Course Overview
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.
Intended Audience
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.
Keywords: Genetics, Genomics, Nucleic acids analysis, NGS
Skill level of training: Beginner
Language: English
Credential awarded: No credential awarded
Type of training: Face-to-face
Venue of the course:
Dates for the course: Every Tuesday and Thursday from 10:30 CAT to 14:30 CAT
Course organisers: H3ABioNet, African Pharmacogenomics Research Consortium, CBIO.
Participation:
Course Sponsors: H3ABioNet, African Pharmacogenomics Research Consortium, CBIO.
Course objectives
  • 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

Registration for classrooms opens: Thu, 01/01/1970
Registration for classrooms closes: Thu, 01/01/1970
Link to classroom application form:
Notification date for successful classrooms: Thu, 01/01/1970
Maximum number of participants that may be accepted per classroom will be capped at

Participant applications

Registration for participants opens: Thu, 01/01/1970
Registration for participants closes: Thu, 01/01/1970
Participant registration link:
Syllabus and Tools

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.

Prerequisites

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

Course limitations
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.
For more information, please visit
Training material availability

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.