The limitation of SNP techniques is that the magnitude of association between a particular allele and a disease have turned out to be rather low - in the order

The limitation of SNP techniques is that the magnitude of association between a particular allele and a disease have turned out to be rather low - in the order of 1-2 times increased risk. This is virtually meaningless on an individual level - for example if there is a 1:1000 risk of a particular disease in the population and you have the risk allele you would still only have a 1:500 risk of getting the condition. A possible explanation for this is that that all of the alleles that are tested in genome wide association studies are found relatively frequently in the population - it may be that rare alleles exist that confer far greater risk e.g. 10-100 increase and it is these that mediate the majority of the inherited risk of a condition. These rare alleles could not be detected by a microarray based approach but would be identified by massive resequencing. A preliminary resequencing effort is already underway: http://www.1000genomes.org/ http://www.1000genomes.org/ and within the next few years whole genome resequencing on an individual basis will become feasible with massively paralell techniques such as Selexa.