Hippocampal atrophy as a quantitative trait in a genome-wide association study identifying novel susceptibility genes for Alzheimer's disease

Potkin, Steven G.; Guffanti, Guia; Lakatos, Anita; Turner, Jessica A.; Kruggel, Frithjof; Fallon, James H.; Saykin, Andrew J.; Orro, Alessandro; Lupoli, Sara; Salvi, Erika; Weiner, Michael; Macciardi, Fabio; for the Alzheimer's Disease Neuroimaging Initiative

doi:10.1371/journal.pone.0006501

Cited by 376Alzheimer's disease research and treatmentsDementia and Cognitive Impairment ResearchGenetic Associations and Epidemiology

Hippocampal atrophy as a quantitative trait in a genome-wide association study identifying novel susceptibility genes for Alzheimer's disease

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Potkin, Steven G., Guffanti, Guia, Lakatos, Anita, Turner, Jessica A., Kruggel, Frithjof, Fallon, James H., Saykin, Andrew J., Orro, Alessandro +5 more·2009·PLoS ONE

DOI 10.1371/journal.pone.0006501PMC PMC2719581

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Abstract

BACKGROUND: With the exception of APOE epsilon4 allele, the common genetic risk factors for sporadic Alzheimer's Disease (AD) are unknown. METHODS AND FINDINGS: We completed a genome-wide association study on 381 participants in the ADNI (Alzheimer's Disease Neuroimaging Initiative) study. Samples were genotyped using the Illumina Human610-Quad BeadChip. 516,645 unique Single Nucleotide Polymorphisms (SNPs) were included in the analysis following quality control measures. The genotype data and raw genetic data are freely available for download (LONI, http://www.loni.ucla.edu/ADNI/Data/). Two analyses were completed: a standard case-control analysis, and a novel approach using hippocampal atrophy measured on MRI as an objectively defined, quantitative phenotype. A General Linear Model was applied to identify SNPs for which there was an interaction between the genotype and diagnosis on the quantitative trait. The case-control analysis identified APOE and a new risk gene, TOMM40 (translocase of outer mitochondrial membrane 40), at a genome-wide significance level of < or =10(-6) (10(-11) for a haplotype). TOMM40 risk alleles were approximately twice as frequent in AD subjects as controls. The quantitative trait analysis identified 21 genes or chromosomal areas with at least one SNP with a p-value < or =10(-6), which can be considered potential "new" candidate loci to explore in the etiology of sporadic AD. These candidates included EFNA5, CAND1, MAGI2, ARSB, and PRUNE2, genes involved in the regulation of protein degradation, apoptosis, neuronal loss and neurodevelopment. Thus, we identified common genetic variants associated with the increased risk of developing AD in the ADNI cohort, and present publicly available genome-wide data. Supportive evidence based on case-control studies and biological plausibility by gene annotation is provided. Currently no available sample with both imaging and genetic data is available for replication. CONCLUSIONS: Using hippocampal atrophy as a quantitative phenotype in a genome-wide scan, we have identified candidate risk genes for sporadic Alzheimer's disease that merit further investigation.

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The TOMM40 gene, and by extension its protein product, could potentially impact LOAD.
“from a strict association perspective it does appear that the TOMM40 gene, and by extension its protein product, could potentially impact LOAD.”
From The Alzheimer’s disease mitochondrial cascade hypothesis: progress and perspectives (2014) · cites this paper as [148]
A large number of novel loci and genes have been nominated by imaging GWAS analyses.
“a large number of novel loci and genes have been nominated by these analyses [222, 229–231]”
From Genetic architecture of Alzheimer's disease (2020) · cites this paper as [230]

