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BackgroundNeurotrophic tyrosine receptor kinase (NTRK) gene fusions are oncogenic drivers in various tumor types. While NTRK gene fusions are predictive of benefit from tropomyosin receptor kinase inhibitors regardless of tumor type, the prognostic significance of NTRK gene fusions in a pan-tumor setting remains unclear.ObjectiveThis study evaluated the characteristics and prognosis of tropomyosin receptor kinase fusion cancer in the real-world setting.Patients and methodsThis retrospective study used a de-identified clinico-genomic database and included patients with cancer who had comprehensive genomic profiling between January 2011 and July 2018. Patients were classified as having cancer with NTRK gene fusions or NTRK wild-type genes. Patients were matched with a 1:4 ratio (NTRK fusion:NTRK wild-type) using the Mahalanobis distance method on demographic and clinical characteristics, including age and Eastern Cooperative Oncology Group performance status. Descriptive analysis of clinical and molecular characteristics was conducted. Kaplan-Meier estimator and Cox regression were used for overall survival analysis.ResultsMedian overall survival was 12.5 months (95% confidence interval 9.5-not estimable) and 16.5 months (95% confidence interval 12.5-22.5) in the NTRK gene fusion (n = 27) and NTRK wild-type cohorts (n = 107), respectively (hazard ratio 1.44; 95% confidence interval 0.61-3.37; p = 0.648). Co-occurrence of select targetable biomarkers including ALK, BRAF, ERBB2, EGFR, ROS1, and KRAS was lower in cancers with NTRK gene fusions than in NTRK wild-type cancers.ConclusionsAlthough the hazard ratio for overall survival suggested a higher risk of death for patients with NTRK gene fusions, the difference was not statistically significant. Co-occurrence of NTRK gene fusions and other actionable biomarkers was uncommon.

Study questionCan whole exome sequencing (WES) and in vitro validation studies be used to find the causative genetic etiology in a patient with primary ovarian failure and infertility?Summary answerA novel follicle-stimulating hormone receptor (FSHR) mutation was found by WES and shown, via in vitro flow cytometry studies, to affect membrane trafficking.What is known alreadyWES may diagnose up to 25-35% of patients with suspected disorders of sex development (DSD). FSHR mutations are an extremely rare cause of 46, XX gonadal dysgenesis with primary amenorrhea due to hypergonadotropic ovarian failure.Study design, size, durationA WES study was followed by flow cytometry studies of mutant protein function.Participants/materials, setting, methodsThe study subjects were two Turkish sisters with hypergonadotropic primary amenorrhea, their parents and two unaffected sisters. The affected siblings and both parents were sequenced (trio-WES). Transient transfection of HEK 293T cells was performed with a vector containing wild-type FSHR as well as the novel FSHR variant that was discovered by WES. Cellular localization of FSHR protein as well as FSH-stimulated cyclic AMP (cAMP) production was evaluated using flow cytometry.Main results and the role of chanceBoth affected sisters were homozygous for a previously unreported missense mutation (c.1222G>T, p.Asp408Tyr) in the second transmembrane domain of FSHR. Modeling predicted disrupted secondary structure. Flow cytometry demonstrated an average of 48% reduction in cell-surface signal detection (P < 0.01). The mean fluorescent signal for cAMP (second messenger of FSHR), stimulated by FSH, was reduced by 50% in the mutant-transfected cells (P < 0.01).Limitations, reasons for cautionThis is an in vitro validation. All novel purported genetic variants can be clinically reported only as 'variants of uncertain significance' until more patients with a similar phenotype are discovered with the same variant.Wider implications of the findingsWe report the first WES-discovered FSHR mutation, validated by quantitative flow cytometry. WES is a valuable tool for diagnosis of rare genetic diseases, and flow cytometry allows for quantitative characterization of purported variants. WES-assisted diagnosis allows for treatments aimed at the underlying molecular etiology of disease. Future studies should focus on pharmacological and assisted reproductive treatments aimed at the disrupted FSHR, so that patients with FSH resistance can be treated by personalized medicine.Study funding/competing interestsE.V. is partially funded by the DSD Translational Research Network (NICHD 1R01HD068138). M.S.B. is funded by the Neuroendocrinology, Sex Differences and Reproduction training grant (NICHD 5T32HD007228). The authors have no competing interests to disclose.

Premature ovarian failure is a major cause of female infertility. The genetic causes of this disorder remain unknown in most patients. Using whole-exome sequence analysis of a large consanguineous family with inherited premature ovarian failure, we identified a homozygous 1-bp deletion inducing a frameshift mutation in STAG3 on chromosome 7. STAG3 encodes a meiosis-specific subunit of the cohesin ring, which ensures correct sister chromatid cohesion. Female mice devoid of Stag3 are sterile, and their fetal oocytes are arrested at early prophase I, leading to oocyte depletion at 1 week of age.

Blepharophimosis syndrome (BPES) is caused by loss-of-function mutations in the single-exon forkhead transcription factor gene FOXL2 and by genomic rearrangements of the FOXL2 locus. Here, we focus on 92 new intragenic FOXL2 mutations, 34 of which are novel. Specifically, we found 10 nonsense mutations (11%), 13 missense mutations (14%), 40 deletions or insertions leading to a frameshift (43%), and 29 in-frame changes (32%), of which 28 (30%) lead to a polyalanine expansion. This study confirms the existence of two previously described mutational hotspots. Moreover, we gained novel insights in genotype-phenotype correlations, emphasizing the need to interpret genotype-phenotype correlations individually and always in the context of further clinical observations.

