A genome-wide search for pleiotropy in more than 100,000 harmonized longitudinal cognitive domain scores
Open accessAbstract
Abstract Background More than 75 common variant loci account for only a portion of the heritability for Alzheimer’s disease (AD). A more complete understanding of the genetic basis of AD can be deduced by exploring associations with AD-related endophenotypes. Methods We conducted genome-wide scans for cognitive domain performance using harmonized and co-calibrated scores derived by confirmatory factor analyses for executive function, language, and memory. We analyzed 103,796 longitudinal observations from 23,066 members of community-based (FHS, ACT, and ROSMAP) and clinic-based (ADRCs and ADNI) cohorts using generalized linear mixed models including terms for SNP, age, SNP × age interaction, sex, education, and five ancestry principal components. Significance was determined based on a joint test of the SNP’s main effect and interaction with age. Results across datasets were combined using inverse-variance meta-analysis. Genome-wide tests of pleiotropy for each domain pair as the outcome were performed using PLACO software. Results Individual domain and pleiotropy analyses revealed genome-wide significant (GWS) associations with five established loci for AD and AD-related disorders ( BIN1 , CR1 , GRN , MS4A6A , and APOE ) and eight novel loci. ULK2 was associated with executive function in the community-based cohorts (rs157405, P = 2.19 × 10 –9 ). GWS associations for language were identified with CDK14 in the clinic-based cohorts (rs705353, P = 1.73 × 10 –8 ) and LINC02712 in the total sample (rs145012974, P = 3.66 × 10 –8 ). GRN (rs5848, P = 4.21 × 10 –8 ) and PURG (rs117523305, P = 1.73 × 10 –8 ) were associated with memory in the total and community-based cohorts, respectively. GWS pleiotropy was observed for language and memory with LOC107984373 (rs73005629, P = 3.12 × 10 –8 ) in the clinic-based cohorts, and with NCALD (rs56162098, P = 1.23 × 10 –9 ) and PTPRD (rs145989094, P = 8.34 × 10 –9 ) in the community-based cohorts. GWS pleiotropy was also found for executive function and memory with OSGIN1 (rs12447050, P = 4.09 × 10 –8 ) and PTPRD (rs145989094, P = 3.85 × 10 –8 ) in the community-based cohorts. Functional studies have previously linked AD to ULK2 , NCALD , and PTPRD . Conclusion Our results provide some insight into biological pathways underlying processes leading to domain-specific cognitive impairment and AD, as well as a conduit toward a syndrome-specific precision medicine approach to AD. Increasing the number of participants with harmonized cognitive domain scores will enhance the discovery of additional genetic factors of cognitive decline leading to AD and related dementias.
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Variant rs73270956 has been linked to memory performance in humans by a GWAS study.
“It is interesting to note that the variant rs73270956 has been linked to memory performance in humans by a Genome-wide association studies (GWAS) study (Kang et al. 2023).”
From The Human Accelerated Region HAR202 Controls <i>NPAS3</i> Expression in the Developing Forebrain Displaying Differential Enhancer Activity Between Modern and Archaic Human Sequences (2024) · cites this paper as Kang et al. 2023
The Results section reports GWAS associations with memory for other variants, including rs6733839 and rs5848 (page unavailable). Searches for rs73270956 and for its alleged link to memory performance returned no passage about that variant, so our copy does not establish the specific claim. (LLM, conf=0.76)
Experimental — accuracy not yet measuredA GWAS catalog SNP included in HAR202 (rs73270956) has been associated with cognitive function, more particularly with memory performance and language impairment.
“we did find a GWAS catalog SNP included in HAR202 that has been associated with cognitive function (rs73270956), more particularly with memory performance and language impairment (Kang et al. 2023).”
From The Human Accelerated Region HAR202 Controls <i>NPAS3</i> Expression in the Developing Forebrain Displaying Differential Enhancer Activity Between Modern and Archaic Human Sequences (2024) · cites this paper as Kang et al. 2023
The Results section reports associations between other SNPs and memory or language, but the passages retrieved for rs73270956 do not mention that variant. A search for HAR202 and the claimed memory-performance and language-impairment association also found no passage addressing it; the paper’s general cognitive-domain findings cannot verify the claim about this specific SNP. (LLM, conf=0.72)
Experimental — accuracy not yet measuredThe variant rs73270956 located in HAR202 has been linked to deficits in memory performance in humans by a GWAS study.
