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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.