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- 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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- Dam, J. S, et al.
(författare)
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Fiber optic system for in vivo real-time determination of tissue optical properties from steady-state diffuse reflectance measurements
- 2000
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Ingår i: PHOTON MIGRATION, DIFFUSE SPECTROSCOPY AND OPTICAL COHERENCE TOMOGRAPHY: IMAGING AND FUNCTIONAL ASSESSMENT. - : SPIE. - 0277-786X .- 1996-756X. - 0819438162 ; 1:31, s. 103-109
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Konferensbidrag (refereegranskat)abstract
- We present a versatile and compact fiber optic probe for real-time determination of the absorption and the reduced scattering coefficients from spatially resolved continuous wave diffuse reflectance measurements. The probe collects the diffuse reflectance at six distances in the range 0.6 - 7.8 mm at four arbitrary wavelengths, which were 660, 785, 805, and 974 nm in these experiments. The maximum sampling rate for one cycle of measurements including all four wavelengths is about 100 Hz. The absorption and the reduced scattering coefficients are extracted real-time from the probe measurements using multivariate calibration methods based on multiple polynomial regression and Newton-Raphson algorithms. The system was calibrated on a 6x7 matrix of Intralipid/ink phantoms with optical properties within typical biological ranges, e.g. at 785 nm, the ranges of the absorption and the reduced scattering coefficients, were 0 - 0.3 /cm and 6 - 16 /cm, respectively. Cross-validation tests shoved that the mean prediction error, relative to the ranges of absorption and the reduced scattering coefficients were 2.8 \% and 1.3 \%, respectively.
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