For each SNP the Cochrane-Armitage trend-test statistic is computed from a 3x2 contingency table

 Cases Controls Row totals AA AB BB Column totals

() and () and () are the total number of occurrences of genotype AA, AB and BB, respectively, for the cases (controls), and

The Cochrane-Armitage trend-test statistic with weights is defined as

The MAX statistics is equal to the maximum of the three Cochrane-Armitage trend-test statistic obtained when assuming a recessive ( ) model, a dominant model ( ) and an additive model ( ). When assuming an additive model( ), the Cochrane-Armitage trend-test statistic is equal to

where , and .

Marit Holden 2008-08-07