This workshop provides an introduction to the computational analyses of NGS data from pre-processing to the identification and annotation of genomic variants and the functional effects of those variants, as well as the use of pharmocogenomic databases.
This workshop is aimed at attendees of the 3rd Pharmacogenetics and Precision Medicine Conference in Africa, geneticists, genetic counselling students/researchers, clinicians and healthcare professionals interested in the use of genomic data for personalising treatment.
- Participants will learn how to execute a web based NGS workflows using Galaxy.
- Participants should come out understanding how to obtain and analyse variants, particularly from NGS data.
- Participants should come out with knowledge on how to predict the significance of identified mutations, checking for pathogenesis, or whether they affect regulatory regions.
- Participants should come out with knowledge on the possible clinical significance (pharmacogenomics relevance) of variants.
Classroom applications
Participant applications
Participants will learn about the handling of NGS data, identification of genomic variants, curated databases that have genomic information/sequences for use; analysis of sequences to look for mutations; evaluation of the significance of mutations observed, pathogenesis and prediction of the functional significance of these variants.
Participants are encouraged to work through the following resources to enable them to gain the most from the workshop:
https://wiki.galaxyproject.org/Learn/GalaxyNGS101
https://usegalaxy.org/u/galaxyproject/p/galaxy-variant-101
https://wiki.galaxyproject.org/Learn/Screencasts
http://www.1000genomes.org/using-1000-genomes-data
http://www.h3abionet.org/tools-and-resources/sops/human-variant-calling
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20120229_tutorial_docs/G1K_web_based_tutorial_exercises_20120217.pdf
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20120229_tutorial_docs/G1K_web_based_tutorial_answers_20120217.pdf
https://www.clinicalgenome.org/data-sharing/clinvar/clinvar-multimedia-tools/
http://www.ensembl.org/info/docs/tools/vep/online/VEP_web_documentation.pdf
This workshop will provide a foundation for continued learning in the bioinformatics handling of NGS data, identification, annotation and functional prediction effects of variants. The workshop will not make one an expert on NGS data, filtering, functional predication and annotation of variants.
Training materials for this course are available as a single downloadable archive here: https://doi.org/10.25375/uct.19129955. Should you re-use any of these materials, please ensure that both the author/s of the material AND H3ABioNet are clearly credited.
