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Meta-Analysis for Genome-Wide Association Study Identifies Multiple Variants at the BIN1 Locus Associated with Late-Onset Alzheimer's Disease

Author

Listed:
  • Xiaolan Hu
  • Eve Pickering
  • Yingxue Cathy Liu
  • Stephanie Hall
  • Helene Fournier
  • Elyse Katz
  • Bryan Dechairo
  • Sally John
  • Paul Van Eerdewegh
  • Holly Soares
  • the Alzheimer's Disease Neuroimaging Initiative

Abstract

Recent GWAS studies focused on uncovering novel genetic loci related to AD have revealed associations with variants near CLU, CR1, PICALM and BIN1. In this study, we conducted a genome-wide association study in an independent set of 1034 cases and 1186 controls using the Illumina genotyping platforms. By coupling our data with available GWAS datasets from the ADNI and GenADA, we replicated the original associations in both PICALM (rs3851179) and CR1 (rs3818361). The PICALM variant seems to be non-significant after we adjusted for APOE e4 status. We further tested our top markers in 751 independent cases and 751 matched controls. Besides the markers close to the APOE locus, a marker (rs12989701) upstream of BIN1 locus was replicated and the combined analysis reached genome-wide significance level (p = 5E-08). We combined our data with the published Harold et al. study and meta-analysis with all available 6521 cases and 10360 controls at the BIN1 locus revealed two significant variants (rs12989701, p = 1.32E-10 and rs744373, p = 3.16E-10) in limited linkage disequilibrium (r2 = 0.05) with each other. The independent contribution of both SNPs was supported by haplotype conditional analysis. We also conducted multivariate analysis in canonical pathways and identified a consistent signal in the downstream pathways targeted by Gleevec (P = 0.004 in Pfizer; P = 0.028 in ADNI and P = 0.04 in GenADA). We further tested variants in CLU, PICALM, BIN1 and CR1 for association with disease progression in 597 AD patients where longitudinal cognitive measures are sufficient. Both the PICALM and CLU variants showed nominal significant association with cognitive decline as measured by change in Clinical Dementia Rating-sum of boxes (CDR-SB) score from the baseline but did not pass multiple-test correction. Future experiments will help us better understand potential roles of these genetic loci in AD pathology.

Suggested Citation

  • Xiaolan Hu & Eve Pickering & Yingxue Cathy Liu & Stephanie Hall & Helene Fournier & Elyse Katz & Bryan Dechairo & Sally John & Paul Van Eerdewegh & Holly Soares & the Alzheimer's Disease Neuroimaging , 2011. "Meta-Analysis for Genome-Wide Association Study Identifies Multiple Variants at the BIN1 Locus Associated with Late-Onset Alzheimer's Disease," PLOS ONE, Public Library of Science, vol. 6(2), pages 1-9, February.
    • Handle: RePEc:plo:pone00:0016616
    DOI: 10.1371/journal.pone.0016616
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    Cited by:

    1. Eduardo Pérez-Palma & Bernabé I Bustos & Camilo F Villamán & Marcelo A Alarcón & Miguel E Avila & Giorgia D Ugarte & Ariel E Reyes & Carlos Opazo & Giancarlo V De Ferrari & the Alzheimer's Disease Neu, 2014. "Overrepresentation of Glutamate Signaling in Alzheimer's Disease: Network-Based Pathway Enrichment Using Meta-Analysis of Genome-Wide Association Studies," PLOS ONE, Public Library of Science, vol. 9(4), pages 1-16, April.
    2. Saar Oz & Yanina Ivashko-Pachima & Illana Gozes, 2012. "The ADNP Derived Peptide, NAP Modulates the Tubulin Pool: Implication for Neurotrophic and Neuroprotective Activities," PLOS ONE, Public Library of Science, vol. 7(12), pages 1-13, December.
    3. Fanggeng Zou & Olivia Belbin & Minerva M Carrasquillo & Oliver J Culley & Talisha A Hunter & Li Ma & Gina D Bisceglio & Mariet Allen & Dennis W Dickson & Neill R Graff-Radford & Ronald C Petersen & th, 2013. "Linking Protective GAB2 Variants, Increased Cortical GAB2 Expression and Decreased Alzheimer’s Disease Pathology," PLOS ONE, Public Library of Science, vol. 8(5), pages 1-11, May.

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