Genomics 1

Why study genomics?

Genomics is an essential subfield of bioinformatics, and a major force in expanding human knowledge of genetic associations with disease and other traits. It is an interdisciplinary field, including the development of methods for DNA sequencing, as well as for big data analysis of genomic sequences. Next-Generation Sequencing (NGS) techniques allow for whole-genome sequencing, and analysis of epigenetic factors such as DNA-protein interactions and DNA methylation with unprecedented efficiency. Massive databases for biological sequence data such as GenBank (National Center for Biotechnology Information), EMBL (European Bioinformatics Institute), and SRA allow for data-driven research and knowledge discovery. Large amounts of data such as from the 1000 Genomes Project are publicly available, providing anyone with the proper analytical skills and resources the opportunity for scientific discovery. While transcriptomics seeks to find variation in gene expression through methods such as RNA sequencing, genomics studies genome-wide genetic variation at the fundamental level of DNA sequences. The understanding of genetic associations provided by genomic research have great value in medicine, agriculture, ecology, biotechnology, and many other industries.

Course description

This course serves as an introduction to the bioinformatics sub-discipline of genomics. Students will be familiarized with the biology of genetics and genetic variation, while considering practical applications of genomics to research and medicine. An example analysis of real-world NGS data is then provided in a tutorial, offering students the chance to employ state-of-the-art genomics algorithms using the T-BioInfo platform. Students will load NGS data, and construct a data analysis pipeline within the platform to identify genetic variants associated with breast cancer.

Student will need access to the T-BioInfo platform to follow the provided data analysis tutorial. Access can be obtained by emailing a request to info@pine-biotech.com. Account information is typically issued within 24 hours of the request. The tutorial also incorporates the Integrative Genomics Viewer, a freely available visualization tool for large-scale genomic data. Integrative Genomics Viewer must be installed locally to perform the analysis detailed in the practical tutorial section of the course.