H3ABioNet

Pan African Bioinformatics Network for H3Africa

Medical population genetics and GWAS for complex diseases

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

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

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

Registration opens: 14th January, 2015

Registration closes: 20th 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

Workshop 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.

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 19th 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 19th of April till the 24th of April (departing on the 25th) 2015 and meals from the 19th of April to the morning of the 25th 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: This email address is being protected from spambots. You need JavaScript enabled to view it.

GWAS data analysis and results interpretation workshop

Lecturers:

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

Mon 20th April

Time

Subject

Lecturer

8:00

Registrations and welcome

 

9:00

Overview on medical population genetics: LD, Population Structure

Bogdan Pasaniuc

10:30

Tea/coffee

 

11:00

GWAS study design:GWAS versus linkage mapping and power calculations

Noah Zaitlen

 

Genotype calling and array QC

Shaun Aron

 

SNP and sample QC

Shaun Aron

13:00

Lunch

 

14:00

Population structure

Scott Hazelhurst

 

Association testing

Scott Hazelhurst

 

Imputation

Noah Zaitlen

15:30

Tea/coffee

 

16:00

Fine mapping

Bogdan Pasaniuc

 

Visualisation and post GWAS analysis

Shaun Aron

Tues 21st April

Time

Subject

Lecturer

9:00

Introduction to PLINK – data formats, loading, manipulation

Scott Hazelhurst

10:30

Tea/coffee

 

11:00

Genotype calling QC

Shaun Aron

 

SNP and sample QC

Shaun Aron

13:00

Lunch

 

14:00

PCA and population structure

Scott Hazelhurst

15:30

Tea/coffee

 

16:00

Preprocessing: imputation, quality control

Bogdan Pasaniuc

Wed 22nd April

Time

Subject

Lecturer

9:00

Introduction to basic statistics, p-values, multiple-testing correction

Bogdan Pasaniuc

10:30

Tea/coffee

 

11:00

Association testing: Example GWAS using linear models. Comparison of F-test and alternatives.

Bogdan Pasaniuc

 

Evaluation of linear fits, pitfalls due to overfitting

Shaun Aron/Scott Hazelhurst

13:00

Lunch

 

14:00

Empirical evaluation of the importance of population structure correction

Scott Hazelhurst

 

Introduction to Meta-analysis and Fine mapping with R

Scott Hazelhurst

15:30

Tea/coffee

 

16:00

Visualisation and post GWAS analysis

Shaun Aron

 

Complete GWAS practical exercise from QC to association results

Shaun Aron/Scott Hazelhurst

Thurs 23rd April

Time

Subject

Lecturer

9:00

Finish exercises

Shaun Aron/Scott Hazelhurst

11:00

Wrap-up and finish

 
  GWAS Symposium starts at 11:30am on Thursday 23rd April at False Bay College Muizenberg campus

 

Advanced GWAS Modelling Workshop Program

Lecturers:

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

Mon 20th April

Time

Subject

Lecturer

8:00

Registrations and welcome

 

9:00

Overview on medical population genetics: LD, Population Structure

Bogdan Pasaniuc

10:30

Tea/coffee

 

11:00

GWAS study design:GWAS versus linkage mapping and power calculations

Noah Zaitlen

 

Genotype calling and array QC

Shaun Aron

 

SNP and sample QC

Shaun Aron

13:00

Lunch

 

14:00

Population structure

Scott Hazelhurst

 

Association testing

Scott Hazelhurst

 

Imputation

Noah Zaitlen

15:30

Tea/coffee

 

16:00

Fine mapping

Bogdan Pasaniuc

 

Visualisation and post GWAS analysis

Shaun Aron

Tues 21st April

Time

Subject

Lecturer

9:00

Using simulations to assess power and false-discovery rate

Noah Zaitlen

10:30

Tea/coffee

 

11:00

Computational hidden Markov model to infer ancestry

Bogdan Pasaniuc

13:00

Lunch

 

14:00

Parameter inference in linear models

Bjarni Vilhjalmsson

 

Statistical testing with linear models

Bjarni Vilhjalmsson

15:30

Tea/coffee

 

16:00

Linear mixed models to correct for confounding variation

Bjarni Vilhjalmsson

Wed 22nd April

Time

Subject

Lecturer

9:00

Computational MCMC methods: Gibbs sampling, Metropolis-Hastings for GWAS

Bjarni Vilhjalmsson

10:30

Tea/coffee

 

11:00

Computational GWAS mixed Models: from genome architecture to environmental influences

Bjarni Vilhjalmsson

13:00

Lunch

 

14:00

Accounting for hidden confounding in high-dimensional studies

Bjarni Vilhjalmsson

 

Segment test and Joint testing of multiple related traits at once

Bjarni Vilhjalmsson

15:30

Tea/coffee

 

16:00

Computing Meta-analysis

Noah Zaitlen

Thurs 23rd April

Time

Subject

Lecturer

9:00

Publication or discussion session

Noah, Bjarni, Bogdan

11:00

Wrap-up and finish

 

GWAS Symposium starts at 11:30am on Thursday 23rd April at False Bay College Muizenberg campus