Population genetic data determined for five different single locus minisatellite probes

Study of three hypervariable DNA loci (D1S7; D7S22 and D12S11) in three European populations

To investigate the population genetic characteristics and genetic affinity, DNA profiles of three highly polymorphic VNTR (variable number of tandem repeats) loci (D1S7; D7S22 and D12S11) were studied in 405 individuals from three major European populations (English, Spanish and Basques). Like other studies on VNTRs, a large significant heterozygote deficiency was observed in all three populations. This decrease was ascribed to the limitation, coalescence and non-detectibility of alleles associated with the RFLP (restriction fragment length polymorphism) technique, through which the VNTR loci are genotyped. When the non-detectable alleles were taken into consideration, analyses of fragment sizes at these loci within each sample, as well as their fixed binned analyses, reveal that the assumptions of independence of allelelic occurrences within and between loci are valid for this European data. By comparing genetic variation at three VNTR loci with 17 blood groups, proteins and HLA loci in three well defined European populations, it is shown that the pattern of differentiation at these sets of loci are in general parallel especially for the hypervariable loci HLA and VNTR. Fixed-bin allele frequencies, therefore, are the best descriptions of such a database both for population genetic and forensic calculation studies. The Basques, with regard to VNTR loci, do not show any reduced genetic variability compared to other two European populations (English and Spanish).

Population genetic and family data for the human minisatellite locus D16S309 (MS205) in Germans

The distribution of restriction fragments at the DNA minisatellite locus D16S309 was estimated by investigating blood samples from 2617 unrelated West German Caucasians and 1269 offspring. Furthermore segregation of fragments was studied in a large family and in trios. Altogether 2296 meioses were studied, revealing 7 paternal and 3 maternal mutations. Inspection of "phenotypes" did not reveal any remarkable deviation from Hardy-Weinberg equilibrium.

Recent observations in human DNA-minisatellite mutations

We report maternal and paternal mutation rates at loci D1S7 (MS1), D7S21 (MS31), D12S11 (MS43A), and D7S22 (G3). The respective mutation rates were as follows: [table: see text] At loci D7S21, D12S11, and D7S22 statistically significant differences in mutation rates exist between the sexes. No such difference was observed at locus D1S7. However inspection of the latter data reveals that by mutation at spermiogenesis approximately two-thirds of the fragments showed an addition of repetitive units, while a 50: 50 ratio was encountered in the series of maternal mutations. We also report the observation of naturally occurring 3-fragment patterns.

DNA fingerprinting used to test for family effects on precocious sexual maturation in two populations of Oncorhynchus tshawytscha (Chinook salmon)

Two single locus Variable Number Tandem Repeat (VNTR) DNA probes were used to test for differences in allele distribution between precociously mature male and immature chinook salmon, Oncorhynchus tshawytscha. Two populations were examined: Robertson Creek (RC) adult salmon, and Nicola River (NR) freshwater juveniles, or parr. Genomic DNA was extracted from 74 RC precociously mature adult males ('jacks') and 94 RC immature adults of the same age and from 45 NR precociously mature parr and 51 NR nonmaturing parr. The genomic DNA was hybridized with a single locus VNTR probe developed for chinook salmon (OtSL1), as well as one developed for Atlantic salmon, Salmo salar (Ssa1). The allele frequency distributions at both loci were significantly different for the RC jacks and immature fish, indicating a family effect on the incidence of precocious maturation in that population. No difference was found between the allele frequency distribution of the NR precocious and immature parr. A bin width sensitivity analysis showed that the comparisons of the allele frequency distributions were insensitive to the choice of bin size. No differences in heterozygosity were found between mature and immature fish at either locus for both stocks. Preliminary testing for family effects on phenotypes of interest, such as alternative life history strategies, can be performed using hypervariable VNTR DNA probes, prior to implementing costly and involved breeding programmes.

Paternity testing with VNTR DNA systems. I. Matching criteria and population frequencies of the VNTR systems D2S44, D5S43, D7S21, D7S22, and D12S11 in Danes

Paternity testing using DNA polymorphism of variable numbers of tandem repeat (VNTR) regions with restriction fragment length polymorphism (RFLP) was implemented. HinfI-digested DNA was separated by electrophoresis in agarose gels and hybridized with radiolabelled probes detecting the VNTR-systems D2S44 (YNH24), D5S43 (MS8), D7S21 (MS31), D7S22 (g3), and D12S11 (MS43a). The intra gel variability of 970 duplicate investigations on the same gel of DNA from 122 individuals showed no differences exceeding 1.25 mm between the positions of the corresponding DNA fragments. The comparison of 1,624 DNA fragments from 342 mother/child pairs showed only one difference above 1.25 mm which was interpreted as a mutation. Based on these observations, we decided to consider an intra gel difference above 1.25 mm between the non-maternal DNA fragment of the child and the nearest DNA fragment of the putative father as an exclusion in paternity testing. This matching criterion was used for the comparisons of 1,197 DNA fragment differences in 247 pairs of children and putative fathers who had not been excluded by conventional marker systems. In all of these cases, the migration differences between the DNA fragments of non-excluded men and the DNA fragments of the children were less than 1.25 mm except in 6 cases (0.5%). The man/child differences in all of 227 false trios exceeded 1.25 mm in 2 or more of the 5 VNTR systems investigated. Matching criteria for inter gel comparisons in paternity testing were established. The frequency distribution of HinfI digested DNA fragments of the 5 VNTR systems in 650 unrelated Danes is presented and the raw data is available.

Paternity testing with VNTR DNA systems. II. Evaluation of 271 cases of disputed paternity with the VNTR systems D2S44, D5S43, D7S21, D7S22, and D12S11

Paternity testing was carried out in 271 cases of disputed paternity using the 5 VNTR systems D2S44 (YNH24), D5S43 (MS8), D7S21 (MS31), D7S22 (g3), and D12S11 (MS43a), and 10-15 conventional marker systems including the HLA-A,B system. By means of the matching criteria for the VNTR systems established elsewhere (Morling & Hansen 1992), all 70 unrelated men who had been excluded by conventional typing were also excluded with 2 or more VNTR systems. Based on the observed exclusion frequencies for the 5 VNTR systems, a theoretical exclusion rate exceeding 0.999 could be obtained. A total of 350 father/child pairs were studied and in 3 paternity cases and one immigrant family, the alleged fathers were excluded solely by one of the 5 VNTR systems possibly reflecting mutations. No mother/child exclusions were observed among 350 mother/child pairs. Linkage analysis between the syntenic systems D7S21 (MS31) and D7S22 (g3) was performed in 29 informative families with 81 children and revealed a recombination distance of about 31 cM. The positive evidence for paternity provided by the 5 VNTR systems in cases with non-exclusions is discussed.