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Take a BIT Module with me: Next-Gen Forensic DNA Analysis

If you have completed BIT410/510, you will be well prepared for how Biotechnology Program lab modules run. These eight-week courses typically consist of a two-hour lecture period and a five-hour lab period each week. When you were told in BIT410/510 that each module has the workload of a four-credit hour class, just for half of the semester, that was not a joke! With the BIT modules, you will put in a lot of work, but get many marketable skills out.

This past eight weeks, during the Spring 2023 session I, I was enrolled in BIT495/595 Next-Gen Forensic DNA Analysis. This course is taught by Dr. Kelly Meiklejohn and her teaching assistant Teresa Tiedge, both from the College of Veterinary Medicine, who have been teaching this course since the Spring of 2020. They told my class many times how much they value student feedback and have made various improvements in the semesters since, including changing the entire structure of the class so the assignment due dates were more spread out and therefore less stressful for the students; we were also able to offer our own feedback at the end of the course. 

If you want to see how a lab module is structured, or if you’re interested in this specific forensics course (offered every spring semester!), follow along as I tell you about my experience.

Week One – Talking about tradition

Lecture: Yay for syllabus week! During today’s lecture, we learned about Dr. Meiklejohn’s background in Australia and with the United States FBI, introduced ourselves to the class, talked about DNA’s traditional role in forensics, and learned the proper ways to collect DNA evidence and process it. DNA swabs look remarkably similar to COVID swabs, except you can just swab it over a door handle with no eye-watering necessary.

Lab: This week was mostly a continuation of the lecture where we expanded on the steps that forensic scientists take for traditional human DNA analysis. We walked through the steps used to produce data from short tandem repeats (STRs), the “gold standard” of most human forensic DNA analysis. The main drawback to STR typing is that you need a relatively high concentration of DNA, which isn’t always possible when you’re swabbing dried blood or collecting a hair. 

Week Two – Was that really grouper…?

Lecture: Since we covered traditional DNA analysis last week, this week we talked about using next-generation sequencing (NGS) in forensics; specifically non-human DNA, which is what Dr. Meiklejohn’s lab works with. As promising as NGS is, it is very hard to introduce new methods into forensic labs that are used in casework since the validation process is so lengthy and will most likely be thrown out in court. 

Lab: Bioinformatics is heavily used in forensics to compare DNA sequences with sequence databases. We were given a mock case involving seafood fraud and the mislabeling of fish. Dr. Meiklejohn had previously gone to the store, bought a bunch of seafood products, and sequenced them. We were then told to use the public database MitoFish to see the species of fish present, BLAST to compare our sequences with the reference genomes in MitoFish, and Excel to organize everything. I am not the most tech-savvy person, but this was surprisingly fun and easy! The protocols for this class are very detailed and easy to follow. Of my two samples, one was improperly labeled (as salmon when it was actually tuna!).

Week Three – The stakes rise

Lecture: After a recap of general STR typing, we talked about alternative methods of collecting DNA for STR analysis, including the popular method of using mitochondrial DNA. After that, we touched on using NGS in human forensics since that’s what we were going to be starting in lab. 

Lab: We started our first wet lab this week! Our mock case was described to be a (fake) bombing that the (fake) FBI was investigating. “Evidence” that had the suspects’ DNA on it was collected and analyzed using STRs. Inconclusive data resulted, so it was our responsibility to run a single nucleotide polymorphism (SNP) panel in order to determine the predicted ancestry of the suspects. This week, we amplified, purified, and quantified the DNA from the “evidence” using PCR, bead purification, and qPCR, respectively. 

Week Four – Building a library, but not of books

Lecture: Dr. Michael Brandhagen from the FBI joined us over Google Meets as a guest speaker to talk about how the FBI takes steps to validate new protocols for DNA analyses. The main takeaway from his talk is that it’s A LOT of work to get a new scientific method approved for use in casework forensics. He was supposed to go over some casework examples, but unfortunately, some technical difficulties forced him to leave early. 

Lab: Our second lab in the wet lab series involved us constructing libraries for NGS and quantifying the DNA in our libraries. Since we are using Illumina sequencing technology, we had to attach specific sequences to our DNA so that it was compatible with the sequencing lawn and software. After that, we quantified our libraries once again. If you take anything away from this, let it be that you always want to know exactly how much DNA you have when you’re working with forensics!

