Evaluating next-generation sequencing in neuromuscular diseases with neonatal respiratory distress

International audienc

Hearing loss in inherited peripheral neuropathies: Molecular diagnosis by NGS in a French series

International audienceBackground: The most common inherited peripheral neuropathy is Charcot-Marie-Tooth disease (CMT), with a prevalence of 1/2500. Other symptoms can be associated to the condition, such as hearing loss. Currently, no global hearing impairment assessment has been determined, and the physiopathology is not well known.Methods: The aim of the study was to analyze among a French series of 3,412 patients with inherited peripheral neuropathy (IPN), the ones who also suffer from hearing loss, to establish phenotype-genotype correlations. An NGS strategy for IPN one side and nonsyndromic hearing loss (NSHL) on the other side, were performed.Results: Hearing loss (HL) was present in only 44 patients (1.30%). The clinical data of 27 patients were usable. Demyelinating neuropathy was diagnosed in 15 cases and axonal neuropathy in 12 cases. HL varied from mild to profound. Five cases of auditory neuropathy were noticed. Diagnosis was made for 60% of these patients. Seven novel pathogenic variants were discovered in five different genes: PRPS1; MPZ; SH3TC2; NEFL; and ABHD12. Two patients with PMP22 variant, had also an additional variant in COCH and MYH14 respectively. No pathogenic variant was found at the DFNB1 locus. Genotype-phenotype correlations do exist, especially with SH3TC2, PRPS1, ABHD12, NEFL, and TRPV4.Conclusion: Involvement of PMP22 is not enough to explain hearing loss in patients suffering from IPN. HL can be due to cochlear impairment and/or auditory nerve dysfunction. HL is certainly underdiagnosed, and should be evaluated in every patient suffering from IPN

Average genome-wide copy number profiles for medullary breast carcinoma (MBC) and basal-like carcinoma (BLC) tumors

<p><b>Copyright information:</b></p><p>Taken from "Identification of typical medullary breast carcinoma as a genomic sub-group of basal-like carcinomas, a heterogeneous new molecular entity"</p><p>http://breast-cancer-research.com/content/9/2/R24</p><p>Breast Cancer Research 2007;9(2):R24-R24.</p><p>Published online 6 Apr 2007</p><p>PMCID:PMC1868916.</p><p></p> Common alterations observed in both the MBC and BLC groups are gains of 1q, 8q and Xq (black arrows). The most frequent specific alteration of MBCs (10p gains) is indicated by a red arrow. Ordinates: loci ratios, abscissa: order of the loci on chromosomes from 1 to Y

Box plot of the bacterial artificial chromosome (BAC) loci in chromosome 10

<p><b>Copyright information:</b></p><p>Taken from "Identification of typical medullary breast carcinoma as a genomic sub-group of basal-like carcinomas, a heterogeneous new molecular entity"</p><p>http://breast-cancer-research.com/content/9/2/R24</p><p>Breast Cancer Research 2007;9(2):R24-R24.</p><p>Published online 6 Apr 2007</p><p>PMCID:PMC1868916.</p><p></p> The results of the statistical comparison of the mean of ratios between clusters 1 and 3-1 are shown. On this figure, the BAC loci that are significantly different between the two clusters by the Welch test (≤ 0.05, Benjamini–Hochberg corrected for genome-wide multiple test) and that lie outside the calculated fold range in at least one cluster are shown in different colors: red, cluster 1; blue, cluster 3-1. The BAC loci that are not significantly different in terms of value and fold range are shown in grey and white, for cluster 1 and cluster 3-1, respectively. The position of the centromere is shown with a vertical pink dashed line

Confirmation of 10p gains with the use of fluorescence hybridization (FISH)

<p><b>Copyright information:</b></p><p>Taken from "Identification of typical medullary breast carcinoma as a genomic sub-group of basal-like carcinomas, a heterogeneous new molecular entity"</p><p>http://breast-cancer-research.com/content/9/2/R24</p><p>Breast Cancer Research 2007;9(2):R24-R24.</p><p>Published online 6 Apr 2007</p><p>PMCID:PMC1868916.</p><p></p> FISH analysis of cases 33 (medullary breast carcinoma) and 26 (basal-like carcinoma) with TelVysion SG 10p (probe 1) shown in green, g1int953 in red (probe 2), and control probe g1int978 in yellow (probe 3)

Caractérisation phénotypique et génomique des patients Becker avec délétion des exons 45-55

