A D19S433 Primer Binding Site Mutation and the Frequency in Japanese of the Silent Allele It Causes

Abstract

Short tandem repeat studies are powerful tools for parentage analysis and for identification of missing persons, victims of murder, and victims of mass fatalities when reference samples are unavailable. The primer in the Identifiler kit failed to amplify an allele at the D19S433 locus, producing a silent ("null") allele. The causal mutation is a base change (G>A) 32 nucleotides downstream from the 3' end of the AAGG repeats. The silent alleles are problematical in parentage analysis because when transmitted, they can cause a parent-child inconsistency that is unrelated to Mendelian genetics. The inconsistency is sometimes termed an "apparent opposite homozygosity" and it produces false evidence of nonparentage. Alternative primers were designed to amplify the D19S433 locus alleles and they detect the silent allele. Frequencies of the (no longer) silent allele were determined to be 0.0114 in 176 people from Shizuoka (Honshu) and 0.0128 in 156 people from Okinawa.

False deletion of the D15S986 maternal allele in a suspected case of Angelman syndrome

“…It is well known that mutations in the primer binding site of STR loci can cause "null alleles" [17][18][19][20], resulting in apparent homozygosis. As a result, caution must be used in the interpretation of a single locus mismatch.…”

Concordance testing between Powerplex ESI 16 Fast System and VeriFiler Express

“…Mizuno and coworkers observed dropout discordance at the D19S433 locus caused by a G → A single nucleotide polymorphism (SNP) that prevented the annealing of the reverse primer at that locus [14]. Similarly, other groups reported primer binding site mutations at specific loci TH01 [15], D8S1179 [16], FGA [17], D18S51 [11],…”

Risk analysis of duo parentage testing with limited STR loci

“…As Tables 1 and 2 show, when genotyped by the Goldeneye 20A system, the cases of C1, C3, and C4 did not reject paternal identity without the mother's information (PI: 0.0005, 0.0091, and 0.0037); only C2 rejected fatherhood (PI < 0.0001). If PCR amplification of STR genotypes fails multiple times, a locus mismatch is produced (Mizuno et al, 2008;Tsuji et al, 2010). We typed these cases using the Identifiler and Goldeneye 20A systems and detected no amplification failure.…”