DOES IT MAKE SENSE TO STUDY AND ANALYSE A RELATIVELY SMALL NUMBER OF POLYMORPHISMS?
Analysing just one polymorphism can lead to spurious associations, among other things, because the variant may be at linkage disequilibrium with other variants, thus forming a characteristic haplotype. Sharma, et al.6 consider that for a candidate gene, selection, genotyping, and frequency analysis of, at least, three common polymorphisms allows identifying variants at linkage disequilibrium and identifying synergies. In a population-based case-control study where proximal SNPs have been genotyped and given that by definition the phase is unknown, haplotypes may be inferred by using genetic software applications: (GDA: http://hydrodictyon.eeb.uconn.edu/people/plewis/software.php and Arlequn: http://lgb.unige.ch/arlequin/), but it should not be determined in its totality, neither should it be associated with a measurable phenotype in a give subject (except those genotyped as homozygous for all the SNPs evaluated in a locus). Nowadays, information on haplotypes begins to be available in
