Novel polymorphism in the FMR1 gene resulting in a "pseudodeletion" of FMR1 in a commonly used fragile X assay

The fragile X syndrome is the most commonly inherited cause of mental retardation. Genetic diagnosis of this disease relies on the detection of triplet repeat expansion in the FMR1 gene on the X chromosome. Although the majority of disease in fragile X patients is due to mutations involving triplet repeat expansion, deletion of various portions of FMR1 has also been described in association with the fragile X syndrome. Here we describe a rare polymorphism in the noncoding region of FMR1 that mimics detection of a deletion in a commonly used assay for fragile X syndrome, which can result in misdiagnosis of the disease.     

Fragile X syndrome: molecular analysis reveals a new mechanism of mutation in human genetic diseases.

The fragile X syndrome belongs to the most common genetic diseases and has a prevalence of one in every 2000 children. The syndrome is named after the fragile site in q27.3 on the X chromosome. The molecular cloning of the DNA containing the fragile site has resulted in the identification of a heritable unstable DNA sequence revealing a new mechanism of mutation in human genetic disorders. This DNA sequence significantly facilitates the diagnosis and provides a rapid method for carrier detection and prenatal diagnosis. The unstable element is located within a candidate gene, FMR1. The FMR1 protein is not made in fragile X patients and nothing is known about its function. We will have to await studies on this protein to be able to understand the variable phenotype of this disease.     

Methylation-specific multiplex ligation-dependent probe amplification enables a rapid and reliable distinction between male FMR1 premutation and full-mutation alleles

Fragile X syndrome is the most common cause of inherited mental retardation and the second most common cause of mental impairment after trisomy 21. It occurs because of a failure to express the fragile X mental retardation protein. The most common molecular basis for the disease is the abnormal expansion of the number of CGG repeats in the fragile X mental retardation 1 gene (FMR1). Based on the number of repeats, it is possible to distinguish four types of alleles: normal (5 to 44 repeats), intermediate (45 to 54), premutation (55 to 200), and full mutation (>200). Today, the diagnosis of fragile X syndrome is performed through a combination of PCR to identify fewer than 100 repeats and of Southern blot analysis to identify longer alleles and the methylation status of the FMR1 promoter. We have developed a methylation-specific multiplex ligation-dependent probe amplification assay to analyze male fragile X syndrome cases with long repeat tracts that are not amplifiable by PCR. This inexpensive, rapid and robust technique provides not only a clear distinction between male pre- and full-mutation FMR1 alleles, but also permits the identification of genomic deletions, a less frequent cause of fragile X syndrome.     

The fragile X syndrome: implications of molecular genetics for the clinical syndrome

Abstract. The fragile X syndrome of mental retardation is one of the most common genetic diseases. Characterization of the mutations involved has greatly improved our knowledge of the transmission of fragile X syndrome and new DNA-based diagnostics tools significantly outperform cytogenetic testing both for establishing the diagnosis and for determining carrier status. Fragile X mutations consist of an expansion of a CGG trinucleotide repeat localized in a gene (FMR-1) that is abnormally methylated in all affected individuals. They are classified as premutations (asymptomatic) and full mutations (associated with the disease). Several different DNA analysis protocols are used for fragile X genotyping but only a few have been tested on large samples of individuals. There are several clinical indications for direct DNA genotyping for fragile X including mental retardation, learning disability or hyperactivity in children with or without a family history of mental retardation, the establishment of carrier diagnosis in fragile X families and prenatal screening of children from carrier women.     

Skewed X inactivation of the normal allele in fully mutated female carriers determines the levels of FMRP in blood and the fragile X phenotype.

BACKGROUND: The variable phenotype in female carriers of a full mutation is explained in part by non-random X-chromosome inactivation. The molecular diagnosis of fragile X syndrome is based on the resolution of the number of CGG triplet repeats and the methylation status of a critical CpG in the fragile X mental retardation gene (FMR1) promoter. Neighboring CpGs in the FMR1 promoter are supposed to be equally methylated or unmethylated. METHOD: Southern blot analysis was performed with double digestion, either with EcoRI/EagI or with HindIII/SacII. The EagI restriction site was studied by sequencing. The fragile X encoded protein (FMRP) was detected in white blood cells by Western blot. The fragile X phenotype was evaluated by specific clinical examinations. RESULTS: Within one family we found three female carriers of a full mutation and a different degree of methylation of the normal allele that correlated with the levels of FMRP in blood and the fragile X phenotype. Complete methylation at the EagI CpG target (but partially methylated SacII CpG site) was associated with extremely skewed X inactivation (confirmed by analysis of the methylation status at the PGK locus), undetectable FMRP in blood, and a male-like phenotype. CONCLUSIONS: In fully mutated female carriers the methylation status at the EagI restriction site correlates with the levels of FMRP in blood and the fragile X phenotype. Neighboring CpG sequences in the FMR1 promoter can be differentially methylated, which should be taken into consideration for molecular diagnosis.     

