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Journal ArticleDOI

Childhood‐onset ataxia: Testing for large CAG‐repeats in SCA2 and SCA7

TL;DR: An assay based on separation of PCR products on an agarose gel, blotting, and hybridization with a (CAG)6 oligonucleotide probe was used to test DNA from individuals more than 10 years of age who had a possible diagnosis of SCA, and provided reliable detection of extreme expansion mutations.
Abstract: Infantile- and juvenile-onset spinal cerebellar ataxia (SCA) is associated with expansion of 130 to more than 200 CAG-repeats in the SCA2 and SCA7 genes. Routine clinical assays for SCA2 and SCA7, which use polymerase chain reaction (PCR) and denaturing PAGE (polyacrylamide gel electrophoresis), will not reliably detect such large expansions. An assay based on separation of PCR products on an agarose gel, blotting, and hybridization with a (CAG)6 oligonucleotide probe was used to test DNA from individuals more than 10 years of age who had a possible diagnosis of SCA. Among 25 cases, the PCR-blot assay confirmed the presence of SCA2 expansions between 230 and 500 repeats in four unrelated individuals, but did not detect any cases of extreme expansion in the SCA7 gene. The PCR-blot assay provides reliable detection of extreme expansion mutations. Routine incorporation of this assay in clinical laboratories may reveal that infantile-juvenile forms of SCA2 and SCA7 are more prevalent than previously recognized.
Citations
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Journal ArticleDOI
TL;DR: SSRs within genes evolve through mutational processes similar to those for SSRs located in other genomic regions including replication slippage, point mutation, and recombination and may provide a molecular basis for fast adaptation to environmental changes in both prokaryotes and eukaryotes.
Abstract: Recently, increasingly more microsatellites, or simple sequence repeats (SSRs) have been found and characterized within protein-coding genes and their untranslated regions (UTRs). These data provide useful information to study possible SSR functions. Here, we review SSR distributions within expressed sequence tags (ESTs) and genes including protein-coding, 3'-UTRs and 5'-UTRs, and introns; and discuss the consequences of SSR repeat-number changes in those regions of both prokaryotes and eukaryotes. Strong evidence shows that SSRs are nonrandomly distributed across protein-coding regions, UTRs, and introns. Substantial data indicates that SSR expansions and/or contractions in protein-coding regions can lead to a gain or loss of gene function via frameshift mutation or expanded toxic mRNA. SSR variations in 5'-UTRs could regulate gene expression by affecting transcription and translation. The SSR expansions in the 3'-UTRs cause transcription slippage and produce expanded mRNA, which can be accumulated as nuclear foci, and which can disrupt splicing and, possibly, disrupt other cellular function. Intronic SSRs can affect gene transcription, mRNA splicing, or export to cytoplasm. Triplet SSRs located in the UTRs or intron can also induce heterochromatin-mediated-like gene silencing. All these effects caused by SSR expansions or contractions within genes can eventually lead to phenotypic changes. SSRs within genes evolve through mutational processes similar to those for SSRs located in other genomic regions including replication slippage, point mutation, and recombination. These mutational processes generate DNA changes that should be connected by DNA mismatch repair (MMR) system. Mutation that has escaped from the MMR system correction would become new alleles at the SSR loci, and then regulate and/or change gene products, and eventually lead to phenotype changes. Therefore, SSRs within genes should be subjected to stronger selective pressure than other genomic regions because of their functional importance. These SSRs may provide a molecular basis for fast adaptation to environmental changes in both prokaryotes and eukaryotes.

