BIO392

This is a repository for materials related to the BIO392 Bioinformatics of Genome Variation introductory course at the University of Zürich, Autumn 2018.

The home page of this repository can be found at baudisgroup.github.io/BIO392-Github/.

Abstract

One of the fastest growing areas of bioinformatics is in the analysis, warehousing and representation of genomic and protein sequence variants, particularly with view on the use of molecular data in personalised health and biomedical applications in general. This course will engage participants to explore common data formats, online resources and analysis techniques, with a focus on human genome variation data.

Links

• BIO392 in the UZH OLAT system
• BIO392 in the UZH directory

Literature and Resources

• Articles and other reading (files)
• Article links
• Resource links (browsers and online repositories)
• Course tasks (to do's and challenges)

Schedule

The course schedule consists of 1 afternoon (Tuesday) and 3 "full" days (Wednesday - Friday) in the first two weeks, with 1.5 days in the last week.

The "full days" run from 09:00 - 17:00, with a break from 12:00 - 13:30.

Conceptually, mornings are predominantly related to introductions, presentations and discussion of the previous days, and are afternoons reserved for independent work on the examples and tasks.

Introduction, File Formats & Genome Browsers (Michael Baudis)

2018-09-18 (Tue), 13-17

• general introduction into the topic (slides)
• schedule adjustment
• guidance about course room and computer use (Tina Siegenthaler)
• reading:
  • 1000 Genomes paper
  • The sequence of sequencers paper
• tasks:
  • Genome Storage Space & Cost

2018-09-19 (Wed), 09-17

• reference genome resources
• reading:
  • "Genomics made easier"
  • UCSC genome browser tutorial
• exercise: UCSC tutorial
• Answer for UCSC tutorial, genelist, genelist_canonical
• genome editions and coordinates
• reading:
  • segment_liftover article
• exercise: genome liftover

2018-09-20 (Thu), 09-17

• Annotating genome variants
• reading:
  • HGVS Recommendations (not for details, though)
  • dbVar "Overview of Structural Variation" (link)
  • info slides from the morning session
• Literature review and discussion

2018-09-21 (Fri), 09-17

• Associating variants with phenotypes and diseases (focus on cancer…)
  • Use of variant databases and annotation tools (CiVIC, OncoKB, ClinGen, arrayMap…)
• info slides from the morning session
• Hands-on analysis of genome data
  • copy number segmentation tutorial Reference publication
  • plink tutorial
  • variant <-> disease mapping exercise

Tools & Programmatic Solutions (Izaskun Mallona)

• SIB Swiss Institute of Bioinformatics tutorial on UNIX
• Unix slides
• Genomic formats slides
• Exercises

2018-09-25 (Tue), 13-17

• How are UCSC Genome Browser data stored? Why?
• Genomics data management: automation
  • Computer basics: plain text files, Unix terminal
  • Reproducibility
  • Systems set up (data download and software installs)

2018-09-26 (Wed), 09-17

• Unix for bioinformatics
  • Chapter 1: What is UNIX
  • Chapter 2: The UNIX filesystem
  • Chapter 3: UNIX shell - first steps
  • Chapter 4: UNIX shell - filesystem commands
  • Chapter 5: UNIX shell - working with files

2018-09-27 (Thu), 09-17

• Overview of the standard genomics data formats (I)
  • FASTA
  • FASTQ
  • SAM
  • BED
• Basic file processing for bioinformatics
  • awk, cut

2018-09-28 (Fri), 09-17

• Overview of the standard genomics data formats (II)
  • GFF/GTF
  • BEDgraphs
  • Wiggle files
  • VCFs
• Indexed genomic data formats
• Exercises

Genome Variants to Modified Proteins (Elif Ozkirimli Olmez)

2018-10-02 (Tue), 13-17

• Protein Structure Slides
  • Protein Data Bank PDB
• Literature
  • Bhattacharya R, Rose PW, Burley SK, Prlić A (2017) Impact of genetic variation on three dimensional structure and function of proteins. PLOS ONE 12(3): e0171355.
  • Zehir, A., Benayed, R., Shah, R. H., Syed, A., Middha, S., Kim, H. R., et al. (2017). Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nature Medicine, 23(6), 703–713.
  • Studer, R. A., Dessailly, B. H., & Orengo, C. A. (2013). Residue mutations and their impact on protein structure and function: detecting beneficial and pathogenic changes. Biochemical Journal, 449(3), 581–594.
• Protein Structure Analysis Task

2018-10-03 (Wed), 09-17

• Go over the protein structure analysis task from Tuesday. All of you did a great job!
• Uniprot slides
  • Uniprot
  • Gene Ontology, GO
• Uniprot introduction video, Uniprot Feature viewer video
• Uniprot activity
• Alignment slides
• Afternoon activity

2018-10-04 (Thu), 09-17

• We start at 9:30
• Oct 4 slides
• Oct 4 activity

2018-10-05 (Fri), 09-17

• Morning: Presentations on your protein
  • Biological relevance of your protein
  • Experimental details/methods
  • 2 key findings
  • Position of mutations on protein structure (structure figure)
  • Discussion
• Afternoon: BLAST task

Review & Write-Up (Michael Baudis)

• 2018-10-09 (Tue), 13-17
• 2018-10-10 (Wed), 09-17
  • Written exam