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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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| 4. |
- Thurtle, D., et al.
(författare)
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Comparative performance and external validation of the multivariable PREDICTProstatetool for non-metastatic prostate cancer: a study in 69,206 men from Prostate Cancer data Base Sweden (PCBaSe)
- 2020
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Ingår i: Bmc Medicine. - : Springer Science and Business Media LLC. - 1741-7015. ; 18:1
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Tidskriftsartikel (refereegranskat)abstract
- Background PREDICTProstateis an endorsed prognostic model that provides individualised long-term prostate cancer-specific and overall survival estimates. The model, derived from UK data, estimates potential treatment benefit on overall survival. In this study, we externally validated the model in a large independent dataset and compared performance to existing models and within treatment groups. Methods Men with non-metastatic prostate cancer and prostate-specific antigen (PSA) < 100 ng/ml diagnosed between 2000 and 2010 in the nationwide population-based Prostate Cancer data Base Sweden (PCBaSe) were included. Data on age, PSA, clinical stage, grade group, biopsy involvement, primary treatment and comorbidity were retrieved. Sixty-nine thousand two hundred six men were included with 13.9 years of median follow-up. Fifteen-year survival estimates were calculated using PREDICTProstatefor prostate cancer-specific mortality (PCSM) and all-cause mortality (ACM). Discrimination was assessed using Harrell's concordance (c)-index in R. Calibration was evaluated using cumulative available follow-up in Stata (TX, USA). Results Overall discrimination of PREDICTProstatewas good with c-indices of 0.85 (95% CI 0.85-0.86) for PCSM and 0.79 (95% CI 0.79-0.80) for ACM. Overall calibration of the model was excellent with 25,925 deaths predicted and 25,849 deaths observed. Within the conservative management and radical treatment groups, c-indices for 15-year PCSM were 0.81 and 0.78, respectively. Calibration also remained good within treatment groups. The discrimination of PREDICT Prostate significantly outperformed the EAU, NCCN and CAPRA scores for both PCSM and ACM within this cohort overall. A key limitation is the use of retrospective cohort data. Conclusions This large external validation demonstrates that PREDICTProstateis a robust and generalisable model to aid clinical decision-making.
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