Lectures/Webinars
Statistical models used for GWAS - Lecture 7 H3ABioNet 2018 GWAS Lecture series
Material type:
Lecture notes/Slides
Submitted by Dr Verena Ras
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Year created: 2018
Year latest update: 2018
Summary:
The seventh and last lecture of the H3ABioNet 2018 GWAS lecture series will cover different types of GWAS depending on data designs: Population-based GWAS (for case/control design or for quantitative traits) and Family-based GWAS (for independent trio data or large pedigrees). This lecture will also provide an overview of test statistics for multi-marker association testing in both type of GWAS. It will discuss the problem of multiple testing, the principal of family wise error rate (FWER) and some proposed methods for P-values correction. The lecture will finally present a set of tools to perform GWAS and to represent results.
Imputation and use in GWAS - Lecture 6 H3ABioNet 2018 GWAS Lecture series
Material type:
Lecture notes/Slides
Submitted by Dr Verena Ras
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Year created: 2018
Year latest update: 2018
Summary:
The sixth of a series of seven H3ABioNet online lectures for Genome Wide Association Studies (GWAS) will introduce the fundamentals of genotype imputation and its importance in GWAS. This lecture will cover the reference panels, file formats, algorithms and tools commonly used for imputation. It will discuss the assessment of the quality of imputation as well as the evaluation of reference panel and imputation methods. The lecture will also explain how imputation enhances the scope a GWAS and describe some of the additional analyses that become possible due to the use of imputed data.
Population structure in GWAS - Lecture 5 H3ABioNet 2018 GWAS Lecture series
Material type:
Lecture notes/Slides
Submitted by Dr Verena Ras
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Year created: 2018
Year latest update: 2018
Summary:
The fifth of a series of seven H3ABioNet online lectures for Genome Wide Association Studies (GWAS) will introduce the concept of population structure/stratification (PS) and suggest why it is critical to consider PS in a GWAS. The lecture will begin by familiarizing the types of PS that are encountered and explain the factors that could cause them to appear in a GWAS dataset. It will then cover the methods that are commonly used to identify PS in a dataset and finally discuss the available computational approaches to correct for PS in a GWAS.
Quality control and its importance in GWAS - Lecture 4 H3ABioNet 2018 GWAS Lecture series
Material type:
Lecture notes/Slides
Submitted by Dr Verena Ras
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Year created: 2018
Year latest update: 2018
Summary:
In the fourth of a series of seven H3ABioNet online lectures for Genome Wide Association Studies (GWAS), the importance of doing good quality control for a GWAS will be discussed. The lecture will cover the types of errors one should control for, the specific bioinformatics tools used for quality control. Specific sample and SNP quality control steps that should be undertaken in a GWAS will be explored using specific examples.
Genotype calling from chip data - Lecture 3 H3ABioNet 2018 GWAS Lecture series
Material type:
Lecture notes/Slides
Submitted by Dr Verena Ras
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Year created: 2018
Year latest update: 2018
Summary:
The third of a series of seven H3ABioNet online lectures for Genome Wide Association Studies (GWAS) will introduce genotyping SNP array chips with particular emphasis on the H3Africa genotype chip. The lecture will cover common file formats when obtaining genotyping chip data from a service provider such as Illumina and software used for genotype calling. This lecture will also cover genotype calling, sample and probe quality control, probe viewing and exporting of data using GenomeStudio. Converting the data to PLINK format and some tips on troubleshooting and common pitfalls will be discussed.
Overview of Genome Wide Association Studies and study designs - Lecture 2 H3ABioNet 2018 GWAS Lecture Series
Material type:
Lecture notes/Slides
Submitted by Dr Verena Ras
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Year created: 2018
Year latest update: 2018
Summary:
The second of a series of seven online lectures for Genome Wide Association Studies (GWAS) will provide a basic overview on genome-wide association studies (GWAS). This is timely with the H3Africa genotyping data becoming available for several of the H3Africa research groups. To enable genomic research, the H3Africa Consortium had to build some of its own resources. This has involved sequencing whole genomes from selected under-represented African populations, analyzing the data to identify common genetic variation across major groups and developing a unique GWAS array, enriched for common African variation. The H3Africa SNP genotyping array, is currently the best-suited array available for African genome-wide association studies.
What does it take to develop a genome study to understand genetic and environmental contributions to complex disease traits? This GWAS lecture will cover the research process from protocol development to data quality control and GWAS analysis approaches. It will include the two main study designs:
Case : control (e.g. diabetes, hypertension, kidney disease)
Continuous trait (e.g. LDL-Cholesterol, body mass index, height) GWAS.
I will discuss the basic building blocks of a GWAS study, the different study designs, power of a study to detect genetic association (based in sample size, allele frequency and expected effect size), and replication studies. The advantages and disadvantages of doing GWAS in African populations will be discussed.
Computational requirements for running the H3ABioNet GWAS workflows. - Lecture 1 H3ABioNet 2018 GWAS Lecture series
Material type:
Lecture notes/Slides
Submitted by Dr Verena Ras
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Year created: 2018
Year latest update: 2018
Summary:
The first of a series of seven online lectures for Genome Wide Association Studies (GWAS) will cover the technical requirements for setting up a your computational environment for running the H3ABioNet GWAS workflows. In this inaugural lecture of the series, Prof. Hazelhurst will cover the the following topics:
1. Installing and using Nextflow
2. Installing and using Github
3. Use of containers for packaging and running tools
4. Pulling the GWAS pipeline from Github and running it
As this lecture aims to provide attendees with an environment to the run the H3ABioNet GWAS workflow at their own pace, there are some preliminary software requirements:
1. Either a Linux machine or an Apple running macOS
2. Ideally you should have machine with at least 2-4 cores and 8GB of RAM.
3. Java 8
4. Nextflow installed (see installation instructions at https://www.nextflow.io/)
5. Python 3
Please also install either Docker OR the following dependencies using pip3:
Pandas, Matplotlib, Openpyxl, SciPy, NumPy
PLINK 1.9
[Please also refer to the following documentation to obtain the H3ABioNet GWAS workflow]:
https://github.com/h3abionet/h3agwas/blob/master/README.md
Wordpress user guide
Material type:
Lecture notes/Slides
Submitted by Ms Kim Gurwitz
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Year created: 2016
Year latest update: 2016
Summary:
Wordpress is a free open-source tool that allows one to create and customise one's own website.
Computational Molecular Biology: Stanford University, Biochem 218
Material type:
Lecture notes/Slides
, Quiz/Assessment
, Videos/Audio
Submitted by Dr Vicky Nembaware
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Year created: 2012
Year latest update: 2012
Summary:
Basics of how computational tools or algorithms can be applied to molecular biology. Link to the videos seem to be working well but not slides