Huan Truong

Notes from a developer


What personal genetics means to a computer nerd

I always consider myself a computer nerd. On this blog, I often write about my hobby-turned-into-a-job as an embedded programmer/security enthusiast/hardware hacker. In real life, I'm a bioinformatics graduate student. My upcoming thesis is about the topic of GPU acceleration of several bioinformatics algorithms. Even so, bioinformatics is a relatively obscure place to be, it's not as flashy as hacking self-driving cars or sending robots on Mars. I think colonizing Mars is something we all dream of but not something we can do now. Plus, it doesn't matter if Elon Musk sends a Tesla to space: You're still here on Earth. Personal genetics is different, it is the stuff that affects our lives right now. If you know it, you make better decisions. It helps you understand part of your destiny to make better choices today. Some people may ask: Do I really want to know that I'm going to die soon? So ask yourself: Would you rather want to know whether it's going to rain tomorrow so you know to prepare an umbrella, or you'd rather have everyday as a complete surprise? It's a personal taste. Maybe you don't want to know, and that's fine. I guess for me and for many of us, knowing part of our destinty is a good thing.

Personal genetics is still a relatively obscure life-hack that not many people are able to tell you, even your doctor won't. I hope to sketch out a layman idea of why a software developer might find personal genetics is a "cool idea" and practical, not something you'd have to be a scientist/strong biology background to understand and act on.

It's also my very personal story. It began 5 years ago when 23andme had the A/B testing 49/68/99 USD random price points for their personal genetics testing. I got the 49USD genetics testing, which was a great deal.

At that point, I actually didn't know what it does. It turned out that 23andme asks you to deposit your saliva into a tube and send back, and it will return your DNA sequence as a result. Technically, it doesn't sequence whole DNA strands. They just put "probes" into certain points of your DNA that each human is known to be different from each other, called the SNPs (pronounced snips). Each of the points has a slight chance of determining what you look like, how tall you are, how much you like sweet stuff, etc.

Here are some of my mysteries uncovered.

You might already know, I'm a Vietnamese national. It was particularly embarrassing when I came to the US for college and had to live and eat in the dorm in the first semester. I had a lot of you knowā€¦ digestive problemsā€¦ bowel movementsā€¦ I had no idea why and thought maybe I wasn't used to the food. Later on, though 23andme, I discovered I am lactose-intolerant. It was like a-ha moment: it's the cereal I ate every once in a while for breakfast in the dorm. Vietnamese people eat noodles (Pho/bun/instant noodles) or baguette for breakfast, so no wonder I'm totally fine in Vietnam, but not in the US. First mystery solved, 5 years too late (but then now I only drink lactose-free milk).

Vietnam is also a hot and sunny country. When I was little, I would get rashes when I played on extremely hot and sunny days. The itchy rashes would go away gradually when I got inside to cool myself down or take a quick shower. My mom thought I was overheated. We never figured out what the that was about, but because I knew how to make it go away, it really was more of an inconvenience than any health concern. I don't think about that much, especially after I moved to the US, which is a much cooler country. 23andme didn't tell me anything cool. One day, I used my genetics data that 23andme provided with another service called Promethease provided by SNPedia. SNPedia is basically a Wikipedia for SNPs - while 23andme only reports what it is confident about, Promethease reports the cutting-edge stuff. I discovered that I have a mild case of the Porphyria aka "vampire disease" and was that another big a-ha moment. It was the generic mutation that inspired people to construct the idea of vampires in folklore. People having the diseases often can't get exposed to sunlight because it would cause rashes. And man, I do have two really scary looking fang teeth too. I never knew the fangs are an indication of my disease. It was right there, and I had no idea.

Other than that, there is even darker, deeper stuff in the mind that I wouldn't have thought it could be influenced by genetics. I know that I'm bad at guessing people's intention and emotions when talking face-to-face. It turns out that there is a chemical molecule called oxytocin that is released when you interact with others (and dogs, too). In people like me, the machine that recognizes oxytocin doesn't work as well, so I feel less empathic to others. It reflected very strongly as I thought about testimonials that ex-girlfriends gave me. Other than that, I am predicted to have bad at avoidance of errors, and more likely to be dependent on stimulants, and have a very high risk of schizophrenia (I have schizophrenic uncle family). All those are very well reflected. Some of the warnings are very helpful, for example, that I am more likely dependant on alcohol and stimulants, so I often remind myself to not getting into troubles.

The cool thing about DNA testing is that it's like the same dataset you generally only need to harvest once. Then you can "plug" whatever fancy algorithm you have in and with better algorithms, it will yield better more accurate results. Or talk like a software engineer: Genetics data is like Java: write once, debug everywhere.

Personal genetics is not something to be afraid of, to quote Marie Curie: "Nothing in life is to be feared, it is only to be understood. Now is the time to understand more, so that we may fear less."

As a social experiment, you can view my personal genetics Promethease report here.