Clinical massively parallel sequencing for the diagnosis of myopathies.

Massively parallel sequencing, otherwise known as high-throughput or next-generation sequencing, is rapidly gaining wide use in clinical practice due to possibility of simultaneous exploration of multiple genomic regions. More than 300 genes have been implicated in neuromuscular disorders, meaning that many genes need to be considered in a differential diagnosis for a patient affected with myopathy. By providing sequencing information for numerous genes at the same time, massively parallel sequencing greatly accelerates the diagnostic processes of myopathies compared to the classical "gene-after-gene" approach by Sanger sequencing. In this review, we describe multiple advantages of this powerful sequencing method for applications in myopathy diagnosis. We also outline recent studies that used this approach to discover new myopathy-causing genes and to diagnose cohorts of patients with muscular disorders. Finally, we highlight the key aspects and limitations of massively parallel sequencing that a neurologist considering this test needs to know in order to interpret the results of the test and to deal with other issues concerning the test.

Adult centronuclear myopathies: A hospital-based study.

INTRODUCTION: Centronuclear myopathies (CNM) are rare inherited disorders characterized by nuclei placed in rows in the central part of the muscle fibres. Three CNM-causing genes have been identified, with MTM1 mutations provoking X-linked myotubular myopathy, DNM2 mutations provoking autosomal dominant (AD) CNM, and BIN1 mutations provoking autosomal recessive (AR) CNM. METHODS: In this retrospective monocentric study, we describe 14 adult patients (age>18 years) diagnosed with CNM in our hospital in the 2000-2012 interval. Twelve patients originated from four families, and two patients presented with sporadic CNM. All patients underwent standardized clinical examinations, biological tests, electrophysiological studies, muscle biopsy, and molecular testing. RESULTS: Seven patients developed CNM before age 15, and seven after age 25. All patients presented with distal upper and lower limbs weakness, and normal CK levels. Disease severity remained mild, with all patients being able to walk without assistance even after decades-long disease duration. Cognitive impairment was found in seven cases, axonal polyneuropathy in six cases and ophthalmoparesis and ptosis in five cases. DNM2 gene mutations were found in eight patients, whereas BIN1 and MTM1 mutations were not observed. Overall, no molecular diagnosis was available for six patients. CONCLUSION: Adult CNM is a slowly progressive distal myopathy with normal CK levels sometimes associated with cognitive impairment, axonal polyneuropathy, and ophthalmoparesis and ptosis. DNM2 mutations were found in eight patients, including AD and sporadic cases, and represent the major cause of CNM in this adult cohort. In contrast, no MTM1 and BIN1 mutations were observed in our series, leaving six patients with no molecular diagnosis. As these six patients presented with AD (3 cases), AR (2 cases), and sporadic (1 case) CNM, it is likely that several CNM-causing genes remain to be discovered.

[Unilateral presentation of X-linked myotubular myopathy (XLMTM) in two out of three female carriers in a family with no affected male]. / Expression hémicorporelle d'une myopathie myotubulaire liée à l'X (XLMTM) chez deux des trois femmes conductrices d'une même famille sans cas masculin.

INTRODUCTION: X-linked myotubular myopathy (XLMTM), a recessive disorder, is caused by mutations affecting the myotubulatin (MTM1) gene located on the X chromosome. Most of the affected males die in the early postnatal period whereas female carriers are usually asymptomatic. CASE REPORTS: We report a family in which two females (45 and 27 years old) in two different generations, presented unilateral weakness which had worsened since adolescence, and one 48-year-old woman presented minimal symptoms. In agreement with the computed tomography and magnetic resonance imaging findings, the EMG was compatible with myopathy. Serum creatine kinase was elevated in the second patient. The histological study showed centronuclear myopathy aspects, more severe in the second patient. Both presented c.1420C>T, p.Arg474X in exon 13 of the MTM1 gene, whereas the third patients with less pronounced manifestation, had a skewed pattern of X chromosome inactivation. DISCUSSION: Symptomatic female carriers of XLMTM can present with asymmetric malformations, which must be distinguished from an autosomal-dominant centronuclear myopathy. CONCLUSION: Unilateral presentation of weakness cannot rule out a diagnosis of myopathy. Detection of symptomatic female carriers of an X linked recessive disease, with a severe presentation in males, is important for genetic counselling.

