Genetic background of Huntington disease in Croatia: Molecular analysis of CAG,CCG, and Δ2642 (E2642del) polymorphisms

This study presents the first molecular data on the basis and the origin of Huntington disease in Croatia and is the first such analysis performed among a Slavic population. We analyzed three trinucleotide polymorphisms in the HD gene: CAG, CCG and GAG Δ2642 (E2642del) triplets. Analysis of the CAG repeat size among 44 Huntington patients (39‐66 CAGs) and 51 normal individuals (9‐34 CAGs) showed that the range of the repeats was similar to previous findings. The frequency of the CCG and Δ2642 polymorphic alleles on N and HD chromosomes was found to correlate well with earlier reports for Western European populations. We found significance for both the CCG7 allele (p=0.004) and the Δ2642 allele (p<0.001) among HD chromosomes. The CCG7 allele was overpresented among affected chromosomes (94.6%), but was also the most frequent CCG allele among normal chromosomes (66.7%). Interestingly, the Δ2642 allele was present on 40.5% HD chromosomes compared to only 9.8% of control chromosomes. Our results indicate that HD mutations in Croatia could be of the same origin as in Western populations and also support the multi‐step hypothesis for generating new HD alleles. Similar frequencies and distributions of both the CCG and the Δ2642 polymorphisms in Croatia and Western European normal chromosomes indicate that the prevalence rate of HD in Croatia may be as high as in Western populations. Since we estimated a lower prevalence rate (1 : 100,000), we assume that there are still many misdiagnosed and/or unrecognized cases of Huntington disease in Croatia. © 2002 Wiley‐Liss, Inc.     

Analysis of CAG and CCG repeats in Huntingtin gene among HD patients and normal populations of India

We have analysed the distribution of CAG and adjacent polymorphic CCG repeats in the Huntingtin gene in 28 clinically diagnosed unrelated Huntington's disease (HD) patients and in normal individuals belonging to different ethnic groups of India. The range of expanded CAG repeats in HD patients varied from 41 to 56 repeats, whereas in normal individuals this number varied between 11 and 31 repeats. We identified six CCG alleles from a total of 380 normal chromosomes that were pooled across different ethnic populations of India. There were two predominant alleles: (CCG)7 (72.6%) and (CCG)10 (20%). We report here for the first time one four-repeat CCG allele which has not been found in any population so far. We found 30 haplotypes (two loci CAG-CCG) for 380 normal chromosomes. In the present study, no statistically significant preponderance of expanded HD alleles was found on either (CCG)7 or (CCG)10 backgrounds. Our studies suggest that the overall prevalence of HD in Indian populations may not be as high as in Western populations. Further studies are necessary to identify the origin of HD mutation in these populations.     

DNA haplotype analysis of Huntington disease reveals clues to the origins and mechanisms of CAG expansion and reasons for geographic variations of prevalence

This study of allelic association using three Intra- and twoextragenlc markers within 150 kb of the Huntlngton disease (HD)mutation has provided evidence for linkage disequilibrium forfour of five markers. Haplotype analysis of 67 HD families usingmarkers in strong linkage disequilibrium with HD Identifiedtwo haplotypes underlying 77.6% of HD chromosomes. Normal chromosomeswith these two haplotypes had a mean number of CAG repeats significantlylarger than and an altered distribution of CAG repeats comparedwith other normal chromosomes. Furthermore, haplotype analysisof five new mutation families reveals that HD has arisen onthese same two chromosomal haplotypes. These findings suggestthat HD arises more frequently on chromosomes with specificDNA haplotypes and higher CAG repeat lengths. We then studiedCAG and CCG repeat lengths In the HD gene on 896 control chromosomesfrom different ancestries to determine whether the markedlyreduced frequency of HD in Finland, Japan, China and AfricanBlacks Is associated with an altered frequency of DNA haplotypesand subsequently lower CAG lengths on control chromosomes comparedto populations of Western European descent. The results showa highly significant positive correlation between CAG size onnormal chromosomes and the frequency of HD and a significantinverse relationship between CAG and CCG repeat lengths. Inpopulations with lowered prevalence rates of HD, CAG repeatlengths are smaller and the distribution of CCG alleles Is markedlydifferent from Western European populations. These findingssuggest that, in addition to European emigration, new mutationsmake a contribution to geographical variation of prevalencerates and is consistent with a multistep model of HD developingfrom normal chromosomes with higher CAG repeat lengths.     

