Discovery and replication of gene influences on brain structure using LASSO regression

Kohannim, O., Hibar, D. P., Stein, J. L., Jahansha, N., Hua, X., Rajagopalan, P., Toga, A. W., Jack Jr, C. R., Weiner, M. W., de Zubicaray, Greig I., McMahon, K. L., Hansell, N. K., Martin, N. G., Wright, M. J., & Thompson, P. M. (2012) Discovery and replication of gene influences on brain structure using LASSO regression. Frontiers in Neuroscience, 6, p. 115.

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We implemented least absolute shrinkage and selection operator (LASSO) regression to evaluate gene effects in genome-wide association studies (GWAS) of brain images, using an MRI-derived temporal lobe volume measure from 729 subjects scanned as part of the Alzheimer's Disease Neuroimaging Initiative (ADNI). Sparse groups of SNPs in individual genes were selected by LASSO, which identifies efficient sets of variants influencing the data. These SNPs were considered jointly when assessing their association with neuroimaging measures. We discovered 22 genes that passed genome-wide significance for influencing temporal lobe volume. This was a substantially greater number of significant genes compared to those found with standard, univariate GWAS. These top genes are all expressed in the brain and include genes previously related to brain function or neuropsychiatric disorders such as MACROD2, SORCS2, GRIN2B, MAGI2, NPAS3, CLSTN2, GABRG3, NRXN3, PRKAG2, GAS7, RBFOX1, ADARB2, CHD4, and CDH13. The top genes we identified with this method also displayed significant and widespread post hoc effects on voxelwise, tensor-based morphometry (TBM) maps of the temporal lobes. The most significantly associated gene was an autism susceptibility gene known as MACROD2.We were able to successfully replicate the effect of the MACROD2 gene in an independent cohort of 564 young, Australian healthy adult twins and siblings scanned with MRI (mean age: 23.8±2.2 SD years). Our approach powerfully complements univariate techniques in detecting influences of genes on the living brain.

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37 citations in Scopus
26 citations in Web of Science®
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ID Code: 85799
Item Type: Journal Article
Refereed: No
Keywords: GWAS, Imaging genetics, LASSO, MACROD2, MRI, Neuroimaging
DOI: 10.3389/fnins.2012.00115
ISSN: 1662-453X
Divisions: Current > QUT Faculties and Divisions > Faculty of Health
Current > Institutes > Institute of Health and Biomedical Innovation
Copyright Owner: Copyright 2012 Kohannim, Hibar, Stein, Jahanshad, Hua, Rajagopalan, Toga, Jack, Weiner, de Zubicaray, McMahon, Hansell, Martin, Wright, Thompson and The Alzheimer’s Disease Neuroimaging Initiative
Copyright Statement: This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and subject to any copyright notices concerning any third-party graphics etc.
Deposited On: 04 Sep 2015 01:24
Last Modified: 14 Sep 2015 08:08

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