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Only a minority of patients with glioblastoma (GBM) respond to immunotherapy, and always only partially. There is a lack of knowledge on immune distribution in GBM and in its tumor microenvironment (TME). To address the question, we used paired primary and recurrent tumors from GBM patients to study the composition and the evolution of the immune landscape upon treatment. We studied the expression of a handful of immune markers (CD3, CD8, CD68, PD-L1 and PD-1) in GBM tissues in 15 paired primary and recurrent GBM. In five selected patients, we used Nanostring Digital Spatial Profiling (DSP) to obtain simultaneous assessments of multiple biomarkers both within the tumor and the microenvironment in paired primary and recurrent GBM. Our results suggest that the evolution of the immune landscape between paired primary and recurrent GBM tumors is highly heterogeneous. However, our study identifies B3-H7 and HLA-DR as potential targets in primary and recurrent GBM. Spatial profiling of immune markers from matched primary and recurrent GBM shows a nonlinear complex evolution during the progression of cancer. Nonetheless, our study demonstrated a global increase in macrophages, and revealed differential localization of some markers, such as B7-H3 and HLA-DR, between GBM and its TME.

Background and objectives According to data from large national registries, almost 20 to 25% of patients with end-stage kidney disease have an undetermined kidney disease (UKD). Recent data have shown that monogenic disease-causing variants are under-diagnosed. We performed exome sequencing (ES) on UKD patients in our center to improve the diagnosis rate. Design, setting, participants, and measurements ES was proposed in routine practice for patients with UKD including kidney biopsy from January 2019 to December 2021. Mutations were detected using a targeted bioinformatic customized kidney gene panel (675 genes). The pathogenicity was assessed using American College of Medical Genetics guidelines. Results We included 230 adult patients, median age 47.5 years. Consanguinity was reported by 25 patients. A family history of kidney disease was documented in 115 patients (50%). Kidney biopsies were either inconclusive in 69 patients (30.1%) or impossible in 71 (30.9%). We detected 28 monogenic renal disorders in 75 (32.6%) patients. Collagenopathies was the most common genetic kidney diagnosis (46.7%), with COL4A3 and COL4A4 accounting for 80% of these diagnoses. Tubulopathies (16%) and ciliopathies (14.7%) yielded respectively the second and third genetic kidney diagnosis category and UMOD-associated nephropathy as the main genetic findings for tubulopathies (7/11). Ten of the 22 patients having ES ‘first’ eventually received a positive diagnosis, thereby avoiding 11 biopsies. Among the 44 patients with glomerular, tubulo-interstitial or vascular nephropathy, 13 (29.5%) were phenocopies. The diagnostic yield of ES was higher in female patients (p = 0.02) and in patients with a family history of kidney disease (p Conclusion Genetic diagnosis has provided new clinical insights by clarifying or reclassifying kidney disease etiology in over a third of UKD patients. Exome ‘first’ may have a significant positive diagnostic yield, thus avoiding invasive kidney biopsy; moreover, the diagnostic yield remains elevated even when biopsy is impossible or inconclusive. ES provides a clinical benefit for routine nephrological healthcare in patients with UKD.

Six Figures and Legends

Purpose: Analyses of the pattern of p53 mutations have been essential for epidemiologic studies linking carcinogen exposure and cancer. We were concerned by the inclusion of dubious reports in the p53 databases that could lead to controversial analysis prejudicial to the scientific community.Experimental Design: We used the universal mutation database p53 database (21,717 mutations) combined with a new p53 mutant activity database (2,300 mutants) to perform functional analysis of 1,992 publications reporting p53 alterations. This analysis was done using a statistical approach similar to that of clinical meta-analyses.Results: This analysis reveals that some reports of infrequent mutations are associated with almost normal activities of p53 proteins. These particular mutations are frequently found in studies reporting multiple mutations in one tumor, silent mutations, or lacking mutation hotspots. These reports are often associated with particular methodologies, such as nested PCR, for which key controls are not satisfactory.Conclusions: We show the importance of accurate functional analysis before inferring any genetic variation. The quality of the p53 databases is essential in order to prevent erroneous analysis and/or conclusions. The availability of functional data from our new p53 web site (http://p53.free.fr and http://www.umd.be:2072/) will allow functional prescreening to identify potential artifactual data.