The CAG repeat at the Huntington disease gene in the Portuguese population: insights into its dynamics and to the origin of the mutation

Huntington disease (HD) is caused by an expansion of a CAG repeat. This repeat is a dynamic mutation that tends to undergo intergenerational instability. We report the analysis of the CAG repeat in a large population sample (2,000 chromosomes) covering all regions of Portugal, and a haplotype study of (CAG)_n and (CCG)_n repeats in 140 HD Portuguese families. Intermediate class 2 alleles represented 3.0% of the population; and two expanded alleles (36 and 40 repeats, 0.11%) were found. There was no evidence for geographical clustering of the intermediate or expanded alleles. The Portuguese families showed three different HD founder haplotypes associated with 7-, 9- or 10-CCG repeats, suggesting the possibility of different origins for the HD mutation among this population. The haplotype carrying the 7-CCG repeat was the most frequent, both in normal and in expanded alleles. In general, we propose that three mechanisms, occurring at different times, may lead to the evolution from normal CAGs to full expansion: first, a mutation bias towards larger alleles; then, a stepwise process that could explain the CAG distributions observed in the more recent haplotypes; and, finally, a pool of intermediate (class 2) alleles more prone to give rise to expanded HD alleles.     

Analysis of triplet repeats in the huntingtin gene in Japanese families affected with Huntington''s disease.

Huntington's disease (HD) is associated with the expansion of a CAG repeat in the huntingtin gene. Molecular analysis of the repeat in Japanese HD patients and normal controls was performed. The size of the CAG repeat ranged from 37 to 95 repeats in affected subjects and from seven to 29 in normal controls. A significant correlation was found between the age of onset and the CAG expansion. The length of the expanded repeat is unstable in meiotic transmission and large increases occur in paternal transmission. At the same time the CCG repeat polymorphism adjacent to the CAG repeat was analysed and haplotypes of HD chromosomes were identified. Strong linkage disequilibrium was found between the CAG repeat expansion and an allele of (CCG)10 in Japanese HD chromosomes. It is distinct from that described previously in western populations. Western HD chromosomes strongly associate with an allele of (CCG)7. Possible mechanisms underlying the disequilibrium in Japan are discussed.     

New Huntington disease mutation arising from a paternal CAG34 allele showing somatic length variation in serially passaged lymphoblasts.

The analysis of somatic CAG triplet variation in lymphoblastoid cell lines from subjects carrying alleles of intermediate length (IA(33CAG) and IA(34CAG)) in Huntington disease (HD) gene disclosed instability in the DNA of the person, from whom a new expansion mutation of 45 triplets originated. The triplet size increased after about 30 passages in cell cultures in lymphoblasts with the IA(34) genotype. Lymphoblasts may provide an appropriate model for studying repeat instability in subjects with poly(CAG) repeat disorders. HD shows somatic, in addition to germ-line instability, highlighting the propensity to somatic CAG variation in human cells even with repeat numbers under the expanded edge. Factors potentially cis acting with the mutation, other than those reported in this study (CCG polymorphic stretch, the deletion of the glutamic acid residue at position 2642 and the 4-codon segment between CAG and CCG polymorphisms), should be searched for and analyzed.     

