title: An application of the elastic net for an endophenotype analysis.
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.
authors.affiliation: Yale University, New Haven, CT, USA.
authors.forename: Dean
authors.initials: D
authors.lastname: Palejev
authors.forename: Wookyeon
authors.initials: W
authors.lastname: Hwang
authors.forename: Nicole
authors.initials: N
authors.lastname: Landi
authors.forename: Maria
authors.initials: M
authors.lastname: Eastman
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Frost
authors.forename: Robert K
authors.initials: RK
authors.lastname: Fulbright
authors.forename: Judith R
authors.initials: JR
authors.lastname: Kidd
authors.forename: Kenneth K
authors.initials: KK
authors.lastname: Kidd
authors.forename: Graeme F
authors.initials: GF
authors.lastname: Mason
authors.forename: W Einar
authors.initials: WE
authors.lastname: Mencl
authors.forename: Carolyn
authors.initials: C
authors.lastname: Yrigollen
authors.forename: Kenneth R
authors.initials: KR
authors.lastname: Pugh
authors.forename: Elena L
authors.initials: EL
authors.lastname: Grigorenko
mesh_terms: D000465:Algorithms; D002648:Child; D002884:Chromosomes, Human, Pair 15 / Q000235:genetics; D002890:Chromosomes, Human, Pair 20 / Q000235:genetics; D004410:Dyslexia / Q000235:genetics* / Q000503:physiopathology*; D058068:Endophenotypes; D005260:Female; D014644:Genetic Variation / Q000235:genetics*; D055106:Genome-Wide Association Study / Q000706:statistics & numerical data*; D005838:Genotype; D006801:Humans; D009682:Magnetic Resonance Spectroscopy; D008297:Male; D008957:Models, Genetic; D009778:Occipital Lobe / Q000503:physiopathology; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D005680:gamma-Aminobutyric Acid / Q000378:metabolism*
chemical_list: D005680:gamma-Aminobutyric Acid