Copy number variants (CNVs) are a major cause of rare pediatric diseases with a broad spectrum of phenotypes. Genetic diagnosis based on comparative genomic hybridization tests typically identifies ∼8-10% of patients as having CNVs of unknown significance, revealing the current limits of clinical interpretation. The adoption of whole-genome sequencing (WGS) as a first-line genetic test has significantly increased the load of CNVs identified in single genomes. Alongside short- and long-read sequencing technologies, a number of pathogenicity scores have been developed for filtering and prioritizing large sets of candidate CNVs in clinical settings. However, current approaches are often based, either explicitly or implicitly, on clinically annotated reference sets, which are likely to bias their predictions. In this study we developed CNVscore, a supervised-learning approach combining tree ensembles and a Bayesian classifier trained on pathogenic and non-pathogenic CNVs from reference databases. Unlike previous approaches, CNVscore couples pathogenicity estimates with uncertainty scores, making it possible to evaluate the suitability of a model for the query CNVs. Comprehensive comparative benchmark tests across independent sets and against alternative methods showed that CNVscore effectively distinguishes between pathogenic and benign CNVs. We also found that CNVs associated with CNVscores of low uncertainty were predicted with significantly higher accuracy than those of high uncertainty. However, the performance of current scoring approaches, including CNVscore, was compromised on CNV sets enriched in highly uncertain variants and presenting unconventional features, such as functionally relevant non-coding elements or the presence of disease genes irrelevant for the clinical phenotypes investigated. Finally, we used the CNVscore framework to guide CNV scoring model selection for the French National Database of Constitutional CNVs (BANCCO), which includes clinical diagnosis annotations. The CNVscore framework provides an objective strategy for leveraging the uncertainty on bioinformatic predictions to enhance the assessment of CNV pathogenicity in rare-disease cohorts. CNVscore is available as open-source software from https://github.com/RausellLab/CNVscore and is integrated into the CNVxplorer webserver http://cnvxplorer.com.

International audience; Background: The difficulty in interpreting somatic alterations is correlated with the increase in sequencing panel size. To correctly guide the clinical management of patients with cancer, there needs to be accurate classification of pathogenicity followed by actionability assessment. Here, we describe a specific detailed workflow for the classification of the pathogenicity of somatic variants in cancer into five categories: benign, likely benign, unknown significance, likely pathogenic and pathogenic.Methods: Classification is obtained by combining a set of eight relevant criteria in favour of either a pathogenic or a benign effect (pathogenic stand-alone, pathogenic very strong, pathogenic strong, pathogenic moderate, pathogenic supporting, benign supporting, benign strong and benign stand-alone).Results: Our guide is concordant with the ACMG/AMP 2015 guidelines for germline variants. Interpretation of somatic variants requires considering specific criteria, such as the disease and therapeutic context, co-occurring genomic events in the tumour when available and the use of cancer-specific variant databases. In addition, the gene role in tumorigenesis (oncogene or tumour suppressor gene) also needs to be taken into consideration.Conclusion: Our classification could contribute to homogenize best practices on somatic variant pathogenicity interpretation and improve interpretation consistency both within and between laboratories.

