26 research outputs found

    ENFI: A System to Promote Reading and Writing

    Get PDF

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

    No full text
    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

    Postsecondary literacy services for persons who are deaf or hard of hearing

    No full text
    Individuals who are deaf or hard of hearing who wish to compete economically must seek literacy services after leaving high school. Prior to this study, there was very little known about these programs. To address this concern, postsecondary institutions and community-based programs claiming to provide literacy services for persons who are deaf or hard of hearing were surveyed about their services in six areas; availability, participants, assessment, instruction, data maintained, and barriers. A subset of the survey respondents participated in in-depth telephone interviews. In comparing and contrasting the two program types it was learned that postsecondary programs were more likely to provide college preparatory work and external accommodations, whereas community-based programs tended to serve participants on an individual basis. The unexpected finding from this study is that overall the two program types were not vastly different. Both types of programs were staffed by predominantly white, hearing women. Both types of programs were frustrated by lack of stable funding and lack of appropriate curriculum. Neither type of program prioritized research or data collection. To address these issues, it was suggested that a national priority be developed to create a uniform database, appropriate curriculum, and a network of service providers who could share ideas and resources rather than compete for them

    Postsecondary literacy services for persons who are deaf or hard of hearing

    No full text
    Individuals who are deaf or hard of hearing who wish to compete economically must seek literacy services after leaving high school. Prior to this study, there was very little known about these programs. To address this concern, postsecondary institutions and community-based programs claiming to provide literacy services for persons who are deaf or hard of hearing were surveyed about their services in six areas; availability, participants, assessment, instruction, data maintained, and barriers. A subset of the survey respondents participated in in-depth telephone interviews. In comparing and contrasting the two program types it was learned that postsecondary programs were more likely to provide college preparatory work and external accommodations, whereas community-based programs tended to serve participants on an individual basis. The unexpected finding from this study is that overall the two program types were not vastly different. Both types of programs were staffed by predominantly white, hearing women. Both types of programs were frustrated by lack of stable funding and lack of appropriate curriculum. Neither type of program prioritized research or data collection. To address these issues, it was suggested that a national priority be developed to create a uniform database, appropriate curriculum, and a network of service providers who could share ideas and resources rather than compete for them

    Sex differences in oncogenic mutational processes

    Get PDF
    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

    Get PDF
    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
    corecore