(1=Married; 2=Widowed; 3=Divorced; 4=Never married), Education length, Retirement (1=Yes; 0=No), and Age. Since Marital Status has four levels, we included three dummy variables. We also included the APOE4 genotype, which has two alleles, as studies have shown that the APOE4 genotypes have significant effect in MCI. The first allele has three genotypes: 2, 3, 4, thus we included two dummy variables for this allele. The second allele has only two genotypes: 3 and 4, so one dummy variable was needed. We also include the ADAS-Cog score, which is a composite score of 11 questions to reflect the severity of AD. In addition, we selected ROIs among the 93 ROI volume data from the Jacob atlas.21 We chose 23 ROIs which may significantly influence MCI progression.10,22,23 The 23 ROIs were bilateral entorhinal cortices, bilateral hippocampal formation, bilateral amygdala, bilateral caudate nuclei, bilateral putamen, bilateral posterior limb of internal capsule including cerebral peduncle, bilateral nucleus accumbens, bilateral lateral ventricles, bilateral thalamus, bilateral fornix, bilateral cingulate and the corpus callosum. Finally, we included information from all the 22 chromosomes. each chromosome contains a number of SNPs, we used principal component analysis for each chromosome and picked the first 2 principal components for each chromosome. We then used the PLINK package ( http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#plink) to perform the principal component analysis for each chromosome. => We then used the PLINK package ( http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#plink) to perform quality control for the genomic data. The principal component analysis for each chromosome was conducted using function in R software. “svd” Hippocampus Preprocessing We adopted a surface fluid registration based hippocampal subregional analysis package,24 which uses isothermal coordinates and fluid registration to generate one-to-one
(1=Married; 2=Widowed; 3=Divorced; 4=Never married), Education length, Retirement (1=Yes; 0=No), and Age. Since Marital Status has four levels, we included three dummy variables. We also included the APOE4 genotype, which has two alleles, as studies have shown that the APOE4 genotypes have significant effect in MCI. The first allele has three genotypes: 2, 3, 4, thus we included two dummy variables for this allele. The second allele has only two genotypes: 3 and 4, so one dummy variable was needed. We also include the ADAS-Cog score, which is a composite score of 11 questions to reflect the severity of AD. In addition, we selected ROIs among the 93 ROI volume data from the Jacob atlas.21 We chose 23 ROIs which may significantly influence MCI progression.10,22,23 The 23 ROIs were bilateral entorhinal cortices, bilateral hippocampal formation, bilateral amygdala, bilateral caudate nuclei, bilateral putamen, bilateral posterior limb of internal capsule including cerebral peduncle, bilateral nucleus accumbens, bilateral lateral ventricles, bilateral thalamus, bilateral fornix, bilateral cingulate and the corpus callosum. Finally, we included information from all the 22 chromosomes. each chromosome contains a number of SNPs, we used principal component analysis for each chromosome and picked the first 2 principal components for each chromosome. We then used the PLINK package ( http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#plink) to perform the principal component analysis for each chromosome. => We then used the PLINK package ( http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#plink) to perform quality control for the genomic data. The principal component analysis for each chromosome was conducted using “svd” function in R software. Hippocampus Preprocessing We adopted a surface fluid registration based hippocampal subregional analysis package,24 which uses isothermal coordinates and fluid registration to generate one-to-one
Molecular_Psychiatry_07212014-3.docx