The Biomolecular Engineering Commission considers that the knowledge acquired in the last three years has provided significant information in reply to the points raised in its review dated 16 February 2001. The Commission has studied the potential environmental impacts associated with large-scale herbicidetolerantGMoilseed rape crops, making a distinction between direct and indirect impacts. Direct impacts stem from the intrinsic properties of herbicide-tolerant GM oilseed rape crops whereas indirect impacts result from practices associated with the farming of these crops. The Commission considers that, in the absence of the use of the herbicide in question in and outside of farmed land, there is no direct environmental risk (development of invasive crops per se) associated with the presence of a herbicide-tolerance gene in oilseed rape (or related species). Nevertheless, since the interest of these tolerant crops lies in the use of the herbicide in question, indirect effects, to varying extents, have been identified and must be taken into account: the use of the herbicide in question, applied to agricultural fields containing the herbicide-tolerant crop could lead to an increase in oilseed rape volunteer populations in crop rotations; the selective pressure exerted by non-specific herbicides (to which the crops have been rendered tolerant) may be very high in cases of continuous and uncontrolled use of these herbicides, and may result in the persistence of rare events such as the reproduction of fertile interspecies hybrids; the change to the range of herbicides used should be conveyed by more effective weed control and, like any change in farming practices, induce indirect effects on the agri-ecosystem, particularly in terms of changes to weeds and the associated animal life. Accordingly, the Biomolecular Engineering Commission recommends a global approach in terms of the large-scale farming of herbicide-tolerant crops that: accounts for the characteristics of the herbicide and its current and future use; accounts for herbicide-tolerant varieties belonging to other species, liable to be farmed in French agriculture in the short term; targets, if applicable, the selection of crop/herbicide combinations according to the constraints associated with French agriculture; coordinates the evaluations conducted on herbicide-tolerant crops and those conducted on herbicides; implements a biovigilance system and its associated resources whenever herbicide-tolerant crop farming is envisaged. Our report highlights the need for the management of any herbicide-tolerant GM oilseed rape crops. Such a management plan must account for the diverse cropping situations, including crop rotations and farming practices. Management should be based on the prior evaluation of situations encountered, the development of measures commensurate with the risks, and a validation of their efficacy through biovigilance. The Biomolecular Engineering Commission considers that the indirect environmental and agronomic impacts associated with current management practices employed for herbicide-tolerant oilseed rape crops can only be determined, in addition to the knowledge acquired, by continuing ongoing experimental studies initiated. Mathematical and computer models – by formalizing complex scenarios that incorporate the functioning of different oilseed rape populations (farmed, spontaneous, volunteer plants) under specific farming practices – enables the simulation of potential impacts and the identification of suitable management measures. Nevertheless, at the present time, the introduction of more extensive farming than that currently practised, or managed progressive introduction, would make it possible to progress in the study of impacts and develop and validate management procedures enabling the limitation of adverse impacts. In the specific case of imports, the Biomolecular Engineering Commission considers that herbicidetolerant GM oilseed rape seed imports for processing and animal feed does not represent additional risks for the environment compared to other oilseed rape varieties on the market. Due to the very low likelihood of the dispersal of tolerant oilseed rape crops from imported seed, the impact of the herbicides used on communication routes is considered to be negligible in the current context. However, in order to supplement the information available on environmental impacts and avert any changes to the current situation, the Commission recommends that a general monitoring plan be implemented in parallel to the introduction of seeds onto the market. Finally, the Biomolecular Engineering Commission considers that biovigilance systems adapted to the various risks should be in place before any farming of commercial herbicide-tolerant varieties is undertaken. The Biomolecular Engineering Commission considers its analysis to be valid for non-selective herbicidetolerant varieties of oilseed rape obtained both by transgenesis and by means of a technique other than transgenesis.

The allelic variability at six Y-chromosome-specific polymorphisms (YAP, DYS19, DYS389-I, DYS390, DYS391, and DYS392) was used to generate male-specific haplotypes in 333 males representing 12 population samples from the region around the Mediterranean sea. Extreme interindividual variation was observed, as more than 160 distinct Y-chromosome variants could be defined as six-locus haplotypes. Concomitant with this high variability, low levels of population genetic structure were observed. In particular, a 'core' of populations directly facing the north and the east of the Mediterranean basin, from the Middle East to the Italian Peninsula, was found to be genetically undifferentiated. This observation, supported by a reanalysis of Y-specific binary polymorphisms in the same populations, suggests that at least part of the male-specific gene pools of these populations has either a very recent common origin (that could be related with the Neolithic demic diffusion hypothesis), and/or that gene flow has played a significant role in shaping the patterns of genetic variability in this region. In agreement with both hypotheses, we found that the spatial distribution of DYS392 alleles revealed a marked differentiation between the East and the West of the Mediterranean area. Through the analysis of microsatellite variation, the time to the most recent common ancestor (TMRCA) of the YAP+ sublineage 4 has been estimated. The estimations, based on two different data sets, turn out to be quite recent (7,000-11,000 YBP), suggesting that this lineage may have been first introduced into Southern Europe through Neolithic migrations from the Middle East. KEY WORDS Y-chromosome; STRs; Mediterranean basin; Neolithic migrations