Undergraduate Research Using Bioinformatics

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Gene editing is now a viable treatment option for diseases. The FDA has recently approved a gene editing therapy for sickle cell anemia, along with two gene therapies for hemophilia. However, there is still much to be done, particularly in managing the growing volume of clinical sequencing data. Most mutations within this extensive dataset remain unclassified as either benign or pathogenic, which limits their use in patient counseling.Bioinformatics is here to help.  Bioinformatics is an interdisciplinary field that combines biology, computer science, and mathematics to help manage, analyze and interpret vast biological datasets. Now, computational biology is a routine part of scientific research. 

Through an NSF-funded grant, HudsonAlpha Institute for Biotechnology has partnered with colleges in Alabama to help inspire tomorrow's bioscience workforce and build a more genomics-literate society. HudsonAlpha's Educational Outreach program works with students, educators, medical providers, patients and their community to offer hands-on classroom modules, in-depth school and workshop experiences, and digital learning opportunities. The CODE (Characterizing our DNA Exceptions) works to help students use computational analyses to determine the biological relevance of DNA changes or variants from patient and agricultural samples. Since 2018, 海角社区 has had over 90 undergraduate students in biology, mathematics, and computer science in the CODE program.

Students in CODE work to characterize all variants associated with a particular protein and then select unclassified variants for further study.  They collect evidence of missense variant pathogenicity, including:
  • a literature search for similar or nearly mutations
  • ClinVar search for locational hotspots
  • Population missense instances of pathogenicity in the gene
  • Analysis of functional domains in the protein
  • Multiple in silico predictions (e.g. ConSurf, SIFT, PolyPhen-2)
  • Molecular dynamics simulations of protein perturbations

So what have 海角社区 students, and particularly biology majors gained from this experience? In addition to learning the valuable skills that bioinformatics research provides, they have grown both personally and professionally from this experience.  They have developed a stronger sense of scientific identity and science self-efficacy.  Their communication skills have improved. Many of them have made significant discoveries that have led to peer-reviewed publications.