1,039 citations

01 Jan 2007
TL;DR: It is concluded that half of all suitable EST databases could be exploited for the population genetic analysis of species of conservation concern and the advantages and disadvantages of EST-SSRs in the context of population genetic applications are discussed.
Abstract: Simple-sequence repeats (SSRs) have increasingly become the marker of choice for population genetic analyses. Unfortunately, the development of traditional ‘anonymous’ SSRs from genomic DNA is costly and time-consuming. These problems are further compounded by a paucity of resources in taxa that lack clear economic importance. However, the advent of the genomics age has resulted in the production of vast amounts of publicly available DNA sequence data, including large collections of expressed sequence tags (ESTs) from a variety of different taxa. Recent research has revealed that ESTs are a potentially rich source of SSRs that reveal polymorphisms not only within the source taxon, but in related taxa, as well. In this paper, we review what is known about the transferability of EST-SSRs from one taxon to another with particular reference to the potential of these markers to facilitate population genetic studies. As an example of the utility of these resources, we then cross-reference existing EST databases against lists of rare, endangered and invasive plant species and conclude that half of all suitable EST databases could be exploited for the population genetic analysis of species of conservation concern. We then discuss the advantages and disadvantages of EST-SSRs in the context of population genetic applications.

520 citations


Cites background from "Childhood‐onset ataxia: Testing for..."

  • ...Indeed, there are examples from the literature wherein certain genic SSRs are known to be associated with various diseases in animals (Zoghbi and Orr, 2000; Mao et al., 2002; Yamada et al., 2002) or pathogenicity/virulence in microbes (Peak et al....

    [...]

  • ...Indeed, there are examples from the literature wherein certain genic SSRs are known to be associated with various diseases in animals (Zoghbi and Orr, 2000; Mao et al., 2002; Yamada et al., 2002) or pathogenicity/virulence in microbes (Peak et al., 1996; Grimwood et al., 2001)....

    [...]

Journal ArticleDOI
23 May 2007-Heredity
TL;DR: In this paper, the authors review what is known about the transferability of EST-SSRs from one taxon to another with particular reference to the potential of these markers to facilitate population genetic studies and conclude that half of all suitable EST databases could be exploited for the population genetic analysis of species of conservation concern.
Abstract: Simple-sequence repeats (SSRs) have increasingly become the marker of choice for population genetic analyses. Unfortunately, the development of traditional 'anonymous' SSRs from genomic DNA is costly and time-consuming. These problems are further compounded by a paucity of resources in taxa that lack clear economic importance. However, the advent of the genomics age has resulted in the production of vast amounts of publicly available DNA sequence data, including large collections of expressed sequence tags (ESTs) from a variety of different taxa. Recent research has revealed that ESTs are a potentially rich source of SSRs that reveal polymorphisms not only within the source taxon, but in related taxa, as well. In this paper, we review what is known about the transferability of EST-SSRs from one taxon to another with particular reference to the potential of these markers to facilitate population genetic studies. As an example of the utility of these resources, we then cross-reference existing EST databases against lists of rare, endangered and invasive plant species and conclude that half of all suitable EST databases could be exploited for the population genetic analysis of species of conservation concern. We then discuss the advantages and disadvantages of EST-SSRs in the context of population genetic applications.

500 citations

Journal ArticleDOI
TL;DR: This review aims to portray the particular profile of the SCA2 disease process and correlate it to the specific features of ataxin-2, a subcellular localization at the Golgi, the endoplasmic reticulum and the plasma membrane.
Abstract: Spinocerebellar ataxia type 2 (SCA2) is an autosomal dominantly inherited, neurodegenerative disease. It can manifest either with a cerebellar syndrome or as Parkinson's syndrome, while later stages involve mainly brainstem, spinal cord and thalamus. This particular atrophy pattern resembles sporadic multi-system-atrophy (MSA) and results in some clinical features indicative of SCA2, such as early saccade slowing, early hyporeflexia, severe tremor of postural or action type, and early myoclonus. For treatment, levodopa is temporarily useful for rigidity/bradykinesia and for tremor, magnesium for muscle cramps, but neuroprotective therapy will depend on the elucidation of pathogenesis. The disease cause lies in the polyglutamine domain of the protein ataxin-2, which can expand in families over successive generations resulting in earlier onset age and faster progression. Genetic testing in SCA2 and other polyglutamine disorders like the well-studied Huntington's disease is now readily available for family planning. Although these disorders differ clinically and in the affected neuron populations, it is not understood how the different polyglutamine proteins mediate such tissue specificity. The neuronal intranuclear inclusion bodies described in other polyglutamine disorders are not frequent in SCA2. For the quite ubiquitously expressed ataxin-2, a subcellular localization at the Golgi, the endoplasmic reticulum and the plasma membrane, in interaction with proteins of mRNA translation and of endocytosis have been observed. As a first victim of SCA2 degeneration, cerebellar Purkinje neurons may be preferentially susceptible to alterations of these subcellular pathways, and therefore our review aims to portray the particular profile of the SCA2 disease process and correlate it to the specific features of ataxin-2.

