[HTML][HTML] Improved genetic prediction of complex traits from individual-level data or summary statistics

Q Zhang, F Privé, B Vilhjálmsson, D Speed - Nature communications, 2021 - nature.com
Most existing tools for constructing genetic prediction models begin with the assumption that
all genetic variants contribute equally towards the phenotype. However, this represents a …

[HTML][HTML] Improved polygenic prediction by Bayesian multiple regression on summary statistics

LR Lloyd-Jones, J Zeng, J Sidorenko, L Yengo… - Nature …, 2019 - nature.com
Accurate prediction of an individual's phenotype from their DNA sequence is one of the great
promises of genomics and precision medicine. We extend a powerful individual-level data …

Mixed-model association for biobank-scale datasets

PR Loh, G Kichaev, S Gazal, AP Schoech, AL Price - Nature genetics, 2018 - nature.com
To the Editor—Despite recent work highlighting the advantages of linear mixedmodel (LMM)
methods for genome-wide association studies (GWAS) in datasets containing relatedness or …

Pitfalls of predicting complex traits from SNPs

NR Wray, J Yang, BJ Hayes, AL Price… - Nature Reviews …, 2013 - nature.com
The success of genome-wide association studies (GWASs) has led to increasing interest in
making predictions of complex trait phenotypes, including disease, from genotype data …

[HTML][HTML] Leveraging functional genomic annotations and genome coverage to improve polygenic prediction of complex traits within and between ancestries

Z Zheng, S Liu, J Sidorenko, Y Wang, T Lin, L Yengo… - Nature Genetics, 2024 - nature.com
We develop a method, SBayesRC, that integrates genome-wide association study (GWAS)
summary statistics with functional genomic annotations to improve polygenic prediction of …

Improving GWAS discovery and genomic prediction accuracy in biobank data

EJ Orliac, D Trejo Banos, SE Ojavee… - Proceedings of the …, 2022 - National Acad Sciences
Genetically informed, deep-phenotyped biobanks are an important research resource and it
is imperative that the most powerful, versatile, and efficient analysis approaches are used …

Genome-wide prediction of traits with different genetic architecture through efficient variable selection

V Wimmer, C Lehermeier, T Albrecht, HJ Auinger… - Genetics, 2013 - academic.oup.com
In genome-based prediction there is considerable uncertainty about the statistical model
and method required to maximize prediction accuracy. For traits influenced by a small …

[HTML][HTML] Regularized machine learning in the genetic prediction of complex traits

S Okser, T Pahikkala, A Airola, T Salakoski… - PLoS …, 2014 - journals.plos.org
Compared to univariate analysis of genome-wide association (GWA) studies, machine
learning–based models have been shown to provide improved means of learning such …

[HTML][HTML] Genome-wide prediction of discrete traits using Bayesian regressions and machine learning

O González-Recio, S Forni - Genetics Selection Evolution, 2011 - Springer
Background Genomic selection has gained much attention and the main goal is to increase
the predictive accuracy and the genetic gain in livestock using dense marker information …

Evaluating and improving heritability models using summary statistics

D Speed, J Holmes, DJ Balding - Nature genetics, 2020 - nature.com
There is currently much debate regarding the best model for how heritability varies across
the genome. The authors of GCTA recommend the GCTA-LDMS-I model, the authors of LD …