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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
Venue of workshop: Medical Campus, University of Cape Town
Dates for the workshop: 22nd February to 24th February, 2016
Workshop organisers: CBIO, Nicola Mulder, Matthew McQueen
Participation: Open application with selection
Workshop Sponsors: CBIO
Syllabus and Tools: Participants will learn about quality control and quality assurance steps of genome-wide data, basic GWAS analysis, construction of genetic risk scores, estimation of genome-wide SNP heritability, an introduction to family-based association approaches and an overview of meta-analytic techniques.
Workshop Trainers: Dr. Matthew McQueen is an Associate Professor and Director of the Public Health Program at the Department of Integrative Physiology at Colorado University, Boulder, USA. His research is focused on a multi-faceted approach to the investigation of genetic determinants underlying complex disease, with a particular interest in psychiatric, behavioral and neurologic disorders. Recent areas of research include the development and application of statistical and epidemiological methods geared towards large-scale genomic analysis in both family-based and population-based samples.
Prerequisites: Participants are encouraged to work through the following resources to enable them to gain the most from the workshop. We will provide a basic overview of the Linux environment as well as work towards gaining an understanding of R.
http://www.ee.surrey.ac.uk/Teaching/Unix/
http://www.r-tutor.com/r-introduction
Objectives: After this workshop participants should be able to:
- Understand the steps necessary to assess the quality of genome-wide data
- Use common software to conduct a basic GWAS analysis
- Conduct relationship-checks and generate components of ancestry
- Aggregate genome-wide association data using GCTA and genetic risk scores
- Understand the features of a family-based association test
- Understand the different techniques to conduct a meta-analysis of genetic results
Workshop limitations: This workshop will only provide a foundation for continued learning in genome wide association testing and studies. Further directions for specific genome-wide approaches will need to be tailored towards particular studies.
Registration: All potential applicants must complete the application form. Incomplete applications will NOTbe reviewed. Successful participants will be notified of their selection for the workshop and will be contacted provide a short biosketch with a recent picture.
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.
Time | Topic | Trainer |
22nd February 2016 | ||
9:00 | Registration and Introductions | |
9:30 | Lecture 1: Introduction to Genome-Wide Approaches | Matthew McQueen |
10:30 | Tea break | |
11:00 | Tutorial 1: Getting Started (Linux) | Matthew McQueen |
12:00 | Lunch | |
1:00 | Lecture 2: Quality Control Procedures for GWAS Data | Matthew McQueen |
2:00 | Tea Break | |
2:30 | Tutorial 2: Data Cleaning, Relationship Checks and Genetic Ancestry (PLINK, R) | Matthew McQueen |
3:30 | Workshop End | |
23rd February 2016 | ||
9:30 | Lecture 3: Genome-Wide Association Approaches | Matthew McQueen |
10:30 | Tea Break | |
11:00 | Tutorial 3: Genome-Wide Association Analysis (PLINK, R) | Matthew McQueen |
12:00 | Lunch | |
1:00 | Lecture 4: Aggregation of GWAS Information | Matthew McQueen |
2:00 | Tea Break | |
2:30 | Tutorial 4: Heritability (GCTA), Genetic Risk Score ® and Pathway Analysis | Matthew McQueen |
3:30 | Workshop End |
24th February 2016 | ||
9:30 | Lecture 5: Introduction to Family-Based Approaches | Matthew McQueen |
10:30 | Tea Break | |
11:00 | Tutorial 5: Family-Based Association Test (FBAT) | Matthew McQueen |
12:00 | Lunch | |
1:00 | Lecture 6: Meta-Analysis of Genetic Results | Matthew McQueen |
2:00 | Tea Break | |
2:30 | Tutorial 6: Meta-Analysis (R) | Matthew McQueen |
3:30 | Workshop End |
Training Materials Availability:
Training materials used for this course were not directly produced by H3ABioNet but may be accessed here: https://doi.org/10.25375/uct.19130048. Please note, these materials may be governed by different sharing/re-use policies, and you are encouraged to follow the policies of the external providers regarding material re-use and/or sharing.
Course Overview: The workshop will be split into two tracks:
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: 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
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
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:
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:
Lecturers:
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 |
Lecturers:
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 |
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.
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