Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Experimental study of Bluetooth, ZigBee and IEEE 802.15.4 technologies on board high-speed trains

This paper studies the feasibility of using low-power wireless technologies such as Bluetooth, IEEE 802.15.4 and ZigBee in high-speed railway scenarios that involve bidirectional ground-to-train communication. The presented results have been obtained through experimental tests conducted at the Madrid-Barcelona high-speed rail line. A multiplatform communication system has been installed in a high-speed train, circulating at velocities up to 300 km/h, whereas autonomous devices have been disseminated along of the railway path to communicate with the onboard devices. The conclusions drawn from this work will be used as guidelines for the future implementation of autonomous communication platforms for high-speed rail connectivity.Peer ReviewedPostprint (published version

Experimental study of bluetooth, ZigBee and IEEE 802.15.4 technologies on board high-speed trains

This paper studies the feasibility of using low-power wireless technologies such as Bluetooth, IEEE 802.15.4 and ZigBee in high-speed railway scenarios that involve bidirectional ground-to-train communication. The presented results have been obtained through experimental tests conducted at the Madrid- Barcelona high-speed rail line. A multiplatform communication system has been installed in a high-speed train, circulating at velocities up to 300 km/h, whereas autonomous devices have been disseminated along of the railway path to communicate with the onboard devices. The conclusions drawn from this work will be used as guidelines for the future implementation of autonomous communication platforms for high-speed rail connectivity.Peer Reviewe

Experimental study of bluetooth, ZigBee and IEEE 802.15.4 technologies on board high-speed trains

This paper studies the feasibility of using low-power wireless technologies such as Bluetooth, IEEE 802.15.4 and ZigBee in high-speed railway scenarios that involve bidirectional ground-to-train communication. The presented results have been obtained through experimental tests conducted at the Madrid- Barcelona high-speed rail line. A multiplatform communication system has been installed in a high-speed train, circulating at velocities up to 300 km/h, whereas autonomous devices have been disseminated along of the railway path to communicate with the onboard devices. The conclusions drawn from this work will be used as guidelines for the future implementation of autonomous communication platforms for high-speed rail connectivity.Peer Reviewe

Uracil/tegafur plus oral calcium folinate in advanced breast cancer

Uracil and tegafur (in a molar ratio of 4:1 [UFT]) has proven activity against breast cancer and is delivered in an easy-to-administer oral formulation. Orzel, which combines UFT with the oral biomodulator, calcium folinate, may provide even greater antitumor efficacy against breast cancer. Here, we describe the preliminary results of this phase H trial investigating the feasibility of 250 mg/m2/day of UFT plus 45 mg/day of oral calcium folinate administered to highly pretreated patients with advanced breast cancer. The results indicate a highly tolerable regimen and an overall response rate of 27.8% in a group of poor-prognosis patients. These findings warrant continued investigation.Fil: Richardet, Eduardo Arnoldo. Universidad Católica de Córdoba. Facultad de Ciencias de la Salud; ArgentinaFil: Pedraza, Cecilia. Universidad Católica de Córdoba. Facultad de Ciencias de la Salud; ArgentinaFil: Mickiewicz, Elizabeth. Universidad Católica de Córdoba. Facultad de Ciencias de la Salud; ArgentinaFil: Lerzo, Guillermo. Universidad Católica de Córdoba. Facultad de Ciencias de la Salud; ArgentinaFil: Bonamasa, Miguel. Universidad Católica de Córdoba. Facultad de Ciencias de la Salud; ArgentinaFil: Coppola, Federico. Universidad Católica de Córdoba. Facultad de Ciencias de la Salud; ArgentinaFil: Elli, Alicia. Universidad Católica de Córdoba. Facultad de Ciencias de la Salud; ArgentinaFil: Uranga, Graciela. Universidad Católica de Córdoba. Facultad de Ciencias de la Salud; ArgentinaFil: Jovtis, Silvia. Universidad Católica de Córdoba. Facultad de Ciencias de la Salud; ArgentinaFil: Bruno, Mario. Universidad Católica de Córdoba. Facultad de Ciencias de la Salud; ArgentinaFil: Ventriglia, Mónica. Universidad Católica de Córdoba. Facultad de Ciencias de la Salud; ArgentinaFil: Cuevas, María Andrea. Universidad Católica de Córdoba. Facultad de Ciencias de la Salud; Argentin

Engaging Researchers with Data Management

Effective Research Data Management (RDM) is a key component of research integrity and reproducible research, and its importance is increasingly emphasised by funding bodies, governments, and research institutions around the world. However, many researchers are unfamiliar with RDM best practices, and research support staff are faced with the diffi cult task of delivering support to researchers across diff erent disciplines and career stages. What strategies can institutions use to solve these problems? Engaging Researchers with Data Management is an invaluable collection of 24 case studies, drawn from institutions across the globe, that demonstrate clearly and practically how to engage the research community with RDM. These case studies together illustrate the variety of innovative strategies research institutions have developed to engage with their researchers about managing research data. Each study is presented concisely and clearly, highlighting the essential ingredients that led to its success and challenges encountered along the way. By interviewing key staff about their experiences and the organisational context, the authors of this book have created an essential resource for organisations looking to increase engagement with their research communities. This handbook is a collaboration by research institutions, for research institutions. It aims not only to inspire and engage, but also to help drive cultural change towards betier data management. It has been writien for anyone interested in RDM, or simply, good research practice

Sex differences in oncogenic mutational processes

Funder: Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology); doi: https://doi.org/10.13039/501100002790Funder: Genome Canada (Génome Canada); doi: https://doi.org/10.13039/100008762Funder: Canada Foundation for Innovation (Fondation canadienne pour l'innovation); doi: https://doi.org/10.13039/501100000196Funder: Terry Fox Research Institute (Institut de Recherche Terry Fox); doi: https://doi.org/10.13039/501100004376Abstract: Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research

Sex differences in oncogenic mutational processes

Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Peer reviewe

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that -80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAFPeer reviewe