An integrated modelling methodology for estimating the prevalence of centronuclear myopathy.

Centronuclear myopathies (CNM) are a group of rare inherited muscular disorders leading to a significantly reduced quality of life and lifespan. To date, CNM epidemiologic reports provide limited incidence and prevalence data. Here, an integrated model utilizing available literature is proposed to obtain a better estimate of overall CNM patient numbers by age, causative gene, severity and geographic region. This model combines published epidemiology data and extrapolates limited data over CNM subtypes, resulting in patient numbers related to age and disease subtype. Further, the model calculates a CNM incidence twofold the current estimates. The estimated incidence of 17 per million births for severe X-linked myotubular myopathy (XLMTM), the main subtype of CNM, corresponds to an estimated prevalence of 2715 in the US, 1204 in the EU, 688 in Japan and 72 in Australia. In conclusion, the model provides an estimate of the CNM incidence, prevalence and survival, and indicates that the current estimates do not fully capture the true incidence and prevalence. With rapid advances in genetic therapies, robust epidemiologic data are needed to further quantify the reliability of incidence, prevalence and survival rates for the different CNM subtypes.

Expression of FMR1, FXR1, and FXR2 genes in human prenatal tissues.

We analyzed the distribution of FMR1, FXR1, FXR2 mRNA, and FMRP in whole normal human embryos and in the brains of normal and fragile X fetuses. The distributions of mRNA for the 3 genes in normal whole embryos and in the brains of normal male and female carrier fetuses were similar, with large amounts of mRNA in the nervous system and in several non-nervous system tissues. No FMR1 (mRNA and protein) was detected and no evident neuropathologic abnormalities found in the brains of male carrier fetuses, suggesting that the FMR1 product (FMRP) may have no crucial function in early stages of nervous system development. FXR1 and FXR2 mRNA had the same distribution and similar intensity in the brains of normal and pathologic fetuses (female and male carriers). The coexpression in the same tissues of FMR1, FXR1, and FXR2, associated with the normal expression of FXR1 and FXR2 and the absence of obvious neuropathological abnormalities in pathological brains, supports the notion that the FXR1 and FXR2 proteins partially compensate for FMRP function. However, the absence of significant overexpression of FXR1 and FXR2 in pathological brains suggests that these genes do not compensate for the lack of FMR1 expression. Alternatively, FMR1, FXR1, and FXR2 proteins may not have compensatory functions, but instead may regulate functions by hetero or homo oligomerization, as suggested by other studies. Thus, a dominant negative effect of abnormal multimeric protein complexes lacking FMRP (e.g. by modification of FXR1 and FXR2 protein functions) may result in the fragile X syndrome phenotype.

Mutational spectrum of the ED1 gene in X-linked hypohidrotic ectodermal dysplasia.

X-linked hypohidrotic ectodermal dysplasia (XLHED) is the most common form of the ectodermal dysplasias characterised by an abnormal development of eccrine sweat glands, hair and teeth. The ED1 gene responsible for the disorder undergoes extensive alternative splicing and to date few studies have concerned the full length transcript. We screened 52 unrelated families or sporadic cases for mutation in the full coding sequence of this gene. SSCA analysis or direct sequencing allowed identification of mutations in 34 families: one initiation defect, twenty-two missenses, two nonsense, eight insertions or deletions, and a large deletion encompassing all the ED1 gene. Fourteen of these mutations have not been previously described, including five missenses. One third of identified mutations were localised in codons 155 and 156, affecting CpG dinucleotides and nine of them correspond to the R156H missense. Hypothesis of a founder effect has been ruled out by haplotype analysis of flanking microsatellites. These recurrent mutations indicate the functional importance of the positively charged domain of the protein. Including our data, there are now 56 different mutations reported in 85 independent patients, that we have tabulated. Review of clinical features in the present series of affected males and female carriers showed no obvious correlation between the type of mutations, the phenotype and its severity. The X-chromosome pattern of inactivation in leucocytes showed little correlation with expressivity of the disease in female carriers. Finally this study is useful for functional studies of the protein and to define a diagnostic strategy for mutation screening of the ED1 gene.

