Power of grammatical evolution neural networks to detect gene-gene interactions in the presence of error.

BMC Research Notes
Alison A Motsinger-ReifMarylyn D Ritchie

Abstract

With the advent of increasingly efficient means to obtain genetic information, a great insurgence of data has resulted, leading to the need for methods for analyzing this data beyond that of traditional parametric statistical approaches. Recently we introduced Grammatical Evolution Neural Network (GENN), a machine-learning approach to detect gene-gene or gene-environment interactions, also known as epistasis, in high dimensional genetic epidemiological data. GENN has been shown to be highly successful in a range of simulated data, but the impact of error common to real data is unknown. In the current study, we examine the power of GENN to detect interesting interactions in the presence of noise due to genotyping error, missing data, phenocopy, and genetic heterogeneity. Additionally, we compare the performance of GENN to that of another computational method - Multifactor Dimensionality Reduction (MDR). GENN is extremely robust to missing data and genotyping error. Phenocopy in a dataset reduces the power of both GENN and MDR. GENN is reasonably robust to genetic heterogeneity and find that in some cases GENN has substantially higher power than MDR to detect functional loci in the presence of genetic heterogeneity. GENN is a pro...Continue Reading

References

Jul 11, 2002·Annals of Medicine·Jason H Moore, Scott M Williams
Nov 4, 2004·Trends in Genetics : TIG·Tricia A Thornton-WellsJonathan L Haines
Jul 27, 2007·Genetic Epidemiology·Marylyn D RitchieAlison A Motsinger
Oct 11, 2007·Pharmacogenomics·Alison A MotsingerDavid M Reif
Feb 1, 2004·Applied Soft Computing·Jason H MooreBill C White
Jul 19, 2011·Artificial Life·X Rosalind WangMikhail Prokopenko

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Citations

Dec 17, 2011·BMC Bioinformatics·Junliang ShangYaling Yin
Dec 25, 2009·BMC Genetics·Frauke GüntherKarin Bammann
Mar 12, 2010·Expert Review of Clinical Pharmacology·Stephen D TurnerMarylyn D Ritchie
Aug 3, 2012·Drug and Alcohol Dependence·R H C PalmerV S Knopik
Jun 19, 2008·Genetic Epidemiology·Alison A Motsinger-ReifMarylyn D Ritchie
Jun 27, 2009·IEEE Transactions on Information Technology in Biomedicine : a Publication of the IEEE Engineering in Medicine and Biology Society·Arpad KelemenYulan Liang
Nov 15, 2013·BioMed Research International·Ching Lee KooAbdul Hakim Mohamed Salleh
Sep 30, 2008·BioData Mining·Alison A Motsinger-Reif, Marylyn D Ritchie
Aug 6, 2010·PloS One·Francesco Lescai, Claudio Franceschi

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Methods Mentioned

BETA
genotyping

Software Mentioned

MDR
GENN

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