Genetic prediction of complex traits with polygenic scores: a statistical review

Accurate genetic and environmental covariance estimation with composite likelihood in genome-wide association studies

(2021) Boran Gao et al.   PLoS Genetics

Evaluation of polygenic prediction methodology within a reference-standardized framework

(2021) Oliver Pain et al.   PLoS Genetics

iCARE: An R package to build, validate and apply absolute risk models

(2020) Parichoy Pal Choudhury et al.   PLoS One

Leveraging effect size distributions to improve polygenic risk scores derived from summary statistics of genome-wide association studies

(2020) Shuang Song et al.   PLoS Computational Biology

Accurate and Scalable Construction of Polygenic Scores in Large Biobank Data Sets

(2020) Sheng Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Non-parametric Polygenic Risk Prediction via Partitioned GWAS Summary Statistics

(2020) Sung Chun et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A penalized regression framework for building polygenic risk models based on summary statistics from genome-wide association studies and incorporating external information

(2020) Ting-Huei Chen et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

A phenome-wide association and Mendelian Randomisation study of polygenic risk for depression in UK Biobank

(2020) Xueyi Shen et al.   Nature Communications

Polygenic risk scores: from research tools to clinical instruments

(2020) Cathryn M. Lewis et al.   Genome Medicine

Combined Utility of 25 Disease and Risk Factor Polygenic Risk Scores for Stratifying Risk of All-Cause Mortality

(2020) Allison Meisner et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Tutorial: a guide to performing polygenic risk score analyses

(2020) Shing Wan Choi et al.   Nature Protocols

Cancer PRSweb: An Online Repository with Polygenic Risk Scores for Major Cancer Traits and Their Evaluation in Two Independent Biobanks

(2020) Lars G. Fritsche et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Deep neural network improves the estimation of polygenic risk scores for breast cancer

(2020) Adrien Badré et al.   JOURNAL OF HUMAN GENETICS

Penalized regression and model selection methods for polygenic scores on summary statistics

(2020) Jack Pattee et al.   PLoS Computational Biology

LDpred2: better, faster, stronger

(2020) Florian Privé et al.   BIOINFORMATICS

15 years of genome-wide association studies and no signs of slowing down

(2020) Ruth J. F. Loos   Nature Communications

Efficient cross-trait penalized regression increases prediction accuracy in large cohorts using secondary phenotypes

(2019) Wonil Chung et al.   Nature Communications

Progress in Polygenic Composite Scores in Alzheimer’s and Other Complex Diseases

(2019) Danai Chasioti et al.   TRENDS IN GENETICS

Clinical use of current polygenic risk scores may exacerbate health disparities

(2019) Alicia R. Martin et al.   NATURE GENETICS

A statistical framework for cross-tissue transcriptome-wide association analysis

(2019) Yiming Hu et al.   NATURE GENETICS

SummaryAUC: a tool for evaluating the performance of polygenic risk prediction models in validation datasets with only summary level statistics

(2019) Lei Song et al.   BIOINFORMATICS

Complex Trait Prediction from Genome Data: Contrasting EBV in Livestock to PRS in Humans

(2019) Naomi R. Wray et al.   GENETICS

Polygenic prediction via Bayesian regression and continuous shrinkage priors

(2019) Tian Ge et al.   Nature Communications

On the utilization of polygenic risk scores for therapeutic targeting

(2019) Greg Gibson   PLoS Genetics

An atlas of polygenic risk score associations to highlight putative causal relationships across the human phenome

(2019) Tom G Richardson et al.   eLife

A flexible and parallelizable approach to genome‐wide polygenic risk scores

(2019) Paul J. Newcombe et al.   GENETIC EPIDEMIOLOGY

Missing heritability of complex diseases: case solved?

(2019) Emmanuelle Génin   HUMAN GENETICS

Analysis of polygenic risk score usage and performance in diverse human populations

(2019) L. Duncan et al.   Nature Communications

Towards clinical utility of polygenic risk scores

(2019) Samuel A Lambert et al.   HUMAN MOLECULAR GENETICS

Improved polygenic prediction by Bayesian multiple regression on summary statistics

(2019) Luke R. Lloyd-Jones et al.   Nature Communications

Making the Most of Clumping and Thresholding for Polygenic Scores

(2019) Florian Privé et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Polygenic Risk Scores in Clinical Psychology: Bridging Genomic Risk to Individual Differences

(2018) Ryan Bogdan et al.   Annual Review of Clinical Psychology

Pleiotropic mapping and annotation selection in genome-wide association studies with penalized Gaussian mixture models

(2018) Ping Zeng et al.   BIOINFORMATICS

Heritability Estimation and Differential Analysis with Generalized Linear Mixed Models in Genomic Sequencing Studies

