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Results for “DNA Repeat Expansion”

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PubMed1999

Anticipation is not associated with CAG repeat expansion in parent-offspring pairs of patients affected with schizophrenia.

With the rationale that a disease that presents with anticipation could be associated with expansion of trinucleotide repeats, we selected parent-offspring pairs of schizophrenia patients with earlier age at onset in the filial generation to measure the expansion of CAG repeats using the repeat expansion detection (RED) method. Intergenerational comparisons were made for age at onset, length of CAG repeats, and clinical variables. Although the patients from the filial generation became affected 13 years earlier than the parents (P < 0.0005), we did not find larger CAG repeats in the offspring. No association was found between size of CAG repeat and age at onset or with any other clinical variable. Overall, the frequency of patients with CAG repeats longer than 40 was 32%, which was similar to that observed in control subjects (27%). It is particularly noteworthy that in 86% of the pairs, the mother was the affected parent. In this Spanish sample with parent-offspring pairs presenting schizophrenia with clinical anticipation and apparent female bias of transmission, neither the phenomenon of anticipation nor disease status was associated with the expansion of CAG repeats.

Adult↗

PubMed2000

Oligonucleotide microarray based detection of repetitive sequence changes.

Prior studies of oligonucleotide microarray-based mutational analysis have demonstrated excellent sensitivity and specificity except in circumstances where a frameshift mutation occurs in the context of a short repeated sequence. To further evaluate this circumstance, a series of nucleic acid samples having heterozygous mutations within repetitive BRCA1 sequence tracts was prepared and evaluated. These mutations included single nucleotide insertions and deletions in homopolymer runs, insertions and deletions of trinucleotide repeats, and duplications. Two-color comparative hybridization experiments were used wherein wild type reference and test targets are co-hybridized to microarrays designed to screen the entire BRCA1 coding sequence for all possible sequence changes. Mutations in simulated heterozygote samples were detected by observing relative losses of test target hybridization signal to select perfect match oligonucleotide probes. While heterozygous mutations could be readily distinguished above background noise in 9/19 cases, it was not possible to detect alterations in a poly dA/dT tract, small triplet repeat expansions, and a 10 bp direct repeat. Unexpectedly, samples containing (GAT)(3) triplet repeat expansions showed significantly higher affinity toward specific perfect match probes relative to their wild type counterparts. Therefore, markedly increased as well as decreased test sample hybridization to perfect match probes should be used to raise a suspicion of repetitive sequence changes.

Algorithms↗

PubMed1999

Linkage disequilibrium and haplotype analysis in German Friedreich ataxia families.

The main mutation causing Friedreich ataxia (FRDA) is the expansion of a GAA repeat localized within the intron between exon 1 and exon 2 of the gene X25. This expansion has been observed in 98% of FRDA chromosomes. To analyze frequencies of markers tightly linked to the Friedreich ataxia gene and to investigate wheter a limited number of ancestral chromosomes are shared by German FRDA families, a detailed analysis employing nine polymorphic markers was performed. We found strong linkage disequilibria and association of FRDA expansions with a few haplotypes. FRDA haplotypes differ significantly from control haplotypes. Our results confirm that GAA repeat expansions in intron 1 of the frataxin gene are limited to a few chromosomes and indicate an obvious founder effect in German patients. Based on these analyses, we estimate a minimum age of the mutation of 107 generations.

Evolution, Molecular↗

PubMed2001

Evidence that the N-terminal extension of the vicieae convicilin genes evolved by intragenic duplications and trinucleotide expansions.

