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Background

Welcome to the Lifecourse-GWAS wiki!

This wiki will guide you through the Lifecourse-GWAS consortium analysis. Here, you will be able to find instructions for data preparation and access code to generate genome-wide association studies (GWASs) on time-varying phenotypes. We are collecting data on a comprehensive list of phenotypes every year up until 18 years of age and every five years after 18 years of age.

We have prepared the pipeline to minimise time and energy required by analysts to contribute data to the overall effort, ensure harmonisation across cohorts, and minimise errors. The use of standardised procedures across all samples is critical in order to increase the effectiveness of the subsequent meta-analyses that we be run internally upon receipt of these GWAS. Because there is always a chance of error, we may ask some analyses to be re-run. We encourage analysts to organize and save their scripts, files, and directories just in case a re-analysis is required.

This pipeline forms part of the overall Analysis plan. Specifically, it implements the per-cohort age-stratified GWAS studies that will contribute to an overall age-stratified meta analysis.

Imputed genotype data

Imputed genotype data

Genotype data QC and standardisation

Genotype data QC and...

Standardised genotype data

Standardised genotyp...

Genotype data processing

Genotype data proces...

Principal components (optionally provided by analyst)

Principal components (...

Sparse GRM

Sparse GRM

List of unrelated individuals

List of unrelated indi...

Phenotype data processing

Phenotype data proce...

Phenotype x age files

Phenotype x age files

Known GWAS hits

Known GWAS hits

LD Matrices

LD Matrices

PRS results

PRS results

Phenotype x age summary statistics

Phenotype x age summar...

Bias checks

Bias checks

GWAS analysis

GWAS analysis

Organised covariates

Organised covariates

Compressed GWAS summary statistics

Compressed GWAS summar...

Covariate file

Covariate file

Phenotype files

Phenotype files

Report

Report

User provided input data

User provided input data

Pipeline steps

Pipeline steps

Pipeline source data

Pipeline source data

Intermediate files (sensitive, not to be shared)

Intermediate files (sensitive, not to be shared)

Results files, to be uploaded to core research team

Results files, to be uploaded to core research teamText is not SVG - cannot display

Principles of collaboration

Please read the Principles of Collaboration here which details information about software and data sharing, publication and authorship, and extensions to the work.

Sign up

If you have a cohort that could make a contribution to these analyses please use the sign up form to register.

Contact details

Questions about this Wiki can be directed to: lifecourse-gwas-group@bristol.ac.uk

The working group for this consortium consists of:

• Grace M. Power
• Genevieve Leyden
• David Carslake
• Eleanor Sanderson
• Gibran Hemani

Lifecourse GWAS consortium website: https://lifecourse-gwas.github.io