Segregation analysis of rare autosomal folate sensitive fragile sites

Fragile sites, chromosomal lesions, tandem repeats, and disease

Expanded tandem repeat DNAs are associated with various unusual chromosomal lesions, despiralizations, multi-branched inter-chromosomal associations, and fragile sites. Fragile sites cytogenetically manifest as localized gaps or discontinuities in chromosome structure and are an important genetic, biological, and health-related phenomena. Common fragile sites (∼230), present in most individuals, are induced by aphidicolin and can be associated with cancer; of the 27 molecularly-mapped common sites, none are associated with a particular DNA sequence motif. Rare fragile sites ( ≳ 40 known), ≤ 5% of the population (may be as few as a single individual), can be associated with neurodevelopmental disease. All 10 molecularly-mapped folate-sensitive fragile sites, the largest category of rare fragile sites, are caused by gene-specific CGG/CCG tandem repeat expansions that are aberrantly CpG methylated and include FRAXA, FRAXE, FRAXF, FRA2A, FRA7A, FRA10A, FRA11A, FRA11B, FRA12A, and FRA16A. The minisatellite-associated rare fragile sites, FRA10B, FRA16B, can be induced by AT-rich DNA-ligands or nucleotide analogs. Despiralized lesions and multi-branched inter-chromosomal associations at the heterochromatic satellite repeats of chromosomes 1, 9, 16 are inducible by de-methylating agents like 5-azadeoxycytidine and can spontaneously arise in patients with ICF syndrome (Immunodeficiency Centromeric instability and Facial anomalies) with mutations in genes regulating DNA methylation. ICF individuals have hypomethylated satellites I-III, alpha-satellites, and subtelomeric repeats. Ribosomal repeats and subtelomeric D4Z4 megasatellites/macrosatellites, are associated with chromosome location, fragility, and disease. Telomere repeats can also assume fragile sites. Dietary deficiencies of folate or vitamin B12, or drug insults are associated with megaloblastic and/or pernicious anemia, that display chromosomes with fragile sites. The recent discovery of many new tandem repeat expansion loci, with varied repeat motifs, where motif lengths can range from mono-nucleotides to megabase units, could be the molecular cause of new fragile sites, or other chromosomal lesions. This review focuses on repeat-associated fragility, covering their induction, cytogenetics, epigenetics, cell type specificity, genetic instability (repeat instability, micronuclei, deletions/rearrangements, and sister chromatid exchange), unusual heritability, disease association, and penetrance. Understanding tandem repeat-associated chromosomal fragile sites provides insight to chromosome structure, genome packaging, genetic instability, and disease.

Diagnostic yield in the clinical genetic evaluation of autism spectrum disorders

PURPOSE

Clinical geneticists are often asked to evaluate patients with autism spectrum disorders (ASDs) in reference to questions about cause and recurrence risk. Recent advances in diagnostic testing technology have greatly increased the options available to them. It is not currently clear what the overall diagnostic yield of a battery of tests, either collectively or individually, might be. The purpose of this study was to evaluate the diagnostic yield of a stepwise approach we have implemented in our clinics.

METHODS

We used a three-tiered neurogenetic evaluation scheme designed to determine the cause of ASDs in patients referred for clinical genetic consultation. We reviewed the results of our diagnostic evaluations on all patients referred with a confirmed diagnosis of autism over a 3-year period.

RESULTS

By using this approach, we found an overall diagnostic yield for ASDs of more than 40%. This represents a significant increase in the diagnostic yield reported just a few years ago.

CONCLUSIONS

Given the implications of these diagnoses on recurrence risk and associated medical conditions, a targeted neurogenetic evaluation of all persons with ASDs seems warranted. We discuss the issues in the future implementation of a fourth tier to the evaluation with the potential for an even higher diagnostic yield.

Prenatal diagnosis of FRA10A: a case report and literature review

We report on the prenatal diagnosis of a familial fra10(q23)/del(10)(q23) detected after cellular cultures in non-folic deprived medium.

Localization of fragile sites in the karyotype of Sus scrofa domestica: present status

Fragile sites were induced to expression in pig lymphocyte chromosomes by in vitro exposure to folate antagonists and BUdR-Hoechst 33258. Expressed fragility was localized according to the presented idiograms and compared with the location of known spontaneous translocations.

Localization of fragile sites in the karyotype of Felis catus

High resolution RBG-banding was induced by exposure of cat fibroblast cultures to a folate antagonist and BUdR. After band induction the chromosomes displayed frequent breaks and gaps. To determine whether the observed aberrations were randomly or non-randomly distributed, a total of 300 metaphases were screened for the presence of breaks, gaps, and deletions. Statistical analysis was performed according to Mariani (1989). The 525 band idiogram presented by Rønne et al. (1994) was used for the calculations, and to determine which bands were harbouring an aberration. Bands with seven or more aberrations were considered to harbour a fragile site (Fh7 < 0.01).

The enigma of common fragile sites

One hundred and fifty breakpoint sites were recorded during an analysis of aphidicolin-ethanol inducible fragile sites (FS) in 56 blood samples and 13 amniocyte cultures and were classified according to the criteria formulated by the Chromosome Coordinating Meeting. The finding of previously unlisted FS in this sample, the altered expression of FS in conditions not usually associated with chromosomal abnormalities and the apparent lack of tissue specificity indicate the importance of one or more fundamental mechanisms operating to produce the diverse associated clinical phenotypes, with the chromosomal fragility representing an intermediate phenotype. Several lines of evidence converge towards the conclusion that FS are a manifestation of an altered state of genetic activity at areas associated with transcriptional regulation, because of their concordance with CpG islands, nuclease sensitive sites, replication origins, zinc finger protein domains and viral integration sites. An investigation is required whether this phenomenon could contribute both to evolutionary diversity through increased recombination, the formation of unstable repeat sequences and variable methylation, and to the expression of multigene disease processes resulting in the production of variable and complex phenotypes, even within families.