Deletion of the MGMT gene in familial melanoma.

The DNA repair gene MGMT (O-6-methylguanine-DNA methyltransferase) is important for maintaining normal cell physiology and genomic stability. Alterations in MGMT play a critical role in the development of several types of cancer, including glioblastoma, lung cancer, and colorectal cancer. The purpose of this study was to explore the function of genetic alterations in MGMT and their connection with familial melanoma (FM). Using multiplex ligation-dependent probe amplification, we identified a deletion that included the MGMT gene in one of 64 families with a melanoma predisposition living in western Sweden. The mutation segregated with the disease as a heterozygous deletion in blood-derived DNA, but a homozygous deletion including the promoter region and exon 1 was seen in tumor tissue based on Affymetrix 500K and 6.0 arrays. By sequence analysis of the MGMT gene in the other 63 families with FM from western Sweden, we identified four common polymorphisms, nonfunctional, as predominantly described in previous studies. We conclude that inherited alterations in the MGMT gene might be a rare cause of FM, and we suggest that MGMT contributes to melanoma predisposition.

Aetiology of severe mental retardation and further genetic analysis by high-resolution microarray in a population-based series of 6- to 17-year-old children.

AIM: To investigate the prevalence, co-morbidities and aetiologies of severe mental retardation (SMR) in a cohort of Swedish children and to further penetrate aetiologies in the group with undetermined causes by application of updated clinical-genetic methods. METHODS: The study was population-based and included children living in the County of Halland in western Sweden in 2004 (born 1987-1998; 46,000 children). Patients were identified through habilitation centres, paediatric clinics and school health services. Patients with unclear prenatal aetiology were investigated with single nucleotide polymorphism (SNP)-array. RESULTS: Severe mental retardation was identified in 133 children from 132 families, corresponding to a prevalence of 2.9 per 1000 children. There were more males than females (90:43).The aetiology was prenatal in 82 (62%), perinatal in 14 (10%) and postnatal in 8 (6%). In 29 (22 %) children, mainly males with autism, the cause could not be related to the time of birth. In the prenatal group, genetic causes dominated, but still 23 children remained undiagnosed; in 5/19 of these patients, a diagnosis could be made after SNP-array analysis. One or more associated neurological handicaps were found in more than half of the children. CONCLUSION: Prevalence and co-morbidity were similar to previous Scandinavian studies. High-resolution chromosomal micro-array techniques are valuable diagnostic tools, reducing the number of patients with unexplained SMR.

Early infantile onset ''congenital'' Rett syndrome variants: Swedish experience through four decades and mutation analysis.

The early infantile onset ''congenital'' variant of Rett syndrome presents with deviations of behavior from very early infancy. Here, we report on a clinical-genetic study in a collected series of 14 Swedish girls with early infantile onset Rett syndrome phenotype. The clinical diagnosis was based on symptom onset before the age of 6 months and the patients fulfilled 3 or more Rett variant criteria and 5 or more supportive criteria. Genotype-phenotype correlation studies in the CDKL5-gene have recently shown clinical associations to early infantile onset Rett variants. Mutation analyses for both the MECP2-gene and the CDKL5-gene were, therefore, performed. Of interest, we found a large deletion covering 2 exons in MECP2, which underlines the importance of MECP2 mutation screening even for the ''atypical'' early infantile onset variants of Rett syndrome. No early infantile onset Rett syndrome patients in this study had the previously well-known hotspot mutations in the MECP2-gene.

Epigenetic mutations in CDKN2A in western Swedish families with hereditary malignant melanoma.

