CAG-encoded polyglutamine length polymorphism in the human genome

Abstract

BackgroundExpansion of polyglutamine-encoding CAG trinucleotide repeats has been identified as the pathogenic mutation in nine different genes associated with neurodegenerative disorders. The majority of individuals clinically diagnosed with spinocerebellar ataxia do not have mutations within known disease genes, and it is likely that additional ataxias or Huntington disease-like disorders will be found to be caused by this common mutational mechanism. We set out to determine the length distributions of CAG-polyglutamine tracts for the entire human genome in a set of healthy individuals in order to characterize the nature of polyglutamine repeat length variation across the human genome, to establish the background against which pathogenic repeat expansions can be detected, and to prioritize candidate genes for repeat expansion disorders.ResultsWe found that repeats, including those in known disease genes, have unique distributions of glutamine tract lengths, as measured by fragment analysis of PCR-amplified repeat regions. This emphasizes the need to characterize each distribution and avoid making generalizations between loci. The best predictors of known disease genes were occurrence of a long CAG-tract uninterrupted by CAA codons in their reference genome sequence, and high glutamine tract length variance in the normal population. We used these parameters to identify eight priority candidate genes for polyglutamine expansion disorders. Twelve CAG-polyglutamine repeats were invariant and these can likely be excluded as candidates. We outline some confusion in the literature about this type of data, difficulties in comparing such data between publications, and its application to studies of disease prevalence in different populations. Analysis of Gene Ontology-based functions of CAG-polyglutamine-containing genes provided a visual framework for interpretation of these genes' functions. All nine known disease genes were involved in DNA-dependent regulation of transcription or in neurogenesis, as were all of the well-characterized priority candidate genes.ConclusionThis publication makes freely available the normal distributions of CAG-polyglutamine repeats in the human genome. Using these background distributions, against which pathogenic expansions can be identified, we have begun screening for mutations in individuals clinically diagnosed with novel forms of spinocerebellar ataxia or Huntington disease-like disorders who do not have identified mutations within the known disease-associated genes.

Unexpanded and intermediate CAG polymorphisms at the SCA2 locus (ATXN2) in the Cuban population: evidence about the origin of expanded SCA2 alleles

“…Normal genetic polymorphism according to CAG repeat length (13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30)(31) The normal CAG repeat size from 2695 (K-S, Po0.01) chromosomes of the Cuban NM population shows a modal distribution (Figure 1a) (mode and median¼22 CAG), with 22 28 The range of the CAG is distributed continuously from 13 to 31 CAG and encompasses almost all the expected allelic classes in this numeric series (17 observed/18 expected) -with a kurtosis of 11.66 and a variance of 3.04 vs 1.21 for other populations worldwide. 27 The allele with 13 CAG repeats is exclusively found in the Cuban population and that with 26 CAG in both Cuban and Czech populations.…”

“…The high odds ratio and the specificity seen in the 27-31 CAG alleles suggest that instabilities would be associated to 27-31 CAG alleles and are more likely to occur in these rather than in the shorter ones (20)(21)(22)(23)(24)(25)(26). The proposed 27 CAG as the lower threshold for intermediate or indeterminate penetrance alleles is in agreement with the situation in SCA7, for which de novo mutations have been proven, and the lower threshold for mitotic and meiotic instabilities has been set at 27 CAG.…”

“…Furthermore, the comparison disclosed highly significant differences and strong effect of the CAG length in the somatic mosaicism, assessed either as mosaicism index (MI) or as peak numbers (F(1,243)¼131.57, P¼0.00, ANOVA followed by Bonferroni post hoc test, 20-26 vs 27-31 CAG range, MI ± SEM: 0.00 ± 0.016, 0.385 ± 0.028, respectively, P¼0.000) (Supplementary Figures S3a and b). According to our current results with regard to the differences between somatic mosaicism and the known phenotypic range of SCA2, we extended the previous comparison to a cohort of 551 alleles with the following ranges: normal (20)(21)(22)(23)(24)(25)(26), large (27)(28)(29)(30)(31), intermediate (32)(33)(34) and expanded . In addition to the differences in normal CAG repeat ranges, the levels of somatic mosaicism of 32-34 CAG alleles were lower than those observed in the full penetrant expanded alleles (35-79 CAG) (MI±SEM: 0.632±0.11 and 2.51±0.25, respectively, P¼0.000) (Figures 3a-c).…”

HTT haplotypes contribute to differences in Huntington disease prevalence between Europe and East Asia

“…This equilibrium is therefore critically dependant on forces that alter the CAG-tract size of normal (o27 CAG) and intermediate alleles (27)(28)(29)(30)(31)(32)(33)(34)(35) of HTT, which are not subject to significant negative selection. Why is the HD mutation more likely to occur on specific HTT haplotypes?…”

“…This conclusion is further supported by a clear precedent for genetic cis-elements influencing CAG instability for other genes. 29 Although there are many CAG-tract-containing genes in the genome, each has a different propensity to CAG instability that is not explained by differences in mean CAG-tract size 30 but could be explained by cis-elements that influence CAG instability. For example, CTCF binding sites located cis to the ATXN7 gene can regulate CAG hyperinstability at that locus.…”