Highly polymorphic minisatellite DNA probes. Further evaluation for individual identification and paternity testing

Genotyping analysis using an RFLP assay

RFLP (Restriction Fragment Length Polymorphism) is a commonly used technique that can be used for genotyping for nearly all organisms, including plants, animals, and humans. RFLP is widely used in genetic and genomic research, such as genome mapping and gene identification. The technique involves DNA digestion, gel electrophoresis, capillary transfer of DNA, and southern hybridization. In this chapter, we aim to give a detailed introduction of how to perform RFLPs for identifying genotypes.

A preliminary study on the incidence of heteroplasmy in mitochondrial DNA from vitreous humour

Vitreous humour is routinely sampled in Forensic Medicine as several post-mortem analyses can be performed. However, it is not used for DNA analyses probably due to its scarce cellularity. In these samples, in which the study of nuclear DNA is difficult, the analysis of mtDNA is an alternative approach. The aim of this study was to investigate the utility of vitreous humour for forensic identification purposes. Samples were collected during vitrectomy from retinopathy patients, in collection bags with saline solution. Blood samples were also obtained in order to contrast results. Before DNA organic extraction, several centrifugation steps were needed to concentrate the vitreous humour samples. Unlike blood, direct amplification of 400-bp fragments of the hipervariable regions I and II (HVI and HVII) was not successful, possibly due to damage to the DNA strand caused by the surgery conditions (UV radiation, oxidative stress). Therefore, amplification of two overlapping fragments for each control region was performed in vitreous humour. In order to eliminate undesired products, all samples were purified by an enzymatic method. Thereafter, mtDNA fragments were sequenced using dye terminators in a MegaBACE 500 capillary sequencer. Sequences of HVI and HVII of approximately 400 bp were obtained from all samples. The sequences obtained from each patient matched almost perfectly those from blood. In summary, herein we describe for the first time a methodology suitable for the mtDNA analysis of vitreous humour samples.

p16INK4A gene alterations are not a prognostic indicator for survival in patients with hepatocellular carcinoma undergoing curative hepatectomy

BACKGROUND AND AIM

Hepatocellular carcinoma (HCC) is a common malignancy worldwide that is highly associated with chronic hepatitis B or C infection and cirrhosis. The tumor suppressor gene p16INK4A is an important component of the cell cycle and inactivation of the gene has been found in a variety of human cancers. The present study was performed to determine genetic and epigenetic alterations in the p16INK4A tumor suppressor gene and the effect of these on HCC progression.

METHODS

The status of p16INK4A was evaluated in 117 HCC tumoral nodules and 110 corresponding peritumoral tissues by loss of heterozigosity (LOH) at the 9p21-22 region, homozygous deletions, single-strand conformation polymorphism-polymerase chain reaction (PCR) mutational analysis and methylation specific PCR.

RESULTS

The most frequent inactivation mechanism was hypermethylation of the promoter region, which was found in 63.2% of the tumor samples and in 28.2% of the peritumoral samples. Loss of heterozygosity at the 9p21 region was detected in 27.3% and 10% of tumor and peritumoral tissues, respectively. Homozygous deletions and mutations were less common events in hepatocarcinogenesis. The authors found 5.9% of the tumor cases with exon 2 homozygous deletions and 8.6% with mutations. Two polymorphisms were detected, one at codon 148 (GCG --> ACG, Ala --> Thr) in three cases and the other in exon 3 at 540 bp (34.2% of the samples). No association was found between inactivation of p16INK4A and clinicopathological characteristics or prognosis.

CONCLUSION

p16INK4A is altered frequently and early in HCC, being the predominant mechanism of inactivation promoter hypermethylation. The present results suggest that the p16INK4A gene plays an important role in the pathogenesis of HCC.

No association between GSTP1 gene aberrant promoter methylation and prognosis in surgically resected hepatocellular carcinoma patients from the Basque Country (Northern Spain)

AIMS

Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide, being linked etiologically to several factors. Glutathione-S-transferases (GSTs) are a family of enzymes that play an important role in detoxification. Hypermethylation of regulatory sequences at glutathione-S-transferase pi class gene (GSTP1) has been found in different human tumor types. In this study, we have studied the methylation status of the GSTP1 promoter region in patients from the Basque Country (Northern Spain) by methylation-specific PCR (MSP).

METHODS AND RESULTS

GSTP1 aberrant promoter methylation was present in 24 of 117 (20.5%) tumor samples being associated with late stages of tumor progression. Patients with multiple HCCs showed different patterns of methylation, which could suggest a different clonal origin of multicentric HCC or different degrees of differentiation. No effect on disease-free survival or overall survival was observed in patients with GSTP1 methylated who underwent curative resection.

CONCLUSIONS

We can conclude that GSTP1 promoter CpG island methylation appears to be a less common event during hepatocarcinogenesis in European populations than in Asian populations, being associated with late stages of tumor progression. These findings could also be useful to provide new therapeutic strategies through the use of demethylating agents.

