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

Omid Kohannim, Derrek P. Hibar, Jason L. Stein, Neda Jahansha, Xue Hua, Priya Rajagopalan, Arthur W. Toga, Clifford R Jr. Jack, Michael W. Weiner, Greig I. de Zubicaray, Katie L. McMahon, Narelle K. Hansell, Nicholas G. Martin, Margaret J. Wright, Paul M. Thompson

Research output: Contribution to journalArticle

56 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Article numberArticle 115
JournalFrontiers in Neuroscience
Issue numberAUG
DOIs
StatePublished - 2012

Fingerprint

Genetic Association Studies
Brain
Genes
Temporal Lobe
Genome-Wide Association Study
Neuroimaging
Single Nucleotide Polymorphism
Autistic Disorder
Siblings
Alzheimer Disease
Genome

Keywords

  • GWAS
  • Imaging genetics
  • LASSO
  • MACROD2
  • MRI
  • Neuroimaging

ASJC Scopus subject areas

  • Neuroscience(all)

Cite this

Kohannim, O., Hibar, D. P., Stein, J. L., Jahansha, N., Hua, X., Rajagopalan, P., ... Thompson, P. M. (2012). Discovery and replication of gene influences on brain structure using LASSO regression. Frontiers in Neuroscience, (AUG), [Article 115]. https://doi.org/10.3389/fnins.2012.00115

Discovery and replication of gene influences on brain structure using LASSO regression. / Kohannim, Omid; Hibar, Derrek P.; Stein, Jason L.; Jahansha, Neda; Hua, Xue; Rajagopalan, Priya; Toga, Arthur W.; Jack, Clifford R Jr.; Weiner, Michael W.; de Zubicaray, Greig I.; McMahon, Katie L.; Hansell, Narelle K.; Martin, Nicholas G.; Wright, Margaret J.; Thompson, Paul M.

In: Frontiers in Neuroscience, No. AUG, Article 115, 2012.

Research output: Contribution to journalArticle

Kohannim, O, Hibar, DP, Stein, JL, Jahansha, N, Hua, X, Rajagopalan, P, Toga, AW, Jack, CRJ, Weiner, MW, de Zubicaray, GI, McMahon, KL, Hansell, NK, Martin, NG, Wright, MJ & Thompson, PM 2012, 'Discovery and replication of gene influences on brain structure using LASSO regression', Frontiers in Neuroscience, no. AUG, Article 115. https://doi.org/10.3389/fnins.2012.00115
Kohannim O, Hibar DP, Stein JL, Jahansha N, Hua X, Rajagopalan P et al. Discovery and replication of gene influences on brain structure using LASSO regression. Frontiers in Neuroscience. 2012;(AUG). Article 115. https://doi.org/10.3389/fnins.2012.00115
Kohannim, Omid ; Hibar, Derrek P. ; Stein, Jason L. ; Jahansha, Neda ; Hua, Xue ; Rajagopalan, Priya ; Toga, Arthur W. ; Jack, Clifford R Jr. ; Weiner, Michael W. ; de Zubicaray, Greig I. ; McMahon, Katie L. ; Hansell, Narelle K. ; Martin, Nicholas G. ; Wright, Margaret J. ; Thompson, Paul M. / Discovery and replication of gene influences on brain structure using LASSO regression. In: Frontiers in Neuroscience. 2012 ; No. AUG.
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