This study was aimed to identify lentil (Lens culinaris subsp. culinaris) convicilin genes and to carry out a comparative analysis of these genes in the tribe Vicieae. Convicilins differ from vicilins, a related group of plant seed storage proteins, mainly by the presence of an additional sequence of amino acids in the sequence corresponding to the first exon, referred as the N-terminal extension. A single gene for convicilin, a component of legume seed storage proteins, was identified in the cultivated lentil. In this species, the N-terminal extension is formed by a stretch of 126 amino acids of which 59.2% are charged amino acids: 29.6% glutamic acid, 3.2% aspartic acid, 14.4% arginine, 8.8% lysine, and 3.2% histidine. This lentil convicilin sequence is similar to the sequence of convicilins in other species of the tribe Vicieae. However, the size of the N-terminal extension clearly differs among convicilins. Sequence comparison and phylogenetic analyses including convicilin and vicilin of Vicieae species indicated that the differentiation between vicilins and convicilins predated the differentiation of the two vicilin gene families (47- and 50-kDa vicilins), and that the N-terminal extension evolved mainly by a series of duplications of short internal sequences and triplet expansions, the predominant one being GAA.

Amino Acid Sequence↗

PubMed1999

Linkage between male infertility and trinucleotide repeat expansion in the androgen-receptor gene.

BACKGROUND: Androgens acting via the androgen receptor bring about stimulation and maintenance of spermatogenesis. If mutations in the androgen-receptor gene interfere with the receptor's function, this effect may partly account for impaired spermatogenesis. We aimed to find out whether expansion of a trinucleotide repeat in the androgen-receptor gene is associated with male infertility. METHODS: We analysed 67 coded semen and blood samples from a predominantly white group of male infertility patients and controls. Clinical analyses included cause of infertility, sperm count, and reproductive hormone concentrations. Analysis of trinucleotide (CAG) repeat length and point mutations in the androgen-receptor gene was done by PCR, single-stranded conformational polymorphism, and DNA sequencing. FINDINGS: Screening and characterisation of the androgen-receptor gene in 35 patients and 32 controls showed no point mutations in the gene. 30 of the infertile patients had idiopathic azoospermia or oligozoospermia, and these men had significantly longer CAG repeat tracts than controls (mean 23.2 [SE 0.7] vs 20.5 [0.3], p=0.0001). The odds of having CAG repeat lengths of 20 were six-fold higher for fertile men than for men with a spermatogenic disorder. INTERPRETATION: Our results indicate a relation between CAG repeat length in the androgen-receptor gene and the risk of defective spermatogenesis. With the use of intracytoplasmic sperm injection, this mutation could be inherited, possibly leading to an increase in male infertility in future generations. Should further elongation of the CAG repeat occur in these future generations, there is an added risk of increased severity of male infertility, and potentially an increased incidence of neurodegenerative disease.

Adult↗

PubMed1998

Trinucleotide repeat DNA structures: dynamic mutations from dynamic DNA.

Models for the disease-associated expansion of (CTG)n.(CAG)n, (CGG)n.(CCG)n, and (GAA)n.(TTC)n trinucleotide repeats involve alternative DNA structures formed during DNA replication, repair and recombination. These repeat sequences are inherently flexible and can form a variety of hairpins, intramolecular triplexes, quadruplexes, and slipped-strand structures that may be important intermediates and result in their genetic instability.

Base Composition↗

PubMed2001

Instability at sequence repeats in melanocytic tumours.

To obtain information on the prevalence of microsatellite mutations in melanomas, we analysed the status of 14 repetitive loci characterized by structurally different non-coding and coding sequence repeats in a panel of 34 primary melanocytic tumours and in lymph node metastases matched to 13 cases. Instability at one or more of the non-coding dinucleotide repeats D2S123, D3S1611, D5S107 and D18S34 was detected in ten out of the 34 primary tumours (29%) and in ten of the 13 metastases (77%). There was no instability at the non-coding mononucleotide repeats BAT25, BAT26 and APDelta3 or at the coding mononucleotide runs within the TGFbetaRII, IGFIIR, BAX, hMSH3 and hMSH6 genes. A five-repeats expansion of the coding E2F4(CAG)n run was found in the only malignant melanoma of soft parts examined, which also showed instability at two dinucleotide loci, and in a superficial spreading melanoma, which was stable at the mononucleotide and dinucleotide repeats but was the only tumour that manifested instability at the SCA1(CAG)n repeat. The absence of mutations at mononucleotide tracts indicates that, in the malignant melanomas tested, microsatellite instability was not associated with the microsatellite mutator phenotype characteristic of mismatch repair-deficient tumours. On the other hand, our results confirm that microsatellite instability at dinucleotide repeats increases with melanoma progression, and indicate that expansions of triplet repeats may occur in melanocytic tumours.