“On the other hand, the variant rs73270956 located in HAR202 has been linked to deficits in memory performance in humans by a GWAS study (Kang et al. 2023), suggesting an involvement in cognitive function.”
From The Human Accelerated Region HAR202 Controls <i>NPAS3</i> Expression in the Developing Forebrain Displaying Differential Enhancer Activity Between Modern and Archaic Human Sequences (2024) · cites this paper as Kang et al. 2023
The Results section reports GWAS associations with memory performance for other variants, but does not identify rs73270956 or HAR202. Searches of our copy for both terms found no passage linking that variant to memory deficits; page numbers were not available. (LLM, conf=0.76)
Experimental — accuracy not yet measured
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- Authors
- Kang, M., Ang, T. F. A., Devine, S. A., Sherva, R., Mukherjee, S., Trittschuh, E. H., Gibbons, L. E., Scollard, P., Lee, M., Choi, S.-E., Klinedinst, B., Nakano, C., Dumitrescu, L. C., Durant, A., Hohman, T. J., Cuccaro, M. L., Saykin, A. J., Kukull, W. A., Bennett, D. A., Wang, L.-S., Mayeux, R. P., Haines, J. L., Pericak-Vance, M. A., Schellenberg, G. D., Crane, P. K., Au, R., Lunetta, K. L., Mez, J. B., & Farrer, L. A.
- Affiliations
- Boston University (US)
- University of Washington (US)
- Vanderbilt University Medical Center (US)
- University of Miami (US)
- Indiana University Indianapolis (US)
- Rush University Medical Center (US)
- University of Pennsylvania (US)
- Columbia University Irving Medical Center (US)
- Case Western Reserve University (US)
- Corresponding author
- Farrer, Lindsay A.
- ORCID
- Ang, Ting Fang Alvin
- Devine, Sherral A.
- Sherva, Richard
- Mukherjee, Shubhabrata
- Trittschuh, Emily H.
- Gibbons, Laura E.
- Scollard, Phoebe
- Lee, Michael
- Choi, Seo-Eun
- Klinedinst, Brandon
- Nakano, Connie
- Dumitrescu, Logan C.
- Hohman, Timothy J.
- Cuccaro, Michael L.
- Saykin, Andrew J.
- Kukull, Walter A.
- Bennett, David A.
- Wang, Li-San
- Mayeux, Richard P.
- Haines, Jonathan L.
- Schellenberg, Gerard D.
- Crane, Paul K.
- Au, Rhoda
- Lunetta, Kathryn L.
- Mez, Jesse B.
- Farrer, Lindsay A.
- Venue
- Molecular Neurodegeneration
- Published
- 2023-06-22
- Volume
- 18
- Issue
- 1
- Pages
- 40-40
- ISSN
- 1750-1326 (ISSN-L)
- PMC
- PMC10286470
- OpenAlex
- W4381716608
- Cited by
- 29
- References
- 112
- Citations by year
- 2026: 9 · 2025: 11 · 2024: 8 · 2023: 1
- FWCI
- 1.32
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Molecular Neurodegeneration (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- IUScholarWorks (Indiana University) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Institute on Aging (U19-AG068753, R01-AG048927, U54-AG052427, U01-AG058654, U01-AG032984, RF1-AG057519, U01-AG062602, P30-AG072878, U24-AG074855, U01-AG068057, R01-AG059716)
- Topics
- Health Sciences › Medicine › Psychiatry and Mental health › Dementia and Cognitive Impairment Research
- Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- pleiotropy, Alzheimer's disease, cognitive domain, executive function, language, memory, endophenotypes, genetic loci, BIN1, complement receptor 1, gene regulatory networks, MS4A6A, apolipoprotein E, ULK2, CDK14
- MeSH terms
- Alzheimer Disease, Cognition, Female, Humans, Male, Cyclin-Dependent Kinases, Genome-Wide Association Study
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