Undergraduate Genomics Research Using Bioinformatics Tools: Recently Completed Student Projects from Amity University, Lucknow
What drives changes in cancer cells? How do viruses evolve and interact with the human body?
As part of the OmicsLogic Biomedical Data Science Research Program, students from Amity University Lucknow explored these questions through hands-on projects in genomics. Using bioinformatics tools, they analyzed mutations, studied viral genomes, and examined gene-level changes linked to disease.
This blog shares highlights from their work, each project offering a focused look at how genomics can support research in healthcare and biology.
Project Summary: This project focused on finding critical genetic mutations in gastric (stomach) cancer using next-generation sequencing (NGS) data. Starting with over 9,000 variants from tumor samples, Kawalpreet narrowed it down to about 50 high-confidence mutations that are likely to affect how the cancer behaves.
“The program is worth opting for, if one wants to explore about a specific topic in detail and the mentors are also very helpful. I enjoyed the research part a lot.” - Kawalpreet Kaur
Most of these were missense mutations (which change a single amino acid in a protein), along with some frameshift and nonsense mutations. Key genes, such as KRAS, TP53, MUC16, SHANK1, and FLNA, showed recurrent changes. By analyzing mutation patterns and visualizing hotspots in the genome, the study revealed the genetic diversity of gastric cancer.
Project Summary: This project looked at how normal breast cells change at the genetic level as they become cancerous. Using whole-genome variant analysis, Akarshika compared two lab-grown breast cell lines: MCF10A (non-tumorigenic) and MCF10CA1 (invasive cancerous).
“I was able to learn so much about bioinformatics. The program was very educational and impactful. I enjoyed the research part a lot.” - Akarshika Choubey
The cancerous MCF10CA1 cells exhibited a higher overall mutation rate, particularly in genes associated with cell cycle regulation, DNA repair, and cancer-related signaling pathways. Two genes—KDM1A (a known biomarker in triple-negative breast cancer) and FUCA1—were consistently mutated across all cancer samples.
This study sheds light on specific genomic changes that may drive breast cancer progression, pointing to potential molecular targets for future research and treatment strategies.
Project Summary: MicroRNAs (miRNAs) are tiny RNA molecules that help control how genes are turned on or off. While they are well-known in humans and other animals, some viruses—large DNA viruses—may also utilize similar molecules to influence both their genes and those of their host.
Monkeypox virus (MPXV), which is related to the variola virus, the causative agent of smallpox, has recently caused concern due to new outbreaks. However, scientists still don’t know much about the small, non-coding parts of its genetic material, like miRNAs.
“On a personal level, it boosted my confidence in handling complex data, problem-solving independently, and communicating scientific ideas clearly.” - Liza Rani Sahu
In this study, Liza used computer-based methods to scan the entire MPXV genome and predict whether it might produce its miRNA-like molecules. Tools like miRNAFold were used to identify hairpin-shaped RNA structures, RNAstructure to assess their stability, and MatureBayes to detect mature miRNAs.
Results provide the first list of possible miRNAs generated by MPXV, which may play a role in the virus's survival, spread, or interaction with the human body. These findings are just the first step; lab experiments are still needed to confirm the function of these miRNAs.
Project Summary: Instead of studying the virus's own genome, Anika’s project focused on the human side of the interaction. She used computational tools to predict which host genes might be involved during a Monkeypox virus infection. By mapping these genes and analyzing them through Gene Ontology (GO) enrichment, the study identified key biological functions likely to be impacted.
“A fun but very informative program that is structured according to our benefit. It brought a whole new experience and taught me about bioinformatics” - Anika Pandey
The analysis highlighted genes involved in immune responses, viral entry, and inflammation, suggesting that MPXV may interfere with pathways crucial to the body's defense against infection. These predictions not only pinpoint potential host targets for future antiviral strategies but also contribute to the growing understanding of how this virus operates at the molecular level. Further lab validation would be needed to confirm these findings.
Project Summary: Torsha’s project investigated the relationship between different strains of the Monkeypox virus. She analyzed complete viral genomes from both past outbreaks (Africa, 1970s) and recent ones (USA and South Korea, 2022) to understand how the virus has changed over time.
“Learning-focused experience that introduces you to real-world research in microbiology and bioinformatics. The research program has positively impacted both my personal and professional life.” - Torsha Das
Using a mix of bioinformatics tools—BLAST for sequence similarity, ClustalW for aligning genomes, and MEGA and IQ-TREE for building phylogenetic trees—evolutionary connections between these strains were mapped. The findings showed that recent outbreak strains are genetically very similar to older West African variants (over 99.9% identical), while Central African strains were more distinct.
Results suggest that new mutations didn’t cause the recent outbreaks, but rather the spread of an already existing viral lineage. The study demonstrates how computational tools can aid in tracking viral evolution and support outbreak monitoring.
As the next step in their journey, the students will begin preparing their projects for academic preprint/publication. Their finalized research will also be shared on our OmicsLogic Platform, making it accessible to peers, educators, and institutions worldwide.
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