Merosin-deficient or LAMA2-related congenital muscular dystrophy (CMD) belongs to a group of muscle diseases with an overlapping diagnostic spectrum. MRI plays an important role in the diagnosis and disease-tracking of muscle diseases. Whole-body MRI is ideal for describing patterns of muscle involvement. We intended to analyze the pattern of muscle involvement in merosin-deficient CMD children employing whole-body muscle MRI. Ten children with merosin-deficient CMD underwent whole-body muscle MRI. Eight of which were genetically-confirmed. We used a control group of other hereditary muscle diseases, which included 13 children (mean age was 13 SD +/- 5.5 years), (8 boys and 5 girls) for comparative analysis. Overall, 37 muscles were graded for fatty infiltration using Mercuri scale modified by Fischer et al. The results showed a fairly consistent pattern of muscle fatty infiltration in index group, which differs from that in control group. There was a statistically significant difference between the two groups in regard to the fatty infiltration of the neck, serratus anterior, intercostal, rotator cuff, deltoid, triceps, forearm, gluteus maximus, gluteus medius, gastrocnemius and soleus muscles. Additionally, the results showed relative sparing of the brachialis, biceps brachii, gracilis, sartorius, semitendinosus and extensor muscles of the ankle in index group, and specific texture abnormalities in other muscles. There is evidence to suggest that whole-body muscle MRI can become a useful contributor to the differential diagnosis of children with merosin deficient CMD. The presence of a fairly characteristic pattern of involvement was demonstrated. MRI findings should be interpreted in view of the clinical and molecular context to improve diagnostic accuracy.

Background: LAMA2-related muscular dystrophy (LAMA2-RD) encompasses a group of recessive muscular dystrophies caused by mutations in the LAMA2 gene, which codes for the alpha-2 chain of laminin-211 (merosin). Diagnosis is straightforward in the classic congenital presentation with no ambulation and complete merosin deficiency in muscle biopsy, but is far more difficult in milder ambulant individuals with partial merosin deficiency. Objective: To investigate the diagnostic utility of muscle imaging in LAMA2-RD using whole-body magnetic resonance imaging (WBMRI). Results: 27 patients (2–62 years, 21–80% with acquisition of walking ability and 6 never ambulant) were included in an international collaborative study. All carried two pathogenic mutations, mostly private missense changes. An intronic variant (c.909 + 7A > G) was identified in all the Chilean cases. Three patients (two ambulant) showed intellectual disability, epilepsy, and brain structural abnormalities. WBMRI T1w sequences or T2 fat-saturated images (Dixon) revealed abnormal muscle fat replacement predominantly in subscapularis, lumbar paraspinals, gluteus minimus and medius, posterior thigh (adductor magnus, biceps femoris, hamstrings) and soleus. This involvement pattern was consistent for both ambulant and non-ambulant patients. The degree of replacement was predominantly correlated to the disease duration, rather than to the onset or the clinical severity. A “COL6-like sandwich sign” was observed in several muscles in ambulant adults, but different involvement of subscapularis, gluteus minimus, and medius changes allowed distinguishing LAMA2-RD from collagenopathies. The thigh muscles seem to be the best ones to assess disease progression. Conclusion: WBMRI in LAMA2-RD shows a homogeneous pattern of brain and muscle imaging, representing a supportive diagnostic tool.

Merosin-deficient or LAMA2-related congenital muscular dystrophy (CMD) belongs to a group of muscle diseases with an overlapping diagnostic spectrum. MRI plays an important role in the diagnosis and disease-tracking of muscle diseases. Whole-body MRI is ideal for describing patterns of muscle involvement. Our purpose is to analyze the pattern of muscle involvement in merosin-deficient CMD children employing whole-body muscle MRI. Ten children with merosin-deficient CMD underwent whole-body muscle MRI. We used a control group of other hereditary muscle diseases, which included 13 children. Overall, 37 muscles were graded for fatty infiltration using Mercuri scale modified by Fischer et al 2008. The results showed a fairly consistent pattern of muscle fatty infiltration in index group, which differed from that in control group. There was a highly statistically significant difference between the two groups in regard to the fatty infiltration of the neck, serratus anterior, rotator cuff, deltoid, forearm, gluteus maximus, gluteus medius, gastrocnemius and soleus muscles. Additionally, results showed relative sparing of the brachialis, biceps brachii, gracilis, sartorius, semitendinosus and extensor muscles of the ankle in index group. There is evidence to suggest that whole-body muscle MRI can become a useful contributor to the differential diagnosis of merosin deficient CMD.Study HighlightsWhole-body muscle MRI is a useful contributor to the differential diagnosis of merosin-deficient (LAMA2-related) congenital muscular dystrophy.The study demonstrated the presence of a fairly characteristic pattern of whole-body muscle MRI in children with merosin-deficient CMD in terms of sensitivity and specificity.The study may be considered as a preliminary step of arriving at an MRI classification system for children with merosin-deficient CMD.

