The sequencing and interpretation of the genome obtained from a Serbian individual

Recent genetic studies and whole-genome sequencing projects have greatly improved our understanding of human variation and clinically actionable genetic information. Smaller ethnic populations, however, remain underrepresented in both individual and large-scale sequencing efforts and hence present an opportunity to discover new variants of biomedical and demographic significance. This report describes the sequencing and analysis of a genome obtained from an individual of Serbian origin, introducing tens of thousands of previously unknown variants to the currently available pool. Ancestry analysis places this individual in close proximity of the Central and Eastern European populations; i.e., closest to Croatian, Bulgarian and Hungarian individuals and, in terms of other Europeans, furthest from Ashkenazi Jewish, Spanish, Sicilian, and Baltic individuals. Our analysis confirmed gene flow between Neanderthal and ancestral pan-European populations, with similar contributions to the Serbian genome as those observed in other European groups. Finally, to assess the burden of potentially disease-causing/clinically relevant variation in the sequenced genome, we utilized manually curated genotype-phenotype association databases and variant-effect predictors. We identified several variants that have previously been associated with severe early-onset disease that is not evident in the proband, as well as variants that could yet prove to be clinically relevant to the proband over the next decades. The presence of numerous private and low-frequency variants along with the observed and predicted disease-causing mutations in this genome exemplify some of the global challenges of genome interpretation, especially in the context of understudied ethnic groups.Comment: 18 pages, 2 figure

Position Statement on the Diagnosis, Treatment, and Response Evaluation to Systemic Therapies of Advanced Neuroendocrine Tumors, With a Special Focus on Radioligand Therapy

Neoadjuvant therapy; Peptide receptor radionuclide therapy; ProgressionTeràpia neoadjuvant; Teràpia amb radionúclids del receptor de pèptids; ProgressióTerapia neoadyuvante; Terapia con radionúclidos del receptor de péptidos; ProgresiónBackground The aim of this study was to provide a guidance for the management of neuroendocrine tumors (NETs) in clinical practice. Material and Methods Nominal group and Delphi techniques were used. A steering committee of 8 experts reviewed the current management of NETs, identified controversies and gaps, critically analyzed the available evidence, and formulated several guiding statements for clinicians. Subsequently, a panel of 26 experts, was selected to test agreement with the statements through 2 Delphi rounds. Items were scored on a 4-point Likert scale from 1 = totally agree to 4 = totally disagree. The agreement was considered if ≥75% of answers pertained to Categories 1 and 2 (consensus with the agreement) or Categories 3 and 4 (consensus with the disagreement). Results Overall, 132 statements were proposed, which incorporated the following areas: (1) overarching principles; (2) progression and treatment response criteria; (3) advanced gastro-enteric NETs; (4) advanced pancreatic NETs; (5) advanced NETs in other locations; (6) re-treatment with radioligand therapy (RLT); (7) neoadjuvant therapy. After 2 Delphi rounds, only 4 statements lacked a clear consensus. RLT was not only recommended in the sequencing of different NETs but also as neoadjuvant treatment, while several indications for retreatment with RLT were also established. Conclusion This document sought to pull together the experts’ attitudes when dealing with different clinical scenarios of patients suffering from NETs, with RLT having a specific role where evidence-based data are limited.This project was funded by Advanced Accelerator Applications, a Novartis company

Review of mastectomy in the department of gynecology at the Treichville teaching hospital, Abidjan-Cote d’Ivoire

Background: Mastectomy plays a key role in the management of breast cancer in our regions of sub-Saharan Africa. Because the advanced forms represent the essential stages of the diagnosis and some therapeutic means remain unavailable. Objective of this study was to report the experience of the practice of mastectomy in the treatment of breast cancer in our service.Methods: This is a retrospective and prospective, descriptive study conducted from January 1, 2013 to May 31, 2017 (age 05) at the University Hospital of Treichville involving 56 breast cancer patients who had undergone a mastectomy.Results: The frequency of the mastectomy was 28.5% and the average age of our patients was 48 years old. The majority of patients had an average socio-economic level (66%). 85.6% of our cancers discovered at advanced stages (T3 and T4). Adenocarcinoma accounted for 96% and infiltrating ductal carcinoma 82% of adenocarcinoma.Patey mastectomy associated with axillary dissection was performed in 96.4% and simple mastectomy in 3.5%. The results of axillary dissection reported lymph node invasion in 38 patients; With an average number of lymph nodes taken from 6.1 and an average number of ganglia affected is 3. Neoadjuvant chemotherapy was administered in 96.4% and adjuvant chemotherapy in 91%. Radiotherapy was performed in 34%. Complications were dominated by lymphoceles in 34% of cases. The 5-year survival of patients operating in the service is 37.8%.Conclusions: Mastectomy is at the forefront of breast cancer surgery in our service. She is supervised by chemotherapy. Radiotherapy remains inaccessible for most patients. Early detection would lead to conservative treatment and a reduction in the postoperative complication rate

