Week Four: PCR Trouble and an Ethical Conversation

Apr 21, 2022

Hello! This week was my first time running through the PCR in the lab at Genspace! The sequencing of the DNA to see which COMT polymorphism I have took about 5 hours total over 2 nights in the lab. Over these 2 nights at the lab, I had many goals before starting the sequencing of my participant’s DNA. Goal 1: Understand the lab space and make sure I knew where all of my materials would be. Goal 2: Practice the protocol for the sequencing with my own DNA to ensure accuracy and efficiency later on in the experiment. Goal 3: Catch any errors with measurements or procedures in my protocol and tweak them before going through the PCR with the participant’s DNA. 

The first day in the lab, my advisor Madison and I prepped my DNA sample with a resin called chelex. Chelex is used to pull ions out of a DNA solution to isolate the DNA so it’s ready for PCR. After cleaning my DNA, we added all of the reagents and buffers to my isolated DNA tube. We also added the primers we made on Benchling in order to target the specific DNA sequence we are looking at. Then we used a machine called a thermo cycler. A thermo cycler is used to heat up, amplify, and replicate the desired DNA sequence in its tubes. This portion of the PCR took up the most of our lab time on Tuesday (about 1.5 hours of waiting for my DNA to be isolated…) After the DNA was heated and amplified, we took my sample out and put it in the freezer until our next lab day.

The second day in the lab, Madison and I added the restriction enzyme to my DNA tube. The restriction enzyme we ordered is called NLaIII. NLaIII cuts the DNA at specific sites (in this case, it cuts the DNA when it sees CAT. This means that on the isolated DNA strand that our primers selected for us (which is a very short 200 base pairs), the enzyme will cut at either 1, 2, or 3 places based on which polymorphism I have. After adding the restriction enzyme we ran the PCR through a gel to see the results. And to our surprise, the PCR failed 🙁 Basically what we saw was the control we placed on the left and blank results for where the bands should have been. We came to the conclusion that we didn’t use a high enough concentration of my DNA. Instead of using 5 microliters, we’re going to use 20 microliters next time and hope for the results to show.

haha this is me loading in the failed PCR into the gel. So sad.

So after two long lab days, Madison and I sat down to talk about my project. She and I talked about the way the second half of my project would go- the experiment and test with participants and comparing their results to the polymorphism. Overall, I was worried about what type of data I should be collecting, if it was ethical, and how I can communicate how our genes do and don’t predict things about us. Originally I wanted to collect quantitative data, aka test scores, and compare it to one’s DNA to see if there was any correlation between the two. However, when I began thinking about it, I wanted to gain more from this experiment than just some numbers and data maybe or maybe not correlating with each other. So I began thinking about the ethics of genetic research overall, and how a lot of emerging research (including research surrounding COMT) has been used to define individuals and place them into distinct categories based on their genetics. I thought to myself, do these studies researching the COMT polymorphism understand the implications of measuring someone’s laziness or productiveness with a gene? I looked back to these studies and none of them touch upon this subject. As someone who loves genetics and biology, it pained me to see how these studies are putting out information where  people could interpret results the wrong way. Placing people into categories based on their genetics is not ethical or morally right whatsoever. None of these studies address the participants and their thoughts about this categorization and correlation, so I want to do just that. My new and kinda in the works idea is to ask these tough questions to my participants, but also try to answer them myself. Do you think your DNA properly defines your abilities? Should we use our genetics to try and define and categorize abstract characteristics like laziness or productiveness? 

Thank you for taking the time to read my long winded rant about the ethics of genetic research and how I believe we can do better with emerging research and addressing the issues that create stigma throughout the scientific community. See you next week! 


3 Replies to “Week Four: PCR Trouble and an Ethical Conversation”

  1. Yasmin B. says:

    Classic Clara! ALWAYS ranting about those genetic research ethics haha. That stigma is so real. Excited to hear more about this shift in your project!

  2. Katie H. says:

    Clara our projects have similar ethical concerns and we also share the experience of our projects taking a turn from what we expected. Super excited to see where this goes!

  3. Luca S. says:

    Damn, it sucks that the PCR test failed….bummer! Glad you took the time to analyze the ethical and moral concerns of your research though! Pretty interesting dilemma you’ve got on your hands haha!

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