(2018) Shiquan Sun et al.   BIOINFORMATICS

The personal and clinical utility of polygenic risk scores

(2018) Ali Torkamani et al.   NATURE REVIEWS GENETICS

Improving genetic prediction by leveraging genetic correlations among human diseases and traits

(2018) Robert M. Maier et al.   Nature Communications

Estimation of complex effect-size distributions using summary-level statistics from genome-wide association studies across 32 complex traits

(2018) Yan Zhang et al.   NATURE GENETICS

Polygenic Risk Scores for Prediction of Breast Cancer and Breast Cancer Subtypes

(2018) Nasim Mavaddat et al.   AMERICAN JOURNAL OF HUMAN GENETICS

SumHer better estimates the SNP heritability of complex traits from summary statistics

(2018) Doug Speed et al.   NATURE GENETICS

Multiethnic polygenic risk scores improve risk prediction in diverse populations

(2017) Carla Márquez-Luna et al.   GENETIC EPIDEMIOLOGY

Polygenic scores via penalized regression on summary statistics

(2017) Timothy Shin Heng Mak et al.   GENETIC EPIDEMIOLOGY

Predictive accuracy of combined genetic and environmental risk scores

(2017) Frank Dudbridge et al.   GENETIC EPIDEMIOLOGY

Genetic architecture: the shape of the genetic contribution to human traits and disease

(2017) Nicholas J. Timpson et al.   NATURE REVIEWS GENETICS

Differential expression analysis for RNAseq using Poisson mixed models

(2017) Shiquan Sun et al.   NUCLEIC ACIDS RESEARCH

Non-parametric genetic prediction of complex traits with latent Dirichlet process regression models

(2017) Ping Zeng et al.   Nature Communications

Leveraging functional annotations in genetic risk prediction for human complex diseases

(2017) Yiming Hu et al.   PLoS Computational Biology

Joint modeling of genetically correlated diseases and functional annotations increases accuracy of polygenic risk prediction

(2017) Yiming Hu et al.   PLoS Genetics

Improving polygenic risk prediction from summary statistics by an empirical Bayes approach

(2017) Hon-Cheong So et al.   Scientific Reports

Local True Discovery Rate Weighted Polygenic Scores Using GWAS Summary Data

(2016) Timothy Shin Heng Mak et al.   BEHAVIOR GENETICS

Meuwissen et al. on Genomic Selection

(2016) Dirk-Jan de Koning   GENETICS

Next-generation genotype imputation service and methods

(2016) Sayantan Das et al.   NATURE GENETICS

Developing and evaluating polygenic risk prediction models for stratified disease prevention

(2016) Nilanjan Chatterjee et al.   NATURE REVIEWS GENETICS

Winner's Curse Correction and Variable Thresholding Improve Performance of Polygenic Risk Modeling Based on Genome-Wide Association Study Summary-Level Data

(2016) Jianxin Shi et al.   PLoS Genetics

Meuwissen et al. on Genomic Selection

(2016) Dirk-Jan de Koning   GENETICS

Joint Analysis of Psychiatric Disorders Increases Accuracy of Risk Prediction for Schizophrenia, Bipolar Disorder, and Major Depressive Disorder

(2015) Robert Maier et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores

(2015) Bjarni J. Vilhjálmsson et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project

(2015) Latarsha J. Carithers et al.   BIOPRESERVATION AND BIOBANKING

Genomic risk prediction of complex human disease and its clinical application

(2015) Gad Abraham et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Genetic variance estimation with imputed variants finds negligible missing heritability for human height and body mass index

(2015) Jian Yang et al.   NATURE GENETICS

Partitioning heritability by functional annotation using genome-wide association summary statistics

(2015) Hilary K Finucane et al.   NATURE GENETICS

An atlas of genetic correlations across human diseases and traits

(2015) Brendan Bulik-Sullivan et al.   NATURE GENETICS

LD Score regression distinguishes confounding from polygenicity in genome-wide association studies

(2015) Brendan K Bulik-Sullivan et al.   NATURE GENETICS

Somatic mutation in cancer and normal cells

(2015) I. Martincorena et al.   SCIENCE

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project

(2015) Latarsha J. Carithers et al.   Biopreservation and Biobanking

A Flexible, Efficient Binomial Mixed Model for Identifying Differential DNA Methylation in Bisulfite Sequencing Data

(2015) Amanda J. Lea et al.   PLoS Genetics

Simultaneous Discovery, Estimation and Prediction Analysis of Complex Traits Using a Bayesian Mixture Model

(2015) Gerhard Moser et al.   PLoS Genetics

Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases

(2014) Alexander Gusev et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Joint Analysis of Functional Genomic Data and Genome-wide Association Studies of 18 Human Traits