Copy number variations (CNVs) are major causative contributors both in the genesis of genetic diseases and human neoplasias. While "High-Throughput" sequencing technologies are increasingly becoming the primary choice for genomic screening analysis, their ability to efficiently detect CNVs is still heterogeneous and remains to be developed. The aim of this white paper is to provide a guiding framework for the future contributions of ELIXIR's recently established h uman CNV Community, with implications beyond human disease diagnostics and population genomics. This white paper is the direct result of a strategy meeting that took place in September 2018 in Hinxton (UK) and involved representatives of 11 ELIXIR Nodes. The meeting led to the definition of priority objectives and tasks, to address a wide range of CNV-related challenges ranging from detection and interpretation to sharing and training. Here, we provide suggestions on how to align these tasks within the ELIXIR Platforms strategy, and on how to frame the activities of this new ELIXIR Community in the international context. The first ELIXIR hCNV Community meeting held in Hinxton (UK) was supported by ELIXIR. The authors declare that no grants were involved in supporting this work

Background Canine models of Duchenne muscular dystrophy (DMD) are a valuable tool to evaluate potential therapies because they faithfully reproduce the human disease. Several cases of dystrophinopathies have been described in canines, but the Golden Retriever muscular dystrophy (GRMD) model remains the most used in preclinical studies. Here, we report a new spontaneous dystrophinopathy in a Labrador Retriever strain, named Labrador Retriever muscular dystrophy (LRMD). Methods A colony of LRMD dogs was established from spontaneous cases. Fourteen LRMD dogs were followed-up and compared to the GRMD standard using several functional tests. The disease causing mutation was studied by several molecular techniques and identified using RNA-sequencing. Results The main clinical features of the GRMD disease were found in LRMD dogs; the functional tests provided data roughly overlapping with those measured in GRMD dogs, with similar inter-individual heterogeneity. The LRMD causal mutation was shown to be a 2.2-Mb inversion disrupting the DMD gene within intron 20 and involving the TMEM47 gene. In skeletal muscle, the Dp71 isoform was ectopically expressed, probably as a consequence of the mutation. We found no evidence of polymorphism in either of the two described modifier genes LTBP4 and Jagged1. No differences were found in Pitpna mRNA expression levels that would explain the inter-individual variability. Conclusions This study provides a full comparative description of a new spontaneous canine model of dystrophinopathy, found to be phenotypically equivalent to the GRMD model. We report a novel large DNA mutation within the DMD gene and provide evidence that LRMD is a relevant model to pinpoint additional DMD modifier genes.

The autosomal recessive Congenital Muscular Dystrophies associated with a merosin deficiency, also known as type 1A muscular dystrophy (MDC1A), results from mutations of the LAMA2 gene. This large gene, composed of 65 exons, encodes the a2-chain subunit of laminin-2 (merosin). For many years, identification of the lack of expression of merosin on muscle biopsies was considered to initiate a molecular analysis by conventional Sanger sequencing. In the majority of cases (80%), the two pathogenic mutations were directly identified by this approach. Nevertheless, for the remaining cases with a single or no mutation, complementary approaches were necessary. They include the detection of large rearrangement; either by MLPA or CGH-array and the search for deep intronic mutations impacting splicing through the mRNA analysis. Altogether, these approaches allowed for the identification of disease-causing mutations in more than 95% of families. Since these early days, patients with partial loss of merosin have been identified. This has paved the way to the identification of a wide range of phenotypes associated with mutations of the LAMA2 gene, ranging from the most severe forms in patients with hypotonia at birth or in the first weeks of life, to rare patients achieving independent ambulation. Most patients, among those with partial laminin-a2 deficiency, belong to this last category. The identification of those milder phenotypes have also led to higher difficulty to select which genes have to be analyzed based on the clinical presentation. This led to the development of NGS gene panels in order to simultaneously screen all genes reported to be associated with congenital muscular dystrophies. Thus, in a single NGS experiment, it is now possible to screen the 19 most commonly involved genes and thus limit the diagnostic wandering. This new technology, while being able to rapidly deliver the sequence of all genes, also place the geneticist in front of multiple candidate mutations, which need to be evaluated prior to reporting the identification of the disease-causing mutation(s) in a family. Not considering the need for large data storage capacity, it is now mandatory to have access to efficient bioinformatics systems and to trained geneticists. In this presentation, I will demonstrate the benefits and limits of this approach for the diagnosis of DMC.

