Proper genomic profiling of (BRCA1-mutated) basal-like breast carcinomas requires prior removal of tumor infiltrating lymphocytes

BRCA1-mutated breast carcinomas may have distinct biological features, suggesting the involvement of specific oncogenic pathways in tumor development. The identification of genomic aberrations characteristic for BRCA1-mutated breast carcinomas could lead to a better understanding of BRCA1-associated oncogenic events and could prove valuable in clinical testing for BRCA1-involvement in patients. Methods: For this purpose, genomic and gene expression profiles of basal-like BRCA1-mutated breast tumors (n=27) were compared with basal-like familial BRCAX (non-. BRCA1/. 2/. CHEK2*1100delC) tumors (n=14) in a familial cohort of 120 breast carcinomas. Results: Genome wide copy number profiles of the BRCA1-mutated breast carcinomas in our data appeared heterogeneous. Gene expression analyses identifi

Next-generation sequencing-based genome diagnostics across clinical genetics centers: Implementation choices and their effects

Implementation of next-generation DNA sequencing (NGS) technology into routine diagnostic genome care requires strategic choices. Instead of theoretical discussions on the consequences of such choices, we compared NGS-based diagnostic practices in eight clinical genetic centers in the Netherlands, based on genetic testing of nine pre-selected patients with cardiomyopathy. We highlight critical implementation choices, including the specific contributions of laboratory and medical specialists, bioinformaticians and researchers to diagnostic genome care, and how these affect interpretation and reporting of variants. Reported pathogenic mutations were consistent for all but one patient. Of the two centers that were inconsistent in their diagnosis, one reported to have found 'no causal variant', thereby underdiagnosing this patient. The other provided an alternative diagnosis, identifying another variant as causal than the other centers. Ethical and legal analysis showed that informed consent procedures in all centers were generally adequate for diagnostic NGS applications that target a limited set of genes, but not for exome- and genome-based diagnosis. We propose changes to further improve and align these procedures, taking into account the blurring boundary between diagnostics and research, and specific counseling options for exome- and genome-based diagnostics. We conclude that alternative diagnoses may infer a certain level of 'greediness' to come to a positive diagnosis in interpreting sequencing results. Moreover, there is an increasing interdependence of clinic, diagnostics and research departments for comprehensive diagnostic genome care. Therefore, we invite clinical geneticists, physicians, researchers, bioinformatics experts and patients to reconsider their role and position in future diagnostic genome care

Evidence for SMAD3 as a modifier of breast cancer risk in BRCA2 mutation carriers

Abstract Introduction Current attempts to identify genetic modifiers of BRCA1 and BRCA2 associated risk have focused on a candidate gene approach, based on knowledge of gene functions, or the development of large genome-wide association studies. In this study, we evaluated 24 SNPs tagged to 14 candidate genes derived through a novel approach that analysed gene expression differences to prioritise candidate modifier genes for association studies. Methods We successfully genotyped 24 SNPs in a cohort of up to 4,724 BRCA1 and 2,693 BRCA2 female mutation carriers from 15 study groups and assessed whether these variants were associated with risk of breast cancer in BRCA1 and BRCA2 mutation carriers. Results SNPs in five of the 14 candidate genes showed evidence of association with breast cancer risk for BRCA1 or BRCA2 carriers (P < 0.05). Notably, the minor alleles of two SNPs (rs7166081 and rs3825977) in high linkage disequilibrium (r 2 = 0.77), located at the SMAD3 locus (15q22), were each associated with increased breast cancer risk for BRCA2 mutation carriers (relative risk = 1.25, 95% confidence interval = 1.07 to 1.45, P trend = 0.004; and relative risk = 1.20, 95% confidence interval = 1.03 to 1.40, P trend = 0.018). Conclusions This study provides evidence that the SMAD3 gene, which encodes a key regulatory protein in the transforming growth factor beta signalling pathway and is known to interact directly with BRCA2, may contribute to increased risk of breast cancer in BRCA2 mutation carriers. This finding suggests that genes with expression associated with BRCA1 and BRCA2 mutation status are enriched for the presence of common genetic modifiers of breast cancer risk in these populations

Knowledge, attitudes and practices of local people on Siberut Island (West-Sumatra, Indonesia) towards primate hunting and conservation

The Mentawai Archipelago (West-Sumatra, Indonesia) harbours a wealth of endemic animals and plants including six unique primate species, all threatened by habitat loss and hunting. Although hunting is known to be widespread, little systematic work has been carried out to examine its scale and impact on Mentawai´s primate populations. Here we report an island-wide survey carried out on Siberut, the archipelago’s largest island, to assess hunting behaviour with respect to the four locally-occurring primate species, as well as the attitudes of indigenous inhabitants to resource utilization. Face-to-face interviews were conducted in mid-2012 with 390 respondents from 50 villages using a structured questionnaire. Overall, ca. one quarter of the respondents (24%) are still active hunters, generally targeting Simias concolor (77%), Macaca siberu (71%) and Presbytis siberu (68%); Hylobates klossii is rarely hunted (3%). Mostly, a single animal is captured per hunt, with average numbers per three months ranging from 1.9-2.3 individuals (for S. concolor, M. siberu and P. siberu). We found that in many aspects our data did not differ between the protected area (Siberut National Park) and the rest of the island, although hunting was significantly more prevalent within the protected area’s boundaries. Our approximation of annual offtake leads us to conclude that no less than 4,800 primates are taken every year (min. 6.4 % of the population). We provide recommendations on how to reduce hunting as a driver for population decline.</a

