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Casting a Wide Net via Case Studies: Educating across the undergraduate to medical school continuum in the biological...Learning ObjectivesAt the end of this lesson, the student should be able to:
- Consider the potential advantages and disadvantages of widespread use of whole genome sequencing and direct-to-consumer genetic testing.
- Explore the critical need to maintain privacy of individual genetic test results to protect patient interests.
- Dissect the nuances of reporting whole genome sequencing results.
- Recognize the economic ramifications of precision medicine strategies.
- Formulate a deeper understanding of the ethical dimensions of emerging genetic testing technologies.
A CURE-based approach to teaching genomics using mitochondrial genomesLearning Objectives
- Install the appropriate programs such as Putty and WinSCP.
- Navigate NCBI's website including their different BLAST programs (e.g., blastn, tblastx, blastp and blastx)
- Use command-line BLAST to identify mitochondrial contigs within a whole genome assembly
- Filter the desired sequence (using grep) and move the assembled mitochondrial genome onto your own computer (using FTP or SCP)
- Error-correct contigs (bwa mem, samtools tview), connect and circularize organellar contigs (extending from filtered reads)
- Transform assembled sequences into annotated genomes
- Orient to canonical start locations in the mitochondrial genome (cox1)
- Identify the boundaries of all coding components of the mitochondrial genome using BLAST, including: Protein coding genes (BLASTx and tBLASTX), tRNAs (proprietary programs such as tRNAscan), rRNAs (BLASTn, Chlorobox), ORFs (NCBI's ORFFinder)
- Deposit annotation onto genome repository (NCBI)
- Update CV/resume to reflect bioinformatics skills learned in this lesson
Cutthroat trout in Colorado: A case study connecting evolution and conservationLearning ObjectivesStudents will be able to:
- interpret figures such as maps, phylogenies, STRUCTURE plots, and networks for species delimitation
- identify sources of uncertainty and disagreement in real data sets
- propose research to address or remedy uncertainty
- construct an evidence-based argument for the management of a rare taxon