is a forum for young forensic researchers and graduate students. The new Investigator blog is an opportunity to meet one of these talented researchers in a place where they can share their achievements and aspirations with peers, friends and colleagues. Read on to find out what first drew this month’s blogger to forensic science. Share with them the excitement of discovery that sustains a passionate commitment to their work.
This new Investigator blog introduces Catarina Xavier, a student in the lab led by Professor Walther Parson at the Institute for Legal Medicine, Medical University of Innsbruck. This active group of scientists has published more than 100 peer-reviewed articles in the forensic and medical genetics field and is internationally recognized as a leader in forensic mitochondrial DNA (mtDNA) analysis.
1. Tell us about your background and how you became interested in forensic science?
I have always been the curious child, mostly interested in how the human body worked and normally the “nerdy” one at school. The first time I had contact with genetics was at 15-years-old when my parents gave me a book The Seven Daughters of Eve, written by Brian Sykes. I was left in awe of mitochondrial genetics and the inferences we could get about human migration and history. Since then, I have always sought a career in natural sciences.
At university, I understood very quickly that I needed to follow a more quantitative approach to biology because of my taste for mathematics and statistics. Therefore, I enrolled in the Master of Forensic Genetics degree and focused on uniparental (maternal) ancestry analysis. The love for forensics in general probably comes from my family entertainment time watching and reading the adventures of the great detectives, Poirot and Sherlock Holmes.
2. Can you provide a summary of the project you are working on?
The main project I am currently working on is called VISAGE (VISible Attributes through GEnomics). It is a Horizon 2020 funded project with various collaborating laboratories. This project is dedicated to designing laboratory and software tools to predict appearance, ancestry and age from an unknown sample, and to validate and implement these into routine forensic laboratories. DNA phenotyping is gaining interest in the forensic genetics field as it may provide investigative leads in cases where standard identification methods fail to provide an answer. Personally, I focus on the appearance and ancestry SNP-based multiplexes.
We have designed two major tools: one basic tool with 153 markers and one enhanced tool with 524 markers. The first contains markers for HirisPlex-S and autosomal ancestry. The second tool also contains markers for other pigmentation traits (such as eyebrow color and freckles), male pattern baldness, hair morphology and both autosomal and paternal ancestry. Furthermore, I have a long-time interest in mtDNA sequencing and analysis, so we can have a good resolution of the entire picture of someone’s background. I am also involved in a series of other projects within the Forensic Genomics group, such as the optimization of bone DNA extraction and methods for DNA quantification.
3. Please describe your typical day in the lab.
I always start my day with an espresso; it’s part of my Portuguese heritage. Then, depending on my lab work of the day, I either go directly into the lab or start by checking my emails. When in the lab, it could be that I am doing quantifications, bone extractions, or library preparations for either of our instruments (Ion S5 [Thermo Fisher] and MiSeq FGx [Verogen and QIAGEN]). Data analysis of such diverse projects can be extremely difficult; I need to be informed and upto- date with numerous types of analysis and software. It also keeps work interesting as I can look at different data and hope to find an answer to a different question every day.
4. What do you find most interesting about your project? Have you seen any surprising results?
One of the most interesting aspects of DNA phenotyping (appearance and ancestry prediction) is the application it has in the real world. The ability to provide any clues to an otherwise “cold” Confidential case is very thrilling! Being a biologist foremost, the increased technical difficulty in building such large multiplexes while keeping similar sensitivity levels as smaller assays is very challenging. Honestly, on a personal level, the challenges make it even a more interesting.
5. What are the benefits of your project?
The true benefits of this project are the potential applications it has in real case scenarios. Imagine a cold case with no DNA match and/or no reference material. Nowadays, we can try to provide a way forward for these cold cases. We can, through the application of DNA phenotyping, give law enforcement some clues to advance an investigation.
6. What are the major challenges faced while working on your project and how do you
The major challenge when trying to design large SNP multiplexes for forensic applications is the balance we want to keep between the high number of markers and the sensitivity of the assay. Of course, some of the phenotyping traits (e.g., male pattern baldness) need several SNPs in order to reach an accurate prediction. Therefore, we need to be able to introduce all these SNPs in one assay, but the more SNPs we add into one assay the higher the probability of having cross-reactions between primers. This makes the design itself more challenging and also means that we might need more starting DNA for a full profile. Since forensic-grade samples can show very low DNA quality and quantity, we must maintain the high sensitivity of the assay. at all costs.
7. Which QIAGEN products do you use and what do you like about the products?
Some QIAGEN products are a must-have in our research lab. We commonly use the QIAampDNA Blood Mini Kit and the EZ1 for extraction of casework “mock” samples, the MinElute PCRPurification Kit for purification of bone extractions, the QIAGEN Multiplex PCR Kit for common multiplex PCRs and have even tested the QIAseq chemistry for the VISAGE basic tool panel.
8. Outside of forensic science, what are your hobbies?
When we have some free time, I like to go hiking and visiting new places with my husband. We love the thrill of travelling and exploring. One of the advantages of living in the center of Europe is the ease of travel into other countries. It is very common to find us trying new shots with a photographic camera. Otherwise, we are always having new ideas; our house is a little laboratory! I am a biologist and my husband is an electronic engineer, so we are always coming up with new ideas for things to test or build.