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. Author manuscript; available in PMC: 2010 Oct 1.
Published in final edited form as: Nat Genet. 2010 Feb 28;42(4):295–302. doi: 10.1038/ng.543

Table 1. Sample collections and genotyping platforms.

Collection Country Celiac disease cases Controls
Sample size
(pre-QC)a 		Sample size
(post-QC)b 		Platformc Sample size
(pre-QC)a 		Sample size
(post-QC)b 		Platformc
Stage 1: Genome wide association
1ef UK 778 737 Illumina Hap300v1-1 2,596j 2,596 Illumina Hap550-2v3
2eg UK 1,922 1,849 Illumina 670-QuadCustom_v1 5,069j 4,936 Illumina 1.2M-DuoCustom_v1
3e Finland 674 647 Illumina 670-QuadCustom_v1 1,839j 1,829 Illumina 610-Quad
4h Netherlands 876 803 Illumina 670-QuadCustom_v1 960 846 Illumina 670-QuadCustom_v1
5e Italy 541 497 Illumina 670-QuadCustom_v1 580 543 Illumina 670-QuadCustom_v1
Analysis of Hap300 markers 4,533 10,750
Analysis of additional Hap550
markers		 3,796 8,154
Stage 2: Follow-up
6 USA 987 973 Illumina GoldenGate 615 555 Illumina GoldenGate
7 Hungary 979 965 Illumina GoldenGate 1,126 1,067 Illumina GoldenGate
8i Ireland 653 597 Illumina GoldenGate 1,499 1,456 Illumina GoldenGate
9 Poland 599 564 Illumina GoldenGate 745 716 Illumina GoldenGate
10 Spain 558 550 Illumina GoldenGate 465 433 Illumina GoldenGate
11e Italy 1,056 1,010 Illumina GoldenGate 864 804 Illumina GoldenGate
12e Finland 270 259 Illumina GoldenGate 653j 653 Illumina 610-Quadd
Subtotal 4,918 5,684
Analysis of Hap300 markers, and
follow-up (91 SNPs)		 9,451 16,434
Analysis of additional Hap550
markers, and follow-up (40 SNPs)		 8,714 13,838
a

Sample numbers attempted for genotyping, before any quality control (QC) steps were applied.

b

Sample numbers after all quality control (QC) steps (used in the association analysis).

c

All platforms contain a common set of Hap300 markers; the Hap550, 610-Quad, 670-Quad and 1.2M contain a common set of Hap550 markers.

d

Finnish stage 2 controls were individuals within the Finrisk collection for whom Illumina 610-Quad genotype data became available after the completion of stage 1.

e

As an additional quality control step, we performed case-case and control-control comparisons for collection 1 versus 2, and collection 3 versus 12, for the 40 SNPs in Table 2 and observed no markers with P<0.01. We did observe (as expected) differences for collection 5 versus 11, from Northern and Southern Italy, respectively.

f

All 737 post-QC cases reported in a previous GWAS1.

g

690 of the post-QC cases and 1150 of the post-QC controls were included in previous GWAS follow-up studies22,32.

h

498 of the post-QC cases and 767 of the post-QC controls were included in previous GWAS follow-up studies22,32.

i

352 of the post-QC cases and 921 of the post-QC controls were included in previous GWAS follow-up studies22,32.

j

Some of these data were generated elsewhere, and some prior quality control steps (information not available) had been applied.