Pathway analysis tools and toxicogenomics reference databases for risk assessment

The pharmaceutical industry has begun to leverage a range of new technologies (proteomics, pharmacogenomics, metabolomics and molecular toxicology [e.g., toxicogenomics]) and analysis tools that are becoming increasingly integrated in the area of drug discovery and development. The approach of analyzing the vast amount of toxicogenomics data generated using molecular pathway and networks analysis tools in combination with analysis of reference data will be the main focus of this review. We will demonstrate how this combined approach can increase the understanding of the molecular mechanisms that lead to chemical-induced toxicity and application of this knowledge to compound risk assessment. We will provide an example of the insights achieved through a molecular toxicology analysis based on the well-known hepatotoxicant lipopolysaccharide to illustrate the utility of these new tools in the analysis of complex data sets, both in vivo and in vitro. The ultimate objective is a better lead selection process that improves the chances for success across the different stages of drug discovery and development.     

Use of risk-reducing surgeries in a prospective cohort of 1,499 BRCA1 and BRCA2 mutation carriers

Inherited mutations in BRCA1 or BRCA2 (BRCA1/2) confer very high risk of breast and ovarian cancers. Genetic testing and counseling can reduce risk and death from these cancers if appropriate preventive strategies are applied, including risk-reducing salpingo-oophorectomy (RRSO) or risk-reducing mastectomy (RRM). However, some women who might benefit from these interventions do not take full advantage of them. We evaluated RRSO and RRM use in a prospective cohort of 1,499 women with inherited BRCA1/2 mutations from 20 centers who enrolled in the study without prior cancer or RRSO or RRM and were followed forward for the occurrence of these events. We estimated the age-specific usage of RRSO/RRM in this cohort using Kaplan–Meier analyses. Use of RRSO was 45 % for BRCA1 and 34 % for BRCA2 by age 40, and 86 % for BRCA1 and 71 % for BRCA2 by age 50. RRM usage was estimated to be 46 % by age 70 in both BRCA1 and BRCA2 carriers. BRCA1 mutation carriers underwent RRSO more frequently than BRCA2 mutation carriers overall, but the uptake of RRSO in BRCA2 was similar after mutation testing and in women born since 1960. RRM uptake was similar for both BRCA1 and BRCA2. Childbearing influenced the use of RRSO and RRM in both BRCA1 and BRCA2. Uptake of RRSO is high, but some women are still diagnosed with ovarian cancer before undergoing RRSO. This suggests that research is needed to understand the optimal timing of RRSO to maximize risk reduction and limit potential adverse consequences of RRSO.     

Entrustable professional activities and facets of competence in a simulated workplace-based assessment for advanced medical students

Abstract

Background: Competence-based assessment formats in medical education usually focus on individual facets of competence (FOCs). The concept of ‘Entrustable Professional Activities’ (EPAs) encompasses supervisors’ decisions on which level of supervision a trainee requires to perform a professional activity including several FOCs. How the different FOCs as perceived by clinician raters contribute to entrustment decisions is yet unclear.

Objective: How do FOC perceptions relate to entrustment-decisions?

Methods: Sixty-seven advanced medical students participated in an assessment simulating the first day of a resident physician. Participants were rated by supervisors for seven FOCs and twelve EPAs.

Results: There was a positive correlation between FOC and EPA scores. Each EPA displayed a different correlation pattern with FOC ratings.

Discussion: For most EPAs high levels of entrustment were associated with high ratings for selected FOCs. The results are in alignment with the assumption that each EPA encompasses a different set of FOCs.

Conclusions: In our simulated workplace-based assessment, entrustment decisions for EPAs reflect the FOCs observed in a trainee. Thus, assessment of FOCs alongside with EPA ratings could add to the understanding of factors contributing to entrustment decisions.     

Fine-scale human genetic structure in Western France

The difficulties arising from association analysis with rare variants underline the importance of suitable reference population cohorts, which integrate detailed spatial information. We analyzed a sample of 1684 individuals from Western France, who were genotyped at genome-wide level, from two cohorts D.E.S.I.R and CavsGen. We found that fine-scale population structure occurs at the scale of Western France, with distinct admixture proportions for individuals originating from the Brittany Region and the Vendée Department. Genetic differentiation increases with distance at a high rate in these two parts of Northwestern France and linkage disequilibrium is higher in Brittany suggesting a lower effective population size. When looking for genomic regions informative about Breton origin, we found two prominent associated regions that include the lactase region and the HLA complex. For both the lactase and the HLA regions, there is a low differentiation between Bretons and Irish, and this is also found at the genome-wide level. At a more refined scale, and within the Pays de la Loire Region, we also found evidence of fine-scale population structure, although principal component analysis showed that individuals from different departments cannot be confidently discriminated. Because of the evidence for fine-scale genetic structure in Western France, we anticipate that rare and geographically localized variants will be identified in future full-sequence analyses.