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

Research output: Contribution to journalArticlepeer-review

243 Scopus citations

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 2010

Bibliographical note

Funding Information:
Data analysis was supported in part by the following grants from the National Institutes of Health : NIA R01 AG19771 to A.J.S. and P30 AG10133 to Bernardino Ghetti, MD and NIBIB R03 EB008674 to L.S., by the Indiana Economic Development Corporation (IEDC 87884 to AJS), by Foundation for the NIH to A.J.S., and by an Indiana CTSI award to L.S.

Funding Information:
Data collection and sharing for this project were funded by the Alzheimer's Disease Neuroimaging Initiative (ADNI; principal investigator: Michael Weiner; NIH grant U01 AG024904 ). ADNI is funded by the National Institute on Aging, the National Institute of Biomedical Imaging and Bioengineering (NIBIB), and through generous contributions from the following: Pfizer Inc., Wyeth Research, Bristol-Myers Squibb, Eli Lilly and Company, GlaxoSmithKline, Merck & Co. Inc., AstraZeneca AB, Novartis Pharmaceuticals Corporation, Alzheimer's Association, Eisai Global Clinical Development, Elan Corporation plc, Forest Laboratories, and the Institute for the Study of Aging, with participation from the U.S. Food and Drug Administration. Industry partnerships are coordinated through the Foundation for the National Institutes of Health. The grantee organization is the Northern California Institute for Research and Education, and the study is coordinated by the Alzheimer's Disease Cooperative Study at the University of California, San Diego. ADNI data are disseminated by the Laboratory of Neuro Imaging at the University of California, Los Angeles.

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