Diagnostic tests for fragile X syndrome

Fragile X syndrome is a common X-linked hereditary disease, characterized by mental retardation, macroorchidism and mild facial abnormalities and is almost always caused by the absence or deficit of the FMR1 protein. In the majority of cases, the disease is associated with an expansion of a CGG repeat, located in the 5' UTR of the FMR1 gene. Diagnostic methods include PCR amplification and Southern blotting, which are performed on DNA isolated from peripheral leukocytes. Recently, varying immunocytochemical tests have been described to identify fragile X patients, based on the detection of FMR1 protein in cells by a monoclonal antibody. This review provides an update on the different DNA methods and gives specific attention to both the newly developed PCR method and antibody methods for prenatal and postnatal diagnosis of the fragile X syndrome.     

Animal Model for Fragile X Syndrome

The fragile X syndrome, one of the most common forms of inherited mental retardation, is caused by an expansion of a polymorphic CGG repeat upstream of the coding region in the FMR1 gene. The expansion blocks expression of the FMR1 gene due to methyla-tion of the FMR1 promoter. Functional studies on the FMR1 protein have shown that the protein can bind RNA and might be involved in transport of RNAs from the nucleus to the cytoplasm. A role of FMR1 protein on translation of certain mRNAs has been suggested. An animal model for fragile X syndrome exists and these mice show some behavioural difficulties mimicking the human fragile X syndrome phenotype. This review presents what is known about the protein and what is learned from the animal model for fragile X syndrome.     

Molecular cytogenetics of fragile X syndrome

Fragile X syndrome is the most common heritable form of mental retardation, and affects 1 in 1500(male)-2500(female), with minor dysmorphic manifestations such as long face with large protruding ears and macro-orchidism in mentally retarded male patients. The syndrome is caused by dynamic mutation(trinucleotide repeat expansion) at FRAXA located on the long arm of X chromosome. Molecular diagnosis enables carrier identification as well as prenatal diagnosis, in which the cytogenetic method was not feasible. Premutation in phenotypically normal carriers and full mutation in mentally retarded patients explain the characteristic inheritance of the disease called anticipation. This article describes the recent advancements in molecular cytogenetics of fragile X syndrome.     

Rare variants in the promoter of the fragile X syndrome gene (FMR1)

Fragile X syndrome, the most common form of familial mental retardation, is mainly caused by the expansion of an unstable region of CGG repeats in the 5' untranslated region of the FMR1 (Fragile X Mental Retardation-1) gene. Molecular tools to detect an abnormal CGG expansion in FMR1 include Southern blot hybridization and PCR amplification. Southern blotting with the StB12.3 probe and Eco RI/Eag I double digestion is widely used as a routine test for fragile X syndrome diagnosis in laboratories around the world. A patient with mental retardation of unknown origin showed absence of digestion for Eag I due to a -149C-->G substitution in the CpG island of the FMR1 gene, which destroys that restriction enzyme site. Screening for other changes around that region also detected a -154insGGC in a patient with a phenotype highly suggestive of fragile X syndrome but without CGG expansion. Expression studies did not show any abnormal changes in FMR1 function. In summary, we have identified two different changes (a C to G substitution at -149 and a GGC insertion at -154) in the promoter of the FMR1 gene. These are the first variants described in the promoter of the FMR1 gene.     

Southern印迹检测智力低下患者的脆性X基因

目的用Southern印迹法检测脆性X基因来确定脆性X基因携带者和脆性X综合征的患者。方法提取27例智力低下患者标本的DNA,用EagI和EcoRI酶切,酶切产物电泳后进行Southern转印,探针杂交后放射自显影,根据DNA片段大小检测脆性X综合征携带者与突变患者。结果检测24位智力低下患者的外周血及3例有智力低下家族史孕妇的羊水后发现3例患者患有脆性X综合征。结论用Southern印迹法诊断脆性X综合征,是一种可靠的首选检测方法,适用于出生后患儿及产前诊断及遗传咨询。     

FMR1 intron 1 methylation predicts FMRP expression in blood of female carriers of expanded FMR1 alleles

