University of Nebraska Five-Year Strategy, Revised August 12, 2020

The University of Nebraska Five-Year Strategy: Trust, Predictability, and Positive Outcomes for Nebraskans In February 2020, the newly named president of the University of Nebraska system, Ted Carter, gathered a diverse 28-member team of students, faculty, staff, and administrators to help chart the path forward for Nebraska’s public university. The team’s goal: At a time of great change in higher education, lay out a vision for what the future should look like for the University of Nebraska. Broad themes quickly emerged, including student access and success, excellence in teaching and research, diversity and inclusion, partnerships, and fiscal effectiveness. Then COVID-19 hit, forcing a pause in the team’s work. The ensuing months showed that the initial priorities identified by the team were not only still relevant, but more important than ever in defining the future of higher education. From that early work has emerged a five-year strategy for growth and success across the four-campus University of Nebraska system. In addition to the strategic planning team, Carter engaged alumni and donors, elected leaders, leaders in business and agriculture, the Board of Regents, NU senior leadership, and others in conversations about the University’s future. The resulting strategy is built around several key principles: The value of higher education is clear and growing. Nebraska’s success is tied to that of its University. Students come first. The University of Nebraska should be the best place in the country to be a student, providing high-quality, affordable, accessible education that prioritizes students’ mental and physical health and prepares them for post-graduation success. Our people are our greatest asset. We will invest accordingly. We have a responsibility to make the best use of every dollar Nebraskans entrust to us. Themes of equity and inclusion touch everything we do. We will be a University for everyone—successful only when all voices are heard. Finally, Nebraskans should know what to expect from their University. We must work every day to maintain the trust and confidence of the people of our state

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

University of Nebraska Five-Year Strategy, Revised August 12, 2020

The University of Nebraska Five-Year Strategy: Trust, Predictability, and Positive Outcomes for Nebraskans In February 2020, the newly named president of the University of Nebraska system, Ted Carter, gathered a diverse 28-member team of students, faculty, staff, and administrators to help chart the path forward for Nebraska’s public university. The team’s goal: At a time of great change in higher education, lay out a vision for what the future should look like for the University of Nebraska. Broad themes quickly emerged, including student access and success, excellence in teaching and research, diversity and inclusion, partnerships, and fiscal effectiveness. Then COVID-19 hit, forcing a pause in the team’s work. The ensuing months showed that the initial priorities identified by the team were not only still relevant, but more important than ever in defining the future of higher education. From that early work has emerged a five-year strategy for growth and success across the four-campus University of Nebraska system. In addition to the strategic planning team, Carter engaged alumni and donors, elected leaders, leaders in business and agriculture, the Board of Regents, NU senior leadership, and others in conversations about the University’s future. The resulting strategy is built around several key principles: The value of higher education is clear and growing. Nebraska’s success is tied to that of its University. Students come first. The University of Nebraska should be the best place in the country to be a student, providing high-quality, affordable, accessible education that prioritizes students’ mental and physical health and prepares them for post-graduation success. Our people are our greatest asset. We will invest accordingly. We have a responsibility to make the best use of every dollar Nebraskans entrust to us. Themes of equity and inclusion touch everything we do. We will be a University for everyone—successful only when all voices are heard. Finally, Nebraskans should know what to expect from their University. We must work every day to maintain the trust and confidence of the people of our state

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

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

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

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