Montpellier University Hospital

Laboratory of molecular genetics: deafness and blindness team

Group :

  • Anne-françoise Roux , Pharm.D, Ph.D, HDR, PH
  • Valérie Faugère
  • Melody Moclin
  • Corinne Baudoin
  • Christel Vaché, Ph.D
  • David Baux

Molecular Diagnosis

  • Usher Syndrome
  • Pendred Syndrome
  • Non Syndromic Hearing Loss (both recessive, dominant or X-linked inheritance)
  • Non Syndromic Retinitis Pigmentosa (recessive inheritance)
  • Choroideremia

Molecular Biology

  • Illumina sequencing: 132 genes custom panel
  • Use of Illumina Nextera, NimbleGen SeqCap, Agilent SureSelect and SureSelect QXT for library preparation
  • Exomes and clinical exomes analysis
  • HRM (High Resolution Melting)
  • SNaPshot® Multiplex system
  • QMPSF (Quantitative Multiplex PCR of Short Fluorescent Fragments)
  • MLPA® (Multiplex Ligation-dependent Probe Amplification)
  • Array-CGH (Comparative Genomics Hybridization)
  • transcripts analysis (RNA, minigenes)

Bioinformatics

  • LSDBs dedicated to Usher syndrome     
  • development of USMA (Usher Syndrome Missense Analysis), an online tool which aims at facilitating missense interpretation
  • development of GSdot (GS data online treatment), a second online tool dedicated to 454 sequencing, using sequence capture, and which aims at facilitating quality assessment and variant prioritising
  • development of a perl client for mutalyzer webservices
  • development of USHVaM and of the new system USHVaM2, our own private LSDB system (source code available upon request, slide show)
  • development of a custom DNA NGS pipeline called nenufaar, running under SLURM at HPC@LR and in the lab

the team in 2016.

In 2010 we contributed to the datation of the most common USH2A mutation (about 6,500 years, Aller et al., 2010).

Still in 2010 we demonstrated the relevancy of the use of nasal cells to study the Usher transcripts (Vaché et al., 2010).

In 2012 we published genotype/phenotype correlations based on an important cohort of Usher type II patients (Abadie et al., 2012).

We described in 2012 the first deep-intronic mutation leading to pseudo-exon insertion in an Usher gene. This variant is now the second most frequent disease-causing variant in Usher type II. (Vaché et al., 2012).

In 2014 we demonstrated the feasibility of the molecular diagnosis of Usher using NGS technology. (Besnard, García-García, Baux et al., 2014).

Meta-analysis of missense variants extracted from LOVD-USHbases plotted against Fibronectin type III domains of usherin (USH2A gene, Baux et al., 2014).

In 2015 we used NGS to perform a full-gene sequencing of USH2A (800kb) to identify new deep intronic mutations (Liquori et al., 2015).

In 2016 we compared 3 different enrichment methods used in NGS (García-García et al., 2016).

USHVaM 2 (internal molecular database) records and annotates each Illumina run.

USHVaM 2 (internal molecular database) computes statistics in real time (here, distribution of deafness deleterious variants per gene.

USMA analyses every missense variant in 9 Usher genes, with orthologuous, domains and 3D (when available) studies.

USMA analyses every missense variant in 9 Usher genes, with orthologuous, domains and 3D (when available) studies.