Assessing models for genetic prediction of complex traits : a comparison of visualization and quantitative methods

Gagliano, Sarah A. and Paterson, Andrew D. and Weale, Michael E. and Knight, Jo (2015) Assessing models for genetic prediction of complex traits : a comparison of visualization and quantitative methods. BMC Genomics, 16: 405. ISSN 1471-2164

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BACKGROUND: In silico models have recently been created in order to predict which genetic variants are more likely to contribute to the risk of a complex trait given their functional characteristics. However, there has been no comprehensive review as to which type of predictive accuracy measures and data visualization techniques are most useful for assessing these models. METHODS: We assessed the performance of the models for predicting risk using various methodologies, some of which include: receiver operating characteristic (ROC) curves, histograms of classification probability, and the novel use of the quantile-quantile plot. These measures have variable interpretability depending on factors such as whether the dataset is balanced in terms of numbers of genetic variants classified as risk variants versus those that are not. RESULTS: We conclude that the area under the curve (AUC) is a suitable starting place, and for models with similar AUCs, violin plots are particularly useful for examining the distribution of the risk scores.

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Journal Article
Journal or Publication Title:
BMC Genomics
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© 2015 Gagliano et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.
?? algorithmsarea under curvecomputer simulationdatabases, geneticgenome, humanhumansmodels, geneticquantitative trait lociroc curverisk ??
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08 Jun 2016 09:34
Last Modified:
31 Dec 2023 00:42