Methods and systems are provided for performing allelic copy number association in genome-wide association studies. Also provided are computer-readable media for storing instructions for performing the genomic marker association studies. The methods include performing genomic marker association studies wherein allelic contrast and copy number are analyzed simultaneously, comprising the steps of receiving measurements of intensity for each of two alleles (A and B) in a biological sample set; computing a sum value (S) and a difference value (D) of the intensities; and employing a statistical model to determine a potential association of the S and/or the D value with an outcome, wherein a statistically significant coefficient of the S intensity indicates an association of the copy number with the outcome and a statistically significant coefficient of the D intensity indicates an association of the allelic contrast with the outcome.
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