During the last 4 years (2012-2016) our research team has acquired unique resources to allow efficient bioinformatics systems development. It allowed us to continue the development of Locus Specific DataBases (LSDB) using the Universal Mutation Database (UMD) system with the creation of 20 new LSDBs. All UMD-LSDB hosted on our servers received an average of 990,840 queries/year, have been valorized through >50 publications (22 since 2012) and 1,847 citations. Two of these database have been licensed through the successful BRCA-Share™ public/private partnership with >1,660 registered users and >15,000 queries/month.

In parallel, we also developed, curate and host various patients' registries including the International Dysferlinopathies registry (www.dysferlinregistry.org), the French observatory of patients affected by the FSHMD (www.fshd.fr), the French registry of Marfan and related diseases (restricted access).

We developed two knowledge base systems, the UMD-Predictor® and Human Splicing Finder® (HSF) systems to predict the pathogenicity of mutations. These two systems are today the most efficient worldwide (Salgado et al. 2016, Desmet et al. 2009 - http://umd-predictor.eu; http://www.umd.be/HSF3/).

Because NGS data are difficult to analyze, we developed the Variant Annotation and Filtration Tool (VarAFT) that has been recently released and is already used in diagnostic and research contexts (http://varaft.eu).

Thanks to its international recognition (participation to 4 EU projects and 2 international projects since 2012) and the quality of these various systems/databases, our team has been labelled as a French National Bioinformatics Platform by the French Bioinformatics Institute (IFB) and is now an Elixir partner. It is leading the "Clinical and Bioinformatics" Work Package of the RD-Connect EU-funded project, which is the flagship for rare diseases in Europe.

CHRISTOPHE BEROUD

PUPH

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Telephone: 04 91 32 44 88

Team members

PUPH 

Mail:

Telephone: 04 91 32 44 88


CRHC 

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Telephone: 04 91 32 49 14


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Beroud, C.  et al. 2016

BRCA Share: A Collection of Clinical BRCA Gene Variants

As next-generation sequencing increases access to human genetic variation, the challenge of determining clinical significance of variants becomes ever more acute. Germline variants in the BRCA1 and...
Hum. Mutat. - issue: 12 - volume: 37 - pages: 1318-1328.

Oetting, WS.  et al. 2016

Clinical Interpretation of Variants from Next-Generation Sequencing: The 2016 Scientific Meeting of the Human Genome Variation Society

WOS:000385805800012
Hum. Mutat. - issue: 10 - volume: 37 - pages: 1110-1113.

Miltgen, M.  et al. 2016

Novel Heterozygous Mutation in ANO3 Responsible for Craniocervical Dystonia

WOS:000382558800031
Mov. Disord. - issue: 8 - volume: 31 - pages: 1251-1252.

Arslan-Kirchner, M.  et al. 2016

Clinical utility gene card for: Hereditary thoracic aortic aneurysm and dissection including next-generation sequencing-based approaches

WOS:000366615000024
Eur. J. Hum. Genet. - issue: 1 - volume: 24 - pages: 146-150.

Rapetti-Mauss, R.  et al. 2015

A mutation in the Gardos channel is associated with hereditary xerocytosis

The Gardos channel is a Ca2+-sensitive, intermediate conductance, potassium selective channel expressed in several tissues including erythrocytes and pancreas. In normal erythrocytes, it is involved...
Blood - issue: 11 - volume: 126 - pages: 1273-1280.

Barckmann, B.  et al. 2015

Aubergine iCLIP Reveals piRNA-Dependent Decay of mRNAs Involved in Germ Cell Development in the Early Embryo

The Piwi-interacting RNA (piRNA) pathway plays an essential role in the repression of transposons in the germline. Other functions of piRNAs such as post-transcriptional regulation of mRNAs are now...
Cell Reports - issue: 7 - volume: 12 - pages: 1205-1216.

Joly, D.  et al. 2015

Rare inherited disorders with renal involvement-approach to the patient

The list of rare inherited disorders with renal involvement is rapidly growing. Many are single gene diseases affecting children, but cases are not restricted to pediatrics and diagnosis is often...
Kidney Int. - issue: 5 - volume: 87 - pages: 901-908.

Manes, G.  et al. 2015

High Prevalence of PRPH2 in Autosomal Dominant Retinitis Pigmentosa in France and Characterization of Biochemical and Clinical Features

PURPOSE: To assess the prevalence of PRPH2 in autosomal dominant retinitis pigmentosa (adRP), to report 6 novel mutations, to characterize the biochemical features of a recurrent novel mutation, and...
Am. J. Ophthalmol. - issue: 2 - volume: 159 - pages: 302-314.

Mazuc, E.  et al. 2014

In-Cell Intrabody Selection from a Diverse Human Library Identifies C12orf4 Protein as a New Player in Rodent Mast Cell Degranulation

The high specificity of antibodies for their antigen allows a fine discrimination of target conformations and post-translational modifications, making antibodies the first choice tool to interrogate...
PLoS One - issue: 8 - volume: 9 - pages: e104998.

Thompson, R.  et al. 2014

RD-Connect: An Integrated Platform Connecting Databases, Registries, Biobanks and Clinical Bioinformatics for Rare Disease Research

Research into rare diseases is typically fragmented by data type and disease. Individual efforts often have poor interoperability and do not systematically connect data across clinical phenotype,...
J. Gen. Intern. Med. - issue: - volume: 29 - pages: S780-S787.

Etienne-Grimaldi, M.  et al. 2014

Molecular patterns in deficient mismatch repair colorectal tumours: results from a French prospective multicentric biological and genetic study

Background: To test the prognostic value of tumour protein and genetic markers in colorectal cancer (CRC) and examine whether deficient mismatch repair (dMMR) tumours had a distinct profile relative...
Br. J. Cancer - issue: 11 - volume: 110 - pages: 2728-2737.

