Towards a Better Molecular Diagnosis of FMR1-Related Disorders-A Multiyear Experience from a Reference Lab.

The article summarizes over 20 years of experience of a reference lab in fragile X mental retardation 1 gene (FMR1) molecular analysis in the molecular diagnosis of fragile X spectrum disorders. This includes fragile X syndrome (FXS), fragile X-associated primary ovarian insufficiency (FXPOI) and fragile X-associated tremor/ataxia syndrome (FXTAS), which are three different clinical conditions with the same molecular background. They are all associated with an expansion of CGG repeats in the 5'UTR of FMR1 gene. Until 2016, the FMR1 gene was tested in 9185 individuals with the pre-screening PCR, supplemented with Southern blot analysis and/or Triplet Repeat Primed PCR based method. This approach allowed us to confirm the diagnosis of FXS, FXPOI FXTAS in 636/9131 (6.96%), 4/43 (9.3%) and 3/11 (27.3%) of the studied cases, respectively. Moreover, the FXS carrier status was established in 389 individuals. The technical aspect of the molecular analysis is very important in diagnosis of FXS-related disorders. The new methods were subsequently implemented in our laboratory. This allowed the significance of the Southern blot technique to be decreased until its complete withdrawal. Our experience points out the necessity of implementation of the GeneScan based methods to simplify the testing procedure as well as to obtain more information for the patient, especially if TP-PCR based methods are used.

Early-onset seizures due to mosaic exonic deletions of CDKL5 in a male and two females.

PURPOSE: Mutations in the CDKL5 gene have been associated with an X-linked dominant early infantile epileptic encephalopathy-2. The clinical presentation is usually of severe encephalopathy with refractory seizures and Rett syndrome (RTT)-like phenotype. We attempted to assess the role of mosaic intragenic copy number variation in CDKL5. METHODS: We have used comparative genomic hybridization with a custom-designed clinical oligonucleotide array targeting exons of selected disease and candidate genes, including CDKL5. RESULTS: We have identified mosaic exonic deletions of CDKL5 in one male and two females with developmental delay and medically intractable seizures. These three mosaic changes represent 60% of all deletions detected in 12,000 patients analyzed by array comparative genomic hybridization and involving the exonic portion of CDKL5. CONCLUSION: We report the first case of an exonic deletion of CDKL5 in a male and emphasize the importance of underappreciated mosaic exonic copy number variation in patients with early-onset seizures and RTT-like features of both genders.

[Angelman syndrome--the research model of epigenetic mechanisms expression genes regulation]. / Zespól Angelmana--model badawczy epigenetycznych mechanizmów regulacji ekspresji genów.

Epigenetics, one of the widely investigated topics in human genetics, refers to phenotypic or gene expression changes caused by specific regulatory mechanisms (eg. DNA methylation, histone proteins modifications, antisense RNA or RNAi expression) that do not involve changes in DNA sequence. The disturbances in epigenetic gene expression regulatory mechanisms might lead to oncogenic transformation as well as monogenic or complex diseases. On the other side, better knowledge about epigenetic causes of certain diseases, gives an opportunity to potential therapies. One of the epigenetic research models in Angelman syndrome (AS). This neurologic disorder associated with improper central nervous system development and function, together with Prader-Willi syndrome are caused by the defects of epigenetic regulation. These disturbances are related to the defects of genomic imprinting, a phenomenon that contributes to allele specific, depending from parental origin, gene expression. In the majority of AS cases, the large deletion in chromosome 15 (15q11-13) of maternal origin (65-75%) or paternal disomy of chromosome 15 (3-7%) are observed. However, in a limited number of cases, other imprinting defects or mosaicism can be found and confirmed by new molecular biology techniques. Investigation of the etiology of the diseases caused by the defects in epigenetic regulation gives a basis to the development of epi-therapy that might be a promising alternative for their treatment. Moreover, knowledge about the epigenome gives an opportunity for prevention of human genetic disorders.

[Analysis of genomic imprinting defects in Angelman syndrome with application of quantitative real-time PCR]. / Badanie defektów rodzicielskiego pietna genomowego w zespole Angelmana z zastosowaniem ilosciowego PCR w czasie rzeczywistym.

BACKGROUND: Angelman Syndrome (AS) is a neurogenetic disorder associated with aberrant genomic imprinting. AS patients with an imprinting defect have only paternal genes expression pattern despite the normal bi-parental inheritance of chromosome 15. In 2-3% of AS cases, the altered gene expression is a consequence of an imprinting defect (ID) such as microdeletions in imprinting centre (IC). Statistically, one third of patients with an imprinting defect and no IC deletion have somatic mosaicism. OBJECTIVES: The objectives of this study were: identification of somatic mosaicism for an imprinting defect in the patients with clinical manifestation of AS and development of a procedure for the identification of IC microdeletion. MATERIAL AND METHODS: Twenty eight AS patients with an aberrant methylation pattern confirmed in methylation screening procedure (MS-PCR) were qualified for mosaicism analysis with quantitative real-time PCR technique. RESULTS: The quantitative analysis of methylated alleles did not confirm the presence of somatic mosaicism in any of the examined patients. CONCLUSIONS: The methods for somatic mosaicism and microdeletion in IC analyses based on quantitative real-time PCR technique can be used in the molecular diagnostic of Angelman syndrome.

[Variability in clinical expression of Noonan syndrome--the report of two familial cases]. / Zmiennosc ekspresji klinicznej zespolu Noonan--analiza dwóch przypadków rodzinnych.