Human genomics is undergoing a step change from being a predominantly research-driven activity to one driven through health care as many countries in Europe now have nascent precision medicine programmes. To maximize the value of the genomic data generated, these data will need to be shared between institutions and across countries. In recognition of this challenge, 21 European countries recently signed a declaration to transnationally share data on at least 1 million human genomes by 2022. In this Roadmap, we identify the challenges of data sharing across borders and demonstrate that European research infrastructures are well-positioned to support the rapid implementation of widespread genomic data access.

International audience; With the rapidly developing high-throughput sequencing technologies known as next generation sequencing or NGS, our approach to gene hunting and diagnosis has drastically changed. In

// Lucile Broncy 1 , Basma Ben Njima 2 , Arnaud Mejean 3 , Christophe Beroud 4, 5 , Khaled Ben Romdhane 2 , Marius Ilie 6 , Veronique Hofman 6 , Jane Muret 7 , Paul Hofman 6 , Habiba Chaabouni Bouhamed 2 , and Patrizia Paterlini-Brechot 1, 8 1 INSERM Unit 1151, Faculte de Medecine Paris Descartes, Paris, France 2 Genetics and Pathology Departments, University of Tunis, Tunis, Tunisia 3 Service d’Urologie, Hopital Europeen Georges Pompidou, Paris, France 4 Aix Marseille University, INSERM, MMG, Marseille, France 5 APHM, Hopital TIMONE Enfants, Laboratoire de Genetique Moleculaire, Marseille, France 6 Laboratoire de pathologie clinique et Biobank BB-0033-00025, Centre Hospitalo-Universitaire de Nice, Nice, France 7 Institut Curie, PSL Research University, Departement d’Anesthesie Reanimation Douleur, Paris, France 8 Laboratoire de Biochimie A, Hopital Necker-Enfants Malades, Paris, France Correspondence to: Patrizia Paterlini-Brechot, email: patrizia.paterlini@inserm.fr Keywords: liquid biopsy; circulating cancer cells; ISET ® (Isolation by Size of Tumour/Trophoblastic Cells) technology; clear cell renal cell carcinoma; VHL mutation Received: October 07, 2017 Accepted: March 24, 2018 Published: April 13, 2018 ABSTRACT Context: Circulating Rare Cells (CRC) are non-haematological cells circulating in blood. They include Circulating Cancer Cells (CCC) and cells with uncertain malignant features (CRC-UMF) according to cytomorphology. Clear cell renal cell carcinomas frequently bear a mutated Von Hippel-Lindau (VHL) gene. Aim: To match blind genetic analysis of CRC and tumor samples with CRC cytopathological diagnosis. Results: 29/30 patients harboured CRC (20 harboured CCC, 29 CRC-UMF) and 25/29 patients carried VHL mutations in their tumour. 205 single CRC (64 CCC, 141 CRC-UMF) provided genetic data. 57/57 CCC and 104/125 CRC-UMF from the 25 patients with VHL-mutated tumor carried the same VHL mutation detected in the tumor. Seven CCC and 16 CRC-UMF did not carry VHL mutations but were found in patients with wild-type VHL tumor tissue. Conclusions: All the CCC and 83,2% (104/125) of the CRC-UMF were found to carry the same VHL mutation identified in the corresponding tumorous tissue, validating cytopathological identification of CCC in patients with clear cell renal cell carcinoma. Methods: The blood of 30 patients with clear cell renal cell carcinoma was treated by ISET ® for CRC isolation, cytopathology and single-cell VHL mutations analysis, performed blindly and compared to VHL mutations of corresponding tumor tissues and leukocytes.

