Summer Spotlight: Hear From National Institute of Genomic Research Intern Cadet Gerardo Quiroga

Soon-to-be junior Cadet Gerardo Quiroga shares his summer internship experience at the National Institute of Genomic Research (INMEGEN) in Mexico City, DF, Mexico. 

Before the Internship 
A few weeks before spring break, I was in the office of one of my school counselors. While talking with Mr. Lucas, I expressed my interest in making the most out of my summer by attending summer programs or having an internship in a lab where I could gain real-life experiences in my favorite fields: biomedicine and genetics. Mr. Lucas was worried that all my enthusiasm would be shattered if I was unable to do one of the things I wished for. He had a lot of faith in me and helped me develop a plan, while also keeping my expectations as realistic as possible, especially since I was applying with tight deadlines. 

Spring break came as fast as it left. My original plan for the break was to spend my time at the beach as others might do during a short vacation. Even though it was tempting, I asked my family for permission to stay in Mexico City for the beginning of the week in hopes of landing an internship. I printed a little over 50 versions of my CV and then very carefully enclosed it in a professionally crafted letter. 

On paper, the plan seemed simple — I would dress in a suit and a red tie, drive to all the potential job locations, and finally, I would get a summer job. But the adventure didn’t go smoothly. First, the heat was unbearable. After giving out all my applications, I had to take my suit off, so it didn’t get drenched in sweat. I was also a bit naïve, as I thought that everyone would be happy to see a kid talking to the directors of the places that I went to, and also there were a bunch of security guards who didn’t let me into the establishments. As a high schooler, there was also an education problem, but I thought, why wouldn’t a top-tier biotech company hire a high school sophomore to work during the summer?

Looking back, I can see how incredible it was for me to receive five emails back. Three places told me that whenever I get a degree, they would be happy to have me, which I wasn’t too happy to read. But then the other two places agreed to interviews. At this point, it was already Wednesday, and we were going to leave the city the next day. I told my parents that I’d love to invest my break in working towards my future rather than have momentary fun at Acapulco.

Both of my interviews were with doctors at the National Institute of Genomic Medicine, which is  INMEGEN in Spanish. I arrived early to the first interview. Dr. Alejandra Cervera gave me directions on how to get to her office, but I had 20 minutes to spare. It was obvious that I stood out, especially because of my red tie, my age and the fact that nobody else was stressed about what they were wearing. I was the only weirdo who was wearing a suit in the 86-degree weather.

Already on the fifth floor where the interview took place, I asked a doctor who was passing by if there was a waiting room. He told me that there wasn’t one on that floor, but he walked me down to the fourth floor where there was a couch where I could wait. 

During the interview with Dr. Cervera, she told me about her project to improve the public health system by properly diagnosing and treating children with B-cell acute lymphoblastic leukemia (B-ALL). She also warned me that the project was not a wet lab. Instead, it was a computational biology. I told her that she could count on me as a summer intern since I have an “all yes” and “all thank you” mentality.

The next day I had a Zoom interview with Dr. Emilio Cordova. Immediately, we recognized each other. He was the doctor who had walked me to the waiting room couch on the fourth floor the previous day! That immediately sparked the conversation, and he offered to teach me about his work at the lab part time to accommodate my work with Dr. Cervera. After an exchange of emails, I had my summer planned out. I would work in INMEGEN from Mondays to Fridays with Dr. Cervera, while visiting visit Dr. Cordova’s lab Tuesdays and Thursdays from 12-2 p.m. The internship would last for the month of June.

A few weeks after returning to school from spring break, I got accepted to NYU’s pre-college program for cellular and molecular biology. For the other half of my summer, I would be attending the NYU program. 

During the Internship 
Leading up to summer, I stayed in contact with Dr. Cervera. We engaged in discussions regarding my proficiency in the programming language R. Dr. Cervera assigned me a few test scripts to gauge my abilities, but unfortunately, they did not meet her initial expectations. This experience quickly taught me that achieving success with a script often requires more than a dozen revisions and iterations. 

Regardless of my experience with the language, my now-tutor Dr. Cervera was patient and helped me learn about B-ALL by sending me helpful scientific literature and solving any of my inquiries regarding the illness. Now, armed with the skills needed to be successful at my future internship, I finished the MMA school year looking forward to the opportunities the summer would bring me.

I was put on my first real project on my first day working at INMEGEN’s office. The script I wrote was the last step of a bigger algorithm that would synthesize the results from the clinical trials of the kids with leukemia. Its main focus was to condense all the valuable information into a data frame with very specific needs from the oncologist. The report file is meant to precisely diagnose the genes and subtypes that the children’s condition presents.

The reason why the five-year survival of B-ALL in the U.S. is over 85% and Mexico’s is less than 20% is because the public health system of Mexico uses only a handful of tests to find specific cancerous genes instead of sequencing the whole genome. If they can’t find the specific gene, they treat the infants with the harshest chemotherapies. In most cases, these treatments lead to chemical toxicity, which causes the premature death of the child. If the child were to be diagnosed correctly, they would have had more than four times the chances of survival.

