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July 8, 2020 | Human ID and Forensics

New Investigator Sofia Antão Sousa on MPS analysis of familial genetic data

Sofia talks about the forensic applications of uncovering mutational mechanisms
July 08, 2020

The new Investigator blog shines a personal spotlight on individual scientists at the exciting early stages of a career working in the field of human identification and forensics. The passion and commitment revealed in their stories are an inspiration to all in our community.

This new Investigator blog is an invitation to meet Sofia Antão Sousa, a Ph.D. candidate working on uncovering mutational mechanisms through MPS analyses at the Faculty of Science at the University of Porto and IPATIMUP/i3S (Instituto de Patologia e Imunologia Molecular da Universidade do Porto/Instituto de Investigação e Inovação em Saúde).

1. Tell us about your background and how you became interested in forensic science?

When I was a little kid, my parents were really into science documentaries and would watch them together with me and my brother at least once a week. I really enjoyed learning about how the natural world works and from a very young age I already told, to anyone who would listen, I wished to be a biologist. Being at the time fascinated with the human body and wanting to be a helper, when the moment came to decide which degree I wanted to pursue, I chose Nursing.

But I soon realized that it wasn’t for me and committed to pursuing a degree in Biology at the University of Porto. I think the feeling of wonder for me comes from the searching for an answer yet unknown, so I thought being a part of a community that dedicates itself to unravel nature’s secrets would be where I belong. During the degree in Biology, we had the freedom to choose classes in different subjects and I experimented with several, ranging from microbiology to paleontology. As the years progressed, it became more and more apparent that all my favorite subjects were in the field of genetics.

After my bachelor’s degree, I did a course in Forensic Sciences and made up my mind to get a master’s degree that combined these two: forensics and genetics. During a class in the first year of my master’s I met, unknowingly, the person who would be my M.Sc. and Ph.D. supervisor. Dr. Nádia Pinto, a mathematician, presented a project which aimed to collect and study Y-chromosomal data in order to learn more about mutation in short tandem repeats (STRs). My M.Sc. co-supervisor was Professor Leonor Gusmão, a biologist with an extensive experience in the field who is currently working at the Laboratório de Diagnósticos por DNA in Rio de Janeiro, Brazil. It captivated me immediately; soon after I told them I was interested in joining the project and had the joy of being accepted. For my PhD supervision, Professor António Amorim joined. He is the group leader of the Population Genetics and Evolution Group at the i3S - Instituto de Investigação e Inovação em Saúde – where my academic journey through forensic genetics began and where I am currently developing my project.

2. Can you provide a summary of the project you are working on?

My PhD project is entitled “Uncovering mutational mechanisms through MPS analyses”. My main goal is to correlate mutation types and rates with different conditions, such as age or sex of the individual, or the type of marker, allele in study, or even with the allele’s repetitive motif. For this, we collect families’ genetic data from published works or generate it in our lab. We compare the haplotypes or genotypes of the individuals of each family and use these data to do
as many analyses as we can. The ultimate goal is to understand and quantify how much each factor affects the frequency and type of occurring mutation.

3. Please describe your typical day in the lab.

The bulk of my work is dry lab. So, as soon as I arrive, I turn on my computer, make myself a cup of tea and sit down to check my email. At the beginning of each day, before I start on any task, I like to write a clear and straightforward to-do list for the day, including every little thing I want to get done. On a typical day, these tasks could be reading a couple of papers, analyzing a set of data, and writing. I regularly attend the seminars my institute hosts and have frequent meetings with my supervisors and colleagues to discuss each other’s latest work, to give and receive feedback and, of course, correct any part of the projects that needs it.

4. What do you find most interesting about your project? Have you seen any surprising results?

Mutational mechanisms are very complex as they are influenced by a variety of aspects. Comprehending these aspects, and in what measure they affect the frequency or type of mutation occurring, has extreme importance in a forensic casework context. In particular, it is important for the correct estimation of mutation rates that allow the analysis, interpretation and proper quantification of likelihood ratios.
As for surprising results, we have seen some unexpected mutational behavior for some markers, but for now I cannot disclose more; we are still working on this. On another work, we have observed a vast disparity in the precision of mutation rates estimates varying with the family transmission analyzed; despite knowing that would happen, its dimension surprised us.

5. What are the benefits of your project?

The study of the biological mechanisms that lead to mutation (and its frequency) is crucial in many studies. These range from linkage and association, where experts need to uncover distant or cryptic relationships to avoid false conclusions on the correlation among (or between) loci and the phenotypes of interest (a disease, for example), to population and evolutionary, forensic and medical studies (for example, microsatellite instability in cancer cells). Additionally, we are able to utilize data already generated for other studies and contexts, for which re-analyses can help boost the state of the art.

6. What are the major challenges faced while working on your project and how do you overcome them?

Because many of the published works we use as data sources include only the number of mutations observed per marker, and do not include both the initial (parental) and final (filial) alleles (complete allelic transfer information), the main challenge I have faced is the lack of the complete data I need to attain better mutation estimates and modelling. To overcome this issue, we generate extra data in our lab and collaborate with other researchers aiming for the enlargement of the dataset. Also, we propose collaborative exercises among several labs aiming for each lab to generate genetic data that will allow us to study the mutation phenomenon.

The latest proposal, at the XXIV GHEP-ISFG Meeting, in Prague, September of 2019, was for two collaborative exercises. These aim to collect complete haplotypic and genotypic information for one generation pedigrees of father-son duos and father-mother-daughter trios, to study mutation in the Y and X chromosomes, respectively. QIAGEN supports the X chromosome collaborative exercise by providing participant laboratories with a generous discount on the amplification kit:
Investigator Argus X-12 QS Kit. All the gathered data will help tremendously to mitigate the issue.

7. Which QIAGEN products do you use and what do you like about the products?

For the amplification of the father-mother-daughter trios processed in our lab, we use the Investigator Argus X-12 QS Kit. This kit already includes a Quality Sensor, which allows the quick realization if the PCR run was successful or if there was no DNA present in the sample. For the PATHS project, the DNA is extracted from FTA cards with the EZ1 DNA Investigator Kit. The EZ1 DNA Investigator Kit reproducibly automates purification of genomic DNA. As some of our samples were noticeably dry, this instrument was crucial to attain the highest quality of genetic profiles possible. It is impressive the fluid workflow this instrument permits.

8. Outside of forensic science, what are your hobbies?

Outside of the lab, I take real pleasure in commanding my own kitchen, which I like to fill to the brim with willing helpers and tasters - my family and close friends - for I love cooking and trying new recipes, particularly savory dishes. If followed by an evening session of boardgame playing, it’s the perfect night! I enjoy reading; my favorite writer is Margaret Atwood. I am fond of sports; I love swimming and I have a soft spot for hiking in the countryside.

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