Splenic diffuse red pulp lymphoma is an indolent small B-cell lymphoma recognized as a provisional entity in the World Health Organization 2008 classification. Its precise relationship to other related splenic B-cell lymphomas with frequent leukemic involvement or other lymphoproliferative disorders remains undetermined. We performed whole-exome sequencing to explore the genetic landscape of ten cases of splenic diffuse red pulp lymphoma using paired tumor and normal samples. A selection of 109 somatic mutations was then evaluated in a cohort including 42 samples of splenic diffuse red pulp lymphoma and compared to those identified in 46 samples of splenic marginal zone lymphoma and eight samples of hairy-cell leukemia. Recurrent mutations or losses in BCOR (the gene encoding the BCL6 corepressor) - frameshift (n=3), nonsense (n=2), splicing site (n=1), and copy number loss (n=4) - were identified in 10/42 samples of splenic diffuse red pulp lymphoma (24%), whereas only one frameshift mutation was identified in 46 cases of splenic marginal zone lymphoma (2%). Inversely, KLF2, TNFAIP3 and MYD88, common mutations in splenic marginal zone lymphoma, were rare (one KLF2 mutant in 42 samples; 2%) or absent (TNFAIP3 and MYD88) in splenic diffuse red pulp lymphoma. These findings define an original genetic profile of splenic diffuse red pulp lymphoma and suggest that the mechanisms of pathogenesis of this lymphoma are distinct from those of splenic marginal zone lymphoma and hairy-cell leukemia.

Charcot-Marie-Tooth disease (CMT) is a hereditary sensory-motor neuropathy characterized by a strong clinical and genetic heterogeneity. Over the past few years, with the occurrence of whole-exome sequencing (WES) or whole-genome sequencing (WGS), the molecular diagnosis rate has been improved by allowing the screening of more than 80 genes at one time. In CMT, except the recurrent PMP22 duplication accounting for about 60% of pathogenic variations, pathogenic copy number variations (CNVs) are rarely reported and only a few studies screening specifically CNVs have been performed. The aim of the present study was to screen for CNVs in the most prevalent genes associated with CMT in a cohort of 200 patients negative for the PMP22 duplication. CNVs were screened using the Exome Depth software on next generation sequencing (NGS) data obtained by targeted capture and sequencing of a panel of 81 CMT associated genes. Deleterious CNVs were identified in four patients (2%), in four genes: GDAP1, LRSAM1, GAN, and FGD4. All CNVs were confirmed by high-resolution oligonucleotide array Comparative Genomic Hybridization (aCGH) and/or quantitative PCR. By identifying four new CNVs in four different genes, we demonstrate that, although they are rare mutational events in CMT, CNVs might contribute significantly to mutational spectrum of Charcot-Marie-Tooth disease and should be searched in routine NGS diagnosis. This strategy increases the molecular diagnosis rate of patients with neuropathy.