International audienceLa dystrophie musculaire de Becker (BMD) est une pathologie liée à l’X qui se caractérise par une dégénérescence des muscles squelettiques et/ou associée à une cardiomyopathie. Les patients Becker BMDdel45-55 présentent une délétion “en phase” des exons 45 à 55 dans le gène DMD. Les introns 44 et 55 qui bordent cette délétion contiennent des séquences régulatrices comme des long-non-coding ARN (lncRNA). Chaque patient BMDdel45-55 présente un point de cassure différent et donc un neo-intron unique avec potentiellement des modifications dans les séquences de lncRNA.L’objectif du projet est d’établir une caractérisation génomique d’une cohorte unique de patients BMDdel45-55 et d’étudier des facteurs impliqués dans leur variabilité phénotypique.Nous avons réalisé (i)une caractérisation phénotypique chez 49 patients, (ii)un séquençage du génome entier chez 19/49 patients et (iii)une étude des lncRNA chez 38/49 patients. Nous avons établi le profil des lncRNA dans des myoblastes immortalisés des sujets sains et DMD avec une délétion des exons 45-52 (Myo-45-52).L’étude phénotypique de notre population identifie une cardiomyopathie dilatée (22%), des difficultés à la marche/course (46%), la fatigabilité (34%). Dans 51% l’âge d’apparition des premiers signes est <18 ans (inconnu 22%). L’étude de la présence de lncRNA au niveau génomique met en évidence plusieurs clusters. L’absence génomique de certains lncRNA s’associe avec un phénotype clinique modéré. L’étude des mêmes lncRNA dans les myoblastes immortalisés a permis d’identifier deux lncRNA non-exprimés dans les Myo-45-52.Notre travail présente une caractérisation phénotypique et génomique de la plus grande cohorte de patients BMDdel45-55. Nous avons identifié des clusters avec un phénotype clinique modéré en fonction du nombre génomique de lncRNA. La caractérisation génomique des candidats pour la thérapie par saut d’exons 45-55 serait favorable dans le design des futures essais cliniques thérapeutiques

Phenotypic and genomic characterization of Becker dystrophy patients with 45 to 55 exons deletion

Becker muscular dystrophy (BMD) is an X linked disorder with 1/30000 life births incidence and is characterized by a progressive muscular dystrophy with or without cardiomyopathy. We present a population of 49 BMD patients with a DMD gene in-phase deletion of exons 45 to 55 (BMDdel45-55). Interestingly, emerging regulatory actors as lncRNA are localized in introns 44 and 55 (Bovolenta et al., 2012). Thus, the specific neo-introns of each patient could create or modify the lncRNA and/or RNA non-coding sequences. The objective of this study is to identify modifier factors involved in phenotypic variability in BMDdel45-55 patients. As described in literature, 63% of Duchenne patients are eligible to a multiexon skipping therapy by skipping exons 45 to 55.We performed (i) a phenotypic characterization of 49 patients, (ii) a lncRNA profile in 40/49patients and (iii) a WGS in 19/49patients. We have established the profile of lncRNA presence at genomic level in healthy subjects, muscle biopsies of BMDdel45-55 and DMD patients and human immortalized myoblasts displaying a deletion of 45-52 exons in DMD gene (Myo-45-52).In our cohort 22% of patients have dilatative cardiomyopathy, interestingly in 51% the first signs age was <18 y.o. After the cardiac involvement, the most disabling complains are the walking/running difficulties (46 %) and fatigue (34%). With the exception of one outlier there is a strong correlation between the age of the first signs and the presence of cardiomyopathy. We have established lncRNA profile in 38/49 patients. The cluster with the less numbers of lncRNA have a “milder” phenotype. In addition, in Myo-45-52 the profile of lncRNA expression investigated by RT-PCR, underlined two lacking lncRNA.This study allowed us to describe phenotypic and genomic profile in the largest reported cohort of BMDdel45-55 patients. We identified a cluster with the less numbers of lncRNA with a “milder” phenotype. Genomic data profiling of the candidates for multiexon skipping therapy of 45 to 55 exons would have a favorable contribution in the design of these therapeutic approaches.Bovolenta, M., Erriquez, D., Valli, E., Brioschi, S., Scotton, C., Neri, M., Falzarano, M.S., Gherardi, S., Fabris, M., Rimessi, P., et al. (2012). The DMD locus harbours multiple long non-coding RNAs which orchestrate and control transcription of muscle dystrophin mRNA isoforms. PloS One 7, e45328