Adult↗

PubMed2003

Triplet repeats in human genome: distribution and their association with genes and other genomic regions.

MOTIVATION: Simple sequence repeats (SSRs) or microsatellite repeats are found abundantly in many prokaryotic and eukaryotic genomes. Among SSRs, triplet repeats are of special significance because some of them have been linked to various genetic disorders. The objective of the study is to analyze the triplet repeats of complete human genome and to identify the genes that contain the triplet repeats in their coding region. The analysis will help us to identify the candidate genes that have potential for repeat expansion. RESULTS: We have analyzed triplet repeats in the complete human genome from the publicly available sequences. Our analysis revealed that AGC and CCG repeat were predominantly present in the coding regions of the genome while UTRs and the upstream sequences contained CCG repeats in relative abundance. Analysis of density of triplet repeats (bp/Mb) revealed that AAT and AAC were the abundant repeats whereas ACT and ACG were the rare repeats found in human genome. We could identify about 2135 known or predicted genes that were associated with at least one of the triplet repeat types. A large proportion of putative transcripts that were identified by gene finding programs were found to be associated with triplet repeats. These transcripts will be the candidate genes for analysis of triplet repeat expansion and a possible association with disease phenotypes. Identification of 171 genes which contain a minimum of ten repeat units will be of particular interest in future in correlating their association with any disease phenotype due to the expansion potential of repeats present in them. The list of genes and other details of analysis are given in the online supplementary data (http://www.ingenovis.com/tripletrepeats).

Databases, Nucleic Acid↗

PubMed1982

Recent duplication and germ-line diversification of rat immunoglobulin kappa chain gene joining segments.

Sequence determination of the joining segment gene (J) cluster in the kappa chain (J kappa) in the embryonic context demonstrates that rat genome contains seven J kappa gene segments that expanded from an ancestral cluster of five J kappa genes. The rat J segments are separated by about 300 base pairs (bp) and are flanked 5' by the presumed variable region (V)/J recombination signal sequence and 3' by the RNA splicing signal. Two of the J gene segments designated J2A and J2B and their 5'-flanking spacer DNA bear striking homology to J2 and its 5'-flanking spacer. Thus, the unit of duplication was the entire J kappa coding region and 5' noncoding spacer (345 bp). The duplication probably occurred as two separate unequal crossing-over (UXO) events. The first UXO event can be confined to recombination within an identical stretch (14 bp long) located at the 3' ends of the coding regions of J1 and J2. The second event could involve a longer segment (372 bp) of tight homology generated by the first UXO event, thus increasing the probability of repeated expansion of the same DNA segment. The sequence homology among the rat duplicated segments (98-99%) is larger than the homology between the corresponding rat and mouse segments (89%), showing that the rat J kappa gene expansion must have occurred after rat and mouse divergence 10 X 10(6) yr ago. We estimate that the first and second UXO events occurred 2 X 10(6) and 1 X 10(6) yr ago, respectively. J3 of rat and mouse share the same mutation (G leads to C) in the RNA splicing signal that presumably inactivates J3. This mutation preceded divergence of the two species. A mutation in the first nucleotide of codon 96 has occurred in both duplicated segments, the only position along 345 bp where J2, J2A, and J2B differ from each other. This results in three different amino acids at position 96 not present in any other J kappa. These mutations are physiologically significant because they diversify the third complementarity-determining region (CDR3) and, thus, may reflect selective pressure to increase antibody diversity. The germ-line diversification of CDR3 was exercised within the last 1-2 X 10(6) yr.