Developmental pathways associated with cancer metastasis: Notch, Wnt, and Hedgehog

Master developmental pathways, such as Notch, Wnt, and Hedgehog, are signaling systems that control proliferation, cell death, motility, migration, and stemness. These systems are not only commonly activated in many solid tumors, where they drive or contribute to cancer initiation, but also in primary and metastatic tumor development. The reactivation of developmental pathways in cancer stroma favors the development of cancer stem cells and allows their maintenance, indicating these signaling pathways as particularly attractive targets for efficient anticancer therapies, especially in advanced primary tumors and metastatic cancers. Metastasis is the worst feature of cancer development. This feature results from a cascade of events emerging from the hijacking of epithelial-mesenchymal transition, angiogenesis, migration, and invasion by transforming cells and is associated with poor survival, drug resistance, and tumor relapse. In the present review, we summarize and discuss experimental data suggesting pivotal roles for developmental pathways in cancer development and metastasis, considering the therapeutic potential. Emerging targeted antimetastatic therapies based on Notch, Wnt, and Hedgehog pathways are also discussed

Virtual Field Studies: Conducting Studies on Public Displays in Virtual Reality

Field studies on public displays can be difficult, expensive, and time-consuming. We investigate the feasibility of using virtual reality (VR) as a test-bed to evaluate deployments of public displays. Specifically, we investigate whether results from virtual field studies, conducted in a virtual public space, would match the results from a corresponding real-world setting. We report on two empirical user studies where we compared audience behavior around a virtual public display in the virtual world to audience behavior around a real public display. We found that virtual field studies can be a powerful research tool, as in both studies we observed largely similar behavior between the settings. We discuss the opportunities, challenges, and limitations of using virtual reality to conduct field studies, and provide lessons learned from our work that can help researchers decide whether to employ VR in their research and what factors to account for if doing so

Salvage carbon dioxide transoral laser microsurgery for laryngeal cancer after (chemo)radiotherapy : a European Laryngological Society consensus statement

Purpose To provide expert opinion and consensus on salvage carbon dioxide transoral laser microsurgery (CO2 TOLMS) for recurrent laryngeal squamous cell carcinoma (LSCC) after (chemo)radiotherapy [(C)RT]. Methods Expert members of the European Laryngological Society (ELS) Cancer and Dysplasia Committee were selected to create a dedicated panel on salvage CO2 TOLMS for LSCC. A series of statements regarding the critical aspects of decision-making were drafted, circulated, and modified or excluded in accordance with the Delphi process. Results The expert panel reached full consensus on 19 statements through a total of three sequential evaluation rounds. These statements were focused on different aspects of salvage CO2 TOLMS, with particular attention on preoperative diagnostic work-up, treatment indications, postoperative management, complications, functional outcomes, and follow-up. Conclusion Management of recurrent LSCC after (C)RT is challenging and is based on the need to find a balance between oncologic and functional outcomes. Salvage CO2 TOLMS is a minimally invasive approach that can be applied to selected patients with strict and careful indications. Herein, a series of statements based on an ELS expert consensus aimed at guiding the main aspects of CO2 TOLMS for LSCC in the salvage setting is presented.Peer reviewe

Operando Laboratory-based Multi-edge X-ray Absorption Near-Edge Spectroscopy of Solid Catalysts

Laboratory-based X-ray absorption spectroscopy (XAS) and especially X-ray absorption near-edge structure (XANES) offers new opportunities in catalyst characterization and presents not only an alternative, but also a complementary approach to precious beamtime at synchrotron facilities. We successfully designed a laboratory-based setup for performing operando , quasi-simultaneous XANES analysis at multiple K edges, more specifically, operando XANES of mono-, bi-, and trimetallic CO 2 hydrogenation catalysts containing Ni, Fe, and Cu. Detailed operando XANES studies of the multi-element solid catalysts revealed metal-dependent differences in the reducibility and re-oxidation behavior and their influence on the catalytic performance in CO 2 hydrogenation. The applicability of operando laboratory-based XANES at multiple K edges paves the way for advanced multi-element catalyst characterization complementing detailed studies at synchrotron facilities

