  In a case-control study aimed at localizing disease variants, association
between a marker and the disease status is often tested by comparing the marker
allele frequencies among cases and controls. These marker allele frequencies
are expected to be different if the marker is associated with the disease. The
power of the commonly used allele based test is based on the marker allele
frequency; markers with a low minor allele frequency have less power to be
detected (if they are associated with the disease), than markers with high
minor allele frequency. Therefore the strategy of selecting markers for
follow-up study based on their p-values, favors markers with a high minor
allele frequency.
  We propose an allele based test that does not have this (unwanted) property
and is therefore more powerful for markers with a low minor allele frequency.
This test may, therefore, be more effective when searching for rare causal
variants. The asymptotic power function of the test is derived and simulation
studies are performed for finite sample properties of the test. Next, the
existing and the proposed tests are applied to data; this is not included yet.
  In the light of the current interest in detecting association between complex
phenotypes and causal variants with a low minor allele frequencies, this test
is expected to be of relevance.
