During routine paternity testing a mutation of a paternal allele at the HPRTB locus was observed. The opportunity was taken to analyse this mutation at a molecular level. The repeat sequence is flanked by an imperfect repeat sequence and this region could be involved in the mutation mechanism. For this reason, we also examined the structure of "intermediate" alleles. Sequencing confirmed the insertion of a perfect repeat motif and revealed a deletion of a dinucleotide some 50 nucleotides downstream from the repeat sequence for the intermediate alleles. It is likely that these intermediate alleles are rare biallelic deletion polymorphisms and are probably not involved in the mutation or variation mechanism of this locus.
STRs have become almost the exclusive tool of genetic scientists in forensic typing work. Consequently, large numbers of samples are genotyped and the detection of rare abnormalities is to be expected. We found rare losses of alleles, also known as drop-out, at the two STR loci D13S317 and CD4. Drop-out at D13S317 was accidentally found in typing of suspects in a murder case and three other examples of drop-out were found at locus CD4 during paternity testing. The lost alleles reappeared when alternative PCR primer pairs were used. Sequences of lost alleles were characterised at the molecular level after cloning. Variations were found in the primer sequences and these are believed to prevent amplification or to reduce amplification yield and to be the origin of the allele drop-out.
In order to apply a set of nine STR loci in parentage testing, we performed a population genetic study on a sample of the Flemish population. Genotypes for HUMHPRTB, HUMFABP, HUMCD4, HUMCSF1PO, HUMTH01, HUMPLA2A, HUMPLA2A1, HUMF13A01, HUMCYAR04 and HUMLIPOL were determined using three triplex PCR reactions and silver staining. Allele frequencies showed no deviation from Hardy-Weinberg equilibrium. The frequency distribution agreed well with other Caucasian populations but three intermediate fragments, not previously found in Caucasians, were observed. We then resolved a series of 151 parentage disputes of which 103 were exclusions. In six cases, evidence for exclusion was obtained by only one informative STR locus out of eight for male children or out of nine for female children. These exclusions were confirmed with additional polymorphic markers. In one case of inclusion, a paternal allele expanded with one repeat unit of HUMHPRTB. This observation illustrates that STRs do not differ from other genetic systems in the fact that more than one excluding locus is required before exclusion is demonstrated.
The allele frequency and sequence structure of the STR locus D12S1090 were investigated in 598 Flemish individuals. The locus shows a complex organisation with repetitions of GATA interrupted by TA and other tetra- and pentanucleotide blocks. No deviation from Hardy-Weinberg equilibrium was observed. The extensive polymorphism makes it a powerful tool for identity as well as paternity testing and even permits differentiation of closely related populations, such as Flemish and Germans. D12S1090 seems to be one of the most informative STRs, however, as seen in other highly variable STRs, the observed mutation frequency of 5.1 x 10(-3), is relatively high. of STR loci is typing highly polymorphic STRs such as ACTBP2 [3]. We thus investigated the tetranucleotide (GATA) repeat locus D12S1090 (GDB accession number GDB:376560, also known as GATA5A09) in a population sample from Flanders, the Dutch speaking part of Belgium. Although this STR is considered to be highly polymorphic [4], compared with other STRs, it has only scarcely been studied.
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