WORKSHOP: Bioinformatics Analysis and Annotation of Variants in NGS Data

WORKSHOP: Bioinformatics analysis and annotation of variants in NGS data

A 3 day workshop will be run prior to the Pharmacogenomics conference on the Analysis of NGS Data for Pharmacogenomics. The workshop is aimed at genetics, genomics and bioinformatics researchers interested in the use of genomic data for personalizing treatment. It will include a combination of lectures and hands-on practical exercises covering topics such as NGS theory (an overview), annotation of variants, including functional analysis and implications.

Workshop Fees and Application:

 If registering for both the conference and workshop, pay your relevant conference registration fees plus only an additional R500  If registering only for the workshop, pay R900  Registration for workshop should be completed online using the conference registration form.

H3ABioNet will provide a limited number of travel fellowships to H3Africa affiliated project members selected on a competitive basis that will cover only the following: an economy return air ticket, accommodation (for up to 5 nights) and registration fee for the workshop. The application for travel fellowships can be completed through the following link: http://surveys.h3abionet.org/h3a2016ngs/

Registration/application for the workshop should be completed on the conference registration form.

Workshop Details:

Venue of workshop: Medical Campus, University of Cape Town, Health-Teaching Lab 1 – 2, Anatomy Building Basement. Dates for the workshop: 4th April to 6th April 2016 Workshop organisers: African Pharmacogenomics Research Consortium, CBIO and H3ABioNet Registration opens: 9th February 2016 Registration closes: 29th February 2016 Travel fellowship application deadline: 1st March 2016 Notification date: 7th March 2016

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 pharmacogenomic 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 understanding the identification and interpretation of human genetic variation.

Syllabus and Tools: Participants will learn about the handling of NGS data (an overview), 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_ba sed_tutorial_exercises_20120217.pdf ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20120229_tutorial_docs/G1K_web_ba sed_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 where to access curated sequence information for different populations. Participants should come out understanding how to 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 genomic variants and the resources available. This workshop will not make attendees experts in NGS data analysis.

Timetable:

Time Topic 8:30 Registration and Introductions 9:00 Introduction to human genomic variation and population genetics (Talk) 9:30 Introduction to NGS data, sequencing platforms, file formats, variant calling and overview of a variant calling workflow (Talk) 10:00 Introduction to the web based Galaxy platform for NGS analysis 10:30 Tea break 11:00 Pre-processing and Quality control of NGS data (Practical) 12:30 Lunch 1:30 Alignment of reads, indel realignment, and variant calling (Practical) 3:00 Tea Break 3:30 VCF file format and tools for manipulation, visualization (Practical) 5:00 Workshop End

9:00 Recap of previous days activities and Q and A session 9:30 Introduction to genome databases (Talk) 10:30 Tea Break 11:00 Introduction to genome databases (Practical) 12:30 Lunch 1:30 NGS variant analysis annotation (Talk and practical) 3:00 Tea Break 3:30 NGS variant analysis annotation (Talk and practical) 5:00 Workshop End

9:00 Recap of previous days activities and Q and A session 9:30 Nano-publications, linking genes and diseases 10:30 Tea Break 11:00 Nano-publications, linking genes and diseases 12:30 Lunch 1:30 Introduction to pharmacogenomics (Talk) Collet 3:00 Tea Break 3:30 Setting up a pharmacogenomics study: critical aspects to consider (Collet) 4:00 Selected presentation from workshop delegate (1) 4:30 Setting up a community of practices for researchers with interest in pharmacogenomics and bioinformatics 5:00 Workshop End