International audience; BackgroundAortic risk has not been evaluated in patients with Marfan syndrome and documented pathogenic variants in the FBN1 gene.ObjectivesThis study sought to describe aortic risk in a population with Marfan syndrome with pathogenic variants in the FBN1 gene as a function of aortic root diameter.MethodsPatients carrying an FBN1 pathogenic variant who visited our reference center at least twice were included, provided they had not undergone aortic surgery or had an aortic dissection before their first visit. Aortic events (aortic surgery or aortic dissection) and deaths were evaluated during the 2 years following each patient visit. The risk was calculated as the number of events divided by the number of years of follow-up.ResultsA total of 954 patients were included (54% women; mean age 23 years). During follow-up (9.1 years), 142 patients underwent prophylactic aortic root surgery, 5 experienced type A aortic dissection, and 12 died (noncardiovascular causes in 3, unknown etiology in 3, post-operative in 6). When aortic root diameter was

Context Multiple endocrine neoplasia type 1 (MEN1) is an autosomal dominant disease caused by mutations in the MEN1 gene characterized by a broad spectrum of clinical manifestations, of which the most frequent are primary hyperparathyroidism, pituitary adenomas, and neuroendocrine tumors. Objective The aim of this work was to facilitate interpretation of variants and improve the genetic counseling and medical care of families of patients with MEN1. Design, Setting, and Patients The TENGEN network (Oncogenetics Network of Neuroendocrine Tumors) has interpreted and collected all allelic variants and clinical characteristics of the MEN1-positive patients identified through genetic testing performed in the French population from 1997 to 2015. Patients and their variants were registered in the locus-specific UMD-MEN1 database (www.umd.be/MEN1/). Main Outcomes Variant classification, age-related penetrance, and odds ratios. Results A total of 370 distinct variants reported in 1676 patients, including 181 unpublished variants, have been registered. This database analysis revealed a low frequency (6.6%) of benign or likely benign missense variants in MEN1. Eight families (1.9%) had members with familial isolated hyperparathyroidism and harbored the same mutations as that found in families with authentic MEN1. An association existed between large rearrangements and an earlier onset of the disease, whereas no difference was observed between truncating and nontruncating variants. Conclusion The UMD-MEN1 database provides an exhaustive overview of the MEN1 variants present in the French population. For each variant, a classification is publicly available. Clinical data collections allow the determination of genotype-phenotype correlation and age-related penetrance of lesions in the cohort.

Background: Both bicuspid aortic valve (BAV) and Marfan syndrome have been associated with aortic dissection risk, but it is unknown whether the presence of BAV is associated with an increased aortic risk in patients with an FBN1 gene mutation. We evaluated aortic diameters, aortic valve function, and aortic shape in Marfan syndrome patients with and without BAV and reported aortic events during follow-up. Methods: All patients with an FBN1 gene mutation evaluated in our clinic were included. Aortic root diameters were measured, and the aortic valve was studied using echocardiography at each visit. Results: Of the 1437 patients with an FBN1 gene mutation, 26 patients (1.8%) had a BAV. Both aortic root maximal diameter and normalized Z score were larger at all ages, in patients with BAV when compared with patients with tricuspid aortic valve. Prophylactic aortic root surgery tended to be performed in younger patients when BAV was present, although aortic diameter threshold was similar in the 2 populations. No aortic dissection was observed in Marfan syndrome patients with BAV. Conclusions: In patients with a FBN1 mutation, BAV is associated with larger aortic root diameter, with no difference in evolution of Z score with age. We found a trend towards prophylactic aortic root surgery at younger ages but similar aortic diameter thresholds without occurrence of aortic dissection. We did not find any evidence for lowering aortic diameter thresholds used to propose preventive aortic root surgery in the presence of BAV in patients with FBN1 mutations.

During early cardiogenesis, progressive addition of distinct cardiac progenitor cells originating from the second heart field (SHF) contributes to elongation of the forming heart. Whereas the subdivision of the SHF into an anterior and posterior domain is essential for morphogenesis of the definitive heart, the transcriptional programs and upstream regulatory events operating in the different progenitor cell populations remain unclear. Here, we characterize the molecular signature and regulation of anterior and posterior sub-populations of SHF cells. We profiled the transcriptome and chromatin accessibility of purified sub-populations at genome-wide levels and demonstrated that the transcriptional regulator Hoxb1 controls the differentiation of the posterior SHF progenitors during heart morphogenesis. Spatial mis-expression of Hoxb1 in anterior SHF progenitors that normally contribute to right ventricular cardiomyocytes results in hypoplastic right ventricle, revealing how deregulation of a specific sub-population of the SHF can result in congenital heart defects. Expanded activation of Hoxb1 perturbs the anterior transcriptional program and induces increased progenitor cell death in anterior SHF progenitors. Moreover, activation of Hoxb1 in embryonic stem cells arrests cardiac differentiation, whereas Hoxb1-deficient embryos display premature differentiation of cardiac progenitor cells. Our results show that Hoxb1 coordinates a cascade of gene-regulatory events in the SHF essential for proper heart development and provide new insights into how deregulation of SHF sub-population identities can induce congenital heart defects.

