H3ABioNet

Pan African Bioinformatics Network for H3Africa

Bioinformatics analysis and annotation of variants in NGS data

This workshop is closed. The training material is available at: http://training.h3abionet.org/h3a2016ngs/?page_id=2

Dates for the workshop: 4th April to 6th April 2016

Venue of workshop: Health Teaching Labs 1, Basement of Anatomy Building, UCT Medical School, Cape Town, South Africa

Workshop organisers and sponsors: H3ABioNet, African Pharmacogenomics Research Consortium, CBIO.

Workshop trainers and support: Amel Ghouila, Gerrit Botha, Colleen Saunders, Luiz Olavo Bonino, Nyarai Soko, Suresh Maslamoney, Sumir Panji, Collet Dandara and Nicola Mulder.

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.

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

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.

Workshop 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.

Workshop program

4th April 2016
Time Topic (Health Teaching Labs 1)
8:30 am Registration
9:00 am Welcome address
9:10 am Participant introductions
9:30 am Introduction to NGS, file formats and workflows (Talk)
10:00 am Introduction to the web based Galaxy platform for NGS analysis (Talk)
10:20 am Register for a Galaxy account (Practical)
10:30 am Tea break (Student Cafeteria)
11:00 am Uploading data into Galaxy, tools, histories and workflow sharing (Practical)
11:20 am Preprocessing and QC of NGS data (Talk)
11:40 am Examining FASTQ files in Galaxy, pre-processing and quality control of NGS data (Practical)
12:20 pm Alignment of reads, reference sequence, indel realignment (Talk)
12:40 pm Submit alignment jobs to Galaxy (Practical)
1:00 pm Lunch (Mac Club)
2:00 pm Alignment of reads, post processing, obtaining statistics, visualising alignments (Practical)
3:00 pm Introduction to variant calling (Talk)
3:20 pm Submit variant calling jobs to Galaxy (Practical)
3:30 pm Tea Break (Student Cafeteria)
4:00 pm Alignment of reads, indel realignment, and variant calling (Practical)
5:00 pm Workshop End
5th April 2016
Time Topic (Health Teaching Labs 1)
9:00 am Recap of previous days activities and Q and A session
9:30 am Overview of variant prioritisation and Introduction to genome databases (Talk)
10:30 am Tea break (Student Cafeteria)
11:00 am Exploring genome databases (Practical)
12:00 pm Lunch (IIDMM Cafeteria)
1:00 pm NGS variant analysis: Annotation and filtering (Talk and practical)
2:30 pm Tea break (Student Cafeteria)
3:30 pm

NGS variant analysis: Exploring links to phenotype and biological function (Talk and practical)

5:00 pm Workshop End
6th April 2016
Time Topic (Health Teaching Labs 1)
9:00 am Recap of previous days activities and Q and A session
9:30 am Findable, accessible, interoperable and reusable (FAIR) Data in Life Sciences (Talk)
10:30 am Tea break (Student Cafeteria)
11:00 am Gene-disease investigation in integrated datasets (Practical)
12:30 pm Lunch (IIDMM Cafeteria)
Venue change to Postgraduate Lecture room 2
1:30 pm Introduction to pharmacogenomics (Talk)
1:45 pm Setting up a pharmacogenomics study: important considerations (Talk)
3:00 pm Tea break (Student Cafeteria)
3:30 pm Pharmacokinetics and pharmacogenetics of rosuvastatin (Talk)
4:00 pm Discussion of project ideas (Group discussion led by Prof. Collet Dandara)
5:00 pm Workshop End