191 citations


Cites background from "Childhood‐onset ataxia: Testing for..."

  • ...For patients with very large CAG-expansions (w200), retinitis pigmentosa (27,28) as frequently found in SCA7 and myoclo- nus-epilepsy as frequently found in DRPLA (29,30) may be part of the SCA2 manifestation....

    [...]

  • ...For patients with very large CAG-expansions (w200), retinitis pigmentosa (27,28) as frequently found in SCA7 and myoclonus-epilepsy as frequently found in DRPLA (29,30) may be part of the SCA2 manifestation....

    [...]

Journal ArticleDOI
TL;DR: Relevance of disease models and recent knowledge of therapeutic possibilities is reviewed, and certain pathomechanistic aspects of PolyQ disorders are discussed here.
Abstract: Expansion of CAG trinucleotide repeat within the coding region of several genes results in the production of proteins with expanded polyglutamine (PolyQ) stretch. The expression of these pathogenic proteins leads to PolyQ diseases, such as Huntington's disease or several types of spinocerebellar ataxias. This family of neurodegenerative disorders is characterized by constant progression of the symptoms and molecularly, by the accumulation of mutant proteins inside neurons causing their dysfunction and eventually death. So far, no effective therapy actually preventing the physical and/or mental decline has been developed. Experimental therapeutic strategies either target the levels or processing of mutant proteins in an attempt to prevent cellular deterioration, or they are aimed at the downstream pathologic effects to reverse or ameliorate the caused damages. Certain pathomechanistic aspects of PolyQ disorders are discussed here. Relevance of disease models and recent knowledge of therapeutic possibilities is reviewed and updated.

184 citations

References
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Journal ArticleDOI
TL;DR: Southern blot analyses and genomic cloning demonstrates the existence of related genes, raising the possibility that similar abnormalities in related genes may give rise to diseases similar to Machado-Joseph disease.
Abstract: We have identified a novel gene containing CAG repeats and mapped it to chromosome 14q32.1, the genetic locus for Machado-Joseph disease (MJD). In normal individuals the gene contains between 13 and 36 CAG repeats, whereas most of the clinically diagnosed patients and all of the affected members of a family with the clinical and pathological diagnosis of MJD show expansion of the repeat-number (from 68-79). Southern blot analyses and genomic cloning demonstrates the existence of related genes. These results raise the possibility that similar abnormalities in related genes may give rise to diseases similar to MJD.

1,704 citations


"Childhood‐onset ataxia: Testing for..." refers background or methods in this paper

  • ...As with other trinucleotide repeat disorders, such as Huntington disease, spinal-bulbar muscular atrophy, and dentatorubral pallidoluysian atrophy (DRPLA), the size of CAG expansion in the SCAs shows a negative correlation with age of onset and a direct correlation with severity and rate of progression [Orr et al., 1993; Kawaguchi et al., 1994; Pulst et al., 1996; Zhuchenko et al., 1997; David et al., 1998]....

    [...]

  • ...In SCA1, 2, 3, 6, and 7, the CAG encodes a polyglutamine tract, whereas the repeat is not translated in SCA8 or SCA12 [Orr et al., 1993; Kawaguchi et al., 1994; Pulst et al., 1996; Zhuchenko et al., 1997; David et al., 1998; Holmes et al., 1999; Evidente et al., 2000]....

    [...]

  • ...Assays for CAG repeat sizes in the SCA1, SCA3, and SCA6 genes also used PCRPAGE with conditions similar to those previously described [Orr et al., 1993; Kawaguchi et al., 1994; Zhuchenko et al., 1997]....

    [...]