Unexpected inheritance of the (CGG)n trinucleotide expansion in a fragile X syndrome family.

The fragile X syndrome is the most frequent cause of inherited mental retardation. CGG repeat alleles are usually classified as normal, premutation, or full mutation based on the length of this triplet in the 5' untranslated region of the FMR1 gene. The pattern of inheritance follows a two-stage intergenerational process in which the premutation evolves into the full mutation. Some reverse mutations have been described, but they appear to be very rare. We describe a family in which a mother of two affected males herself carried a full mutation. Surprisingly, her clinically normal daughter, initially considered to be a carrier by linkage analysis, carried a very short premutation. Findings from our family study corroborate the hypothesis that the expansion during female transmission could be a postzygotic event and raise the problem of mosaicism.

On some technical aspects of direct DNA diagnosis of the fragile X syndrome.

Direct DNA analysis of fragile X [Fra(X)] mutations has already shown its clear superiority for postnatal and prenatal diagnosis of the disorder and for carrier detection. However, it is of great importance to have conditions which guarantee optimal reliability and sensitivity. Some mutations may be more difficult to detect, especially in female carriers: this is the case for small amplifications of the CGG repeat (premutations) or for smears which can be generated by the instability of the full mutation in somatic tissues. We present the various alternatives (probe/enzymes combinations) for Southern blot based diagnosis, the possible artefacts and our detailed experimental protocol, which has given excellent results on a large number of families. While detection of amplification, using for instance EcoRI, appears sufficient for initial testing of mentally retarded patients, once the fra(X) diagnosis has been established, we favor the use of an EcoRI+EagI digest, which detects both amplification and abnormal methylation, for analysis of the family, including carrier detection and prenatal diagnosis. We discuss the place of proposed PCR based techniques for detection of mutations, or for indirect tracking using polymorphic microsatellites in the immediate vicinity of the fra(X) locus.

Direct DNA analysis of fragile X syndrome in Spanish pedigrees.

Eleven complete Spanish pedigrees with fragile X syndrome were analysed by Southern blotting with the DNA probe StB12.3 previously isolated and described by Oberlé et al. [1991]. This probe allowed the direct detection of affected males and carrier females and was able to distinguish between normal males and normal transmitting males (NTMs). One hundred and twenty three individuals were analyzed, 115 from the pedigrees and 8 from the general population. Five mosaic cases were found (4 males and one female) showing both the premutation and the full mutation. One half of the females with the full mutation were mentally retarded but no female with mental retardation carried the premutated pattern, suggesting that the absence of the full mutation in females is a very good criterion for pre-or postnatal diagnosis of normal mental status.

Analysis of full fragile X mutations in fetal tissues and monozygotic twins indicate that abnormal methylation and somatic heterogeneity are established early in development.

The fragile X syndrome, the most common cause of inherited mental retardation, is characterized by unique genetic mechanisms, which include amplification of a CGG repeat and abnormal DNA methylation. We have proposed that 2 main types of mutations exist. Premutations do not cause mental retardation, and are characterized by an elongation of 70 to 500 bp, with little or no somatic heterogeneity and without abnormal methylation. Full mutations are associated with high risk of mental retardation, and consist of an amplification of 600 bp or more, with often extensive somatic heterogeneity, and with abnormal DNA methylation. To analyze whether the latter pattern is already established during fetal life, we have studied chorionic villi from 10 fetuses with a full mutation. In some cases we have compared them to corresponding fetal tissues. Our results indicate that somatic heterogeneity of the full mutation is established during (and possibly limited to) the very early stages of embryogenesis. This is supported by the extraordinary concordance in mutation patterns found in 2 sets of monozygotic twins (9 and 30 years old). While the methylation pattern specific of the inactive X chromosome appears rarely present on chorionic villi of normal females, the abnormal methylation characteristic of the full mutation was present in 8 of 9 male or female chorionic villi analyzed. This suggests that the methylation mechanisms responsible for establishing the inactive X chromosome pattern and the full mutation pattern are, at least in part, distinct. Our results validate the analysis of chorionic villi for direct prenatal diagnosis of the fragile X syndrome.

