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.

Course Overview: This workshop provides an overview on medical population genetics, PLINK and basic statistics and practicals in order to build a foundational knowledgebase for genome wide association testing. The workshop will consist of a series of theory lectures and a “hands on” practical lab session at the end.

Course Overview: The post-genomic era has been characterized by the rapid advance of genotyping technology resulting in a wealth of new, high-quality data that may hold promise for the further elucidation of genetic factors underlying complex disease. Without the proper tools and methods, the ultimate utility of such rich data may be limited in scope as the field attempts to process and interpret the growing amount of information being generated. For this workshop, we will adopt a hands-on approach to navigate some of the more popular genome-wide software packages available. A general overview of the topics to be covered is as follows. After a brief introduction on the current state of genetic research, we will begin with a discussion of the key quality assurance and quality control steps that are necessary to any genome-wide analysis. We will then transition to the analysis phase with a focus on genome-wide association using unrelated samples, including an overview of the analysis of gene pathways. Next, we will discuss the use of genome-wide data to estimate heritability, construction of genetic risk scores and pathway analysis. We will conclude with an introduction to family-based analysis and an overview of meta-analytic techniques.

Intended Audience: This workshop is aimed at beginning and intermediate level graduate students, postdoctoral researchers and faculty.

Keywords: Genetics, Genomics, Nucleic acids analysis, GWAS

Language: English

Skill level: Intermediate

Type of training: Face-to-face /  in person

Credential awarded:  none

Course Overview: The workshop will be split into two tracks:

1. An introductory track that will cover fundamental assumptions, showcase recent successes and discuss limitations of current GWAS approaches in the field of complex diseases, particularly in the case of African populations with known low linkage disequilibrium (LD). It will also provide a ‘hands-on’ experience of data analysis and a stage for shaping the next generation of GWAS scientists/researchers.
2. An advanced track which will draw upon the audience’s interdisciplinary expertise in mathematics, simulation studies, statistics and machine learning to overcome present challenges and identify the most promising avenues of future research for effective phenotype–genotype association.

Intended Audience: The target audience includes H3Africa project members who will be involved in the design and analyses of population genetics data and genome wide association testing, technicians, graduate students, postdocs and established and young investigators entering the field of complex trait genetics from a variety of backgrounds such as biological, bioinformatics, statistics, mathematics and computer science.

Keywords: Genetics, Genomics, Nucleic acid analysis, Biostatistics

Langiage: English

Skill level: Intermediate

Type of training: face-to-face / in person

Credential awarded: none

Venue of workshop: The African Institute for Mathematical Sciences (AIMS),Cape Town, South Africa.

Dates for the workshop: 20^th-22^nd April, 2015, followed by a symposium from the 23^rd-24^th April, 2015

Workshop organisers: H3ABioNet, the African Institute for Mathematical Sciences (AIMS) and the CPGR node of H3ABioNet

Registration opens: 14^th January, 2015

Registration closes: 20^th February, 2015

Notification date: March, 2015

Link to application form:https://bioweb.cpgr.org.za/redcap/surveys/?s=4L3ANT998T

Workshop Sponsors: H3ABioNet and the African Institute for Mathematical Sciences

Participation: Open application with selection for H3Africa consortium members, African Institute for Mathematical Sciences (AIMS) students and interested participants. The selection procedure will give priority to those with demonstrated need for this training, particularly those with data available or soon to be available. A total of 50 participants will be selected.

Syllabus and Tools: Participants will learn about the design and analyses of population data and genome wide association testing. On the second day, participants will be split into two groups

1. Hands on data processing, analysis and the interpretation of results
2. Advanced mathematical population genetics and disease scoring statistics

Objectives: This workshop aims to introduce an interdisciplinary audience to the potential of GWAS and to key strategic considerations in designing and performing Genome-wide Association studies, as well as to bring all participants up to speed on the basic principles of human genetic variation, genotyping and disease scoring statistics. In addition, this workshop aims to bridge the gap between statistics, bioinformatics and genetics. We envisage that researchers in machine learning and statistics who have an interest in genetic architecture of complex diseases, as well as statistical geneticists looking for using or improved tools for GWAS will benefit from participating in this workshop.

Workshop limitations: This workshop will provide a foundation for continued learning in medical genetics and GWAS studies for the introductory track and will not make one an expert in medical population genetics and genome wide association testing and studies. The advanced track will provide the cover current mathematical and statistical models and simulations methods used in population genetics and GWAS and will not make one an expert in simulations, mathematical and statistical modelling and methodology development for population genetics and GWAS studies.

Trainers and support staff:

1. Organizers: Prof. Nicola Mulder, Dr. Emile Chimusa, Dr. Judit Kumuthini and Dr. Gaston Kuzamunu
2. Trainers: Prof. Scott Hazelhurst, Dr. Noah Zaitlen, Dr. Bogdan Pasaniuc, Dr. Bjarni Vilhjalmsson and Shaun Aron

Prerequisites: Selected participants will need to work through the following resources to enable them to gain the most from the workshop:
http://www.ee.surrey.ac.uk/Teaching/Unix/
http://www.r-tutor.com/r-introduction
https://www.python.org/
http://onlinestatbook.com/2/ 
A pre-workshop course on an Introduction to Linux/R/python will take place on the 19^th April 2015.

Registration: All interested applicants must complete the application form and upload a motivation letter from their supervisor. Incomplete applications will NOT be reviewed. The successful applicants for the workshop, will be contacted to complete an airline ticket booking form, a short biosketch with a recent picture and the H3ABioNet workshop policy. The workshop will be followed by a symposium which workshop participants will automatically attend and are encouraged to submit an abstract for either oral or poster presentations.

H3ABioNet will cover the costs of a return economy air ticket to Cape Town. AIMS will cover the cost of accommodation from the night of the 19^th of April till the 24^th of April (departing on the 25^th) 2015 and meals from the 19^th of April to the morning of the 25^th of April 2015. H3ABioNet and AIMS will NOT cover the costs of visa fees, vaccinations, airport transfers from your local area or any other costs.

Please note, if a participant is unable to attend this workshop after acceptance, their place will be passed onto to applicants on the waiting list and not to other recommended members from their Institution or Research project.

If you would like any additional information, please do not hesitate to contact the symposium and workshop organizers: 

GWAS data analysis and results interpretation workshop

Advanced GWAS Modelling Workshop Program

Lecturers:

• Bogdan Pasaniuc (UCLA)
• Noah Zaitlen (UCSF)
• Bjarni Vilhjalmsson (HSPH)
• Shaun Aron (Wits)
• Scott Hazelhurst (Wits)

Training Materials Availability:

Training materials for this course are available as a single downloadable archive here: https://doi.org/10.25375/uct.19130000. Should you re-use any of these materials, please ensure that both the author/s of the material AND H3ABioNet are clearly credited.