On 21/08/2023, 12:45, "A UK-based worldwide e-mail broadcast system mailing list on behalf of Speed, Doug" <[log in to unmask] <mailto:[log in to unmask]> on behalf of [log in to unmask] <mailto:[log in to unmask]>> wrote:
Hi all
Myself and David Balding will run the next edition of our one-day workshop on GWAS, heritability analysis and prediction in Bloomsbury, London, on Thursday 19th October.
See text below for more details, and visit the Eventbrite page to register:
https://www.eventbrite.com/e/methods-and-software-for-analysing-complex-trait-gwas-data-tickets-700562741017?aff=oddtdtcreator <https://www.eventbrite.com/e/methods-and-software-for-analysing-complex-trait-gwas-data-tickets-700562741017?aff=oddtdtcreator>
If you have any questions, email [log in to unmask] <mailto:[log in to unmask]>
Thanks, Doug
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Methods and Software for Analysing Complex Trait GWAS Data
Course Leaders
David Balding, Melbourne Integrative Genomics, University of Melbourne , Australia, and UCL Genetics Institute, London.
Doug Speed, Center for Quantitative Genetics and Genomics, Aarhus University, Denmark.
Cost
GBP 100, which includes refreshments, light lunch and Eventbrite fees. Automatic refunds available if you cancel more than 7 days before the event, except for Eventbrite fee which is not refundable.
Course outline
This workshop will cover analysis of genome-wide association studies (GWAS), both using individual-level genetic data (e.g. GCTA and LDAK software) and using summary statistics (LDSC, SumHer). It will include latest developments in heritability analyses, such as assessing heritability enrichment in functionally-annotated regions, genetic correlation and prediction (polygenic scores, BLUP and MultiBLUP). The common elements of these methods will be emphasised, highlighting a modelling framework that has emerged for genome-wide SNP analysis, while also contrasting the differences in modelling assumptions underlying the different software.
The practicals will provide step-by-step details for analysing genetic data, starting either with individual-level data (e.g. PLINK files or the output from IMPUTE2) or summary statistics (p-values from a GWAS). There will be worked examples; to take part in the practicals, participants should bring a laptop computer with a recent version of R installed. LDAK and other scientific software require the Linux Operating System, which is available under MAC OS using Terminal.app, and under Windows 10 or later using Windows Subsystem for Linux (WSL), see https://docs.microsoft.com/en-us/windows/wsl/install <https://docs.microsoft.com/en-us/windows/wsl/install>
Prerequisites
Participants should be proficient in statistics including maximum-likelihood estimation, hypothesis testing, correlation and regression, preferably some familiarity with random-effects regression models and experience of computer-based data analysis. In genetics, it is expected that participants will have some knowledge of SNP genotyping including basic QC, and Hardy-Weinberg and linkage equilibria. Optional background information introducing these and related topics will be sent a week before the course date. Computer scripts and output will be discussed that assume some familiarity with scientific computing using Linux. Some familiarity with PLINK would be helpful but is not essential.
Venue: Bloomsbury, London W1, (Goodge St, Russell Square, Warren St, Euston Square, Euston and Kings Cross stations all within walking distance)
Provisional Timetable
9:30 - 10:00 Coffee, snack and registration.
10:00 - 12:30: Lecture 1 followed by Practical 1
Introduction to analysing GWAS data analysis using individual genotype data, kinship and heritability, both classical and SNP-based. Effect of LD, MAF and genotyping quality on heritability. GCTA and LDAK software. Methods based on summary statistics, enrichment of functional categories. LDSC, SumHer software.
12:30 - 13:30: Lunch (a light lunch will be provided)
13.30 - 16:00: Lecture 2 followed by Practical 2
The effects of confounding in association analysis. Genetic correlations. Genomic prediction using enhanced polygenic risk scores.
16:00 - 16:30 Optional wrap up session. The course leaders will be available for informal Q&A.
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