Fragile X syndrome (FXS) is caused by loss of the fragile X mental retardation gene protein product (FMRP) through promoter hypermethylation, which is usually associated with CGG expansion to full mutation size (>200 CGG repeats). Methylation-sensitive Southern blotting is the current gold standard for the molecular diagnosis of FXS. For females, Southern blotting provides the activation ratio (AR), which is the proportion of unmethylated alleles on the active X chromosome. Herein, we examine the relationship of FMRP expression with methylation patterns of two fragile X-related epigenetic elements (FREE) analyzed using matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry and the AR. We showed that the differential methylation of the FREE2 sequence within fragile X mental retardation gene intron 1 was related to depletion of FMRP expression. We also show that, using the combined cohort of 12 females with premutation (55 to 200 CGG repeats) and 22 females with full mutation alleles, FREE2 methylation analysis was superior to the AR as a predictor of the proportion of FMRP-positive cells in blood. Because matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry is amenable to high-throughput processing and requires minimal DNA, these findings have implications for routine FXS testing and population screening.     

病因不明型精神发育迟滞儿童1 088例发病相关因素分析

背景儿童病因不明型的精神发育迟滞 (mental retardation,MR)与遗传因素、性别、环境因素有何关系? 目的探讨病因不明型 MR发生的相关因素. 设计以诊断为依据的横断面研究. 地点,对象和方法研究对象为 1 500例 MR患者,主要来自南京及南京周边的城市和农村,年龄为 2个月～ 15岁. 采用韦氏智力评定,将 1 500例 MR患者按轻、中、重分组,对疑为脆性 X综合征患者进行染色体及脆性位点检查. 主要观察指标受检 MR患者的病因分布,性别构成以及染色体及脆性位点检查. 结果从 1 500例精神发育迟滞患者中共发现 1 088例病因不明 MR患者,对这 1 088例患者进行分析,中度智力低下所占比率较高( 51.68%),男性( 642例)多于女性( 446例). 1 088例患者中,共发现 112例 Fra(X)患者,其中 97%的 Fra(X)有 FMR-1基因突变. 结论病因不明型 MR的发生有遗传因素的作用.     

The fragile X syndrome.

An amplification of a highly unstable DNA element has been identified at the fragile X locus in Xq27.3. This sequence appears to be both the source of the primary mutation causing the fragile X syndrome, apparently having its causative effect through the methylation of the FMR-1 HTF island and the region of cytogenetic fragility. The direct analysis of the genotype of carrier and affected individuals can be used as a direct diagnosis tool which will improve both the accuracy and speed of diagnosis. The identification of hereditary unstable DNA in a disease with such a wide level of non-penetrance and variable phenotype may give clues as to the basis of non-penetrance in other human genetic disorders.     

Consensus characterization of 16 FMR1 reference materials: a consortium study

Fragile X syndrome, which is caused by expansion of a (CGG)(n) repeat in the FMR1 gene, occurs in approximately 1:3500 males and causes mental retardation/behavioral problems. Smaller (CGG)(n) repeat expansions in FMR1, premutations, are associated with premature ovarian failure and fragile X-associated tremor/ataxia syndrome. An FMR1-sizing assay is technically challenging because of high GC content of the (CGG)(n) repeat, the size limitations of conventional PCR, and a lack of reference materials available for test development/validation and routine quality control. The Centers for Disease Control and Prevention and the Association for Molecular Pathology, together with the genetic testing community, have addressed the need for characterized fragile X mutation reference materials by developing characterized DNA samples from 16 cell lines with repeat lengths representing important phenotypic classes and diagnostic cutoffs. The alleles in these materials were characterized by consensus analysis in nine clinical laboratories. The information generated from this study is available on the Centers for Disease Control and Prevention and Coriell Cell Repositories websites. DNA purified from these cell lines is available to the genetics community through the Coriell Cell Repositories. The public availability of these reference materials should help support accurate clinical fragile X syndrome testing.     

Simplified molecular diagnosis of fragile X syndrome by fluorescent methylation-specific PCR and GeneScan analysis

BACKGROUND: Fragile X syndrome (FXS), the most common cause of inherited mental impairment, is most commonly related to hyperexpansion and hypermethylation of a polymorphic CGG trinucleotide repeat in the 5' untranslated region of the FMR1 gene. Southern blot analysis is the most commonly used method for molecular diagnosis of FXS. We describe a simplified strategy based on fluorescent methylation-specific PCR (ms-PCR) and GeneScan analysis for molecular diagnosis of fragile X syndrome. METHODS: We used sodium bisulfite treatment to selectively modify genomic DNA from fragile X and normal lymphoblastoid cell lines and from patients. We then performed ms-PCR amplification using fluorescently-labeled primers complementary to modified methylated or unmethylated DNA. Amplification products were resolved by capillary electrophoresis. FMR1 mutational status was determined by a combination of fluorescent peak sizes and patterns on the GeneScan electropherogram. RESULTS: DNA samples from male and female persons with known NL, PM, and FM FMR1 CGG repeats were analyzed. Each FMR1 genotype produced a unique GeneScan electropherogram pattern, thus providing a way to identify the various disease states. The number of CGG repeats in all NL and PM alleles were determined accurately. Analysis by both the new assay and Southern blot of a family segregating with FXS showed complete concordance between both methods. CONCLUSIONS: This simplified molecular diagnostic test, based on fluorescent methylation-specific PCR, may be a suitable alternative or complement to Southern blot analysis for the diagnosis of FXS.     