Journal ArticleDOI
TL;DR: There is a direct correlation between the size of the (CAG)n repeat expansion and the age–of–onset of SCA1, with larger alleles occurring in juvenile cases.
Abstract: Spinocerebellar ataxia type 1 (SCA1) is an autosomal dominant disorder characterized by neurodegeneration of the cerebellum, spinal cord and brainstem. A 1.2-Megabase stretch of DNA from the short arm of chromosome 6 containing the SCA1 locus was isolated in a yeast artificial chromosome contig and subcloned into cosmids. A highly polymorphic CAG repeat was identified in this region and was found to be unstable and expanded in individuals with SCA1. There is a direct correlation between the size of the (CAG)n repeat expansion and the age-of-onset of SCA1, with larger alleles occurring in juvenile cases. We also show that the repeat is present in a 10 kilobase mRNA transcript. SCA1 is therefore the fifth genetic disorder to display a mutational mechanism involving an unstable trinucleotide repeat.

1,586 citations


"Childhood‐onset ataxia: Testing for..." refers background or methods in this paper

  • ...As with other trinucleotide repeat disorders, such as Huntington disease, spinal-bulbar muscular atrophy, and dentatorubral pallidoluysian atrophy (DRPLA), the size of CAG expansion in the SCAs shows a negative correlation with age of onset and a direct correlation with severity and rate of progression [Orr et al., 1993; Kawaguchi et al., 1994; Pulst et al., 1996; Zhuchenko et al., 1997; David et al., 1998]....

    [...]

  • ...In SCA1, 2, 3, 6, and 7, the CAG encodes a polyglutamine tract, whereas the repeat is not translated in SCA8 or SCA12 [Orr et al., 1993; Kawaguchi et al., 1994; Pulst et al., 1996; Zhuchenko et al., 1997; David et al., 1998; Holmes et al., 1999; Evidente et al., 2000]....

    [...]

  • ...Assays for CAG repeat sizes in the SCA1, SCA3, and SCA6 genes also used PCRPAGE with conditions similar to those previously described [Orr et al., 1993; Kawaguchi et al., 1994; Zhuchenko et al., 1997]....

    [...]

Journal ArticleDOI
TL;DR: It is concluded that a small polyglutamine expansion in the human α1A calcium channel is most likely the cause of a newly classified autosomal dominant spinocerebellar ataxia, SCA6.
Abstract: A polymorphic CAG repeat was identified in the human α1A voltage-dependent calcium channel subunit. To test the hypothesis that expansion of this CAG repeat could be the cause of an inherited progressive ataxia, we genotyped a large number of unrelated controls and ataxia patients. Eight unrelated patients with late onset ataxia had alleles with larger repeat numbers (21‐27) compared to the number of repeats (4‐16) in 475 non‐ataxia individuals. Analysis of the repeat length in families of the affected individuals revealed that the expansion segregated with the phenotype in every patient. We identified six isoforms of the human α1A calcium channel subunit. The CAG repeat is within the open reading frame and is predicted to encode glutamine in three of the isoforms. We conclude that a small polyglutamine expansion in the human α1A calcium channel is most likely the cause of a newly classified autosomal dominant spinocerebellar ataxia, SCA6.

1,558 citations


"Childhood‐onset ataxia: Testing for..." refers background or methods in this paper

  • ...As with other trinucleotide repeat disorders, such as Huntington disease, spinal-bulbar muscular atrophy, and dentatorubral pallidoluysian atrophy (DRPLA), the size of CAG expansion in the SCAs shows a negative correlation with age of onset and a direct correlation with severity and rate of progression [Orr et al., 1993; Kawaguchi et al., 1994; Pulst et al., 1996; Zhuchenko et al., 1997; David et al., 1998]....

    [...]

  • ...Assays for CAG repeat sizes in the SCA1, SCA3, and SCA6 genes also used PCRPAGE with conditions similar to those previously described [Orr et al., 1993; Kawaguchi et al., 1994; Zhuchenko et al., 1997]....

    [...]

  • ...In SCA1, 2, 3, 6, and 7, the CAG encodes a polyglutamine tract, whereas the repeat is not translated in SCA8 or SCA12 [Orr et al., 1993; Kawaguchi et al., 1994; Pulst et al., 1996; Zhuchenko et al., 1997; David et al., 1998; Holmes et al., 1999; Evidente et al., 2000]....