A CCG repeat polymorphism adjacent to the CAG repeat in the Huntington disease gene: implications for diagnostic accuracy and predictive testing

The polymorphic CAG repeat that is expanded on Huntington disease(HD) chromosomes is flanked by a CCG repeat. Here we show thatthis CCG tract, previously assumed to be invariant at sevenCCG repeats, is also polymorphic. We have identified five CCGalleles from 205 normal chromosomes, with 137 (67%) having allelesof seven repeats, five (2%) with nine repeats, 61 (30%) with10 repeats, one (0.5%) with 11 repeats and one (0.5%) with 12repeats. In contrast, analysis of 113 HD chromosomes revealedthat the majority (105 chromosomes, 93%) contained seven CCGrepeats, while the remaining eight chromosomes (7%) had allelesizes of 10 CCG repeats. Despite evidence that both CAG andCCG are polymorphic on normal chromosomes, we have found thatit is only the CAG length that has a significant impact on ageof onset. The discovery of larger sized CCG alleles, however,has significant implications for the assessment of CAG repeatlength, particularly for persons with estimated CAG size of36–42 repeats, since an overestimation of CAG length inthis range could result in erroneous information being impartedto patients.     

Polymorphisms in the CAG repeat--a source of error in Huntington disease DNA testing

Five of 400 patients (1.3%), referred for Huntington disease DNA testing, demonstrated a single allele on CAG alone, but two alleles when the CAG + CCG repeats were measured. The PCR assay failed to detect one allele in the CAG alone assay because of single-base silent polymorphisms in the penultimate or the last CAG repeat. The region around and within the CAG repeat sequence in the Huntington disease gene is a hot-spot for DNA polymorphisms, which can occur in up to 1% of subjects tested for Huntington disease. These polymorphisms may interfere with amplification by PCR, and so have the potential to produce a diagnostic error.     

Mosaicism of the CAG repeat sequence in the Huntington disease gene in a pair of monozygotic twins

We report on a pair of monozygotic twins belonging to a family segregating Huntington disease (HD). In routine DNA analysis of blood cells, they displayed three alleles of the CAG repeat sequence in the HD gene. Two different cell lines, carrying the normal allele together with either an expanded allele with 47 CAGs or an intermediate allele with 37 CAGs, were detected in blood and buccal epithelium from both twins. To our knowledge, this is the first case described of HD gene CAG repeat length mosaicism in blood cells. Haplotype analysis established that the 37 CAG allele most likely arose by contraction of the maternal 47 CAG allele. The contraction must have taken place postzygotically, possibly at a very early stage of development, and probably before separation of the twins. One of the twins has presented symptoms of HD for 4 years; his skin fibroblasts and hair roots carried only the cell line with the 47 CAG repeat allele. The other twin, who is without symptoms at present, displayed mosaicism in skin fibroblasts and hair roots. If the proportion of the two cell lines in the brain of each twin resembles that of their hair roots (another tissue originating from the ectoderm), the mosaicism in the unaffected twin would mean that only a part of his brain cells carried the expanded allele, which could explain why he, in contrast to his brother, has no symptoms at this time.     

Sequence analysis of the CCG polymorphic region adjacent to the CAG triplet repeat of the HD gene in normal and HD chromosomes.

The CAG expansion responsible for Huntington's disease (HD) is followed by an adjacent polymorphic CCG repeat region which may interfere with a PCR based diagnosis. We have sequenced this region in 52 unrelated HD patients, from both normal and HD chromosomes. Fifty percent of the normal alleles were (CCG)7(CCT)2, 48% (CCG)10(CCT)2, and 2% (CCG)7(CCT)3. In contrast (CCG)7(CCT)2 was found in 85% of the HD alleles which represents significant linkage disequilibrium with the HD mutation.     

