Genotype-based Prediction (GenoPred)

Welcome!

This website provides details of a project evaluating methods for genotype-based prediction. The website will be updated continuously as the project develops.

Please see our GenoPred pipeline (GenoPredPipe), providing a one-liner for ancestry inference and polygenic score calculation.

Data Preparation
- Genetic
- Phenotypic
  - Target phenotypic
Main Research Questions
Side Questions
- Standardised vs. non-standardised
- Estimating significance of model comparisons
Future developments
- Stratification using pathway/tissue-specific genetic scores
- Gene expression risk scores using observed expression

Help

This website was created by Oliver Pain (oliver.pain@kcl.ac.uk). Please get in touch if you have any questions or comments. Also, follow me on twitter and GitHub for updates.

Acknowledgments

I would like to thank the following people who have contributed to this project so far:

Cathryn Lewis
Lasse Folkersen
Kylie Glanville
Saskia Hagenaars
Saskia Selzam
Anna Fürtjes
Helena Gaspar
Jonathon Coleman
Gerome Breen
Robert Plomin
Alex Gillett
Ken Hanscombe
Ryan Arathimos
Toshiki Kono

Funding:

This work is funded by the MRC (MR/N015746/1), and the National Institute for Health Research (NIHR) Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London. The authors acknowledge use of the research computing facility at King’s College London, Rosalind (https://rosalind.kcl.ac.uk), which is delivered in partnership with the NIHR Maudsley BRC, and part-funded by capital equipment grants from the Maudsley Charity (award 980) and Guy’s & St. Thomas’ Charity (TR130505). The views expressed are those of the authors and not necessarily those of the NHS, the NIHR or the Department of Health and Social Care.

Change log:

24/06/2020:

Change log started
Updated Ancestry_identifier.R to use proper grid search in enet, allow other modelling methods to be specified, and improve model performance reporting.

13/08/2020:

Add comparison between standardised and non-standardised polygenic scores.

10/02/2021:

PRS comparison: Added LDPred2 and DBSLMM methods. Added prostate and breast cancer. Add polygenicity and ancestry senstivity analysis.
GeRS comparison: Minor formatting changes.

13/04/2021

PRS comparison: Evaluated new version of GCTB v2.03
PRS conversion to absolute scale: Updated html

22/08/2021

Added GenoPredPipe documentation