Abstract
We provide an illustration of an application of the elastic net to a large number of common genetic variants in the context of the search for the genetic bases of an endophenotype conceivably related to individual differences in learning. GABA concentration in the occipital cortex, a critical area for reading, was obtained in a group (n = 76) of children aged 6–10 years. Two extreme groups, high and low, were selected for genotyping with the 650Y Illumina array chip (Ilmn650Y). An elastic net approach was applied to the resulting SNP dataset; 100 SNPs were identified for each chromosome as “interesting” based on having the highest absolute value coefficients. The analyses highlighted chromosomes 15 and 20, which contained 55 candidate genes. The STRING partner analyses of the associated proteins pointed to a number of related genes, most notably, GABA and NTRK receptors.
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Acknowledgements
Preparation of this article was supported in part by the following research grants from the National Institutes of Health: HD048830, HD001994, HD053409, AA009379, GM057672, HD052120, DC007665, and TW008274. Grantees undertaking such projects are encouraged to express their professional judgment freely. Therefore, this article does not necessarily reflect the position or policies of the National Institutes of Health, and no official endorsement should be inferred. We are thankful to Ms. Mei Tan for her editorial assistance.
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Palejev, D., Hwang, W., Landi, N. et al. An Application of the Elastic Net for an Endophenotype Analysis. Behav Genet 41, 120–124 (2011). https://doi.org/10.1007/s10519-011-9443-8
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DOI: https://doi.org/10.1007/s10519-011-9443-8