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Deutelmoser, H.* ; Scherer, D.* ; Brenner, H.* ; Waldenberger, M. ; Suhre, K.* ; Kastenmüller, G. ; Lorenzo Bermejo, J.*

Robust Huber-LASSO for improved prediction of protein, metabolite and gene expression levels relying on individual genotype data.

Brief. Bioinform. 22:bbaa230 (2021)
Verlagsversion DOI PMC
Open Access Gold (Paid Option)
Creative Commons Lizenzvertrag
Least absolute shrinkage and selection operator (LASSO) regression is often applied to select the most promising set of single nucleotide polymorphisms (SNPs) associated with a molecular phenotype of interest. While the penalization parameter λ restricts the number of selected SNPs and the potential model overfitting, the least-squares loss function of standard LASSO regression translates into a strong dependence of statistical results on a small number of individuals with phenotypes or genotypes divergent from the majority of the study population-typically comprised of outliers and high-leverage observations. Robust methods have been developed to constrain the influence of divergent observations and generate statistical results that apply to the bulk of study data, but they have rarely been applied to genetic association studies. In this article, we review, for newcomers to the field of robust statistics, a novel version of standard LASSO that utilizes the Huber loss function. We conduct comprehensive simulations and analyze real protein, metabolite, mRNA expression and genotype data to compare the stability of penalization, the cross-iteration concordance of the model, the false-positive and true-positive rates and the prediction accuracy of standard and robust Huber-LASSO. Although the two methods showed controlled false-positive rates ≤2.1% and similar true-positive rates, robust Huber-LASSO outperformed standard LASSO in the accuracy of predicted protein, metabolite and gene expression levels using individual SNP data. The conducted simulations and real-data analyses show that robust Huber-LASSO represents a valuable alternative to standard LASSO in genetic studies of molecular phenotypes.
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Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
Korrespondenzautor
Schlagwörter Huber Loss Function ; Lasso ; Genetic Prediction ; Molecular Data ; Robust Statistics; Regression; Association; Selection; Atlas
ISSN (print) / ISBN 1467-5463
e-ISSN 1477-4054
Zeitschrift Briefings in Bioinformatics
Quellenangaben Band: 22, Heft: 4, Seiten: , Artikelnummer: bbaa230 Supplement: ,
Verlag Oxford University Press
Verlagsort Great Clarendon St, Oxford Ox2 6dp, England
Nichtpatentliteratur Publikationen
Begutachtungsstatus Peer reviewed
Institut(e) Institute of Epidemiology II (EPI2)
Institute of Computational Biology (ICB)
Förderungen National Institute on Aging
Biomedical Research Program at Weill Cornell Medicine in Qatar, a program funded by the Qatar Foundation
European Union's Horizon 2020 research and innovation programme
Federal Ministry of Education and Research Germany (Bundesministerium fur Bildung und Forschung, BMBF)