The CASECONTROL Procedure

Marker information can be used to help locate the genes that affect susceptibility to a disease. The CASECONTROL procedure is designed for the interpretation of marker data when random samples are available from the populations of unrelated individuals who are either affected or unaffected by the disease. Several tests are available in PROC CASECONTROL that compare marker allele and/or genotype frequencies in the two populations, with frequency differences indicating an association of the marker with the disease. Although such an association can point to the proximity of the marker and disease genes in the genome, it can also reflect population structure, so care is needed in interpreting the results; association does not necessarily imply linkage.

The three chi-square tests available for testing case-control genotypic data are the genotype case-control test, which tests for dominant allele effects on the disease penetrance, and the allele case-control test and linear trend test, which test for additive allele effects on the disease penetrance. Since the allele case-control test requires the assumption of Hardy-Weinberg equilibrium (HWE), it might be desirable to run the ALLELE procedure on the data to perform the HWE test on each marker (see Chapter 3: The ALLELE Procedure, for more information) prior to applying PROC CASECONTROL.