Week Five – Saving the day

Lecture: At the beginning of the semester we either chose a partner or were assigned a partner to create a presentation on an assigned forensics manuscript. My partner and I got lucky with a relatively short paper, but it meant we had to fully understand most details of the paper so we had enough to talk about for the 15-minute presentation. Our assigned paper focused on using Y-STRs, which are found on the male Y chromosome, in forensics to identify males from females in sexual assault cases. Dr. Meiklejohn asked my partner and me a question, and since we were able to provide answers to the class, we successfully completed our presentation. Each group was asked a few questions just to ensure their understanding, but everyone did great!

Lab: Last week marked the last of our sample prep, so today we took the results from the NGS and did some bioinformatics magic. Before class, Teresa ran all of our results through the published CLC workflow and Python script, providing us with files that were compatible with our computers and Excel. We used the Frog-KB database to compare our SNPs with and predict the ancestry of our evidence samples, just in time for the (fake) FBI to narrow down their suspect list.

Week Six – Your motivation to dust

Lecture: This week we had lecture over Zoom because I was unlucky enough to catch COVID, in addition to many other students being sick this week. Since Dr. Brandhagen’s connection was cut during his original lecture, he joined us for approximately 15 minutes to finish talking about some of the case examples he has worked on. Dr. Meiklejohn lectured on using NGS with non-human forensic evidence, including fungi, dust, and soil metabarcoding. Did you know your DNA can be identified from dust collected from your bedroom? Finally, we watched a pre-recorded guest lecture from Dr. Jessica Metcalf on using the microbiome in forensics.

Lab: No lab this week while Dr. Meiklejohn and Teresa attended a scientific conference. They recommended we use this time to knock out a big chunk of our 10-page manuscript that was based on labs three through five. I would definitely recommend starting this at least one week before it’s due, because maybe it’s the COVID talking, but 10 pages is not easy.

Week Seven – Go pack!

Lecture: No lecture this week to keep the lectures aligned with the labs. If you stayed up late working on your manuscript, this was a great time to take a nap!

Lab: We had another bioinformatics-heavy lab today, but this time looking at what SNPs and primers people could use to get the most distinguishing power between canid (dogs, wolves, foxes, etc.) species, which is a huge problem in wildlife forensics. Up until today, my technologically-challenged self was able to keep up, but using the CLC Genomics Workbench did throw me for a bit of a loop. We were analyzing full mitochondrial genomes, creating alignments between the reference genome and our samples, looking at different primers, and the amount of SNPs in concentrated areas within the primers. It was a lot of looking at tiny letters and seemingly endless scrolling, but in the end, we got to make phylogenetic trees with our results. I love visual results, so this is exactly what I needed to re-spark my interest in the lab.

Week Eight – The coolest career

Lecture: Today’s lecture expanded upon Dr. Brandhagen’s talk on forensic laboratory accreditation, specifically with regard to NGS. We discussed why it’s almost impossible to build a case in court using new technologies/techniques and what the underlying ethics are surrounding these issues. We also were introduced to the idea of genetic genealogy, or how various companies are able to form family trees from a DNA test, and how the government can use this information in forensics.

Lab: In honor of our last class, we had an untraditional lab today. First we watched the first episode of The Genetic Detective, a TV show about the most famous genetic genealogist, CeCe Moore. This episode focused on how she became one of the first genetic genealogists and her process behind solving the Jay Cook and Tanya Van Cuylenborg cold case from 1987. After learning about the process and power of genetic genealogy, we were split into two groups to prepare for a mock Frye court admissibility hearing, arguing “for” or “against” the practice. I was in the group arguing “for ” genetic genealogy, and in an hour we had prepared a presentation complete with three main points and closing remarks. I’m not one for public speaking, let alone arguing, but this was a fun way to wrap up the class and learn about something that is changing the face of forensic science as we know it.

Dr. Meiklejohn is a wonderful professor who is always full of joy and fun facts. Even though this class is a lot of bioinformatics and computer work, her classroom atmosphere makes up for it. The prelab readings are quite dense, but all of the assignments are spread out in a fashion that you won’t have to work on more than one thing at a time. 

I hope anyone who is interested in forensics, next-gen sequencing, and/or bioinformatics gets the opportunity to take this class. It will be offered again next spring during the second eight-week period. BIT495/595 Next-Gen Forensic DNA Analysis is a fun way to experience forensics, plus the next-gen sequencing and bioinformatics skills you gain will be plenty to aid you in a future in biotechnology.