Genome Analysis Module:�Course Introduction
Dr. Phillip Richmond�UBC MSc Genetic Counselling�October 31st, 2022
Today’s Outline (October 31st)
Today’s Outline (October 31st)
Happy Halloween!
Teacher Bio
Dr. Phillip Richmond
PhD in Bioinformatics (October 2020), Wasserman Lab, UBC
Staff Scientist, PHSA, BCCHR, Precision Health Initiative
Website: www.philliprichmond.com
Twitter: @Phil_A_Richmond
Research:�Maximizing the Utility of Whole Genome Sequencing in the Diagnosis of Rare Genetic Disorders�
Previous work in Genomics: Genomic Contributions to Ethanol Sensitivity in Mice, Polyploid Evolution in Yeast, Brewing Yeast Genomics, Cancer Cell Epigenetics, Addiction Predisposition
Also loves teaching genomics, and my dog Sherlock Holmes.
Today’s Outline (October 31st)
Goal of the course
To get hands-on experience using whole genome sequencing in the diagnosis of rare genetic disorders.
How are we going to do it?
During this course, you will identify as a genome analyst.
Each of you will have a case to work on. All of the cases are different.
How are we going to do it?
During this course, you will identify as a genome analyst.
Each of you will have a case to work on. All of the cases are different.
Throughout the course, we will slowly build your toolkit with the ability to process, visualize, and interpret whole genome sequencing data.
The course will end with a presentation of the case to your peers with your proposed candidate variant.
https://www.clinicalpathwaysresearch.com/blog/2014/06/09/rbm-round-table-discussion
Course Syllabus
Accessing Course Content
How to keep up
With this class size we will not leave anyone behind!
You should work together!
Ask lots of questions, no question is “dumb”!
Celebrate the little wins!
For some sessions, we’ll do: watch me do it, do it with me, do it by yourself (problem sets)
Join the slack channel
https://join.slack.com/t/gcgenomeanalysis/shared_invite/zt-1h6ux1awi-dODwvMAfc6UkDbUEchpVzA
This is easiest for me to answer questions outside of class, and post links to slides.
Today’s Outline (October 31st)
Slide Deck
Suggested reading
1. Boycott KM, Hartley T, Biesecker LG, Gibbs RA, Micheil Innes A, Riess O, et al. A Diagnosis for All Rare Genetic Diseases: The Horizon and the Next Frontiers. Cell. 2019. pp. 32–37. doi:10.1016/j.cell.2019.02.040
3. Ouwehand WH, on behalf of the NIHR BioResource and the, 000 Genomes Project. Whole-genome sequencing of rare disease patients in a national healthcare system. doi:10.1101/507244
4. Smedley D, Jacobsen JOB, Jäger M, Köhler S, Holtgrewe M, Schubach M, et al.
Today’s Outline (October 31st)
Try logging in to the cluster
You need:
ssh sophie.albert@gpcc-node01.bcricwh.lan�
Today’s Outline (October 31st)
Case Assignments
Sophie - Case 1
Kelvin - Case 5
Mitch - Case 6
Tessa - Case 7
Yvette - Case 8
Sydney - Case 10
Today’s Outline (October 31st)
Software
You should have: