Guidelines for complex genetic analysis of hereditary breast ovarian cancer syndrome in slovak population

Genetic diagnostics of hereditary breast and ovarian cancer (HBOC) has been performed in Slovakia in many different forms before the year 2000. Complex HBOC genetic analysis consists of many steps, including the initial genetic consultation, laboratory testing of genes associated with HBOC, interpretation and report of DNA analysis results, secondary explanatory genetic consultation and recommendation of clinical management for pathological mutation carriers. Many clinicians are participating on this workflow, such as clinical geneticists, laboratory diagnosticians as well as gynaecologists, oncologists or radio-diagnosticians. Currently, genetic testing is still technically and financially demanding and aimed only at selected families or patients who fulfil the defined clinical indication criteria.

Positive result of DNA analysis, that is, detection of pathological mutation in genes associated with HBOC syndrome means that the risk of breast/ovarian cancer onset in mutation carriers is amplified. This predisposition markedly affects the clinical management and treatment of patient and other members of the family, thus creating the demand to establish widely accepted specific recommendations for genetic diagnostics of HBOC. In the past, the analysis of HBOC in Slovakia followed various technical approaches and indication criteria depending on the workflow of specific laboratory. The guidelines reported below adhere to the current trends in DNA analysis and clinical healthcare, define the criteria for diagnostic laboratories, conditions for genetic testing and determine indications for selection of HBOC families and further clinical management of mutation carriers.

Clustering of mutations in the 5' tertile of the NF1 gene in Slovakia patients with optic pathway glioma

Optic pathway gliomas (OPG) occur in 15% of patients with neurofibromatosis type 1 (NF1; OMIM 162200). Genotype-phenotype correlations in patients with NF1 may help to determine the risk group for developing complications such as OPG in coincidence with other NF1.features. We evaluated 52 patients with NF1 (25 with OPG and 27 without OPG). All subjects underwent a clinical examination focused on neurofibromatosis type 1 and molecular diagnostics of NF1 gene using protocol based on RNA analysis confirming the diagnosis of NF1. In the group with OPG patients, there was a significantly higher incidence of freckling (P=0.017), neurofibromatosis bright objects (NBO) (P=0.0038), compared to the group without OPG. The differences between the groups with respect to Lisch nodules were on the borderline of statistical significance (P=0.088). The frequency of neurofibromas in the group with OPG was not significant (P=0.9). From all patients with the mutation localized in the first tertile of the NF1 gene majority (71%) had optic glioma compared to individuals who didn't have the OPG 29% (P=0.0049). Our results present the clustering of mutations in the 5'tertile of NF1 gene in patients with optic nerve glioma and suggest higher incidence of freckling and neurofibromatosis brain objects in these patients. Molecular analysis of NF1 gene is important part in complex management of NF1 patients and contributes to a better understanding of clinical picture of NF1 patients. .

The impact of thiopurine-S-methyltransferase genotype on the adverse drug reactions to azathioprine in patients with inflammatory bowel diseases

BACKGROUND AND AIMS

The thiopurine drugs, azathioprine (AZA) and 6-mercaptopurine, are established in the treatment of inflammatory bowel diseases (IBD). Polymorphisms in thiopurine S-methyltransferase (TPMT) gene have been associated with adverse drug reactions (ADRs) to AZA.

METHODS

The aim of this study was to evaluate TPMT polymorphisms and AZA-related toxicity in a Slovak cohort of 220 IBD patients treated with AZA. In every patient, the dose and duration of AZA therapy, concomitant 5-aminosalicylate (5-ASA) medication, frequency, type, time to onset, dose of ADR and concomitant 5-ASA at the onset of ADR were recorded. Each patient was also genotyped for the presence of variant TPMT alleles (*2,*3A,*3B,*3C). Frequency, type and circumstances of ADRs were compared according to TPMT status.

RESULTS

Of the 220 patients, 205 (93.2 %) were wild-type (TPMT*1/*1), one (0.5%) carried a TPMT*1/*3C allele, 13 (5.9 %) carried TPMT *1/*3A allele and one was homozygous for TMPT *3A allele. No TPMT *2 mutation was found. The incidence of adverse drug reactions was 62/205 (30.2 %) in the wild-type group as compared to 13/15 (86.7 %) in the TPMT mutation group, p=2.10-5. Leukopenia (WBC< 3.0*10^9/L) occurred in 21/205 (10.2 %) patients with wild type TPMT versus 11/15 (73.3 %) patients with TPMT mutations, p=0.000001. There was no significant difference between TMPT groups in gastrointestinal or other ADRs. No impact of 5-ASA on the incidence and severity of AZA adverse drug reactions was observed.

CONCLUSION

The incidence of leukopenia in TPMT mutant patients was significantly higher and more severe as compared to TPMT wild type patients. We observed no impact of concomitant 5-ASA therapy on AZA induced toxicity (Tab. 4, Fig. 2, Ref. 37).