Fragile X mental retardation syndrome: from pathogenesis to diagnostic issues.

The Fragile X (FRAXA) syndrome is the most common cause of familial (monogenic) mental retardation and is widespread in human populations. This syndrome is characterised by an unusual mode of transmission for an X-linked disease. In affected families, one frequently finds clinically normal transmitting males, whose daughters - also clinically normal - have a high risk of having affected children. The risk of developing the disease (penetrance) thus appears to increase in successive generations of the same family through maternal transmission. As shown by molecular cloning of the fragile X locus, Fragile X mutations are unstable expansions of a CGG trinucleotide repeat, located in the first exon (non-protein-coding) of the FMR1 gene (for Fragile X Mental Retardation). Two main types of mutation are observed in affected families. A full mutation is found in patients with mental retardation and corresponds to large expansions of the repeat. Premutations are moderate expansions and are found in normal transmitting males and in the majority of clinically normal carrier females. About 15% of patients show a mosaic pattern consisting of both full mutations and premutations. Although analysis of the CGG expansion has led to the establishment of reliable tests for diagnosis and genetic counseling of Fragile X syndrome, care must be exercised to use these tools to answer the concerns of the families and avoid doing harm. In our opinion, testing in children should be restricted to those who show a developmental delay, cognitive deficits and/or abnormal behavior evocative of the syndrome. A carrier diagnosis in a girl who is clinically normal should probably only be performed at an age where she can understand the consequences for family planning and the options of prenatal diagnosis. When testing children with borderline cognitive deficits, a positive diagnosis should be used to improve educational strategies for the children - and not to stigmatise them.

Genotype-phenotype relationship in female carriers of the premutation and full mutation of FMR-1.

The present French-German cooperative study focuses on the genotype-phenotype relationship of mutations of the FMR-1 gene and psychiatric conditions in mothers with a full mutation in the FMR-1 gene of fra-X children (n=13), mothers with a premutation in the FMR-1 gene of fra-X children (n=61), as well as premutated siblings of these mothers without affected children (n=17) and two non-mutated control groups: (1) siblings of these mothers with normal CGG repeat (n=18); and (2) mothers of non-fra-X autistic children (n=42). Mothers with a full mutation in the FMR-1 gene and mothers with a premutation in the FMR-1 gene did not differ in the frequency of any axis I disorder; however, both groups were diagnosed with social phobia more often than the control group of mothers of autistic children. Moreover, mothers with a premutation in the FMR-1 gene of fra-X children and their siblings with the premutation (without affected offspring) revealed a similar frequency of social phobia. Furthermore avoidant personality disorder was more common in groups of carriers of the full premutation than in siblings without mutation or than the control group of mothers with autistic children. On the basis of our data, we therefore suggest that social avoidance (expressed as social phobia or avoidant personality disorder) has been underestimated in previous studies of carriers with the FMR-1 full mutation or premutation. Comorbidity of axis I and axis II psychiatric diagnoses was mainly restricted to the group of carriers of the full mutation and carriers of the premutation of FMR-1. Correlations between size of CGG repeat and IQ as well as CGG and age of onset of axis I diagnosis were non-significant. IQ of subjects had no impact on presence or absence of axis I and/or axis II diagnoses.

[Fragile X syndrome is still unrecognized: efficacy of molecular diagnosis in mentally retarded probands]. / Le syndrome X fragile est encore méconnu: efficacité du diagnostic moléculaire chez les proposants avec retard mental.