Nucleotide substitution in the 5' flanking region of D1S80 locus

We have analyzed a mutation responsible for a Hinf I polymorphism of the D1S80 system by Taq dye deoxy terminator cycle sequencing. A G-T transversion at the 58th nucleotide from the 5' end of the forward primer was identified. This mutation has been firmly established by the restriction enzymes. The type G was digested with Hinf I but not with Tsp 509 I. Conversely, the type T was digested with Tsp 509 I but not with Hinj I. We applied this technique to analyze D1S80 system in German and Japanese populations. In the Japanese population, the type T frequencies were much lower than those in the German population, and the type T was almost exclusively observed in the allele 24.

Allele frequency distributions of D1S80 in the Polish population

The polymorphism of the D1S80 locus has been analyzed in a population sample of 208 unrelated individuals in the Southeast Poland and 103 mother/child pairs. PCR amplified alleles were separated by a vertical discontinuous polyacrylamide gel electrophoresis system. Nineteen different alleles and 52 phenotypes could be distinguished. The alleles 18 (f = 0.267) and 24 (f = 0.300) were most common in Poland. D1S80 genotype frequencies of Poland population do not deviate from Hardy-Weinberg equilibrium. All mother/child pairs shared at least one D1S80 allele.

Use of single- and multi-locus and polymerase chain reaction systems for zygosity determination--clinical application in twins with clefts of the lip and palate

Precision of zygosity determination in twins can be improved by the use of modern methods of DNA analysis. The clinical application of 4 single- (SLS) and 2 multi-locus (MLS), and 6 PCR (polymerase chain reaction) systems for zygosity determination in 12 twin pairs with oral clefts was compared with regard to the quality and quantity of sample material required and the probability of error in monozygosity determination. PCR systems proved to be superior to SLS or MLS, as DNA sampling is much more convenient, while its level of accuracy still fulfils clinical requirements. For this reason, PCR systems should be considered a basic method in modern clinical twin research.

Clefts of the lip and palate in twins: use of DNA fingerprinting for zygosity determination

The study of twins is a well-established method for evaluating the relative roles of heredity and environmental factors in the etiology of diseases. Conclusions depend on zygosity determination and on the classification of minor forms of diseases. This paper reports on ten (5 mono- and 5 dizygotic) out of thirteen twin pairs among 1039 patients with cleft lip and palate (n = 677) or cleft palate (n = 362). Zygosity was determined using "DNA fingerprinting" on blood samples in all 10 pairs and on cleft-associated tissue in one pair. Including minor forms of clefting, two of five pairs of monozygotic and two of five pairs of dizygotic twins of the same sex showed concordance. "DNA fingerprinting" should be established as a definitive method for zygosity determination, and the calculation of concordance rates should always include minor forms of diseases.

Distribution of alleles and genotypes from three hypervariable DNA loci in individuals from central and southern Italy

Three hypervariable locus-specific DNA probes (D2S44, alpha globin 3'HVR, D12S11) used in the routine typing activities of our laboratory have been studied using a representative sample of individuals from central and southern Italy. We report allele and genotype distribution of these systems, and discuss several problems met when typing quasi-continuous arrays of restriction fragments.

DNA fingerprinting--a valuable new technique for the characterisation of cell lines

DNA fingerprinting is an important new development for the authentication of cell lines. Multilocus methods such as those developed by Alec Jeffreys provide information on a wide range of genetic loci throughout the human genome and thus give a useful genetic "snap-shot" of a cell culture. Our work has shown that Jeffreys multilocus fingerprinting method can be applied to cell lines from a wide range of animals including reptiles, birds, fish and diverse mammals. It can also differentiate very closely related cell lines including those from the same mouse strain. Routine fingerprint analysis has enabled an unprecedented level of confidence in the consistency of cell stocks. Our results demonstrate that this straightforward method represents a powerful and readily interpreted system for cell authentication and exclusion of cross-contamination.

Female twin with Hunter disease due to nonrandom inactivation of the X-chromosome: a consequence of twinning

We report the occurrence of Hunter disease (mucopolysaccharidosis type II) in a karyotypically normal girl who was one of identical twins. Molecular studies showed nonrandom X-inactivation in both her fibroblasts and lymphocytes, while her normal twin showed equal usage of both X chromosomes. In view of previous reports of 7 pairs of identical female twins in which one had Duchenne muscular dystrophy, it seems that twinning may be strongly associated with nonrandom X-inactivation, and is not specific to the properties of the disease causing gene.