Cell free circulating tumor DNA in cerebrospinal fluid detects and monitors central nervous system involvement of B-cell lymphomas

The levels of cell free circulating tumor DNA (ctDNA) in plasma correlate with treatment response and outcome in systemic lymphomas. Notably, in brain tumors, the levels of ctDNA in the cerebrospinal fluid (CSF) are higher than in plasma. Nevertheless, their role in central nervous system (CNS) lymphomas remains elusive. We evaluated the CSF and plasma from 19 patients: 6 restricted CNS lymphomas, 1 systemic and CNS lymphoma, and 12 systemic lymphomas. We performed whole exome sequencing or targeted sequencing to identify somatic mutations of the primary tumor, then variant-specific droplet digital polymerase chain reaction was designed for each mutation. At time of enrollment, we found ctDNA in the CSF of all patients with restricted CNS lymphoma but not in patients with systemic lymphoma without CNS involvement. Conversely, plasma ctDNA was detected in only 2 out of 6 patients with restricted CNS lymphoma with lower variant allele frequencies than CSF ctDNA. Moreover, we detected CSF ctDNA in one patient with CNS lymphoma in complete remission and in one patient with systemic lymphoma, 3 and 8 months before CNS relapse was confirmed, indicating that CSF ctDNA might detect CNS relapse earlier than conventional methods. Finally, in two cases with CNS lymphoma, CSF ctDNA was still detected after treatment even though no tumoral cells were observed by flow cytometry (FC), indicating that CSF ctDNA detected residual disease better than FC. In conclusion, CSF ctDNA can detect CNS lesions better than plasma ctDNA and FC. In addition, CSF ctDNA predicted CNS relapse in CNS and systemic lymphomas

The sequencing and interpretation of the genome obtained from a Serbian individual

Recent genetic studies and whole-genome sequencing projects have greatly improved our understanding of human variation and clinically actionable genetic information. Smaller ethnic populations, however, remain underrepresented in both individual and large-scale sequencing efforts and hence present an opportunity to discover new variants of biomedical and demographic significance. This report describes the sequencing and analysis of a genome obtained from an individual of Serbian origin, introducing tens of thousands of previously unknown variants to the currently available pool. Ancestry analysis places this individual in close proximity to Central and Eastern European populations; i.e., closest to Croatian, Bulgarian and Hungarian individuals and, in terms of other Europeans, furthest from Ashkenazi Jewish, Spanish, Sicilian and Baltic individuals. Our analysis confirmed gene flow between Neanderthal and ancestral pan-European populations, with similar contributions to the Serbian genome as those observed in other European groups. Finally, to assess the burden of potentially disease-causing/clinically relevant variation in the sequenced genome, we utilized manually curated genotype-phenotype association databases and variant-effect predictors. We identified several variants that have previously been associated with severe early-onset disease that is not evident in the proband, as well as putatively impactful variants that could yet prove to be clinically relevant to the proband over the next decades. The presence of numerous private and low-frequency variants, along with the observed and predicted disease-causing mutations in this genome, exemplify some of the global challenges of genome interpretation, especially in the context of under-studied ethnic groups

Mechanistic insight into acrylate metabolism and detoxification in marine dimethylsulfoniopropionate-catabolizing bacteria

Dimethylsulfoniopropionate (DMSP) cleavage, yielding dimethyl sulfide (DMS) and acrylate, provides vital carbon sources to marine bacteria, is a key component of the global sulfur cycle and effects atmospheric chemistry and potentially climate. Acrylate and its metabolite acryloyl-CoA are toxic if allowed to accumulate within cells. Thus, organisms cleaving DMSP require effective systems for both the utilization and detoxification of acrylate. Here, we examine the mechanism of acrylate utilization and detoxification in Roseobacters. We propose propionate-CoA ligase (PrpE) and acryloyl-CoA reductase (AcuI) as the key enzymes involved and through structural and mutagenesis analyses, provide explanations of their catalytic mechanisms. In most cases, DMSP lyases and DMSP demethylases (DmdAs) have low substrate affinities, but AcuIs have very high substrate affinities, suggesting that an effective detoxification system for acylate catabolism exists in DMSP-catabolizing Roseobacters. This study provides insight on acrylate metabolism and detoxification and a possible explanation for the high Km values that have been noted for some DMSP lyases. Since acrylate/acryloyl-CoA is probably produced by other metabolism, and AcuI and PrpE are conserved in many organisms across all domains of life, the detoxification system is likely relevant to many metabolic processes and environments beyond DMSP catabolism