Sold Out

UCL Genetics Short Course 2 - Methods for Analysing Complex Trait GWAS Data

Event Information

Share this event

Date and Time

Location

Location

University College London

University College London

Gower Street

London

WC1E 6BT

United Kingdom

View Map

Refund Policy

Refund Policy

Refunds up to 7 days before event

Friends Who Are Going
Event description

Description

Understanding the genetic architecture of complex traits through SNP-based heritability analysis

Date: Thursday 14th September, University College London, 10-4pm

Tutors: Prof David Balding (Melbourne and UGI) and Dr Doug Speed (UGI)

Cost: £40 (or £30 for UCL Members)

Advance Registration is REQUIRED

Note, this is duplicate of our course on Tuesday 5th September, which is now full up.

-------------------------------------------------

Background: In recent years there has been great progress in developing genome-wide statistical analyses for detecting causal variants, constructing prediction models and better understanding the genetic architecture of complex traits. However the underlying regression model involves very large numbers of predictors, and strong modelling assumptions are required to tackle the consequent problem of over-fitting. The results can be sensitive to these assumptions, and also to the effects of population structure, genotyping errors and the extent to which rare SNPs are included.

Course outline: We will cover mixed-model association analysis (e.g., Fast-LMM, GEMMA), risk prediction (e.g., polygenic risk scores, BLUP and MultiBLUP) and heritability analyses (GCTA, LDAK, LDSC), both using individual-level genetic data and summary statistics. We will emphasise the common elements of these methods, highlighting a standard framework that has emerged for genome-wide SNP analysis, while also contrasting the differences in underlying modelling assumptions.

The practicals will provide step-by-step details for analysing genetic data, starting either with indvidual-level data (e.g., PLINK files or the output from IMPUTE2) or summary statistics (p-values from a GWAS). There will be a selection of worked examples; to take part in the practicals, participants should bring a laptop with either MAC or LINUX OS

Prerequisites: Participants should be proficient in statistics including some familiarity with random-effects regression models. In genetics, knowledge of SNP genotypes and Hardy-Weinberg and linkage equilibrium will be assumed. 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.

-------------------------------------------------

Provisional Timetable

10:00 - 12:40: Lecture 1 followed by Practical 1

Introduction to analysing GWAS data, including QC, single-SNP analysis,polygenic risk scores, mixed-model analysis and gene-based analysis

12:40 - 13:20: Lunch

13.20-16:00: Lecture 2 followed by Practical 2

Estimating heritability, bivariate correlations and enrichment of functional categories


Room details will be provided closer to the time; any questions, email doug[dot]speed[at]ucl.ac.uk

Share with friends

Date and Time

Location

University College London

University College London

Gower Street

London

WC1E 6BT

United Kingdom

View Map

Refund Policy

Refunds up to 7 days before event

Save This Event

Event Saved