Extensive progress in human genetics and clinical diagnostics allowed identification of the majority of genetically-related diseases. Still, the genes responsible for numerous diseases have not been recognized and frequently the disease etiology remains unknown. This is true for keratoconus, the study subject of this article. Therefore, before mutation analysis or other sequence variant assessment, it is essential to identify the chromosomal region, where a gene or genes causing the disease phenotype are located. To achieve that, advanced bioinformatics methods are applied to data obtained from molecular research to narrow the chromosomal region containing the disease locus.