Amino Acid Sequence↗

PubMed1998

The correlation of clinical phenotype in Friedreich ataxia with the site of point mutations in the FRDA gene.

Most cases of Friedreich ataxia (FRDA) are due to expansions of a GAA trinucleotide repeat sequence in the FRDA gene coding for frataxin, a protein of poorly understood function which may regulate mitochondrial iron transport. However, between 1% and 5% of mutations are single base changes in the sequence of the FRDA gene, causing missense, nonsense, or splicing mutations. We describe three new mutations, IVS4nt2 (T to G), R165C, and L182F, which occur in patients in association with GAA expansions. These cases, and a further five reported cases of point mutations causing FRDA, demonstrate that splicing, nonsense, or initiation codon mutations (which cause a complete absence of functional frataxin) are associated with a severe phenotype. Missense mutations, even in highly evolutionally conserved amino acids, may cause a mild or severe phenotype.

Adaptor Proteins, Signal Transducing↗

PubMed2026

Multiomic approaches identify a rare CCG repeat expansion in BCLAF3 in neurodevelopmental disorders.

BACKGROUND: Tandem repeat expansions have been implicated in various neurological conditions. Here, we present a novel hypermethylated CCG repeat expansion on Xp22 in the 5'UTR of BCLAF3 in males with neurodevelopmental disorders. METHODS: We used patient-derived fibroblasts and neuronal models from a family with BCLAF3 repeat expansions to generate multiomic data and investigate downstream molecular consequences of the repeat expansion. To identify additional affected individuals with BCLAF3 repeat expansions, we screened methylation arrays (n = 12,375) and short-read genomes (n = 15,963) from probands with neurodevelopmental presentations. We also characterized BCLAF3 repeat expansions in the general population using long-read sequencing data (n = 793) and population-level short-read sequencing data (n = 410,076). RESULTS: Long-read sequencing validated hypermethylation of expanded repeats. Patient-derived cells showed repressed BCLAF3 RNA and protein expression. We show that the BCLAF3 CCG repeat expansion constitutes a previously uncharacterized fragile site (FRAXG) that shifts the surrounding chromatin compartment from open euchromatin to closed heterochromatin. Using our multiomic screening approaches, we identified three additional unrelated males and one related male cousin with long-read sequencing validated (n = 2) or short-read sequencing predicted (n = 2) repeat expansions. In one family, the BCLAF3 repeats segregate with more severe phenotypes than expected for the primary diagnoses. Long-read sequencing in three carrier mothers showed skewed X-inactivation against the repeat expansion, highlighting the potential deleterious effect of an allele with an expansion. Expansions were absent in long-read sequencing data from control populations. Assessment of the BCLAF3 repeat expansion in the UK Biobank indicates that it may be ~ 20X rarer than FMR1 repeat expansions. CONCLUSIONS: CCG repeat expansions in the 5'UTR of BCLAF3 likely constitute a novel genetic etiology associated with X-linked neurodevelopmental phenotypes in males. Future work will be essential to delineate the phenotypic spectrum and determine a disease pathomechanism.

BCLAF3↗

PubMed1999

Clinical and neuroimaging study of central nervous system in congenital myotonic dystrophy.

We present the clinical and neuroimaging findings of five patients (four males, one female; mean age 12 years) affected by congenital myotonic dystrophy and the correlation with their molecular genetic analysis. At birth all five presented severe muscular weakness and hypotonia, associated with feeding difficulties and respiratory distress. In the same patients, congenital clubfoot or more generalized arthrogryposis was also evident. Lymphocyte DNA was characterized in each by a CTG repeat longer than 1300 in the region of the myotonic dystrophy gene in chromosome 19. The patients' neurological condition was evaluated by clinical examination, intelligence tests, electroencephalography, and brain magnetic resonance imaging. All five suffered from some impairment of intellectual function (IQ ranged from 52 to 79). In three a longitudinal evaluation of the cognitive deficit detected no deterioration. In all patients magnetic resonance imaging showed some degree of ventricular dilatation, loosely correlated to the cognitive impairment; in three there was hypoplasia of the corpus callosum and in two mild abnormalities of supratentorial white matter. The relationship between the size of the CTG repeat expansion found in lymphocyte DNA and the cerebral abnormalities appeared inconsistent in this unusual myoencephalopathy of the newborn.