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Retracted
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“…previously implicated in AD (including APOE and PICALM (Furney et al., 2011)) have been associated with imaging endophenotypes, a large number of novel loci and genes have been nominated by these analyses (Risacher et al., 2009; Furney et al., 2011; Potkin et al., 2009; Stein et al., 2010) (Fig.”
Background
A large scale multivariate parallel ICA method reveals novel imaging–genetic relationships for Alzheimer's disease in the ADNI cohort
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Journal of Parkinson’s disease & Alzheimer’s disease
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Hippocampal atrophy as a quantitative trait in a genome-wide association study identifying novel susceptibility genes for alzheimer's disease. PLoS One 40
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Authors: Potkin, S. G., Guffanti, G., Lakatos, A., Turner, J. A., Kruggel, F., Fallon, J. H., Saykin, A. J., Orro, A., Lupoli, S., Salvi, E., Weiner, M., Macciardi, F., & Initiative, F. T. A. D. N.
Affiliations: University of California, Irvine (US)
University of Milan (IT)
Indiana University Indianapolis (US)
Institute of Biomedical Technologies (IT)
Vita-Salute San Raffaele University (IT)
University of California, San Francisco (US)
Corresponding author: Potkin, Steven G.
ORCID: Potkin, Steven G.
Lakatos, Anita
Turner, Jessica A.
Kruggel, Frithjof
Saykin, Andrew J.
Orro, Alessandro
Salvi, Erika
Weiner, Michael
Macciardi, Fabio
Venue: PLoS ONE
Publisher: Public Library of Science (PLoS)
Published: 2009-08-07
Volume: 4
Issue: 8
Pages: e6501
ISSN: 1932-6203 (ISSN-L)
DOI: 10.1371/journal.pone.0006501
PMC: PMC2719581
OpenAlex: W2162988145
Cited by: 376
References: 71
Citations by year: 2026: 2 · 2025: 8 · 2024: 15 · 2023: 17 · 2022: 15 · 2021: 6 · 2020: 22 · 2019: 14 · 2018: 21 · 2017: 25 · 2016: 21 · 2015: 27 · 2014: 28 · 2013: 36 · 2012: 36
FWCI: 25.99
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (unspecified)
Locations: PLoS ONE (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano) (submittedVersion, other-oa)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
eScholarship (California Digital Library) (submittedVersion, cc-by)
Figshare (submittedVersion, cc-by)
IUScholarWorks (Indiana University) (submittedVersion, cc-by)
Funders: Foundation for the National Institutes of Health (U01AG024904, AG024904)
Alzheimer's Association (U01 AG024904)
Bristol-Myers Squibb (U01 AG024904, AG024904)
Eli Lilly and Company (U01 AG024904, AG024904)
Pfizer (AG024904, U01 AG024904)
AstraZeneca
GlaxoSmithKline
Alzheimer's Disease Neuroimaging Initiative (3U01AG024904-03S5, ADNI U01 AG024904-01, U01AG024904, AG024904)
Novartis Pharmaceuticals Corporation (U01 AG024904, AG024904)
Northern California Institute for Research and Education (U01 AG024904)
Vanda Pharmaceuticals
Elan (U01 AG024904)
Eisai (U01 AG024904, AG024904)
National Institutes of Health (3u01ag024904-03s5, U01-AG024904, AG024904, ADNI U01 AG024904)
U.S. Food and Drug Administration
University of California, Los Angeles
University of California, San Diego
National Institute on Alcohol Abuse and Alcoholism
National Institute on Aging (U01-AG-024904, U01 AG024904-01, AG 024904, 3U01AG024904-03S5, U19AG010483, U24AG021886, 3U01AG024904)
National Institute of Biomedical Imaging and Bioengineering (U01 AG024904, AG024904)
National Center for Research Resources (U24RR021992, FBIRN U24-RR021992, RR021992, P20RR020837, TIGC-P20 RR020837-01, U01 AG024904)
Topics: Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
Health Sciences › Medicine › Psychiatry and Mental health › Dementia and Cognitive Impairment Research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
Keywords: Alzheimer's disease, hippocampal atrophy, genetic susceptibility, genome-wide association study, quantitative traits, apolipoprotein E, TOMM40, ephrin-A5, CAND1, MAGI2, arsB, single nucleotide polymorphisms, MRI phenotypes, sporadic Alzheimer's disease, ADNI
MeSH terms: Adult, Alzheimer Disease, Female, Hippocampus, Humans, Magnetic Resonance Imaging, Male, Case-Control Studies, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Genome-Wide Association Study

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Hippocampal atrophy as a quantitative trait in a genome-wide association study identifying novel susceptibility genes for Alzheimer's disease

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