Whole genome association study of brain-wide imaging phenotypes for identifying quantitative trait loci in MCI and AD: A study of the ADNI cohort

Li Shen, Sungeun Kim, Shannon L. Risacher, Kwangsik Nho, Shanker Swaminathan, John D. West, Tatiana Foroud, Nathan Pankratz, Jason H. Moore, Chantel D. Sloan, Matthew J. Huentelman, David W. Craig, Bryan M. DeChairo, Steven G. Potkin, Clifford R. Jack, Michael W. Weiner, Andrew J. Saykin

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Abstract

A genome-wide, whole brain approach to investigate genetic effects on neuroimaging phenotypes for identifying quantitative trait loci is described. The Alzheimer's Disease Neuroimaging Initiative 1.5 T MRI and genetic dataset was investigated using voxel-based morphometry (VBM) and FreeSurfer parcellation followed by genome-wide association studies (GWAS). One hundred forty-two measures of grey matter (GM) density, volume, and cortical thickness were extracted from baseline scans. GWAS, using PLINK, were performed on each phenotype using quality-controlled genotype and scan data including 530,992 of 620,903 single nucleotide polymorphisms (SNPs) and 733 of 818 participants (175 AD, 354 amnestic mild cognitive impairment, MCI, and 204 healthy controls, HC). Hierarchical clustering and heat maps were used to analyze the GWAS results and associations are reported at two significance thresholds (p<10-7 and p<10-6). As expected, SNPs in the APOE and TOMM40 genes were confirmed as markers strongly associated with multiple brain regions. Other top SNPs were proximal to the EPHA4, TP63 and NXPH1 genes. Detailed image analyses of rs6463843 (flanking NXPH1) revealed reduced global and regional GM density across diagnostic groups in TT relative to GG homozygotes. Interaction analysis indicated that AD patients homozygous for the T allele showed differential vulnerability to right hippocampal GM density loss. NXPH1 codes for a protein implicated in promotion of adhesion between dendrites and axons, a key factor in synaptic integrity, the loss of which is a hallmark of AD. A genome-wide, whole brain search strategy has the potential to reveal novel candidate genes and loci warranting further investigation and replication.

Original languageEnglish (US)
Pages (from-to)1051-1063
Number of pages13
JournalNeuroImage
Volume53
Issue number3
DOIs
StatePublished - Nov 1 2010

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Quantitative Trait Loci
Genome-Wide Association Study
Neuroimaging
Single Nucleotide Polymorphism
Cohort Studies
Phenotype
Brain
Genome
Genes
Homozygote
Dendrites
Cluster Analysis
Axons
Alzheimer Disease
Hot Temperature
Alleles
Genotype
Gray Matter
Proteins

ASJC Scopus subject areas

  • Neurology
  • Cognitive Neuroscience

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Whole genome association study of brain-wide imaging phenotypes for identifying quantitative trait loci in MCI and AD : A study of the ADNI cohort. / Shen, Li; Kim, Sungeun; Risacher, Shannon L.; Nho, Kwangsik; Swaminathan, Shanker; West, John D.; Foroud, Tatiana; Pankratz, Nathan; Moore, Jason H.; Sloan, Chantel D.; Huentelman, Matthew J.; Craig, David W.; DeChairo, Bryan M.; Potkin, Steven G.; Jack, Clifford R.; Weiner, Michael W.; Saykin, Andrew J.

In: NeuroImage, Vol. 53, No. 3, 01.11.2010, p. 1051-1063.

Research output: Contribution to journalArticle

Shen, L, Kim, S, Risacher, SL, Nho, K, Swaminathan, S, West, JD, Foroud, T, Pankratz, N, Moore, JH, Sloan, CD, Huentelman, MJ, Craig, DW, DeChairo, BM, Potkin, SG, Jack, CR, Weiner, MW & Saykin, AJ 2010, 'Whole genome association study of brain-wide imaging phenotypes for identifying quantitative trait loci in MCI and AD: A study of the ADNI cohort', NeuroImage, vol. 53, no. 3, pp. 1051-1063. https://doi.org/10.1016/j.neuroimage.2010.01.042
Shen, Li ; Kim, Sungeun ; Risacher, Shannon L. ; Nho, Kwangsik ; Swaminathan, Shanker ; West, John D. ; Foroud, Tatiana ; Pankratz, Nathan ; Moore, Jason H. ; Sloan, Chantel D. ; Huentelman, Matthew J. ; Craig, David W. ; DeChairo, Bryan M. ; Potkin, Steven G. ; Jack, Clifford R. ; Weiner, Michael W. ; Saykin, Andrew J. / Whole genome association study of brain-wide imaging phenotypes for identifying quantitative trait loci in MCI and AD : A study of the ADNI cohort. In: NeuroImage. 2010 ; Vol. 53, No. 3. pp. 1051-1063.
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