Genome-Wide Association Meta-analysis of Neuropathologic Features of Alzheimer's Disease and Related Dementias
Open accessAbstract
Alzheimer's disease (AD) and related dementias are a major public health challenge and present a therapeutic imperative for which we need additional insight into molecular pathogenesis. We performed a genome-wide association study and analysis of known genetic risk loci for AD dementia using neuropathologic data from 4,914 brain autopsies. Neuropathologic data were used to define clinico-pathologic AD dementia or controls, assess core neuropathologic features of AD (neuritic plaques, NPs; neurofibrillary tangles, NFTs), and evaluate commonly co-morbid neuropathologic changes: cerebral amyloid angiopathy (CAA), Lewy body disease (LBD), hippocampal sclerosis of the elderly (HS), and vascular brain injury (VBI). Genome-wide significance was observed for clinico-pathologic AD dementia, NPs, NFTs, CAA, and LBD with a number of variants in and around the apolipoprotein E gene (APOE). GalNAc transferase 7 (GALNT7), ATP-Binding Cassette, Sub-Family G (WHITE), Member 1 (ABCG1), and an intergenic region on chromosome 9 were associated with NP score; and Potassium Large Conductance Calcium-Activated Channel, Subfamily M, Beta Member 2 (KCNMB2) was strongly associated with HS. Twelve of the 21 non-APOE genetic risk loci for clinically-defined AD dementia were confirmed in our clinico-pathologic sample: CR1, BIN1, CLU, MS4A6A, PICALM, ABCA7, CD33, PTK2B, SORL1, MEF2C, ZCWPW1, and CASS4 with 9 of these 12 loci showing larger odds ratio in the clinico-pathologic sample. Correlation of effect sizes for risk of AD dementia with effect size for NFTs or NPs showed positive correlation, while those for risk of VBI showed a moderate negative correlation. The other co-morbid neuropathologic features showed only nominal association with the known AD loci. Our results discovered new genetic associations with specific neuropathologic features and aligned known genetic risk for AD dementia with specific neuropathologic changes in the largest brain autopsy study of AD and related dementias.
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When loci that were associated with clinically defined AD are examined against autopsy-defined AD, many of these loci have no association with neuritic plaques and neurofibrillary degeneration but rather with other pathologic findings such as cerebrovascular disease.
“When loci that were associated with clinically defined AD are examined against autopsy-defined AD, many of these loci have no association with neuritic plaques and neurofibrillary degeneration but rather with other pathologic findings such as cerebrovascular disease [217].”
From NIA‐AA Research Framework: Toward a biological definition of Alzheimer's disease (2018) · cites this paper as [217]
Split into 2 atoms — 0 confirmed, 1 partially supported, 1 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
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Experimental — accuracy not yet measuredAPOE4 allelic dose was associated with significantly higher odds ratios for CAA and DLB, before and after adjustment for the presence or absence of AD, and not with VBI or HS.
“In contrast, APOE4 allelic dose was associated with significantly higher ORs for CAA and DLB, before and after adjustment for the presence or absence of AD, and not with VBI or HS11.”
From Exceptionally low likelihood of Alzheimer’s dementia in APOE2 homozygotes from a 5,000-person neuropathological study (2020) · cites this paper as [11]
The Results (Genome-wide association; page unavailable) report significant APOE-locus associations with CAA and Lewy body disease (LBD), but not strong associations with VBI or HS. The passages do not establish an APOE ε4 allelic-dose effect or show that these associations remained significant both before and after adjustment for AD. The Discussion mentions ε4 risk for dementia with Lewy bodies in the absence of AD, but attributes that finding to a separate study. (LLM, conf=0.86)
Experimental — accuracy not yet measuredDue to prioritized ascertainment, the number of misclassified cases and controls available through the AD Genetics Consortium is much smaller than the estimated number of neuropathologically misclassified cases and controls, limiting the ability to clarify the impact of brain donation on APOE ORs in post hoc analyses.
“Due to the prioritized ascertainment of those cases who met the clinical and neuropathological criteria for Alzheimer’s dementia and those unimpaired controls without AD, the number of misclassified cases and controls available through the AD Genetics Consortium12 is much smaller than our estimated number of neuropathologically misclassified cases and controls8–11, limiting our ability to clarify”
From Exceptionally low likelihood of Alzheimer’s dementia in APOE2 homozygotes from a 5,000-person neuropathological study (2020) · cites this paper as [11]
Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measuredAPOE ε4 is known to associate with accumulation of β-amyloid pathology and cognitive decline.