(2014) Joseph K. Pickrell   AMERICAN JOURNAL OF HUMAN GENETICS

PRSice: Polygenic Risk Score software

(2014) Jack Euesden et al.   BIOINFORMATICS

MultiBLUP: improved SNP-based prediction for complex traits

(2014) Doug Speed et al.   GENOME RESEARCH

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

Efficient multivariate linear mixed model algorithms for genome-wide association studies

(2014) Xiang Zhou et al.   NATURE METHODS

Measuring missing heritability: Inferring the contribution of common variants

(2014) David Golan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Defining functional DNA elements in the human genome

(2014) M. Kellis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Explaining additional genetic variation in complex traits

(2014) Matthew R. Robinson et al.   TRENDS IN GENETICS

Integrating Functional Data to Prioritize Causal Variants in Statistical Fine-Mapping Studies

(2014) Gleb Kichaev et al.   PLoS Genetics

Data augmentation for non-Gaussian regression models using variance-mean mixtures

(2013) N. G. Polson et al.   BIOMETRIKA

Improving genetic risk prediction by leveraging pleiotropy

(2013) Cong Li et al.   HUMAN GENETICS

Projecting the performance of risk prediction based on polygenic analyses of genome-wide association studies

(2013) Nilanjan Chatterjee et al.   NATURE GENETICS

Pitfalls of predicting complex traits from SNPs

(2013) Naomi R. Wray et al.   NATURE REVIEWS GENETICS

Correction: Power and Predictive Accuracy of Polygenic Risk Scores

(2013) Frank Dudbridge   PLoS Genetics

Polygenic Modeling with Bayesian Sparse Linear Mixed Models

(2013) Xiang Zhou et al.   PLoS Genetics

Five Years of GWAS Discovery

(2012) Peter M. Visscher et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Multiple-Trait Genomic Selection Methods Increase Genetic Value Prediction Accuracy

(2012) Yi Jia et al.   GENETICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Genome-wide efficient mixed-model analysis for association studies

(2012) Xiang Zhou et al.   NATURE GENETICS

Risk Prediction of Complex Diseases from Family History and Known Susceptibility Loci, with Applications for Cancer Screening

(2011) Hon-Cheong So et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Estimating Missing Heritability for Disease from Genome-wide Association Studies

(2011) Sang Hong Lee et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Bayesian variable selection regression for genome-wide association studies and other large-scale problems

(2011) Yongtao Guan et al.   Annals of Applied Statistics

Extension of the bayesian alphabet for genomic selection

(2011) David Habier et al.   BMC BIOINFORMATICS

Genetic risk prediction in complex disease

(2011) Luke Jostins et al.   HUMAN MOLECULAR GENETICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

Genotype Imputation with Thousands of Genomes

(2011) Bryan Howie et al.   G3-Genes Genomes Genetics

Beyond Missing Heritability: Prediction of Complex Traits

(2011) Robert Makowsky et al.   PLoS Genetics

Evidence for Polygenic Susceptibility to Multiple Sclerosis—The Shape of Things to Come

(2010)   AMERICAN JOURNAL OF HUMAN GENETICS

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Common SNPs explain a large proportion of the heritability for human height

(2010) Jian Yang et al.   NATURE GENETICS

Genetic Architecture of Complex Traits and Accuracy of Genomic Prediction: Coat Colour, Milk-Fat Percentage, and Type in Holstein Cattle as Contrasting Model Traits

(2010) Ben J. Hayes et al.   PLoS Genetics

Predicting Quantitative Traits With Regression Models for Dense Molecular Markers and Pedigree

(2009) G. de los Campos et al.   GENETICS

Accuracy of genomic selection using stochastic search variable selection in Australian Holstein Friesian dairy cattle

(2009) KLARA L. VERBYLA et al.   Genetics Research

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

Common polygenic variation contributes to risk of schizophrenia and bipolar disorder

(2009) Shaun M. Purcell et al.   NATURE

Human genetic variation and its contribution to complex traits

(2009) Kelly A. Frazer et al.   NATURE REVIEWS GENETICS

The Bayesian Lasso

(2008) Trevor Park et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Genome-wide association studies for complex traits: consensus, uncertainty and challenges

(2008) Mark I. McCarthy et al.   NATURE REVIEWS GENETICS

Heritability in the genomics era — concepts and misconceptions

(2008) Peter M. Visscher et al.   NATURE REVIEWS GENETICS

Genetic architecture of complex traits: Large phenotypic effects and pervasive epistasis

(2008) H. Shao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simultaneous Analysis of All SNPs in Genome-Wide and Re-Sequencing Association Studies

(2008) Clive J. Hoggart et al.   PLoS Genetics