Adolescent↗

PubMed1997

Repeat expansion detection analysis of (CAG)n tracts in tumor cell lines, testicular tumors, and testicular cancer families.

The mutational expansion of triplet repeat microsatellite sequences underlies the transmission of a number of heritable neurological disorders. However, this form of microsatellite instability has not previously been observed in association with malignant disease. Because trinucleotide expansions can dramatically alter gene expression and protein function, we hypothesized that they might occur in neoplastic cells as a mechanism through which to alter cancer genes. Accordingly, we used the repeat expansion detection technique to determine whether (CAG)n triplet repeat expansions were present in DNA from malignant cells. No expansions were observed in a survey of 20 tumor cell lines derived from neoplasms of the breast, ovary, cervix, endometrium, lung, colon, placenta, or hematopoietic system. However, we did observe expanded (CAG)n tracts in DNA from 5 of 11 testicular tumor cell lines and in 1 of 11 sporadic testicular tumors. Examination of the corresponding normal DNA, when available, revealed that some of the expansions were germline in nature. To assess the possibility that (CAG)n expansions underlie some cases of inherited testicular cancer, we also analyzed germline DNA from members of five kindreds predisposed to this malignancy. An increase in (CAG)n tract size was observed in all five families and was particularly striking in one large pedigree in which expansions were observed in three of four affected siblings. These observations raise the possibility that the germline transmission of expanded (CAG)n tracts may play a role in testicular tumorigenesis.

Adenine↗

PubMed2003

Somatic instability of the androgen receptor CAG repeat in a normal female.

The polyglutamine repeat disorders represent a family of degenerative neurological diseases which are characterized by expansions of tandemly repeated CAG repeats. Investigations have demonstrated that in Huntington disease, dentatorubral pallidoluysian atrophy, and the spinocerebellar ataxias type 1, 2, and 3, the polyglutamine expansions show both meiotic and mitotic instability. However, previous studies have suggested that the polyglutamine motif within exon 1 of the androgen receptor gene (AR) which expands in cases of spinobulbar muscular atrophy differs in that it is apparently mitotically stable. During linkage analysis in a family with FG syndrome, a rare condition mapped to Xq12-q22.1, we detected the presence of an unusually small AR allele segregating within the pedigree. Sequencing, cytogenetic analysis, and PCR of flanking markers indicate that this allele arose by a somatic contraction of seven CAG repeats in the proband's mother, representing the first report of mitotic instability of an AR CAG repeat of normal size.

Adult↗

PubMed2000

Phenotypic manifestations associated with CAG-repeat expansion in the androgen receptor gene in male patients and heterozygous females: a clinical and molecular study of 30 families.

Spinal and bulbar muscular atrophy (Kennedy disease) is an adult form of X-linked motor neuron disease caused by the expansion of a polymorphic CAG-repeat sequence in the first exon of the androgen receptor gene. We studied clinical and molecular features of 36 patients and 19 heterozygous females. Phenotypic manifestations and disease severity broadly varied among our spinal and bulbar muscular atrophy patients. The size of CAG expansion significantly influences the age of disease onset, but neither clinical features nor disease severity. The majority of carrier women presented signs of chronic denervation at neurophysiological examination and, in three cases, low-amplitude sensory action potentials were recorded. Notably, a few women developed mild signs of bulbar motor neuron impairment later in life. The identification of a large number of patients by the use of the molecular test further supports the hypothesis that Kennedy disease had been previously underdiagnosed, probably because of the great variability of clinical presentation. Although an early diagnosis may not be crucial for treatment, given the lack of effective therapy, the molecular testing can be of great relevance for disease prognosis and genetic counseling.

