TY - JOUR
T1 - Whole genome association analysis shows that ACE is a risk factor for Alzheimer's disease and fails to replicate most candidates from meta-analysis
AU - Webster, Jennifer
AU - Reiman, Eric M.
AU - Zismann, Victoria L.
AU - Joshipura, Keta D.
AU - Pearson, John V.
AU - Hu-Lince, Diane
AU - Huentelman, Matthew J.
AU - Craig, David W.
AU - Coon, Keith D.
AU - Beach, Thomas
AU - Rohrer, Kristen C.
AU - Zhao, Alice S.
AU - Leung, Doris
AU - Bryden, Leslie
AU - Marlowe, Lauren
AU - Kaleem, Mona
AU - Mastroeni, Diego
AU - Grover, Andrew
AU - Rogers, Joseph
AU - Heun, Reinhard
AU - Jessen, Frank
AU - Kölsch, Heike
AU - Heward, Christopher B.
AU - Ravid, Rivka
AU - Hutton, Michael L.
AU - Melquist, Stacey
AU - Petersen, Ron C.
AU - Caselli, Richard J.
AU - Papassotiropoulos, Andreas
AU - Stephan, Dietrich A.
AU - Hardy, John
AU - Myers, Amanda
PY - 2010
Y1 - 2010
N2 - For late onset Alzheimer's disease (LOAD), the only confirmed, genetic association is with the apolipoprotein E (APOE) locus on chromosome 19. Meta-analysis is often employed to sort the true associations from the false positives. LOAD research has the advantage of a continuously updated meta-analysis of candidate gene association studies in the web-based AlzGene database. The top 30 AlzGene loci on May 1st, 2007 were investigated in our whole genome association data set consisting of 1411 LOAD cases and neuropathologically verified controls genotyped at 312,316 SNPs using the Affymetrix 500K Mapping Platform. Of the 30 "top AlzGenes", 32 SNPs in 24 genes had odds ratios (OR) whose 95% confidence intervals that did not include 1. Of these 32 SNPs, six were part of the Affymetrix 500K Mapping panel and another ten had proxies on the Affymetrix array that had >80% power to detect an association with α=0.001. Two of these 16 SNPs showed significant association with LOAD in our sample series. One was rs4420638 at the APOE locus (uncorrected p-value=4.58E-37) and the other was rs4293, located in the angiotensin converting enzyme (ACE) locus (uncorrected pvalue=0.014). Since this result was nominally significant, but did not survive multiple testing correction for 16 independent tests, this association at rs4293 was verified in a geographically distinct German cohort (pvalue=0.03). We present the results of our ACE replication along with a discussion of the statistical limitations of multiple test corrections in whole genome studies.
AB - For late onset Alzheimer's disease (LOAD), the only confirmed, genetic association is with the apolipoprotein E (APOE) locus on chromosome 19. Meta-analysis is often employed to sort the true associations from the false positives. LOAD research has the advantage of a continuously updated meta-analysis of candidate gene association studies in the web-based AlzGene database. The top 30 AlzGene loci on May 1st, 2007 were investigated in our whole genome association data set consisting of 1411 LOAD cases and neuropathologically verified controls genotyped at 312,316 SNPs using the Affymetrix 500K Mapping Platform. Of the 30 "top AlzGenes", 32 SNPs in 24 genes had odds ratios (OR) whose 95% confidence intervals that did not include 1. Of these 32 SNPs, six were part of the Affymetrix 500K Mapping panel and another ten had proxies on the Affymetrix array that had >80% power to detect an association with α=0.001. Two of these 16 SNPs showed significant association with LOAD in our sample series. One was rs4420638 at the APOE locus (uncorrected p-value=4.58E-37) and the other was rs4293, located in the angiotensin converting enzyme (ACE) locus (uncorrected pvalue=0.014). Since this result was nominally significant, but did not survive multiple testing correction for 16 independent tests, this association at rs4293 was verified in a geographically distinct German cohort (pvalue=0.03). We present the results of our ACE replication along with a discussion of the statistical limitations of multiple test corrections in whole genome studies.
KW - ACE
KW - Genome-wide association study
KW - Late-onset alzheimer disease
KW - Metaanalysis
KW - Single nucleotide polymorphism
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M3 - Article
C2 - 21537449
AN - SCOPUS:77954641948
SN - 1948-1756
VL - 1
SP - 19
EP - 30
JO - International Journal of Molecular Epidemiology and Genetics
JF - International Journal of Molecular Epidemiology and Genetics
IS - 1
ER -