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Table 1 A toy example illustrating how MDR collapses two 3 × 3 genotype tables to a 2 × 2 contingency table

From: The choice of null distributions for detecting gene-gene interactions in genome-wide association studies

Case

BB

Bb

bb

Control

BB

Bb

bb

MDR table

Case

Control

AA

179

119

18

AA

199

126

15

   

Aa

315

173

26

Aa

306

164

17

Low-risk

399

443

aa

101

59

10

aa

118

49

6

High-risk

601

557

  1. Suppose the threshold of the odds ratio in MDR is specified to be τ OR = 1. Then the 2 × 2 contingency table is obtained by MDR in the following way: For the cells whose odd-ratio is higher than τ OR will be considered as high-risk. For case genotypes, the bold numbers indicate these genotypes are considered as high-risk. Their summation equals to 601 as shown in bold font in the MDR table. For control genotypes, the italic numbers also indicate these genotypes are considered as high-risk. Their summation equals to 557 as shown in italic font in the MDR table. For the low-risk cells, this is done in the same way. Statistical tests can be conducted based on the 2 × 2 contingency table: χ2 = 3.9711 for the Pearson χ2 test and χ2 = 3.9726 for the likelihood ratio test.