This summer, I’ve been working at American Molecular Laboratories as a data analyst. In the winter, I was able to get some lab experience, working as a lab assistant before transitioning to helping out with COVID testing. This time, I was stationed just outside the laboratory, working at a desk and analyzing the data provided by the lab workers. The computer I had utilized Next Generation Sequencing (NGS) to find mutations in the forward and reverse DNA strands. I would then look at the mutations and determine which ones were indicative of H-pylori positive results. It was my first time applying data analysis to a modern problem, and it was an informative and enjoyable experience.
For background, Helicobacter pylori (H-pylori) is a type of bacteria that inhabits the digestive tract when it enters a host. This can lead to ulcers and damage to the stomach lining and the upper small intestine. If these get infected, it can lead to stomach cancer. There are medicines that can treat H-pylori and soothe ulcers, but clean water and sanitation is the best way to prevent it in the first place. Next-generation sequencing is a DNA sequencing technology that yields the nucleotide sequence of entire genomes very quickly. Also called massive parallel sequencing, NGS has high sensitivity to low frequency mutations while operating at a fast rate.
To test for this, the lab uses fresh stool or tissue samples to obtain the DNA. Once the DNA is extracted, it is sequenced, then analyzed—the job I did. Analyzing the data wasn’t overly difficult; I utilized the research of other workers at the company as well as previous studies to figure out which DNA mutations were indicative of H-pylori. I compared these to the ones that were listed in the table by the NGS software and listed the common mutations in an Excel sheet. It was great to get some experience in the data analysis industry, and also apply some of the knowledge I learned in Biology this past school year.
Most of the samples I tested were clinical. That is, people that went to the lab for testing because they were sick. However, some of the samples I tested were from the Boston Children’s Hospital for a study conducted by Harvard, so it was an incredible feeling to know that I was helping with something much greater than myself.
Image Link:
https://www.labmanager.com/product-focus/the-third-wave-of-next-generation-sequencing-22898
