Phenotype versus genotype reporting for DNA polymorphisms

Abstract In the College of American Pathologists' (CAP) 2001 PI-A survey, consensus was not achieved for the child's phenotype at the HUMTH01 locus. Two alleles (6 and 9.3) were reported by 37 laboratories, and only one allele (9.3) by 30 laboratories. Analysis of the results showed that this discrepancy was related to the kits used. This was attributed to a primer binding site mutation. The mother's phenotype was 8,9.3 and the tested man's 9,9.3. Participants who detected the “6” allele in the child reported a PI of 0, while participants who did not detect it reported a median PI of 1.43. Two participants reported the inferred genotype of 9.3,9.3. This is clearly an incorrect response. This case illustrates that for DNA polymorphisms the phenotypes detected may depend on the testing method used. Thus reporting phenotypes only is sound and scientifically accurate.