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- Campbell, PJ, et al.
(author)
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Pan-cancer analysis of whole genomes
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Journal article (peer-reviewed)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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3. |
- Bayley, PJ, et al.
(author)
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2013 SYR Accepted Poster Abstracts
- 2013
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In: International journal of yoga therapy. - 1531-2054. ; 23:1, s. 32-53
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Journal article (peer-reviewed)
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- Abazov, V. M., et al.
(author)
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Search for pair production of second generation scalar leptoquarks
- 2009
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In: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 671:2, s. 224-232
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Journal article (peer-reviewed)abstract
- We report on a search for the pair production of second generation scalar leptoquarks (LQ) in p (p) over bar collisions at the center of mass energy root s- = 1.96 TeV using a data set corresponding to an integrated luminosity of 1.0 fb(-1) collected with the D empty set experiment at the Fermilab Tevatron Collider. Topologies arising from the LQ (LQ) over bar -> mu q nu q and LQ (LQ) over bar -> mu q mu q decay modes are investigated. No excess of data over the standard model prediction is observed and upper limits on the leptoquark pair production cross section are derived at the 95% C.L. as a function of the leptoquark mass and the branching fraction beta for the decay LQ -> mu q. These are interpreted as lower limits on the leptoquark mass as a function of beta. For beta = 1 (0.5), scalar second generation leptoquarks with masses up to 316 GeV (270 GeV) are excluded.
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- Amgad, M, et al.
(author)
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Report on computational assessment of Tumor Infiltrating Lymphocytes from the International Immuno-Oncology Biomarker Working Group
- 2020
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In: NPJ breast cancer. - : Springer Science and Business Media LLC. - 2374-4677. ; 6:1, s. 16-
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Journal article (peer-reviewed)abstract
- Assessment of tumor-infiltrating lymphocytes (TILs) is increasingly recognized as an integral part of the prognostic workflow in triple-negative (TNBC) and HER2-positive breast cancer, as well as many other solid tumors. This recognition has come about thanks to standardized visual reporting guidelines, which helped to reduce inter-reader variability. Now, there are ripe opportunities to employ computational methods that extract spatio-morphologic predictive features, enabling computer-aided diagnostics. We detail the benefits of computational TILs assessment, the readiness of TILs scoring for computational assessment, and outline considerations for overcoming key barriers to clinical translation in this arena. Specifically, we discuss: 1. ensuring computational workflows closely capture visual guidelines and standards; 2. challenges and thoughts standards for assessment of algorithms including training, preanalytical, analytical, and clinical validation; 3. perspectives on how to realize the potential of machine learning models and to overcome the perceptual and practical limits of visual scoring.
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