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Table 1 Late-onset Alzheimer disease genome-wide association study: summary of methodologies.

From: Genetics of Alzheimer disease in the pre- and post-GWAS era

       Discovery series Replication series  
Reference Ethnicity/Source Samples Study design Genotyping platform SNPsa AD patients Controls AD patients Controls Follow-up criteria
Grupe et al. [50], February 2007 UK/US Case control 1 discovery (pooled DNA) and 5 replication series (1 pooled) Gene-based putative functional polymorphisms 17,343 (in 11,211 genes) 380 396 1,428 1,666 P < 0.075 or P < 0.1 and biology (stage 1)
P < 0.15 and same risk allele (stage 2)
P < 0.05 in UK1 and WU and P meta < 0.005 (stage 3)
Coon et al. [51], April 2007 US/The Netherlands Case control Single-stage study Affymetrix 500K 502,627 664 422 - - Single-stage
Reiman et al. [52], June 2007b US/The Netherlands Case control 1 discovery and 2 replication series Affymetrix 500K 312,316 446 290 415 260 All SNPs genotyped in both stages.
Li et al. [53], January 2008 Canada/UK Case control 1 discovery and 1 replication series Affymetrix 500K 469,438 753 736 418 249 Top 120 SNPs
Abraham et al. [54], September 2008 UK Case control Single-stage study (first pooled, hen individual enotyping) Illumina HumanHap300 and llumina Sentrix umanHap240S 561,494 1,082 1,239 - 1,400 Passed three criteria and could be genotyped (stage 1) ≤ 0.05 (stage 2)
Bertram et al. [55], November 2008 US Family-based 1 discovery and 3 replication series Affymetrix 500K 404,604 941 404 1,767 838 Significance after weighted-Bonferroni correction
Beecham et al. [56], January 2009 US Case control 1 discovery and 1 replication series Illumina HumanHap550 532,000 492 496 238 220 Significance after FDR-BUM criteria
Feulner et al. [57], January 2009 Germany Case control Single-stage study Illumina HumanHap550 555,000 491 479 - - Single-stage
Poduslo et al. [58], January 2009b US Family-based and case control 1 discovery and 2 replication series Affymetrix 500K 469,218 19
(family members)
60
(CEPH)
140
(family members)
199
(unrelated)
85
(unrelated)
Genome-wide significance after Bonferroni correction
Carrasquillo et al. [59], February 2009b US Case control 3 discovery and 4 replication series Illumina HumanHap300 313,504 844 1,255 1,547 1,209 25 top SNPs
Harold et al. [60], September 2009b US/Europe Case control 13 discovery and 5 replication series Illumina 610-quad, Illumina umanHap550, or umanHap300 529,205 (up to) 3,941 7,848 2,023 2,340 Genome-wide significance after Bonferroni correction + 12 other CLU/PICALM SNPs
Lambert et al. [61], September 2009b Europe Case control 1 discovery and 4 replication series (15 centers) Illumina Human 610-Quad BeadChip 537,029 2,032 5,328 3,978 3,297 P < 10-5
  1. The study designs of the 11 independent late-onset Alzheimer disease genome-wide association studies are depicted. The Coon et al. [51] and Reiman et al. [52] studies are overlapping. Abraham et al. [54], Grupe et al. [50], and Harold et al. [60] also have overlapping samples. Carrasquillo et al. [59] contributed data to the Harold et al. [60] study. aNumber of single-nucleotide polymorphisms (SNPs) in the initial genotyping stage. bStudies hat yield non-APOE associations that are significant at the genome-wide level after Bonferroni corrections. AD, Alzheimer disease; CEPH, Centre d'Etude du Polymorphisme Humain; FDR-BUM, false discovery rate-beta uniform mixture.