Identification of small FRAXA premutations.

BACKGROUND: Diagnosis of fragile X syndrome in mentally retarded individuals is satisfactorily achieved using a Southern blot test that detects the typical triplet repeat expansion (>200 repeats) within the FMR1 gene. All such individuals inherit the mutation from a carrier, who usually shows a lower triplet repeat number and may be asymptomatic. Having identified a fragile X proband, it is necessary to identify related carriers of this familial X-linked dominant mutation to provide family counseling and testing. METHODS AND RESULTS: For one family in which a fragile XA repeat expansion occurs, Southern blot hybridization did not give accurate sizing data because of the very small premutation associated with the unstable allele. PCR sizing methods and linkage analysis were adapted to identify family members with the premutation. CONCLUSION: Although most carriers can be detected using Southern blot and/or direct PCR sizing tests, very small expansions (55-70 repeats) are difficult to distinguish from larger, normal alleles. We have used linkage analysis in combination with direct allele analysis to identify carriers of very small expansions of a fragile X chromosome in a four-generation family.     

A pseudo-full mutation identified in fragile X assay reveals a novel base change abolishing an EcoRI restriction site

Diagnostic testing for the fragile X syndrome is designed to detect the most common mutation, a CGG expansion in the 5'-untranslated region of the fragile X mental retardation (FMRI) gene. PCR can determine the number of CGG repeats less than 100, whereas Southern analysis can detect large premutations, full mutations, and their methylation status. Bands larger than 5.8 kb observed via Southern analysis are usually considered a methylated full mutation, causing fragile X syndrome in males and varied clinical presentations in females. We observed a 10.9-kb band on a Southern blot assay from an autistic girl with language delay. Further investigation identified a novel G-to-A transition at an EcoRI cleavage site, upstream of the CGG repeat region of the FMRI gene. This base change abolished the EcoRI restriction site, resulting in a 10.9-kb pseudo-full mutation. This G-to-A base change has not been previously reported and was not identified in a subsequent analysis of 105 male and 30 female patient samples. The clear 10.9-kb band detected on a Southern blot assay for fragile X syndrome mimics a large, methylated full mutation, which could result in a misdiagnosis without the benefit of family studies and further testing.     

A simple and rapid analysis of triplet repeat diseases by expand long PCR.

It is now known that 15 monogenic, mostly neurological, disorders are caused by the same type of mutations that occur in trinucleotide repeat sequences in certain genes. Since they share a nonspecific and variable phenotype, the accurate diagnosis could be made only by DNA analysis. We developed an Expand Long PCR assay that provides more reliable molecular diagnosis of such disorders. Its main characteristics are robust amplification of expanded alleles, simplicity, low cost and speed. We suggest the use of Expand Long PCR for routine molecular diagnosis of triplet repeat diseases, and present such analysis of the fragile X syndrome, myotonic dystrophy and Huntington's disease.     

Epstein-Barr virus transformation of human lymphoblastoid cells from patients with fragile X syndrome induces variable changes on CGG repeats size and promoter methylation.

BACKGROUND: Our understanding of fragile X syndrome can be improved by reversing the expression of the silenced fragile X mental retardation 1 (FMR1) gene in immortalized cells from these patients. Epstein-Barr virus (EBV) infection has been extensively used to transform B cells into a permanent lymphoblastoid cell line. METHODS: We immortalized B lymphocytes from three different fragile X patients and one normal male. We analyzed the CGG triplet repeats and methylation status of the FMR1 and interferon (IFN)-gamma promoter. We also assayed FMR1 mRNA levels by real-time PCR and FMR1 protein (FMRP) by Western blot. RESULTS: We observed that EBV transformation may induce the instability of CGG repeats and DNA demethylation that can lead to the modification of mRNA expression. CONCLUSIONS: EBV transformation may induce variable changes in the genome that can lead to the misinterpretations of experimental data obtained from these cells. Thus, periodic testing of DNA from immortalized cells should be routinely undertaken to detect undesired effects.