BACKGROUND: The fragile X mental retardation syndrome is the most common cause of inherited mental retardation. Identification of the unstable mutation responsible for the disease has allowed the design of a fully reliable molecular test for the diagnosis of the disease and for genetic counselling (identification of clinically normal carriers and prenatal diagnosis). We started in July 1991 to search for the mutation in mentally retarded probands, with no known cause for their phenotype. We present the results of a 42-month experience. POPULATION AND METHODS: One thousand and one hundred fourty-nine probands were analysed. In case of a positive diagnosis, an extension of the molecular study to relatives was proposed. DNA samples were studied by Southern blot following EcoRI or EcoRI + EagI digestion. Clinical data were collected from referring clinicians. RESULTS: Seventy-three carriers of a full mutation were identified, belonging to 52 families. The mean age of the fragile X probands was 16 +/- 14 years, which is very surprising for a disease that causes significant manifestations by the age of 2 to 3 years. This indicates an insufficient knowledge about this disease in France. Most of the demands for the test were from clinical geneticists. This diagnosis is of major importance for genetic counselling, as illustrated by the following study of 108 women at risk in these families. CONCLUSIONS: The importance of an early diagnosis followed by an extended family study, for carrier screening and prevention of this severe disease, justifies molecular testing on any child with mental retardation or significant language delay of unknown cause, in the absence of clinical signs formally excluding a fragile X diagnosis.

Measurement of XeI and XeII velocity in the near exit plane of a low-power Hall effect thruster by light induced fluorescence spectroscopy.

Near exit plane non-resonant light induced fluorescence spectroscopy is performed in a Hall effect low-power Xenon thruster at discharge voltage of 250 V and anode flow rate of 0.7 mg/s. Measurements of the axial and radial velocity components are performed, exciting the 6s(2)[3/2]2(o)→6p(2)[3/2]2 transition at 823.16 nm in XeI and the 5d[4]7/2→6p[3]5/2(o) transition at 834.724 nm in XeII. No significant deviation from the thermal velocity is observed for XeI. Two most probable ion velocities are registered at a given position with respect to the thruster axis, which are mainly attributed to different areas of creation of ions inside the acceleration channel. The spatial resolution of the set-up is limited by the laser beam size (radius of the order of 0.5 mm) and the fluorescence collection optics, which have a view spot diameter of 8 mm.

A room-temperature alternating current susceptometer--data analysis, calibration, and test.

An AC susceptometer operating in the range of 10 Hz to 100 kHz and at room temperature is designed, built, calibrated, and used to characterize the magnetic behaviour of coated magnetic nanoparticles. Other weakly magnetic materials (in amounts of some millilitres) can be analyzed as well. The setup makes use of a digital acquisition system in order to determine the amplitude and the phase of the sample magnetization as a function of the frequency of the driving magnetic field, which is powered by a digital waveform generator. A specific acquisition strategy makes the response directly proportional to the sample susceptibility, taking advantage of the differential nature of the coil assembly. A calibration method based on conductive samples is developed.

Identification of a mutation in the MTM1 gene, associated with X-linked myotubular myopathy, in a Greek family.

X-linked myotubular myopathy (XLMTM) is a rare congenital myopathy, usually characterized by severe hypotonia and respiratory insufficiency at birth, in affected, male infants. The disease is causally associated with mutations in the MTM1 gene, coding for phosphatase myotubularin. We report a severe case of XLMTM with a novel mutation, at a donor splicing site (c.1467+1G) previously associated with severe phenotype. The mutation was also identified in the patient's mother, providing an opportunity for sound genetic counseling.

Stray magnetic field compensation with a scalar atomic magnetometer.

We describe a system for the compensation of time-dependent stray magnetic fields using a dual channel scalar magnetometer based on nonlinear Faraday rotation in synchronously optically pumped Cs vapor. We detail the active control strategy, with an emphasis on the electronic circuitry, based on a simple phase-locked-loop integrated circuit. The performance and limits of the system developed are tested and discussed. The system was applied to significantly improve the detection of free induction decay signals from protons of remotely magnetized water precessing in an ultralow magnetic field.