Dr. Carmen Alaez, director of the leukemia initiative, tests eight individuals at a time to sequence their DNA and feeds the algorithm with the information she receives. The problem with massive gene sequencing is that it is very expensive and takes too much time, so she implements a novel way of breaking down the whole genome into little fragments of genetic code that are then sequenced more efficiently all at the same time.

The first algorithm I collaborated on focused on reordering genetic material and analyzing the entirety of the genome to extract relevant information for oncologists. Broadly speaking, my contribution to the algorithm involved developing the "prep_summary" script. This script effectively identified cancerous fusion genes, the corresponding detection methods, single nucleotide variants, focal deletions, gene expression levels in multiple genes and gene duplications. These findings, in simpler terms, aid in determining the most suitable clinical treatments for each patient's specific condition, therefore elevating the survival rate of sick infants.

Outside of the office, the environment was unexpectedly easygoing. Everyone at the institute had a very friendly energy, and I was enthused to meet new people. I was particularly delighted by one aspect that truly stood out to me — our incredibly affordable $3 meals. The dinner, supported by the government, provided a delectable three-course homemade feast. It consisted of a comforting hot soup, a satisfying main course, a delightful side dish, such as fruit, and a delicious dessert. Additionally, the meal came with a pack of tortillas and a refreshing drink made from the fruit of the day.

My second contribution at the internship was a multi-version genotype proof and data compiler script. I worked on this code to replace a commercial service that Dr. Alaez hired to interpret the leukemia genes database, and it aims to reduce a big percentage of the whole project’s cost. It worked by using the specific gene name as a key to the Ensembl database, a free online server with information on many genes. With Ensembl, we could access lots of specific and updated information regarding the genes we were working with. A problem that I encountered with this server was that a significant number of genes had their names changed in recent updates, so I had to create a function to look for the missing genes on older versions of Ensembl.

Another thing that kept me excited during the internship was my lessons at Dr. Cordova’s labs. Not related to the leukemia initiative, Dr. Cordova investigates the wet lab part of T-cell chronic myeloid leukemia, which was very different from what I was studying with Dr. Cervera. Since my primary practices were with Dr. Cervera, Dr. Cordova gave me the opportunity to learn at his lab twice a week, which totaled four hours.    

Dr. Cordova put me under the charge of Dr. Omar, one of his lab assistants. At first, I learned how to manage lab tools, especially the pipette. Dr. Omar put me on to pipette almost 1,000 times with water, 200 times with 5 microliters, 200 with 7.5 microliters and 300 times with 10 microliters to put the water dropper back and forth. It was great to learn how to use the pipette, especially when I tried my first method — DNA electrophoresis with agar gel. After several learning sessions in the lab, I developed sufficient proficiency in assisting Dr. Cordova's team with creating a plaque by using their MYC DNA.

One of my favorite things at the institute was the seminars. I got to create good connections inside and outside of INMEGEN, since I was actively trying to meet new people. At my first seminar, the doctor presenting mentioned that he used an algorithm in R to research their desired topic, and at the end of the talk, I walked up to him and started a conversation. My interaction with him resulted in gaining him as a contact in WhatsApp, as well as receiving the script they used on my computer. Since this networking technique worked, I thought to use it in the next seminar I attended, and certainly enough, I created a connection with Dr. Fausto. Dr. Fausto worked at the cardiology center a couple of blocks away, and he shared with me that he had been planning a new research project where he wanted to understand the evolutive part that miRNAs have had in the metabolism of our immune cells. He also added that he needed someone who could build a data analyzer to interpret the data. I told him that I was familiar with R and would gladly help him in any way I could. He promised to give me a call when he starts the new project.

On my last week working for Dr. Cervera, she took me and another her student out for lunch. On our way back, she stayed to talk to another doctor. Apparently, they were talking about their students and how I was very young for what I was achieving in the lab. Dr. Humberto suggested that it would look great for my resume and the report that she had to write to the investigators committee if I helped publish a scientific article. Of course, I got super excited about Dr. Humberto’s news, and I wanted to get a research topic assigned to me to eventually write an article on. Dr. Cervera told me that as soon as she could talk to Dr. Alaez, she would tell me if I got the project. I waited in deep suspense.

For the next couple of days, I didn’t get news about the project. Finally, Dr. Cervera told me that she signed for me to be registered in the INMEGEN system for another year. This meant that I would have a username for INMEGEN’s server, and I would keep my student ID. But most importantly, it meant I had a project with them! The new project’s goal is to create a case study of each individual gene that is over-expressed or not normally in non-leukemic Mexican children. The study also involves investigating the genetic pool and evaluating the prognosis of the disease in other countries with the genes as a variable. I look forward to working on this project!

At the end of the internship, Dr. Cervera wrote a recommendation for me about my work with her and posted it on LinkedIn to show her gratefulness for my contributions and achievements during my time at INMEGEN. 

And with the many achievements I've made so far this summer, I am ready to take on my next adventure at NYU!