Allelic variation and mutation at human hypervariable minisatellite loci.

Human polymorphic tandemly repeated loci have been exploited in linkage analysis and have also had a profound impact on forensic and legal medicine. Most DNA typing systems assay allelic length variation at tandem repetitive loci such as minisatellites. Although these include the most informative loci in the human genome, their forensic application is limited by innaccuracies in allele length measurement, and the need to make population genetic assumptions in statistical analysis. Minisatellite alleles frequently vary not only in repeat copy number, but also in the interspersion pattern of variant repeat units, which can be assayed by minisatellite variant repeat mapping (MVR). This technique uses either restriction analysis, or more efficiently MVR-PCR, to display minisatellite allele internal structures as digital codes that can theoretically distinguish millions of alleles. MVR-PCR profiles from the hypervariable minisatellites MS31A and MS32 generate extraordinarily heterogenous codes, reflecting extreme levels of allelic variability, far in excess of that detectable by allele length analysis. These codes are appropriate for forensic investigations and for analysing allelic diversity and mutation. Comparison of MVR structures showed that most alleles at both loci were different, implying the existence of many thousands of alleles worldwide. Variation between groups of alleles with related MVR-structures was largely confined to one end of the locus, providing evidence for a localised mutation "hotspot". This was confirmed by using MVR-PCR to characterise de novo mutation events at both loci. Most mutations involved gains of small numbers of repeats at the ultravariable end of the tandem repeat array, by highly polar intra- and interallelic unequal conversion-like processes. Evidence suggested that this mechanism was male germline-specific, and possibly meiotic. Less frequent intraallelic deletions were seen in male and female germline and in somatic tissues. These observations suggest that the same mechanisms of repeat unit turnover may operate at different hypervariable minisatellites.