“consistent with this haplotype’s known associations with accumulation of β-amyloid pathology and cognitive decline29.”
From A molecular network of the aging human brain provides insights into the pathology and cognitive decline of Alzheimer’s disease (2018) · cites this paper as [29]
The AD GWAS for Braak stages (Beecham et al., 2014) was used as the gold standard for AD association.
“using an AD GWAS for Braak stages (NFT pathology-based staging) (Beecham et al., 2014) as gold standard and the ECII-specific functional network neighborhoods as features, we applied NetWAS 2.0 with n = 10,000 to rank each of the 23,950 genes for potential association to AD.”
From Selective Neuronal Vulnerability in Alzheimer’s Disease: A Network-Based Analysis (2020) · cites this paper as Beecham et al., 2014
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- Authors
- Beecham, G. W., Hamilton, K., Naj, A. C., Martin, E. R., Huentelman, M., Myers, A. J., Corneveaux, J. J., Hardy, J., Vonsattel, J.-P., Younkin, S. G., Bennett, D. A., De Jager, P. L., Larson, E. B., Crane, P. K., Kamboh, M. I., Kofler, J. K., Mash, D. C., Duque, L., Gilbert, J. R., Gwirtsman, H., Buxbaum, J. D., Kramer, P., Dickson, D. W., Farrer, L. A., Frosch, M. P., Ghetti, B., Haines, J. L., Hyman, B. T., Kukull, W. A., Mayeux, R. P., Pericak-Vance, M. A., Schneider, J. A., Trojanowski, J. Q., Reiman, E. M., the Alzheimer's Disease Genetics Consortium (ADGC), Schellenberg, G. D., & Montine, T. J.
- Affiliations
- University of Miami (US)
- University of Pennsylvania (US)
- Translational Genomics Research Institute (US)
- University College London (GB)
- Columbia University (US)
- Mayo Clinic (US)
- Rush University (US)
- Kaiser Permanente Washington Health Research Institute (US)
- University of Washington (US)
- University of Pittsburgh (US)
- Vanderbilt University (US)
- Mount Sinai Hospital (US)
- Oregon Health & Science University (US)
- Boston University (US)
- Massachusetts General Hospital (US)
- Indiana University Indianapolis (US)
- Case Western Reserve University (US)
- Harvard University (US)
- Rush University Medical Center (US)
- University of Arizona (US)
- Corresponding author
- Montine, Thomas J.
- ORCID
- Beecham, Gary W.
- Naj, Adam C.
- Martin, Eden R.
- Myers, Amanda J.
- Hardy, John
- Bennett, David A.
- Larson, Eric B.
- Crane, Paul K.
- Kamboh, M. Ilyas
- Kofler, Julia K.
- Mash, Deborah C.
- Gilbert, John R.
- Buxbaum, Joseph D.
- Dickson, Dennis W.
- Farrer, Lindsay A.
- Frosch, Matthew P.
- Ghetti, Bernardino
- Haines, Jonathan L.
- Hyman, Bradley T.
- Kukull, Walter A.
- Mayeux, Richard P.
- Schneider, Julie A.
- Trojanowski, John Q.
- Reiman, Eric M.
- Schellenberg, Gerard D.
- Montine, Thomas J.
