Pooling/bootstrap-based GWAS (pbGWAS) identifies new loci modifying the age of onset in PSEN1 p.Glu280Ala Alzheimer's disease
Open accessAbstract
The literature on GWAS (genome-wide association studies) data suggests that very large sample sizes (for example, 50,000 cases and 50,000 controls) may be required to detect significant associations of genomic regions for complex disorders such as Alzheimer's disease (AD). Because of the challenges of obtaining such large cohorts, we describe here a novel sequential strategy that combines pooling of DNA and bootstrapping (pbGWAS) in order to significantly increase the statistical power and exponentially reduce expenses. We applied this method to a very homogeneous sample of patients belonging to a unique and clinically well-characterized multigenerational pedigree with one of the most severe forms of early onset AD, carrying the PSEN1 p.Glu280Ala mutation (often referred to as E280A mutation), which originated as a consequence of a founder effect. In this cohort, we identified novel loci genome-wide significantly associated as modifiers of the age of onset of AD (CD44, rs187116, P=1.29 × 10⁻¹²; NPHP1, rs10173717, P=1.74 × 10⁻¹²; CADPS2, rs3757536, P=1.54 × 10⁻¹⁰; GREM2, rs12129547, P=1.69 × 10⁻¹³, among others) as well as other loci known to be associated with AD. Regions identified by pbGWAS were confirmed by subsequent individual genotyping. The pbGWAS methodology and the genes it targeted could provide important insights in determining the genetic causes of AD and other complex conditions.
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A previous genome-wide association study by the authors found that genome-wide intronic variants are significantly associated as modifiers of age of onset in the E280A pedigree.
“Indeed, a previous analysis by our group using a genome-wide association study approach found that genome-wide intronic variants significantly associated as ADAOO modifiers.10”
From APOE*E2 allele delays age of onset in PSEN1 E280A Alzheimer’s disease (2016) · cites this paper as [10]
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Swaroop, A., Marchal, C., Gaur, M., Kumari, A., Mohan, S. V., Brooks, M. J., Jaeger, C., Advani, J., Campello, L., English, M. A., et al. (2026) · Research Square · doi:10.21203/rs.3.rs-10017071/v1
- Authors
- Vélez, J. I., Chandrasekharappa, S. C., Henao, E., Martinez, A. F., Harper, U., Jones, M., Solomon, B. D., Lopez, L., Garcia, G., Aguirre-Acevedo, D. C., Acosta-Baena, N., Correa, J. C., Lopera-Gómez, C. M., Jaramillo-Elorza, M. C., Rivera, D., Kosik, K. S., Schork, N. J., Swanson, J. M., Lopera, F., & Arcos-Burgos, M.
- Affiliations
- National Institutes of Health (US)
- Universidad de Antioquia (CO)
- Universidad Nacional de Colombia (CO)
- University of California, Santa Barbara (US)
- Scripps Research Institute (US)
- Florida International University (US)
- ORCID
- Venue
- Molecular Psychiatry
- Published
- 2012-06-19
- Volume
- 18
- Issue
- 5
- Pages
- 568-575
- ISSN
- 1359-4184 (ISSN-L)
- 1476-5578
- PMC
- PMC3596442
- OpenAlex
- W2015628552
- Cited by
- 44
- References
- 45
- Citations by year
- 2026: 2 · 2025: 3 · 2024: 4 · 2023: 2 · 2022: 2 · 2021: 6 · 2020: 4 · 2019: 3 · 2018: 4 · 2017: 3 · 2016: 5 · 2015: 3 · 2014: 1 · 2013: 2
- FWCI
- 1.29
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Molecular Psychiatry (publishedVersion, cc-by-nc-sa)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-sa)
- PubMed Central (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- Florida International University Digital Commons (Florida International University) (submittedVersion, cc-by-nc-sa)
- eScholarship (California Digital Library) (submittedVersion)
- ANU Open Research (Australian National University) (submittedVersion)
- Repositorio Digital - Academia Colombiana de Ciencias Exactas, Fisicas y Naturales (submittedVersion, other-oa)
- Funders
- Departamento Administrativo de Ciencia, Tecnología e Innovación (COLCIENCIAS)
- Australian National University
- Curtin University of Technology
- Universidad de Antioquia
- National Institutes of Health
- National Human Genome Research Institute (ZICHG200346)
- NHLBI Division of Intramural Research
- 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, early-onset Alzheimer's disease, PSEN1 E280A mutation, age of onset, genetic modifiers, bootstrapping, CD44, NPHP1, GREM2, founder effect, multigenerational pedigree, statistical power
- MeSH terms
- Alanine, Alzheimer Disease, Female, Gene Frequency, Genotype, Humans, Male, Mutation, Cohort Studies, Databases, Factual, Age of Onset, Glutamic Acid, Founder Effect, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Presenilin-1, Genome-Wide Association Study
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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.
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