This approach is more difficult because researchers have to contend with recombination events that have accumulated over, perhaps, tens of thousands of years. In a sense, recombination has had time to shuffle the DNA into smaller blocks, and that requires more markers. To cover the entire genome, anywhere from 100,000 to 1,000,000 markers might be needed for an association study, compared with 2000-3000 markers for a linkage analysis. Although association studies have been less common, they have been successful, according to Aravinda Chakravarti of Case Western University. We use this principle over and over again.
Preliminary evidence suggests the approach also can be used in more complex diseases.
The researchers concentrated on a 4-Mb region around the gene and identified 51 SNPs. Ten of those SNPs had frequencies greater than expected, suggesting that they could be used as disease markers. The researchers compared these results with other marker methods and found that SNPs provided a more efficient way of identifying the gene. So have Celera and Genset. But, because the SNP map is not complete, nobody has ever been in a position to fully test the whole-genome method.