Action Potentials↗

PubMed2002

Paternal transmission of the congenital form of myotonic dystrophy type 1: a new case and review of the literature.

Myotonic dystrophy type 1 (DM1) is an autosomal dominant trinucleotide repeat disorder that shows anticipation. The mildest manifestations of the DM gene are usually noted in individuals with the smallest repeat sizes, while congenital myotonic dystrophy (CDM) is the most common clinical outcome of the larger expansions. For many years, it was thought that CDM could only be maternally transmitted. However, in the last few years, cases of paternal transmission of CDM have been described. We report a child with the CDM phenotype and 1, 800 CTG repeats born to an asymptomatic father with 65 repeats and compare this case to the four currently in the literature. We note that polyhydramnios was present in the majority of cases and that all fathers whose status was known had small repeat sizes and/or were asymptomatic at the time of their child's birth. Although it may be unusual, the possibility of the paternal transmission of CDM should be mentioned when counseling families with DM. The men who are at highest risk may be those who have small repeats sizes and are asymptomatic.

Adult↗

PubMed2005

Spinocerebellar ataxia type 2: polyQ repeat variation in the CACNA1A calcium channel modifies age of onset.

Nine neurodegenerative diseases, collectively referred to as polyglutamine (polyQ) diseases, are caused by expansion of a coding CAG DNA trinucleotide repeat. PolyQ diseases show a strong inverse correlation between CAG repeat length and age of disease onset (AO). Despite this, individuals with identical repeat expansion alleles can have highly variable disease onset indicating that other factors also influence AO. We examined AO in 148 individuals in 57 sibships from the SCA2 founder population in Cuba. The mutant CAG repeat allele explained 57% of AO variance. To estimate heritability of the residual variance after correction for SCA2 repeat length, we applied variance component analysis and determined the coefficient of intraclass correlation. We found that 55% of the residual AO variance was familial. To test candidate modifier alleles in this population, we selected 64 unrelated individuals from a set of 394 individuals who were highly discordant for AO after correction for SCA2 CAG repeat length. We hypothesized that long normal alleles in the other 8 polyQ disease genes were associated with premature disease onset in SCA2. Of the 8 genes tested, only long normal CAG repeats in the CACNA1A gene were associated with disease onset earlier than expected based on SCA2 CAG repeat size using non-parametric tests for alleles (P < 0.04) and genotypes (P < 0.023) after correction for multiple comparisons. CACNA1A variation explained 5.8% of the residual variation in AO. The CACNA1A calcium channel subunit represents an excellent candidate as a modifier of disease in SCA2. It is highly expressed in Purkinje cells (PCs) and is essential for the generation of the P/Q current and the complex spike in PCs. In contrast to other polyQ proteins, which are nuclear, the CACNA1A and SCA2 proteins are both cytoplasmic. Furthermore, small pathologic expansions of the polyQ domain in the CACNA1A protein lead to PC degeneration in SCA6. Future studies are needed to determine whether the modifier effect of CACNA1A relates to neuronal dysfunction or cell death of Purkinje neurons.

Adult↗

PubMed2006

Intergeneration CAG expansion and contraction in a Chinese HD family.

The prevalence of juvenile-onset Huntington's disease (HD) is about ten times lower than adult HD. Here we report a Chinese HD family showing both intergeneration CAG expansion and contraction. The expansion resulted from a paternal transmission which leads to juvenile-onset HD for a 17-year-old Chinese boy (III-5). More interestingly, a contraction was noticed in a maternal transmission (III-3), which changed the CAG repeat from an expanded, disease-causing allele (48 repeats) to a normal or intermediate allele (34 repeats). Of note, the contraction resulted in a deletion of 14 CAG repeats, which is much larger than previously reported contractions. Our results are consistent with previous observations in Western Caucasians that juvenile-onset HD is more likely inherited through the male germline.

Adolescent↗