| 1. |
- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)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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- Noguchi, S, et al.
(författare)
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FANTOM5 CAGE profiles of human and mouse samples
- 2017
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Ingår i: Scientific data. - : Springer Science and Business Media LLC. - 2052-4463. ; 4, s. 170112-
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Tidskriftsartikel (refereegranskat)abstract
- In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.
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| 13. |
- Biedron, Sandra G., et al.
(författare)
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Measurements of nonlinear harmonic generation at the Advanced Photon Source's SASE FEL
- 2002
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Ingår i: Nuclear Instruments & Methods in Physics Research. Section A: Accelerators, Spectrometers, Detectors, and Associated Equipment. - 0167-5087. ; 483:1-2, s. 94-100
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Tidskriftsartikel (refereegranskat)abstract
- SASE saturation was recently achieved at the Advanced Photon Source's SASE FFL in the low-energy undulator test line at 530 nm and 385 urn. The electron beam microbunching becomes more and more prominent until saturation is achieved. This bunching causes nonlinear harmonic emission that extends the usefulness of a SASE system in achieving shorter FEL wavelengths for the same electron beam energy. We have investigated the intensity of the fundamental and second harmonic undulator radiation as a function of distance along the undulator line and present the experimental results and compare them to numerical simulations. In addition, we have measured the single-shot second harmonic spectra as well as the simultaneous fundamental and second harmonic spectra and present the experimental results. (C) 2002 Elsevier Science B.V. All riudits reserved.
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| 14. |
- Forrest, ARR, et al.
(författare)
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A promoter-level mammalian expression atlas
- 2014
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 507:7493, s. 462-
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Tidskriftsartikel (refereegranskat)
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| 15. |
- Lewellen, JW, et al.
(författare)
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Present status and recent results from the APS SASE FEL
- 2002
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Ingår i: Nuclear Instruments & Methods in Physics Research. Section A: Accelerators, Spectrometers, Detectors, and Associated Equipment. - 0167-5087. ; 483:1-2, s. 40-45
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Tidskriftsartikel (refereegranskat)abstract
- The Low-Energy Undulator Test Line (LEUTL) at the Advanced Photon Source, Argonne National Laboratory, is intended to demonstrate the basic operation of a SASE-based free-electron laser. Goals include comparison of experimental results With theoretical predictions and scaling laws, identification of problems relevant to fourth-generation light source construction and operation and the means of addressing them, the development of operational and diagnostic techniques to optimize SASE FEL performance and increase repeatability from run to run. and performance of initial pioneering experiments capable of exploiting the unique properties of the laser. The basic layout and operational philosophy of the LEUTL experiment is presented. A summary of past results, including saturation, is reviewed, and a description of recent results is presented. We conclude with future plans, which include pressing to shorter wavelengths and incorporating user experiments into the LEUTL experimental program.
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