Contribution of DNA sequence and CAG size to mutation frequencies of intermediate alleles for Huntington disease: evidence from single sperm analyses

New mutations for Huntington disease (HD) arise from intermediate alleles (IAs) with between 29 and 35 CAG repeats that expand on transmission through the paternal germline to 36 CAGs or greater. Using single sperm analysis, we have assessed CAG mutation frequencies for four IAs in families with sporadic HD (IANM) and IAs ascertained from the general population (IAGP) by analyzing 1161 single sperm from three persons. We show that IANM are more unstable than IAGP with identical size and sequence. Furthermore, comparison of different sized IAs and IAs with different sequences between the CAG and the adjacent CCG tracts indicates that DNA sequence is a major influence on CAG stability. These studies provide estimates of the likelihood of expansion of IANM and IAGP to > or = 36 CAG repeats for these individuals. For an IA with a CAG of 35 in this family with sporadic HD, the likelihood for siblings to inherit a recurrent mutation > or = 36 CAG is approximately 10%. For IAGP of a similar size, the risk of inheriting an expanded allele of > or = 36 CAG through the paternal germline is approximately 6%. These risk estimates are higher than previously reported and provide additional information for counselling in these families. Further studies on persons with IAs will be needed to determine whether these results can be generalized to other families.      

Haplotype analysis of the 4p16.3 region in Portuguese families with Huntington's disease

Huntington's disease (HD) is a neurodegenerative disorder characterized by involuntary choreic movements, cognitive impairment, and behavioral changes, caused by the expansion of an unstable CAG repeat in HTT. We characterized the genetic diversity of the HD mutation by performing an extensive haplotype analysis of ～1Mb region flanking HTT in over 300 HD families of Portuguese origin. We observed that haplotype A, marked by HTT delta2642, was enriched in HD chromosomes and carried the two largest expansions reported in the Portuguese population. However, the most frequent HD haplotype B carried one of the largest (+12 CAGs) expansions, which resulted in an allele class change to full penetrance. Despite having a normal CAG distribution skewed to the higher end of the range, these two core haplotypes had similar expanded CAG repeat sizes compared to the other major core haplotypes (C and D) and there was no statistical difference in transmitted repeat instability across haplotypes. We observed a diversity of HTT region haplotypes in both normal and expanded chromosomes, representative of more than one ancestral chromosome underlying HD in Portugal, where multiple independent events on distinct chromosome 4 haplotypes have given rise to expansion into the pathogenic range. © 2015 Wiley Periodicals, Inc.     

Ancestral differences in the distribution of the {Delta}2642 glutamic acid polymorphism is associated with varying CAG repeat lengths on normal chromosomes: insights into the genetic evolution of Huntington disease

This study addresses genetic factors associated with normalvariation of the CAG repeat in the Huntington disease (HD) gene.To achieve this, we have studied patterns of variation of threetrinucleotide repeats in the HD gene including the CAG and adjacentCCG repeats as well as a GAG polymorphism at residue 2642 (     

Ancient origin of the CAG expansion causing Huntington disease in a Spanish population

Huntington disease (HD) is an autosomal dominant neurodegenerative disorder characterized clinically by progressive motor impairment, cognitive decline, and emotional deterioration. The disease is caused by the abnormal expansion of a CAG trinucleotide repeat in the first exon of the huntingtin gene in chromosome 4p16.3. HD is spread worldwide and it is generally accepted that few mutational events account for the origin of the pathogenic CAG expansion in most populations. We have investigated the genetic history of HD mutation in 83 family probands from the Land of Valencia, in Eastern Spain. An analysis of the HD/CCG repeat in informative families suggested that at least two main chromosomes were associated in the Valencian population, one associated with allele 7 (77 mutant chromosomes) and one associated with allele 10 (two mutant chromosomes). Haplotype A-7-A (H1) was observed in 47 out of 48 phase-known mutant chromosomes, obtained by segregation analysis, through the haplotype analysis of rs1313770-HD/CCG-rs82334, as it also was in 120 out of 166 chromosomes constructed by means of the PHASE program. The genetic history and geographical distribution of the main haplotype H1 were both studied by constructing extended haplotypes with flanking short tandem repeats (STRs) D4S106 and D4S3034. We found that we were able to determine the age of the CAG expansion associated with the haplotype H1 as being between 4,700 and 10,000 years ago. Furthermore, we observed a nonhomogenous distribution in the different regions associated with the different extended haplotypes of the ancestral haplotype H1, suggesting that local founder effects have occurred.     

