Identification of novel genes implicated in structural congenital myopathies by exome sequencing – CM-WES

Rare monogenic diseases are inherited diseases due to defect in a single gene, and target less than 1 in 2,000 people. Taken together, several hundred thousand persons are affected in Europe. Huge progress in human genetics the past 25 years led to the identification of the molecular basis for about 3000 of them. However, the cause of more than half of these rare genetic diseases is still unknown, despite huge research effort. This is mainly due to genetic heterogeneity and to the lack of large families and large panel of patients. Neuromuscular diseases and especially congenital myopathies are debilitating diseases with a strong impact on the individuals and the society. These pathologies are present in all populations, affecting children as well as adults. Additional genes implicated in congenital myopathies remain to be identified. To this aim, we propose here to use exome capture and massive parallel sequencing.

1) We will collect clinical and morphological data and build cohorts of patients with the following structural congenital myopathies: a) Congenital myopathies with central nuclei (centronuclear myopathies), b) Congenital myopathies with protein aggregates (thin filaments accumulation, cap disease, nemaline myopathy), c) Congenital myopathies with cores (cores myopathies), d) Tubular aggregate.
2) Exome liquid capture followed by massive parallel DNA sequencing technologies will be used to identify all the sequence variants present in the affected individuals. Indeed most disease-causing mutations are located in coding regions (that represent only 1.5% of the genome), and since January 2010 several publications reported the first success of this strategy to identify novel genes implicated in monogenic diseases.
3) One main challenge will be to determine the disease-causing mutation among all the detected variants. Indeed, genomes sequenced and the 1000 genome project revealed that a given individual harbors about 10,000 non-synonymous variants. We plan to develop a relational database to integrate the experimental design and variants analysis and ranking, in order to focus on the most likely deleterious variants.
4) While our whole exome sequencing project will be applied to a subset of patients for each cohort, we will confirm the implication of novel genes by sequencing the whole panel. The pathological effect of the mutations found will be confirmed by genetic and functional analysis.

Both partners previously collaborated and were implicated in the identification of genes mutated in congenital myopathies through classical methods. Importantly, partner 2 (a pediatrician and histopathologist) already assembled several patient cohorts. Being part of a national medical center for neuromuscular pathologies, her expertise warrants the further characterization of homogeneous cohorts. Partner 1 (a molecular geneticist and a sequencing platform) performed several whole exome sequencing experiments in-house, established a first bioinformatic analysis pipeline, and could detect different classes of known mutations.

The identification of novel genes implicated in congenital myopathies is necessary for accurate diagnosis, improved health care, genetic counselling, and will provide novel therapeutic targets. The knowledge of the disease-causing mutation is also a pre-requisite for inclusion in therapeutic trials. This emerging strategy is very likely to become a standard tool for the discovery of genes underlying rare monogenic diseases (and later polygenic diseases), and may be applicable to routine genetic diagnosis.