STR null alleles complicate parentage testing in South Africa.

BACKGROUND: Null alleles complicate parentage testing because they do not contribute positively to phenotypes.Objectives. To survey South African populations for null alleles at short tandem repeat (STR) loci used in parentage testing. METHODS: Paternity case data were scanned for apparent contradictions compared with Mendelian inheritance that could be due to null alleles. Estimates of null allele frequencies were obtained from tallies of apparent carriers. RESULTS: Three of 15 loci appeared to have null alleles at appreciable frequencies and five showed no evidence of null alleles. A null allele at the vWA locus reached a frequency of ~0.3% in the black population and approximately three times this frequency in the coloured population. No apparent vWA null carriers were detected in whites suggesting that the Khoisan were the major contributors of the null alleles to coloureds. The apparent genotypes of a sample of TPOX null carriers changed from homozygous to heterozygous when they were retyped using different polymerase chain reaction primers. The revealed allele was allele 6 in every case. A D13S317 null allele was detected at relatively low frequencies in the black and coloured samples but 2/145 Indian (Asian) parents appear to be carriers, suggesting that it could be common in Indians. CONCLUSION: Three of the 15 forensically relevant STR loci investigated had null alleles at significant frequencies in South African populations. Failure to allow for the presence of null alleles can have a large impact on the outcome of parentage tests.

Chitotriosidase deficiency: a mutation update in an african population.

Human plasma chitotriosidase activity is a commonly used diagnostic and therapeutic biomarker for non-neuronopathic Gaucher disease. Chitotriosidase deficiency is common in non-African populations and is primarily caused by a 24 bp duplication in the encoding gene (CHIT1). Allele frequencies for the 24 bp duplication range from 20-50 % outside Africa. The present study found chitotriosidase deficiency to be rare in the South African Black population (1.6 %) and the otherwise common 24 bp duplication is absent in this African population. Instead, chitotriosidase deficiency is caused by a 4 bp deletion across the exon/intron 10 boundary (E/I-10_delGAgt) of the CHIT1 gene. The exact position of this mutation was found to differ from the previously reported location. Allele frequencies for six coding variants of CHIT1 (p.G102S, p.G354R, 24 bp duplication, E/I-10_delGAgt, p.A442V/G) were determined and the 4 bp deletion was found to be in complete linkage disequilibrium (LD) with two of the coding variants (p.G354R and p.A442V). The in silico assessments of the two missense mutations in LD predict a protein-damaging nature and functional studies are needed to clarify if one or both abolish the enzyme's activity. Overall, the low frequency of chitotriosidase deficiency in South African Blacks makes chitotriosidase activity an excellent biomarker of choice in this population.