Noonan syndrome (NS) belongs to one of the most frequent genetic disorders with autosomal dominant pattern of inheritance. The main symptoms of NS are short stature, congenital heart defects, thorax deformities and specific dysmorphic features: hypertelorism, low set ears. short and wide neck, wide spaced nipples. The clinical picture ofNS changes with the age, which impedes the proper diagnosis in adults. We present two familial cases of Noonan syndrome with mutated PTPN11 gene in probands and one of their parents and siblings. We analyzed clinical features with regards to NS diagnostic criteria.

Identification of mutations in the NF2 gene in Polish patients with neurofibromatosis type 2.

Point mutation and loss of heterozygosity (LOH) analyses were performed in 12 Polish patients with a classic symptom of NF2 - bilateral vestibular schwannomas (BVS). In 5 patients (41.7%), germline mutations were found in the NF2 gene: 2 previously reported substitutions (c.592C>T and c.52C>T) and 3 novel mutations (c.1001_1002insG, c.1029_1030insCC, c.774_778dupGAATG). In addition, LOH analysis of 30 tumour samples from 10 patients revealed a molecular basis of NF2 in 3 patients (25%) that did not have any germline mutation. The molecular defects in sporadic cases of NF2 are still being discussed.

[Clinical symptoms and molecular pathogenesis of Noonan syndrome--current concepts]. / Charakterystyka kliniczna i podloze molekularne zespolu Noonan--aktualny stan wiedzy.

Noonan syndrome (NS; MIM 163950) is an autosomal dominant disorder. With incidence of 1/1000 to 1/2500 live births, NS belongs to the most common genetic disorders. Typical features of NS are: short stature, chest deformities, congenital heart defects, cryptorchidism and dysmorphic features. Mutations of PTPN11 gene (located on chromosome 12q24.1) are responsible for NS and are identified in 33-60% cases. Less than half of the cases are familial. This paper presents current opinion on clinical symptoms, molecular pathogenesis and possibilities of growth hormone therapy. The genotype--phenotype correlation is also discussed.

Mutation incidence in folate metabolism genes and regulatory genes in Polish families with neural tube defects.

Neural tube defects (NTDs) are a common cause of disability or death of new-borns, but the aetiology and genetic background of this disease are still poorly understood. Therefore, it was decided to determine the conditions for the identification of several polymorphisms and to perform a preliminary study on Polish NTD patients and their parents. According to the results of this study, the genetic predisposition to NTD can be correlated with the 677TT genotype in the MTHFR gene, 677CT/1298AC haplotype (the MTHFR gene), 2756G allele in the MTR gene, 66AG variant and minisatellite sequence with 5 or 10 repeats in intron 6 of the MTRR gene. The 530GG and TIVS7-2/TIVS7-2 genotypes in the T gene could also be considered as a risk factor for NTD. The analysis also revealed no correlation between neurulation disturbances and A4956G and A1186G mutations in the BRCA1 gene and the 844ins68bp in CBS gene. Although a correlation was found of some molecular markers with NTD, an additional examination should be conducted on more numerous groups to obtain statistically significant results.

Genetic basis of neural tube defects. II. Genes correlated with folate and methionine metabolism.

Effective supplementation with folate, which prevents neural tube defect (NTD) occurrence, and high homocysteine levels in the blood of NTD children's mothers suggest that genes involved in folate and homocysteine metabolism can be involved in NTD aetiology. Genes encoding methylenetetrahydrofolate reductase (MTHFR) or methylenetetrahydrofolate dehydrogenase (MTHFD) belong to the first group. Genes encoding methionine synthase (MTR), its regulator - methionine synthase reductase (MTRR) and also cystathionine synthase (CBS) can be included in the second group. We present a current list of the folate and homocysteine metabolism genes that are known to be involved in NTD and pay special attention to primary and secondary NTD prevention.

Genetic basis of neural tube defects. I. Regulatory genes for the neurulation process.

Neural tube defects (NTD) together with cardiovascular system defects are the most common malformations in the Polish population (2.05-2.68/1000 newborns). They arise during early embryogenesis and are caused by an improper neural groove closure during the neurulation process. NTD can arise from the influence of specific environmental factors on the foetus. The genetic factor is also very important, because NTDs have multigenetic conditioning. It was suggested that genes connected with the regulation of neurulation could also be involved in NTD aetiology, especially when their deletion or modification leads to neural tube defects in the mouse model. Examples are genes from the PAX family, T (Brachyury), BRCA1 and PDGFRA genes.

[Mutations of MTHFR, MTR, MTRR genes as high risk factors for neural tube defects]. / Analiza mutacji w genach MTHFR, MTR, MTRR w rodzinach ryzyka wad cewy nerwowej.

Neural tube defects (NTDs) have a polygenic background. There are numerous genes known to be high-risk genetic factors for NTDs. Ones of them are mutations of foliate metabolisms pathways genes. This paper shows the results of analysis of common mutations of MTHFR, MTR and MTRR genes. Results of screening mutations 2756A-->G and 66A-->G in MTR and MTRR genes respectively show that are might have an effect on NTDs incidence among the examined population. Analysis of data for the studied population does not prove the influence of mutations 677C-->T and 1298A-->C of MTHFR gene on NTDs.

[Genetic risk factors of neural tube defects]. / Genetyczne czynniki ryzyka wad cewy nerwowej.

Neural tube defects (NTDs) are a group of diseases caused by a failure of closure of the neural tube. Its aetiology contains both environmental and genetic factors. NTDs have a polygenic background. Genes, which are linked with NTDs occurrence, are both directly and indirectly connected with controlling the process of closure of the neural tube. Ones of those are genes of metabolism of folic acid as MTHFR, MTR, MTRR, CBS, MTHFD, folic acid receptors (FR) regulator genes from PAX family, T, PDGFRA and BRCA1 genes.