Socialising adolescent volunteering : How important are parents and friends? Age dependent effects of parents and friends on adolescents' volunteering behaviours

This study examined the relative importance of best friend's and parents' volunteering and civic family orientation (combined with open family communication) in adolescent volunteering, and the moderating effect of age. Results, involving 698 adolescents (M age. = 15.19; SD= 1.43), revealed that adolescents were more likely to volunteer when their best friend and parents volunteered, and volunteered more frequently when their family had a stronger civic orientation combined with more open family communication. Clear age differences were found: when adolescents get older, friends become more important for whether they volunteer, and the family's civic orientation becomes important for their volunteering frequency. An implication of these findings may be that, depending on adolescents' age and the aspect of volunteering, interventions may focus on targeting parents' or friend's civic behaviour to stimulate adolescent volunteering

Socialising adolescent volunteering: How important are parents and friends? Age dependent effects of parents and friends on adolescents' volunteering behaviours

This study examined the relative importance of best friend's and parents' volunteering and civic family orientation (combined with open family communication) in adolescent volunteering, and the moderating effect of age. Results, involving 698 adolescents (M age. = 15.19; SD= 1.43), revealed that adolescents were more likely to volunteer when their best friend and parents volunteered, and volunteered more frequently when their family had a stronger civic orientation combined with more open family communication. Clear age differences were found: when adolescents get older, friends become more important for whether they volunteer, and the family's civic orientation becomes important for their volunteering frequency. An implication of these findings may be that, depending on adolescents' age and the aspect of volunteering, interventions may focus on targeting parents' or friend's civic behaviour to stimulate adolescent volunteering

Operational experience of the Dutch helicopter emergency medical services (HEMS) during the initial phase of the COVID-19 pandemic: jeopardy on the prehospital care system?

Purpose: The SARS-CoV-2 virus has disrupted global and local medical supply chains. To combat the spread of the virus and prevent an uncontrolled outbreak with limited resources, national lockdown protocols have taken effect in the Netherlands since March 13th, 2020. The aim of this study was to describe the incidence, type and characteristics of HEMS and HEMS-ambulance ‘Lifeliner 1’ dispatches during the initial phase of the COVID-19 pandemic compared to the same period one year prior. Methods: A retrospective review of all HEMS and HEMS-ambulance ‘Lifeliner 1’ dispatches was performed from the start of Dutch nationwide lockdown orders from March 13th until May 13th, 2020 and the corresponding period one year prior. Dispatch-, operational-, patient-, injury-, and on-site treatment characteristics were extracted for analysis. In addition, the rate of COVID-19 positively tested HEMS personnel and the time physicians were unable to take call was described. Results: During the initial phase of the COVID-19 pandemic, the HEMS and HEMS-ambulance was requested in 528 cases. One year prior, a total of 620 requests were received. The HEMS (helicopter and ambulance) was cancelled after deployment in 56.4% of the COVID-19 cohort and 50.7% of the historical cohort (P = 0.05). Incident location type did not differ between the two cohorts, specifically, there was no significant difference in the number of injuries that occurred at home in pandemic versus non-pandemic circumstances. Besides a decrease in the number of falls, the distribution of mechanisms of injury remained similar during the COVID-19 study period. There was no difference in self-inflicted injuries observed. Prehospital interventions remained similar during the COVID-19 pandemic compared to one year prior. Specifically, prehospital intubation did not differ between the two cohorts. The rate of COVID-19 positively tested HEMS personnel was 23.1%. Physicians who tested positive were unable to take call for a mean of 25 days (range 8–53). Conclusion: A decrease in the number of deployments and increase in the number of cancelled missions was observed during the COVID-19 study period. No major differences in operational- and injury characteristics were found for HEMS and HEMS-ambulance dispatches between the initial phase of the COVID-19 pandemic in the Netherlands and the same period one year prior. These findings highlight the importance of continued operability of the HEMS, even during pandemic circumstances. Level of evidence: III, retrospective comparative study

Surfactant-free colloidal particles with specific binding affinity

Colloidal particles with specific binding affinity are essential for in vivo and in vitro biosensing, targeted drug delivery, and micrometer-scale self-assembly. Key to these techniques are surface functionalizations that provide high affinities to specific target molecules. For stabilization in physiological environments, current particle coating methods rely on adsorbed surfactants. However, spontaneous desorption of these surfactants typically has an undesirable influence on lipid membranes. To address this issue and create particles for targeting molecules in lipid membranes, we present here a surfactant-free coating method that combines high binding affinity with stability at physiological conditions. After activating charge-stabilized polystyrene microparticles with EDC/Sulfo-NHS, we first coat the particles with a specific protein and subsequently covalently attach a dense layer of poly(ethyelene) glycol. This polymer layer provides colloidal stability at physiological conditions as well as antiadhesive properties, while the protein coating provides the specific affinity to the targeted molecule. We show that NeutrAvidin-functionalized particles bind specifically to biotinylated membranes and that Concanavalin A-functionalized particles bind specifically to the glycocortex of Dictyostelium discoideum cells. The affinity of the particles changes with protein density, which can be tuned during the coating procedure. The generic and surfactant-free coating method reported here transfers the high affinity and specificity of a protein onto colloidal polystyrene microparticles