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2014-09-04
- Volume
- 10
- Issue
- 9
- Pages
- e1004606
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- PMC
- PMC4154667
- OpenAlex
- W2105752911
- Cited by
- 343
- References
- 28
- Citations by year
- 2026: 13 · 2025: 17 · 2024: 19 · 2023: 31 · 2022: 25 · 2021: 38 · 2020: 36 · 2019: 34 · 2018: 50 · 2017: 29 · 2016: 31 · 2015: 17 · 2014: 3
- FWCI
- 3.13
- Type
- journal article
- Language
- en
- Update notices
- correction (2014-11-12)
- Open access
- gold
- doi.org
- Locations
- PLoS Genetics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- D-Scholarship@Pitt (University of Pittsburgh) (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- UCL Discovery (University College London) (submittedVersion)
- Figshare (submittedVersion, cc-by)
- Funders
- U.S. Department of Veterans Affairs (U01 AG024904)
- Alzheimer's Association (IIRG-05–14147, K01 AG030514, U01 AG016976, U01 AG032984, IIRG-08-89720, U01 AG024904, U24AG021886)
- Dana Foundation (K01 AG030514, U01 AG024904)
- Bristol-Myers Squibb (U01 AG024904, AG024904)
- Eli Lilly and Company (U01 AG024904, AG024904)
- Pfizer (AG024904, U01 AG024904)
- AstraZeneca
- GlaxoSmithKline
- Novartis
- Office of Research and Development
- F. Hoffmann-La Roche (AG024904, U01 AG024904)
- Medpace (U01 AG024904)
- Synarc (U01 AG024904, K01 AG030514)
- Northern California Institute for Research and Education (U01 AG024904, K01 AG030514)
- Alzheimer's Research Trust
- Newcastle University
- Stichting MS Research
- Elan (U01 AG024904)
- Eisai (U01 AG024904, AG024904)
- North Bristol NHS Trust
- Universitat de Barcelona
- Hersenstichting
- National Institutes of Health (5rc2ag036502-02, 5r01ag027944-05, 5u01ag024904-10, 7r01ag019757-06, 5r37ag015473-15, AG016976, U01-AG024904, AG024904, MH60451)
- Genentech (AG024904, U01 AG024904)
- Medical Research Council (U01 AG024904, K01 AG030514)
- National Institute on Aging (U01-AG-024904, R01AG017917, P01AG010491, P50 AG016575, AG 016976, AG05 128, P30AG010129, P30AG010133, R01AG019085, P30 AG 08051, P50AG005144, U01‐AG10483, R01AG33193, P50 AG016576, R01AG030146, AG021547, R01 AG30146, AG036535, AG010491, R01‐AG17917, AG-05144, U24 AG026390, P30AG028383, R01 AG15819, P30AG012300, R01AG041718, AG 025688, P50AG016577, P50AG005133, R01-AG027944, AG 024904, AG 030,514, P30AG028377, U01AG006781, U01AG016976, P50AG005131, R01-AG019757, R01AG034504, R37-AG015473, P50AG005138, R01AG026390, R01AG022374, P50AG016570, K01AG030514, AG036528, P50AG005128, P30AG010124, P50AG016573, AG019757, R01AG021547, R01AG041232, R01AG030653, U01AG010483, R01AG015819, P30AG008017, P30AG010161, U01AG032984, R01AG012101, R01AG031581, P30AG008051, R01AG041797, RC2-AG036502, P50AG016582, P50AG008702, AG032984, P50AG005681, P50AG005142, P50AG008671, P30AG019610, R01AG026916, P50AG005146, P01 AG0 3991, P01AG003991, 1RC2AG036502, U24AG026395, P30AG013846, P50AG005136, P50AG005134, RC2AG036535, P30AG013854, R01AG025259, P50AG025688, AG026395, R01AG017173, RC2AG036528, R01AG033193, P01AG002219, RF1AG015819, AG021886, R01AG013616, P30 AG-10133, U24AG056270, P01AG019724, U24AG021886, P30AG062421, P50AG023501, AG027944, R01AG020688, AG 030653, P50AG016574, R01AG035137, AG041232, UO1-AG06781)
- National Institute of Mental Health (U01 AG024904, MH60451, R01MH080295, P50MH060451)
- National Human Genome Research Institute (UO1 HG004610, U01HG004610)
- National Cancer Institute (R01CA129769, U54CA137788, U54CA132378)
- National Institute of Neurological Disorders and Stroke (NS3 9764, R01NS059873, MH60451, NIMH MH60451, P50NS039764)
- National Institute of Biomedical Imaging and Bioengineering (U01 AG024904, AG024904)
- National Center for Research Resources (MO1 RR000-96, UL1RR02777, UL1RR029893, M01RR000096)
- 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, related dementias, genetic susceptibility loci, neuritic plaques, neurofibrillary tangles, cerebral amyloid angiopathy, Lewy body disease, vascular brain injury, apolipoprotein E, GALNT7, ABCG1, complement receptor 1, BIN1, clusterin, MS4A6A, PICALM, ABCA7, CD33, Pyk2, SORL1, MEF2C, brain autopsy
- MeSH terms
- ATP Binding Cassette Transporter, Subfamily G, Member 1, Alzheimer Disease, Brain, Chromosome Mapping, Chromosomes, Human, Pair 18, Chromosomes, Human, Pair 9, Dementia, Hippocampus, Humans, Phenotype, Odds Ratio, Case-Control Studies, N-Acetylgalactosaminyltransferases, ATP-Binding Cassette Transporters, Genetic Predisposition to Disease, Quantitative Trait Loci, Genome-Wide Association Study, Plaque, Amyloid
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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