Boennemann, CG.  et al. 2014

Diagnostic approach to the congenital muscular dystrophies

Congenital muscular dystrophies (CMDs) are early onset disorders of muscle with histological features suggesting a dystrophic process. The congenital muscular dystrophies as a group encompass great...
Neuromusc. Disord. - issue: 4 - volume: 24 - pages: 289-311.

Robellet, X.  et al. 2014

A Genetic Screen for Functional Partners of Condensin in Fission Yeast

Mitotic chromosome condensation is a prerequisite for the accurate segregation of chromosomes during cell division, and the conserved condensin complex a central player of this process. However, how...
G3-Genes Genomes Genet. - issue: 2 - volume: 4 - pages: 373-381.

Bladen, CL.  et al. 2014

Mapping the differences in care for 5,000 Spinal Muscular Atrophy patients, a survey of 24 national registries in North America, Australasia and Europe

Spinal muscular atrophy (SMA) is an autosomal recessive genetic disorder characterised by the degeneration of motor neurons and progressive muscle weakness. It is caused by homozygous deletions in the...
J. Neurol. - issue: 1 - volume: 261 - pages: 152-163.

Callier, P.  et al. 2013

Systematic molecular and cytogenetic screening of 100 patients with marfanoid syndromes and intellectual disability

The association of marfanoid habitus (MH) and intellectual disability (ID) has been reported in the literature, with overlapping presentations and genetic heterogeneity. A hundred patients (71 males...
Clin. Genet. - issue: 6 - volume: 84 - pages: 507-521.

Bladen, CL.  et al. 2013

The TREAT-NMD Duchenne Muscular Dystrophy Registries: Conception, Design, and Utilization by Industry and Academia

Duchenne muscular dystrophy (DMD) is an X-linked genetic disease, caused by the absence of the dystrophin protein. Although many novel therapies are under development for DMD, there is currently no...
Hum. Mutat. - issue: 11 - volume: 34 - pages: 1449-1457.

Humbertclaude, V.  et al. 2013

Phenotypic heterogeneity and phenotype-genotype correlations in dystrophinopathies: Contribution of genetic and clinical databases

The objective of this work was to study the natural history of dystrophinopathies and the genotype-phenotype correlations made possible by the development of the clinical part of the French DMD...
Rev. Neurol. - issue: 8-9 - volume: 169 - pages: 583-594.

McDonnell, CM.  et al. 2013

Ecto- and endoparasite induce similar chemical and brain neurogenomic responses in the honey bee (Apis mellifera)

Background: Exclusion from a social group is an effective way to avoid parasite transmission. This type of social removal has also been proposed as a form of collective defense, or social immunity, in...
BMC Ecol. - issue: - volume: 13 - pages: 25.

Carmignac, V.  et al. 2012

In-Frame Mutations in Exon 1 of SKI Cause Dominant Shprintzen-Goldberg Syndrome

Shprintzen-Goldberg syndrome (SGS) is characterized by severe marfanoid habitus, intellectual disability, camptodactyly, typical facial dysmorphism, and craniosynostosis. Using family-based exome...
Am. J. Hum. Genet. - issue: 5 - volume: 91 - pages: 950-957.

Salgado, D.  et al. 2012

MyMiner: a web application for computer-assisted biocuration and text annotation

Motivation: The exponential growth of scientific literature has resulted in a massive amount of unstructured natural language data that cannot be directly handled by means of bioinformatics tools....
Bioinformatics - issue: 17 - volume: 28 - pages: 2285-2287.

Boehm, J.  et al. 2012

Mutation Spectrum in the Large GTPase Dynamin 2, and Genotype-Phenotype Correlation in Autosomal Dominant Centronuclear Myopathy

Centronuclear myopathy (CNM) is a genetically heterogeneous disorder associated with general skeletal muscle weakness, type I fiber predominance and atrophy, and abnormally centralized nuclei....
Hum. Mutat. - issue: 6 - volume: 33 - pages: 949-959.

Humbertclaude, V.  et al. 2012

Motor and respiratory heterogeneity in Duchenne patients: Implication for clinical trials

Aims: Our objective was to clarify the clinical heterogeneity in Duchenne muscular dystrophy (DMD). Methods: The French dystrophinopathy database provided clinical, histochemical and molecular data of...
Eur. J. Paediatr. Neurol. - issue: 2 - volume: 16 - pages: 149-160.

Bonnans, C.  et al. 2012

Essential requirement for beta-arrestin2 in mouse intestinal tumors with elevated Wnt signaling

beta-Arrestins (Arrb) participate in the regulation of multiple signaling pathways, including Wnt/beta-catenin, the major actor in human colorectal cancer initiation. To better understand the roles of...
Proc. Natl. Acad. Sci. U. S. A. - issue: 8 - volume: 109 - pages: 3047-3052.

Samadi, A.  et al. 2012

Surgical management of patients with Marfan syndrome: Evolution throughout the years

Aim. To evaluate the evolution of surgical management in a large population of patients with Marfan syndrome. Methods. This is a retrospective study of patients fulfilling the Ghent criteria for...
Arch. Cardiovasc. Dis. - issue: 2 - volume: 105 - pages: 84-90.

Jondeau, G.  et al. 2012

Aortic Event Rate in the Marfan Population A Cohort Study

Background-Optimal management, including timing of surgery, remains debated in Marfan syndrome because of a lack of data on aortic risk associated with this disease. Methods and Results-We used our...
Circulation - issue: 2 - volume: 125 - pages: 226-232.