[RNAseq in routine oncology]

High throughput RNA sequencing, also know as RNAseq, can easily be performed on the gold-standard technique of formalin-fixed paraffin-embedded tissue, which has long been successfully used in routine practice by pathologists. For this reason, RNAseq has been fully adopted in a very short period of time in most French molecular platforms of cancer genotyping, generating "high throughput" data, both qualitative (mutations, fusions) and quantitative (gene expression profiles). This technique opens new perspectives in oncology practice: from a diagnostic point of view (some gene fusions are specific of some diagnoses, some transcriptomic signatures suggest some types of cancer), but also from a prognostic point of view (gene expression profile of an aggressive tumor, or conversely of an indolent one), and above all from a predictive point of view, guiding the choice of potential targeted therapies (example of ALK, ROS1 or NTRK translocations). This technical approach has many advantages, first and foremost it detects, at one go, a plethora of molecular alterations which were previously analyzed sequentially using heterogenous assays (immunohistochemistry, DNA genotyping, fluorescent in situ hybridization, etc.). However, it also presents several drawbacks which may easily be overcome if certain pre-analytic parameters are correctly controlled, mainly aiming at the preservation of the quality of nucleic acids. In any event, the widespread use of RNAseq has had a profound impact on the algorithms of tumor tissue processing, shaping a new, holistic era in oncology.

[Pharmacogenetics for patient care in France: A discipline that evolves!]

Pharmacogenetics, which concepts are known for a long time, is entering a new period at least as far as its practical applications for patients are concerned. In recent years there have been more and more initiatives to promote widespread dissemination, and health authorities are increasingly incorporating these concepts into drug labels. In France, the national network of pharmacogenetics (RNPGx) works to promote these activities, both with health actors (biologists, clinicians) and health authorities. This article reviews the current situation in France and the milestones of the year 2018. It highlights recent advances in this field, in terms of currently recommended analyses, sharing of information or technological developments, and the prospects for future developments in the near future from targeted pharmacogenetics to eventually preemptive approaches.

Molecular perspectives in differentiated thyroid cancer

Progress in understanding the molecular genetics of thyroid cancer in the last 20 years has accelerated recently with the advent of high-throughput sequencing technologies known as Next-Generation Sequencing. Besides classical molecular abnormalities involving the MAPK (Mitogen Activated Protein Kinase) and PI3K (PhosphoInositide 3-Kinase) pathways that play a key role in follicular-derived thyroid tumorigenesis, new molecular abnormalities have been discovered. The major advances in recent years have been the discovery of new somatic driver gene point mutations (such as RASAL1 [RAS protein activator Like 1] mutations in follicular cancer) and/or mutations that have prognostic value (such as TERT [Telomerase reverse transcriptase] promoter mutations); new chromosomal rearrangements, usually having close connection with exposure to ionizing radiation (such as ALK [Anaplastic Lymphoma Kinase] rearrangements); and deregulation of some gene or microRNA expression representing a molecular signature. Progress made in understanding the molecular mechanisms of thyroid cancer offers new perspectives for the diagnosis of the benign or malignant status of a thyroid nodule, to refine prognosis and offer new perspectives of targeted therapy for radioiodine-refractory cancers.

Clinical massively parallel sequencing for the diagnosis of myopathies

Massively parallel sequencing, otherwise known as high-throughput or next-generation sequencing, is rapidly gaining wide use in clinical practice due to possibility of simultaneous exploration of multiple genomic regions. More than 300 genes have been implicated in neuromuscular disorders, meaning that many genes need to be considered in a differential diagnosis for a patient affected with myopathy. By providing sequencing information for numerous genes at the same time, massively parallel sequencing greatly accelerates the diagnostic processes of myopathies compared to the classical "gene-after-gene" approach by Sanger sequencing. In this review, we describe multiple advantages of this powerful sequencing method for applications in myopathy diagnosis. We also outline recent studies that used this approach to discover new myopathy-causing genes and to diagnose cohorts of patients with muscular disorders. Finally, we highlight the key aspects and limitations of massively parallel sequencing that a neurologist considering this test needs to know in order to interpret the results of the test and to deal with other issues concerning the test.