H3ABioNet 2018 Genotyping Chip Data Analysis and GWAS lecture series - Lecture 1
20 August 2018H3ABioNet 2018 Genotyping Chip Data Analysis and GWAS lecture series - Lecture 1 https://www.youtube.com/watch?v=4_-pxWFUpfU&list=PLcQ0XMykNhCQJPz0amnbz9BPM4Bu0Nkgf https://tess.elixir-europe.org/events/h3abionet-2018-genotyping-chip-data-analysis-and-gwas-lecture-series #### Computational requirements for running the H3ABioNet GWAS workflows 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: Installing and using Nextflow Installing and using Github Use of containers for packaging and running tools 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: Either a Linux machine or an Apple running macOS Ideally you should have machine with at least 2-4 cores and 8GB of RAM. Java 8 Nextflow installed (see installation instructions at https://www.nextflow.io/) 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 2018-08-20 15:00:00 UTC 2018-08-20 16:30:00 UTC H3ABioNet Population genomics Genotyping experiment Computational biology Workflows GWAS study Bioinformatics H3ABioNet email@example.com H3ABioNet Anyone intersted in GWAS and using the H3Africa genotyping chipAnyone who wants to learn more about GWAS workshops_and_courses  NextflowDockerH3ABioNetGWASWorkflowsGenotyping array analysis bioinformaticsAfricaPopulation GenomicsReproducible ScienceH3Africa genotyping arrayHigh performance computingCloud computingGWAS workflowH3ABioNet GWAS 2018 Lecture Series
H3ABioNet 2018 Genotyping Chip Data Analysis and GWAS lecture series - Lecture 2
22 August 2018H3ABioNet 2018 Genotyping Chip Data Analysis and GWAS lecture series - Lecture 2 https://www.youtube.com/watch?v=4_-pxWFUpfU&list=PLcQ0XMykNhCQJPz0amnbz9BPM4Bu0Nkgf https://tess.elixir-europe.org/events/h3abionet-2018-genotyping-chip-data-analysis-and-gwas-lecture-series-4a0ce1cc-f48d-4f1e-98b5-2bfc55abce6a ### Overview of Genome Wide Association Studies and study designs 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. 2018-08-22 15:00:00 UTC 2018-08-22 17:00:00 UTC H3ABioNet Genotyping experiment Population genetics Population genomics GWAS study H3ABioNet firstname.lastname@example.org H3ABioNet Anyone intersted in GWAS and using the H3Africa genotyping chip workshops_and_courses  H3ABioNetGWASH3AfricaH3Africa genotyping arrayAfrican populationsStudy designAWI-GENAfrican genomicsPopulations GenomicsGenetic DiversityH3Africa genotyping arrayCase Control studyGenotypesComplex traitsGWAS study designsAllelic associationGenotype associationGWAS workflowQuantitative traitsSample sizeCommon and rare variantsAfrican genome structureH3ABioNet GWAS 2018 Lecture Series
H3ABioNet 2018 Genotyping Chip Data Analysis and GWAS lecture series - Lecture 5
3 September 2018H3ABioNet 2018 Genotyping Chip Data Analysis and GWAS lecture series - Lecture 5 http://meeting.uct.ac.za/h3abionet_gwas/ https://tess.elixir-europe.org/events/h3abionet-2018-genotyping-chip-data-analysis-and-gwas-lecture-series-ce96b48a-423a-435c-beae-9ddfcaba38a6 ### Population structure in GWAS 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. Date: 3rd September 2018 Time: 2pm WAT / 3pm CAT / 4pm EAT [Url to join the lecture]: http://meeting.uct.ac.za/h3abionet_gwas/ 2018-09-03 15:00:00 UTC 2018-09-03 16:30:00 UTC H3ABioNet Genotyping experiment Bioinformatics GWAS study Population genetics Population genomics H3ABioNet email@example.com H3ABioNet Anyone intersted in GWAS and using the H3Africa genotyping chip 150 meetings_and_conferencesworkshops_and_courses first_come_first_served Population structureGWASCorrect for population structureH3ABioNetH3AfricaAWI-GEN
H3ABioNet 2018 Genotyping Chip Data Analysis and GWAS lecture series - Lecture 6
5 September 2018H3ABioNet 2018 Genotyping Chip Data Analysis and GWAS lecture series - Lecture 6 http://meeting.uct.ac.za/h3abionet_gwas/ https://tess.elixir-europe.org/events/h3abionet-2018-genotyping-chip-data-analysis-and-gwas-lecture-series-lecture-6 ### Imputation and its importance in GWAS 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. 2018-09-05 15:00:00 UTC 2018-09-05 16:30:00 UTC H3ABioNet Population genetics Population genomics Computational biology Bioinformatics Genotyping experiment GWAS study H3ABioNet firstname.lastname@example.org H3ABioNet Anyone intersted in GWAS and using the H3Africa genotyping chip 150 workshops_and_courses first_come_first_served ImputationGWASAfrican populationsImputation panel
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