Late development of renal carcinoma in allograft kidney

The Cincinnati Transplant Tumor Registry recorded 169 cases of renal carcinoma developing in transplant recipients. The great majority of these cases were of primary renal cell carcinoma developing in the recipient native kidneys. Renal carcinoma developing de novo in the renal allograft occurred 17 times, with a maximal interval to clinical development of 85 months after transplantation. The development of multicentric renal cell carcinoma in an allograft 156 months after transplantation is described. The 24-year-old white male recipient with Alport's syndrome received a cadaver renal allograft from a healthy 27-year-old black man who had died of a cerebral hemorrhage in 1977. At 13 years after transplantation the recipient had upper abdominal pain. Ultrasound revealed 2 incidental renal masses and a renal cyst in the allograft. Partial nephrectomy confirmed the presence of multicentric renal carcinoma. The graft was left in situ and immunosuppression was maintained. The recipient continued to do well with no evidence of disease 1 year postoperatively. Deoxyribonucleic acid banding demonstrated that the tumor and recipient blood were of different patterns.

Multilocus DNA fingerprint analysis of cellbanks: Stability studies and culture identification in human B-lymphoblastoid and mammalian cell lines

The technique of multilocus DNA fingerprinting has great potential for the authentication of animal cell cultures and in identification of cross-contamination. The Alec Jeffreys probes 33.6 and 33.15 were used as multilocus probes to demonstrate the consistent DNA fingerprint profiles in human peripheral blood and its derivative Epstein-Barr virus (EBV) transformed B-lymphoblastoid cultures maintained by repeated subculture for six months. However, fingerprint analysis of EBV transformed cultures generated from small numbers of cells showed that the majority (seven of eight cultures) had anomalous profiles. Some of these altered profiles shared common features not seen in the peripheral blood pattern. Analysis of seven murine hybridoma clones from a single fusion experiment revealed only two clones which could not be distinguished using probe 33.15. Further studies of master and distribution cell banks for eleven cell lines demonstrated consistent fingerprint profiles in all cases except one (U937). However, this cell line showed only minor differences in the master and distribution bank profiles. These data indicate that, while changes in fingerprint profile may be identified in exceptional instances, the multilocus fingerprinting method using probes 33.6 and 33.15 is a powerful and reliable tool in the quality control of animal cell cultures.

Statistical analysis of the measurement errors in the determination of fragment length in DNA-RFLP analysis

DNA from human whole blood samples was digested with the restriction enzyme HinfI and RFLP analysis performed using the single locus probes MS1, MS31, MS43a and YNH24. The intergel variation of 3291 duplicate measurements of fragment lengths in terms of basepairs was investigated. The difference between two measurements of the same fragment on different gels increased approximately exponentially with increasing fragment length. After transformation of the fragment length into a normalized migration distance it was found that the difference between two transformed measurements was normally distributed with a S.D. (0.70 mm) which was independent of the fragment length. The errors of band 1 and band 2 on the same lane were correlated (r2 = 0.8). It is useful in the calculation of frequencies and in retrieval procedures and also in the calculation of likelihood ratios to be able to use a S.D. which is independent of the fragment length.

Allele frequency distributions of four variable number tandem repeat (VNTR) loci in the London area

Allele frequency distributions of four hypervariable minisatellite loci were obtained from a large sample of individuals in the London area. The sample is subdivided into three major ethnic groups; Caucasian, Afro-Caribbean and Asian, and histograms for these groups are displayed for comparison. The distributions are discussed in relation to mutation rates, heterozygosity and the computer analysis and processing of results.

Repeat unit multipriming and hybridisation--a novel method for the production of DNA fingerprints using minisatellite probes

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Population and family data of RFLP's using selected single- and multi-locus systems

The multi-locus systems (MLS) 33.15 and 33.6 (Jeffreys et al 1985a) and the single-locus systems (SLS) MS 1, MS 8, MS 31 and MS 43 (Wong et al. 1987) were investigated. The number of bands and the rate of band sharing were determined for both multi-locus systems and compared to the results of an English survey. Additionally 73 families were investigated using the multi-locus probes and the results compared to those obtained for the traditional blood grouping systems. The results were in full agreement so that no evidence of new mutations could be found. The fragment distribution was calculated for each of the 4 single-locus systems and compared to the values reported in an English survey (Smith et al. 1990b). Distinct discrepancies were seen in the systems MS 1 and MS 8. Family analyses were carried out for the 4 single-locus systems and compared to English data (Jeffreys et al. 1988) to look for any indications of possible new mutations. Only one isolated exclusion could be demonstrated with MS 1.

Highly polymorphic minisatellite sequences: allele frequencies and mutation rates for five locus-specific probes in a Caucasian population

Six human minisatellite sequences (MS1, MS8, MS29, MS31, MS43, g3) have been subcloned into a stable host/vector system. Allele frequencies at the hypervariable loci detected by five of these probes were determined in a Caucasian population (200 individuals). Mendelian inheritance has been demonstrated in 5 large multi-generation pedigrees. The mutation rate has been determined in 59 families. The highest mutation rate was observed with MS1, as might be predicted from the observed high heterozygosity and in agreement with previous direct measurement of germ line mutation rates. The data presented on allele frequencies and mutation rates provide preliminary data supporting the use of these probes in paternity analysis and forensic investigations.