International audience; In 2015, the ACMG-AMP guidelines provided a general procedure for the objective and reproducible classification of genomic variants. While the benefits of this framework are of major importance, its adaptation for locus-specific use is needed. Multiple Endocrine Neoplasia type 1 (MEN1) occurs due to inactivating mutations in the tumour suppressor gene MEN1, including 20% of missense variants. The classification of these variants may be extremely challenging. Here, we compared the interpretation of the 122 MEN1 missense variants, identified in the French population over the past 15 years by the TENGEN network (French oncogenetics network of neuroendocrine tumors) versus by using the ACMG-AMP guidelines, and analyzed the causes of discordance. A total of 59.8% of missense variants were termed as (likely)-pathogenic variants by TENGEN versus only 28.7% using ACMG-AMP guidelines. Actually, 53.4% (39/73) of TENGEN (likely)-pathogenic variants were declassified in variant of uncertain significance (VUS) by using ACMG-AMP guidelines, thereby affecting the clinical management of patients and their families. Twenty of these ACMG-AMP VUS were found in patients with a clinically authentic MEN1 disease. Here, TENGEN proposes adjustments to the ACMG-AMP framework for the interpretation of MEN1 missense variants. These propositions merge both the classification systems, and are particularly interesting, as MEN1 is included in the ACMG secondary findings list for reporting in clinical genomic sequencing.

Background Facioscapulohumeral muscular dystrophy is a rare inherited neuromuscular disease with an estimated prevalence of 1/20,000 and France therefore harbors about 3000 FSHD patients. With research progress and the development of targeted therapies, patients’ identification through registries can facilitate and improve recruitment in clinical trials and studies. Results The French National Registry of FSHD patients was designed as a mixed model registry involving both patients and physicians, through self-report and clinical evaluation questionnaires respectively, to collect molecular and clinical data. Because of the limited number of patients, data quality is a major goal of the registry and various automatic data control features have been implemented in the bioinformatics system. In parallel, data are manually validated by molecular and clinical curators. Since its creation in 2013, data from 638 FSHD patients have been collected, representing about 21% of the French FSHD population. The mixed model strategy allowed to collect 59.1% of data from both patients and clinicians; 26 and 14.9% from respectively patients and clinicians only. With the identification of the FSHD1 and FSHD2 forms, specific questionnaires have been designed. Though FSHD2 patients are progressively included, FSHD1 patients still account for the majority (94.9%). The registry is compatible with the FAIR principles as data are Findable, Accessible and Interoperable. We thus used molecular standards and standardized clinical terms used by the FILNEMUS French network of reference centers for the diagnosis and follow-up of patients suffering from a rare neuromuscular disease. The implemented clinical terms mostly map to dictionaries and terminology systems such as SNOMED-CT (75% of terms), CTV3 (61.7%) and NCIt (53.3%). Because of the sensitive nature of data, they are not directly reusable and can only be accessed as aggregated data after evaluation and approval by the registry oversight committee. Conclusions The French National Registry of FSHD patients belongs to a national effort to develop databases, which should now interact with other initiatives to build a European and/or an international FSHD virtual registry for the benefits of patients. It is accessible at www.fshd.fr and various useful information, links, and documents, including a video, are available for patients and professionals. Electronic supplementary material The online version of this article (10.1186/s13023-018-0960-x) contains supplementary material, which is available to authorized users.