Gene deletions causing human genetic disease: mechanisms of mutagenesis and the role of the local DNA sequence environment

Abstract

Reports describing short (less than 20 bp) gene deletions causing human genetic disease were collated in order to study underlying causative mechanisms. Deletion breakpoint junction regions were found to be non-random both at the nucleotide and dinucleotide sequence levels, an observation consistent with an endogenous sequence-directed mechanism of mutagenesis. Direct repeats of between 2bp and 8bp were found in the immediate vicinity of all but one of the 60 deletions analysed. Direct repeats are a feature of a number of recombination, replication or repair-based models of deletion mutagenesis and the possible contribution of each to the spectrum of mutations examined was assessed. The influence of parameters such as repeat length and length of DNA between repeats was studied in relation to the frequency, location and extent of these deletions. Findings were broadly consistent with a slipped mispairing model but the predicted deletion of one whole repeat copy was found only rarely. A modified version of the slipped mispairing hypothesis was therefore proposed and was shown to possess considerable explanatory value for approximately 25% of deletions examined. Whereas the frequency of inverted repeats in the vicinity of gene deletions was not significantly elevated, these elements may nevertheless promote instability by facilitating the formation of secondary structure intermediates. A significant excess of symmetrical sequence elements was however found at sites of single base deletions. A new model to explain the involvement of symmetric elements in frameshift mutagenesis was devised, which successfully accounted for a majority of the single base deletions examined. In general, the loss of one or a few base pairs of DNA was found to be more compatible with a replication-based model of mutagenesis than with a recombination or repair hypothesis. Seven hitherto unrecognized hotspots for deletion were noted in five genes (AT3, F8, HBA, HBB and HPRT). Considerable sequence homology was found between these different sites, and a consensus sequence (TGA/GA/GG/TA/C) was drawn up. Sequences fitting this consensus (i) were noted in the immediate vicinity of 41% of the other (sporadic) gene deletions, (ii) were found frequently at sites of spontaneous deletion in the hamster APRT gene, (iii) were found to be associated with many larger human gene deletions/translocations, (iv) act as arrest sites for human polymerase alpha during DNA replication and (v) have been shown by in vitro studies of human polymerase alpha to be especially prone to frameshift mutation.(ABSTRACT TRUNCATED AT 400 WORDS)

Comprehensive analysis of 989 patients with breast or ovarian cancer provides BRCA1 and BRCA2 mutation profiles and frequencies for the German population

“…34 The independent origin of the 4bp deletions might be caused by slippage effects during replication. 38,39 Missense mutations in the BRCA genes Most mutations reported in the BIC database are small deletions, small insertions and nonsense mutations, all predicted to cause premature termination of translation and thus are considered as predisposing. In the absence of functional tests for the BRCA1 and BRCA2 proteins, most missense mutations, in frame deletions, or certain intronic substitutions pose serious problems for the interpretation of their effects on tumorigenesis.…”

Assessment of genomic instability in breast cancer and uveal melanoma by random amplified polymorphic DNA analysis

“…Human gene mutations appear to be caused by multiple mechanisms whose relative importance is probably governed by local primary and secondary DNA structure. 7 We have searched for consensus sequences located in the immediate vicinity of gene mutations and for "hot spots" that mediate illegitimate recombinations, a mechanism that is suggested to be crucial for the generation of genomic instability and cancer. …”

Novel germline mutations of the MEN1 gene in Japanese patients with multiple endocrine neoplasia type 1

“…Among these mutations, Bassett et al (1998) reported hot spots for small deletions and insertions in exons 2, 3, and 10. The mutations identified in the present study are also located at exons 2 and 3, where misalignment of the dinucleotide repeat during replication could easily be expected from the nucleotide sequence of this region (Krawczak and Cooper 1991). Irrespective of these mutational hot spots, the mutation sites are fundamentally distributed over the entire exon.…”