Human minisatellite alleles detectable only after PCR amplification

Comparison of germ line minisatellite mutation detection at the CEB1 locus by Southern blotting and PCR amplification

Identification of de novo minisatellite mutations in the offspring of parents exposed to mutagenic agents offers a potentially sensitive measure of germ line genetic events induced by ionizing radiation and genotoxic chemicals. Germ line minisatellite mutations (GMM) are usually detected by hybridizing Southern blots of unamplified size-fractionated genomic DNA with minisatellite probes. However, this consumes a relatively large amount of DNA, requires several steps and may lack sensitivity. We have developed a polymerase chain reaction (PCR)-based GMM assay, which we applied to the hypermutable minisatellite, CEB1. Here, we compare the sensitivity and specificity of this assay with the conventional Southern hybridization method using DNA from 10 spouse pairs, one parent of each pair being a survivor of cancer in childhood, and their 20 offspring. We report that both methods have similar specificity but that the PCR method uses 250 times less DNA, has fewer steps and is better at detecting GMM with single repeats provided that specific guidelines for allele sizing are followed. The PCR GMM method is easier to apply to families where the amount of offspring DNA sample is limited.

Human minisatellite loci composed of interspersed GGA-GGT triplet repeats

We have isolated two tandemly repeated loci from human DNA which contain long blocks of GGA and GGT trinucleotide repeats. These two repeat unit types, together with other less common variants, are apparently irregularly interspersed along each repeat array. Genotyping methods have been developed for these highly polymorphic loci, including typing by polymerase chain reaction followed by Southern blot hybridization. Linkage analysis in Centre d'Etude du Polymorphisme Humain (CEPH) pedigrees has been used to map the loci to chromosomes 15 and 22. In normal individuals, alleles at these loci can contain thousands of repeats, greatly exceeding repeat copy number at most trinucleotide and other simple repeat loci. No evidence for longer, higher-order repeats was observed among the limited number of repeats sequenced. These loci may represent a transitional state between simple repeat loci and some minisatellites.

Microsatellite polymorphisms reveal phylogenetic relationships in primates

We amplified, via PCR, DNA segments from intron 1 of the tyrosine hydroxylase gene (TH01) and intron 40 of the von Willebrand factor gene (VWA) in ten nonhuman primate genera. In humans both introns contain polymorphic microsatellites with tetrameric repeats. Compared to the allelic ranges in human populations relatively short repeat arrays could be detected for the nonhuman primates typed, presumably reflecting an ancient precursor state at both microsatellite loci. Furthermore, our results provide evidence for an association of the average number of repeats present in different primate genera and their divergence time from man. DNA sequencing of VWA orthologues revealed a relatively high variability in the arrangement of repeats in the 5'-repeat arrays, the generation of which could probably be explained by polar mutational events.

The detection of subtelomeric chromosomal rearrangements in idiopathic mental retardation

A major challenge for human genetics is to identify new causes of mental retardation, which, although present in about 3% of individuals, is unexplained in more than half of all cases. We have developed a strategy to screen for the abnormal inheritance of subtelomeric DNA polymorphisms in individuals with mental retardation and have detected three abnormalities in 99 patients with normal routine karyotypes. Pulsed-field gel electrophoresis and reverse chromosome painting showed that one case arose from an interstitial or terminal deletion and two from the de novo inheritance of derivative translocation chromosomes. At least 6% of unexplained mental retardation is accounted for by these relatively small chromosomal abnormalities, which will be an important resource in the characterization of the genetic basis of neurodevelopment.

Minisatellite DNA markers in the chicken genome. II. Isolation and characterization of minisatellite loci

The isolation of chicken minisatellites is reported. Two charomid libraries were constructed from fractions of size-selected MboI-digested genomic DNA. A total of 5985 colonies were screened with the multilocus probes 33.6 and 33.15; 137 positives were obtained (2.35%). A total of 55 clones were tested against four unrelated chickens; 30 revealed variable single locus patterns. More detailed characterization was made of 15 probes, which were tested against four families comprising a total of 53 offspring. Of parent/offspring comparisons 51% were informative for segregation. No mutations were detected. Three minisatellites were linked on the same autosome, implying that these loci may occur in clusters, and one was Z chromosome-linked. Heterozygosity and allelic variability were measured in 67 individuals from several different strains and breeds. Mean heterozygosity ranged from 50 to 84%. Minisatellite loci appear to be highly variable in the chicken and should provide highly informative markers in intraspecific crosses in genome mapping studies.