    [...]

Journal ArticleDOI
TL;DR: A CAG trinucleotide repeat with CAA interruptions that was expanded in patients with SCA2, which is a member of a novel gene family and not highly polymorphic in normal individuals is identified.
Abstract: The gene for spinocerebellar ataxia type 2 (SCA2) has been mapped to 12q24.1. A 1.1-megabase contig in the candidate region was assembled in P1 artificial chromosome and bacterial artificial chromosome clones. Using this contig, we identified a CAG trinucleotide repeat with CAA interruptions that was expanded in patients with SCA2. In contrast to other unstable trinucleotide repeats, this CAG repeat was not highly polymorphic in normal individuals. In SCA2 patients, the repeat was perfect and expanded to 36-52 repeats. The most common disease allele contained (CAG)37, one of the shortest expansions seen in a CAG expansion syndrome. The repeat occurs in the 5'-coding region of SCA2 which is a member of a novel gene family.

1,094 citations


"Childhood‐onset ataxia: Testing for..." refers background or methods in this paper

  • ...Both SCA2 and SCA7 are progressive neurological disorders most commonly seen in adult patients, with age of onset in the 30s to 40s [Pulst et al., 1996; David et al., 1998; Evidente et al., 2000]....

    [...]

  • ...As with other trinucleotide repeat disorders, such as Huntington disease, spinal-bulbar muscular atrophy, and dentatorubral pallidoluysian atrophy (DRPLA), the size of CAG expansion in the SCAs shows a negative correlation with age of onset and a direct correlation with severity and rate of progression [Orr et al., 1993; Kawaguchi et al., 1994; Pulst et al., 1996; Zhuchenko et al., 1997; David et al., 1998]....

    [...]

  • ...Primers used to amplify the repeat regions were 2A: 50-GGGCCCCTCACCATGTCG and 2B: 50-CGGGCTTGCGGACATTGG for SCA2 [Pulst et al., 1996]; 7A: 50-GTAGGAGCGGAAAGAATGTC and 7B: 50-CCCCGACCGTCGCCATTG for SCA7 (designed in-house)....

    [...]

  • ...In SCA1, 2, 3, 6, and 7, the CAG encodes a polyglutamine tract, whereas the repeat is not translated in SCA8 or SCA12 [Orr et al., 1993; Kawaguchi et al., 1994; Pulst et al., 1996; Zhuchenko et al., 1997; David et al., 1998; Holmes et al., 1999; Evidente et al., 2000]....

    [...]

Journal Article
TL;DR: The length of FA alleles ranged from 201 to 1,186 repeat units, with no overlap with the normal range, and showed a negatively skewed distribution with a peak between 800 and 1,000 repeats, and the FA repeat showed meiotic instability with a median variation of 150 repeats.
Abstract: Friedreich ataxia (FA) is associated with the expansion of a GAA trinucleotide repeat in the first intron of the X25 gene. We found both alleles expanded in 67 FA patients from 48 Italian families. Five patients from three families were compound heterozygotes with expansion on one allele and an isoleucine-->phenylalanine change at position 154 on the other one. We found neither expansions nor point mutations in three patients. The length of FA alleles ranged from 201 to 1,186 repeat units, with no overlap with the normal range, and showed a negatively skewed distribution with a peak between 800 and 1,000 repeats. The FA repeat showed meiotic instability with a median variation of 150 repeats. The lengths of both larger and smaller alleles in each patient inversely correlated with age at onset of the disorder. Smaller alleles showed the best correlation, accounting for approximately 50% of the variation of age at onset. Mean allele length was significantly higher in patients with diabetes and in those with cardiomyopathy.

489 citations


"Childhood‐onset ataxia: Testing for..." refers background in this paper

  • ...PCR-based assays for other trinucleotide repeats show that the PCR can produce products for alleles containing more than 1,000 repeats, although amplification efficiency declines with increasing repeat size [Pergolizzi et al., 1992; Filla et al., 1996]....

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