Integrative genetic risk prediction using non-parametric empirical Bayes classification

DOI10.1111/BIOM.12619zbMATH Open1372.62090arXiv1607.06976OpenAlexW2509807924WikidataQ39238156 ScholiaQ39238156MaRDI QIDQ5283313FDOQ5283313

Authors: Sihai Dave Zhao 

Publication date: 21 July 2017

Published in: Biometrics (Search for Journal in Brave)

Abstract: Genetic risk prediction is an important component of individualized medicine, but prediction accuracies remain low for many complex diseases. A fundamental limitation is the sample sizes of the studies on which the prediction algorithms are trained. One way to increase the effective sample size is to integrate information from previously existing studies. However, it can be difficult to find existing data that examine the target disease of interest, especially if that disease is rare or poorly studied. Furthermore, individual-level genotype data from these auxiliary studies are typically difficult to obtain. This paper proposes a new approach to integrative genetic risk prediction of complex diseases with binary phenotypes. It accommodates possible heterogeneity in the genetic etiologies of the target and auxiliary diseases using a tuning parameter-free nonparametric empirical Bayes procedure, and can be trained using only auxiliary summary statistics. Simulation studies show that the proposed method can provide superior predictive accuracy relative to non-integrative as well as integrative classifiers. The method is applied to a recent study of pediatric autoimmune diseases, where it substantially reduces prediction error for certain target/auxiliary disease combinations. The proposed method is implemented in the R package ssa.

Full work available at URL: https://arxiv.org/abs/1607.06976

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zbMATH Keywords

empirical Bayesnonparametric maximum likelihoodGWAShigh-dimensional classificationintegrative genomicsgenetic risk prediction

Mathematics Subject Classification ID

Nonparametric estimation (62G05) Classification and discrimination; cluster analysis (statistical aspects) (62H30) Applications of statistics to biology and medical sciences; meta analysis (62P10) Empirical decision procedures; empirical Bayes procedures (62C12)

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Cited In (14)

• Something Borrowed, Something New: Precise Prediction of Outcomes from Diverse Genomic Profiles
• Title not available (Why is that?)
• An empirical Bayes risk prediction model using multiple traits for sequencing data
• A weighted empirical Bayes risk prediction model using multiple traits
• Jackknife model averaging prediction methods for complex phenotypes with gene expression levels by integrating external pathway information
• An intuitive risk factors search algorithm: usage of the Bayesian network technique in personalized medicine
• Risk classification with an adaptive naive Bayes kernel machine model
• Simultaneous estimation of normal means with side information
• Multi-modal genotype and phenotype mutual learning to enhance single-modal input based longitudinal outcome prediction
• Structure-leveraged methods in breast cancer risk prediction
• Structure-leveraged methods in breast cancer risk prediction
• Kernel Machine Approach to Testing the Significance of Multiple Genetic Markers for Risk Prediction
• Risk scores and their predictive ability for common complex diseases
• Title not available (Why is that?)

Uses Software

• R
• PLINK
• saa
• REBayes
• LDpred
• LDAK

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