A multistep mutation mechanism drives the evolution of the CAG repeat at MJD/SCA3 locus

Despite the intense debate around the repeat instability reported on the large group of neurological disorders caused by trinucleotide repeat expansions, little is known about the mutation process underlying alleles in the normal range that, ultimately, expand to pathological size. In this study, we assessed the mutation mechanisms by which wild-type Machado-Joseph disease (MJD) alleles have been generated throughout human evolution. Haplotypes including the CAG repeat, six intragenic SNPs and four flanking microsatellites were analysed in 431 normal chromosomes of European, Asian and African origin. A bimodal CAG repeat length frequency distribution was found in the four most frequent wild-type lineages (H1-GCGGCA; H2-GTGGCA; H3-TTAGAC and H4-TTACAC). Based on flanking microsatellite haplotypes, the variance calculated by analysis of molecular variance between modal (CAG)n alleles was little or null in lineages H1, H2 and H4, as were the pairwise differences. Moreover, genetic distances among all the alleles from each lineage did not reflect the allele sizes differences, as expected if a stepwise mutation model was the main process of evolution. On the contrary, when exposed in maximum parsimonious phylogenetic trees, a large number of mutation steps separated same-size alleles, whereas several microsatellite haplotypes were shared by modal CAGs. In conclusion, our results suggest that the main mutation mechanism occurring in the evolution of the polymorphic CAG region at MJD/SCA3 locus is a multistep one, either by gene conversion or DNA slippage; repeats with 14, 21, 23 and 27 CAGs are the main alleles involved in this process.     

A single allele from the polymorphic CCG rich sequence immediately 3' to the unstable CAG trinucleotide in the IT15 cDNA shows almost complete disequilibrium with Huntington's disease chromosomes in the Scottish population

The CCG rich sequence immediately 3' to the CAG repeat thatis expanded in Huntington's disease (HD) has recently been shownto be polymorphic with at least 4 alleles differing by multiplesof 3 bp being found in the normal population. We have studiedthe allele distribution in 180 HD families resident in Scotlandand have found very strong evldence for disequilibrium in thispopulation. For the 131 families where phase was unambiguouslydetermined, 130 were shown to have a CCG repeat allele of 176bp cosegregating with the HD chromosome. This observation issignificantly different to the normal population distributionwhere 31% of people have an allele of 185 bp. The evidence forand against a possible founder effect in the Scottish HD populationis discussed. We propose the hypothesis that we may have identifieda region of the IT15 gene that is critical in Huntington's disease.     

Interaction of normal and expanded CAG repeat sizes influences age at onset of Huntington disease

Huntington disease (HD) is a neurodegenerative disorder caused by the abnormal expansion of CAG repeats in the HD gene on chromosome 4p16.3. Past studies have shown that the size of expanded CAG repeat is inversely associated with age at onset (AO) of HD. It is not known whether the normal Huntington allele size influences the relation between the expanded repeat and AO of HD. Data collected from two independent cohorts were used to test the hypothesis that the unexpanded CAG repeat interacts with the expanded CAG repeat to influence AO of HD. In the New England Huntington Disease Center Without Walls (NEHD) cohort of 221 HD affected persons and in the HD-MAPS cohort of 533 HD affected persons, we found evidence supporting an interaction between the expanded and unexpanded CAG repeat sizes which influences AO of HD (P = 0.08 and 0.07, respectively). The association was statistically significant when both cohorts were combined (P = 0.012). The estimated heritability of the AO residual was 0.56 after adjustment for normal and expanded repeats and their interaction. An analysis of tertiles of repeats sizes revealed that the effect of the normal allele is seen among persons with large HD repeat sizes (47-83). These findings suggest that an increase in the size of the normal repeat may mitigate the expression of the disease among HD affected persons with large expanded CAG repeats.     