Charomid cloning vectors meet the pedipalpal chelae: single-locus minisatellite DNA probes for paternity assignment in the harlequin beetle-riding pseudoscorpion

We describe the first application of the charomid-cloning method for developing single-locus minisatellite DNA probes in a terrestrial arthropod. From a genomic library of the neotropical pseudoscorpion, Cordylochernes scorpioides, we have isolated two probes with heterozygosities exceeding 95%. These probes yielded single-locus patterns after only low stringency washing and in the absence of genomic competitor DNA. Analysis of three pedigrees indicated germline stability and showed no evidence of linkage between the loci. Patterns of allelic transmission generally conformed closely to Mendelian expectations but large offspring numbers did enable detection of one example of significant bias in allele inheritance. Two test cases are presented to illustrate the clarity and power with which these probes can establish paternity: (i) a female mated to three unrelated males, and (ii) a female mated to two of her brothers. In both cases, a single probe could be used to assign the paternity of all offspring.

Identification, isolation and characterization of canine minisatellite sequences

A Charomid ordered-array library containing a 2-16 Kb size fraction of MboI-digested canine genomic DNA has been screened with the Jeffreys multilocus probes, 33.6 and 33.15, to identify and isolate canine minisatellite sequences. Of the 48 positive clones identified, 7 were found to contain polymorphic minisatellites with heterozygosities in the range 20-88%. The majority of the remainder were either monomorphic or dimorphic in the animals tested. Analysis of intrabreed variation in Bedlington Terriers using two polymorphic minisatellites has shown that a significant reduction occurs in the number of alleles seen compared to an agglomerated population sample, correlating with the high level of inbreeding within this breed. Flanking DNA sequence and partial repeat sequence is presented for the most polymorphic minisatellite thus far identified, cCfaMP5. The variable region in this minisatellite is similar to human minisatellites which show a distinct purine or pyrimidine strand bias.

Allele frequency data for VNTR locus D17S79: identification of an internal HaeIII polymorphism in the black population

D17S79 is one of several highly polymorphic VNTR loci commonly used to generate DNA profiles for forensic identity testing and parentage determination. In this study, we used Southern hybridization analysis of HaeIII-digested genomic DNA to compile D17S79 allele frequency databases for the Caucasian, Southeast Asian, East Indian, and Black populations of Southern Ontario. In our Black population sample, low-molecular-weight D17S79 alleles are relatively common and approximately 7% of the individuals have three-band hybridization patterns due to a HaeIII restriction site polymorphism within a common D17S79 allele. The internal HaeIII site generates an allele consisting of two HaeIII fragments of approximately 980 and 420 bp. The estimated frequency of this "split-allele" in our Black population is 0.035. Since this allele was not observed in the other population groups, the internal HaeIII polymorphism probably originated within the Black population. Although the existence of low-molecular-weight alleles and the internal HaeIII polymorphism could affect the interpretation of some VNTR patterns, they are of little or no forensic consequence to the frequencies assigned to VNTR profiles.

Origins of polymorphism at a polypurine hypervariable locus

We present characterisation of a hypervariable locus, D8S210, mapped to the telomeric region of the short arm of chromosome 8. The locus is highly polymorphic with alleles varying in size from 1.8 kb to 24 kb. Sequence data from 7 alleles shows that the variable region is entirely polypurine on one strand with a tetranucleotide repeating unit GGAA at the margins and diverged versions of this motif internally. The margins are conserved between alleles; polymorphism occurring in the internal regions of the repeat. Alleles are inherited in a Mendelian manner and one new mutation has been observed in analysis of 51 meioses. Use of single copy flanking sequences to elaborate the polymorphism revealed loss of single copy DNA in 3 unrelated families and in 2 other unrelated individuals. Restriction mapping shows that this loss is similar for different sized alleles in all three families suggesting that it was an early event that may have involved a flanking Alu sequence. We present evidence that the polypurine region can adopt triplex conformations in vitro. Such structures may facilitate loss or gain of unique sequences in the genome, contribute to mutation at conformation transition points and drive the hypervariability (> 99% heterozygosity) of this locus.

Chemiluminescent DNA probes: evaluation and usefulness in forensic cases

Five phosphatase-labelled oligonucleotide probes were evaluated in respect to their sensitivity, with the help of an optimized chemiluminescent protocol, for DNA-VNTR polymorphism determination. Their usefulness for the identification of biological traces is illustrated with casework examples.

Comparison of five tandem repeat loci between humans and chimpanzees

Five tandem repeat loci were studied in humans and chimpanzees using VNTR probes derived from human DNA. Shared alleles were found at three loci and were often the modal allele in one species but never in both. There was no difference in the mean number of alleles per locus. However, these species exhibited substantially different levels of gene diversity, with chimpanzees monomorphic at two loci. Evidence of reduced variability in chimpanzees corroborates earlier comparisons using isozymes and plasma proteins. Molecular mechanisms, population dynamics, or both may be responsible for these differences. Equal numbers of alleles per locus may reflect high mutation rates. By one test, chimpanzees were out of equilibrium at one locus, which may reflect a typing error or population substructure. The long divergence time, and the high probability of backward mutations, precludes accurate estimation of genetic distance between these species.