An association or linkage between a genetic locus and a disease phenotype is identified by confirming that a test population comprising a plurality of humans is an index founder population (IFP). This is accomplished by determining that (i) the consanguinity rate of a test population is greater than ten percent and (ii) at least five percent of a portion of the autosomal genome, from which marker genotypes have been measured at an average marker density of at least 1 marker per 100 kilobases of genome in each human in at least fifty percent of the humans in the test population, is encompassed by homozygous marker tract lengths that are at least one megabase long. A genetic analysis between (i) the disease phenotype exhibited by the IFP, and (ii) IFP genome variation is performed to find the genetic locus linked with or associated with the disease phenotype.