This study aimed to identify the molecular genetic variations associated with an increased risk of hereditary malignant melanoma (HMM) in the western Swedish population. In 68 families with increased hereditary susceptibility to malignant melanoma, we previously reported a low frequency of alterations in the CDKN2A gene, which is regarded as the major melanoma predisposition gene. Among these alterations, we identified a novel mutation in 3 families (Asp108Tyr). In the present study, we focused on the possible role of heritable epimutations as a cause of the silencing of the CDKN2A gene. We used two different technical approaches to detect changes in CpG methylation in the promoter region of the CDKN2A gene; methylation-specific PCR (MSP) analysis of bisulfite-converted DNA and methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA). From families who tested negative for germ-line CDKN2A mutations, 64 unrelated patients with hereditary melanoma were included in the study. We showed a consistent lack of hypermethylation in the promoter region of CDKN2A in patients with HMM in our western Swedish population. A putative germ-line methylation of the CDKN2A, if any, is therefore likely to be a rare event in hereditary melanoma. This study demonstrates that there are probably additional and as yet unknown genetic factors present in western Swedish HMM families.

Novel CDKN2A mutations detected in western Swedish families with hereditary malignant melanoma.

We have examined alterations in the cyclin-dependent kinase inhibitor 2A (CDKN2A), a major melanoma predisposing gene, in a western-Swedish hereditary melanoma population comprising 107 patients from 68 families. Using sequence analysis and multiplex ligation-dependent probe amplification, we found a novel mutation (Asp108 Tyr), segregating with the disease in three families. This mutation has previously been detected as a somatic mutation in other cancers. We found a previously described Swedish founder mutation (ins113Arg) in one family and a large duplication encompassing the CDKN2A gene locus in another family. Moreover, a debated polymorphism (Ala148Thr) was found in nine families, in which the polymorphism did not segregate with the disease.

MECP2 abnormality phenotypes: clinicopathologic area with broad variability.

Rett syndrome is a neurodevelopmental disorder that occurs worldwide and predominantly affects girls. The MECP2 gene has been put forward as the underlying gene. Interestingly, other clinical presentations in addition to Rett syndrome have been reported to be the results of deviations in MECP2. This prompted us to outline a working hypothesis of how these diverse phenotypes are connected. Our aim was to summarize the clinical picture of deviations in MECP2 at this moment to obtain a comprehensive overview. Thus, we have attempted to create a gradient, starting at the left with the most severely affected MECP2-deviant subgroups, represented by boys who are diseased in the intrauterine phase or as neonates, and at the right, the most mildly affected subgroup, female asymptomatic carriers. In the center, with dominant numbers, we have placed classic Rett syndrome presentations, together with the late-onset Rett syndrome variant and preserved speech variant. In conclusion, we feel that it is important to emphasize that Rett syndrome is a strictly clinical diagnosis that is not identical to the far broader concept of MECP2 deviations.

Multiplex ligation-dependent probe amplification (MLPA) detects large deletions in the MECP2 gene of Swedish Rett syndrome patients.

Mutations in the methyl-CpG-binding protein-2 (MECP2) gene on Xq28 have been found to be a cause of Rett syndrome (RS). In a previous mutation screening, we found MECP2 mutations in 81% of Swedish classical Rett women. In this study, we have analyzed 22 patients for MECP2 deletions using multiplex-ligation-dependent probe amplification (MLPA). Clinically, 11 of the patients who were classical Rett women, 3 were forme fruste, 1 was congenital RS, and 7 were Rett variants. As inclusion criteria, we used DNA from patients in whom previous sequencing results showed no mutations in coding portions of the MECP2 gene. MLPA is a method based on multiplex PCR. In one PCR, as many as 40 probes are amplified with the same primers. The specificity of the amplification products is determined by the site-specific hybridization of each probe construct, prior to amplification. Each PCR product has a unique length, which makes it possible to identify it by size separation. In 3 of 11 (27%) classical Rett women, we detected large deletions in MECP2 using MLPA. All these patients had deletions covering two exons; in 2 cases the deletion involved exons 3 and 4 and, in one case, exons 1 and 2 were missing. In the forme fruste, congenital and Rett-variant patients, we found no large deletions. We have found that MLPA is useful when it comes to finding large deletions compromising whole exons in MECP2. Used as a complementary method to DNA sequencing, it revealed new MECP2 mutations in classical RS patients.