Study of the Huntington''s disease (HD) gene CAG repeats in schizophrenic patients shows overlap of the normal and HD affected ranges but absence of correlation with schizophrenia.

The CAG repeats in the Huntington's disease gene were investigated in chromosomes from 71 unrelated schizophrenic persons and 18 patients with schizoaffective disorder in order to determine if any of these patients had abnormal expansions. All of the probands had repeat sizes in the normal range (< 35 repeats) and there was no significant difference between the allele distributions of these patients and the normal controls. The families of two patients with 32 repeats and one patient with 34 repeats were investigated further and showed no uniform segregation of the disease with the large repeat alleles. The proband with 34 repeats inherited a chromosome that originally had 36 repeats in her father. The presence of 36 CAG repeats in members of her family and in HD patients suggests that there is an overlap between the normal and Huntington's disease CAG repeat size ranges. The more recently described CCG polymorphism in this gene was also examined in the schizophrenic and schizoaffective persons. All patients had alleles in the normal range.     

Huntington disease-like 2: the first patient with apparent European ancestry

Huntington disease-like 2 (HDL2) is a rare autosomal dominant disorder of the nervous system, apparently indistinguishable from Huntington disease (HD). HDL2 is caused by the expansion above 40 CTG/CAG repeats, in a variably spliced exon of the junctophilin-3 gene, on chromosome 16q24.3. All patients described so far have been of African ancestry. A clinical evaluation, including the Unified Huntington's Disease Rating Scale, and brain M agnetic resonance imaging were achieved in a 48-year-old Brazilian man of apparent European extraction, and presenting a picture very suggestive of HD. Gene mutation analysis (HD, HDL1, HDL2, dentatorubralpallidoluysian atrophy and spinocerebellar ataxia 17) was performed. After exclusion of the HD mutation and other HDL disorders, we identified an expansion of 47 CTG/CAG at the HDL2 locus. To clarify the origin of the mutation and estimate the patient's ancestry, we performed haplotype studies and used the insertion/deletion polymorphisms method. Despite the fact that this patient had an estimated likelihood of 97.4% of being of European ancestry, the haplotype containing the expanded allele has been found only in Africans. Thus, this is the first HDL2 case reported in a patient with an apparent European ancestry, although bearing an African HDL2 haplotype. This work stresses the importance of performing the diagnosis of HDL2 in HD-like patients of various ethnicities, and particularly in highly mixed populations.     

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

Huntington disease (HD) results from CAG expansion in the huntingtin (HTT) gene. Although HD occurs worldwide, there are large geographic differences in its prevalence. The prevalence in populations derived from Europe is 10-100 times greater than in East Asia. The European general population chromosomes can be grouped into three major haplogroups (group of similar haplotypes): A, B and C. The majority of HD chromosomes in Europe are found on haplogroup A. However, in the East-Asian populations of China and Japan, we find the majority of HD chromosomes are associated with haplogroup C. The highest risk HD haplotypes (A1 and A2), are absent from the general and HD populations of China and Japan, and therefore provide an explanation for why HD prevalence is low in East Asia. Interestingly, both East-Asian and European populations share a similar low level of HD on haplogroup C. Our data are consistent with the hypothesis that different HTT haplotypes have different mutation rates, and geographic differences in HTT haplotypes explain the difference in HD prevalence. Further, the bias for expansion on haplogroup C in the East-Asian population cannot be explained by a higher average CAG size, as haplogroup C has a lower average CAG size in the general East-Asian population compared with other haplogroups. This finding suggests that CAG-tract size is not the only factor important for CAG instability. Instead, the expansion bias may be because of genetic cis-elements within the haplotype that influence CAG instability in HTT, possibly through different mutational mechanisms for the different haplogroups.