Prevalence of mutations in thiopurine S-methyltransferase gene among Slovak IBD patients

BACKGROUND

Thiopurine S-methyltransferase (TPMT) plays an important role in the metabolism of thiopurines. It has been suggested that TPMT genetic polymorphisms lead to dose-related hematopoietic toxicity. Since there are major ethnic differences in the prevalence of particular TPMT variants, it is important for each country to study their own prevalence in order to estimate the role of TPMT variants-related thiopurines toxicity in population suffering from particular inflammatory bowel disease (IBD).

AIMS

The aim of this study was to determine the frequency of the four most common allelic variants of TPMT gene in the population of Slovak IBD patients.

METHODS

TPMT genetic polymorphisms (TPMT*2, TPMT*3A, TPMT*3B, TPMT*3C) were amplified using PCR and consequently genotyped with genetic analyzer. The allele frequencies of particular allelic variants were calculated and compared with other Caucasian populations reported so far.

RESULTS

Three hundred and thirty IBD patients were included; 196/132/2 cases of Crohn´s disease/ulcerative colitis/unclassified colitis; 180 (55 %) males. Ninety-three percent of patients were homozygous for wild-type TPMT variant. Heterozygous genotype of any of the studied polymorphisms was present in 6 % of patients while only one patient was homozygous for TPMT*3A allele (0.3 %). The most prevalent mutant allele was that of TPMT*3A (3.2 %). The distribution of most common allelic variants of TPMT gene among Slovak IBD patients was in accordance with previously reported prevalence in Caucasian populations.

CONCLUSION

This study shows the prevalence of TPMT genetic polymorphisms in population of Slovak IBD patients. As in other Caucasian populations, the most common mutant allelic variant is that of TPMT*3A while the prevalence of homozygosity is relatively low (Tab. 3, Ref. 22).

Rapid detection methods for five HGO gene mutations causing alkaptonuria

Alkaptonuria (AKU) is an autosomal recessive disorder caused by the deficiency of homogentisate 1,2 dioxygenase (HGO) activity. The disease is characterized by homogentisic aciduria, ochronosis and ochronotic arthritis. AKU shows a very low prevalence (1:250 000), in most ethnic groups. Altogether 43 HGO mutations have been identified in approximately 100 patients. In Slovakia, however, the incidence of this disorder rises up to 1:19 000, and 10 different AKU mutations have been identified in this relatively small country. Here, we report detection methods developed for rapid identification of five HGO mutations. PCR primers were designed enabling detection of mutations IVS5 + 1G-->A, R58fs, and V300G by restriction digestion of amplification-created restriction sites (ACRS). Mutation G152fs is readily identified by heteroduplex analysis, and G161R by amplification refractory mutation system (ARMS) PCR.

TaqI digestion of PCR product increases the informativity of St14 VNTR for the diagnosis of hemophilia A

Recently, a pair of PCR primers have been described that make it possible to amplify a highly polymorphic VNTR locus DX552 (St14). PCR products range in size from approximately 650 to 3000 bp. Ninety X chromosomes from unrelated Caucasian subjects were investigated. Digestion of the PCR products with TaqI revealed the presence of a polymorphic TaqI restriction site within the product 200 bp from the end. This restriction site is present on 60% and absent on 40% of all alleles, but the absence is confined solely to the alleles 1690 bp (39%) and 2100 bp (1%). Thus, there is a strong allelic association between the most frequent 1690 bp allele and the absence of the TaqI restriction site. Determination of this polymorphisms within the St14 VNTR region increases the expected heterozygosity at the DXS52 locus from 72% to 80%. This increases the fraction of hemophilia A families where this marker is informative for indirect prenatal diagnosis and carrier identification.

Deletion analysis of DMD/BMD families from the German Democratic Republic and selected regions of Czechoslovakia and Hungary

Over the last two years we have screened 183 DMD/BMD families requesting prenatal diagnosis. Using cDNA probes cf56a,b we have detected exon deletions in 72 of them. In 62 cases the deletion was also detectable with currently available PCR primers. Deletion analysis for exons 8, 17, and 19, using either PCR or Southern blotting techniques, was performed for 65 of the 111 families which showed no deletions with cf56a,b. Eight of them were deleted for one or more of these exons. PCR offers new possibilities for deletion analysis in families without a living patient using either Guthrie papers or histologically conserved material from the dead patient. In 20 of 25 patients, we observed concordance between the clinical picture and the molecular deletion analysis in accordance with the open reading frame hypothesis. Five patients, however, presented with DMD in spite of our analysis showing an in frame deletion. Carrier determination in families in which DMD is caused by a deletion using linkage, dosage, or breakpoint analysis is discussed.