| 1. |
- Menden, MP, et al.
(författare)
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Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen
- 2019
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1, s. 2674-
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Tidskriftsartikel (refereegranskat)abstract
- The effectiveness of most cancer targeted therapies is short-lived. Tumors often develop resistance that might be overcome with drug combinations. However, the number of possible combinations is vast, necessitating data-driven approaches to find optimal patient-specific treatments. Here we report AstraZeneca’s large drug combination dataset, consisting of 11,576 experiments from 910 combinations across 85 molecularly characterized cancer cell lines, and results of a DREAM Challenge to evaluate computational strategies for predicting synergistic drug pairs and biomarkers. 160 teams participated to provide a comprehensive methodological development and benchmarking. Winning methods incorporate prior knowledge of drug-target interactions. Synergy is predicted with an accuracy matching biological replicates for >60% of combinations. However, 20% of drug combinations are poorly predicted by all methods. Genomic rationale for synergy predictions are identified, including ADAM17 inhibitor antagonism when combined with PIK3CB/D inhibition contrasting to synergy when combined with other PI3K-pathway inhibitors in PIK3CA mutant cells.
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| 4. |
- Demichelis, F., et al.
(författare)
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TMPRSS2:ERG gene fusion associated with lethal prostate cancer in a watchful waiting cohort
- 2007
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Ingår i: Oncogene. - Basingstoke : Nature Publ. Group. - 0950-9232 .- 1476-5594. ; 26:31, s. 4596-4599
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Tidskriftsartikel (refereegranskat)abstract
- The identification of the TMPRSS2:ERG fusion in prostate cancer suggests that distinct molecular subtypes may define risk for disease progression. In surgical series, TMPRSS2:ERG fusion was identified in 50% of the tumors. Here, we report on a population-based cohort of men with localized prostate cancers followed by expectant (watchful waiting) therapy with 15% (17/111) TMPRSS2:ERG fusion. We identified a statistically significant association between TMPRSS2:ERG fusion and prostate cancer specific death (cumulative incidence ratio=2.7, P<0.01, 95% confidence interval=1.3–5.8). Quantitative reverse-transcription–polymerase chain reaction demonstrated high estrogen-regulated gene (ERG) expression to be associated with TMPRSS2:ERG fusion (P<0.005). These data suggest that TMPRSS2:ERG fusion prostate cancers may have a more aggressive phenotype, possibly mediated through increased ERG expression.
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| 6. |
- Hwang, W, et al.
(författare)
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CREDO: Highly confident disease-relevant A-to-I RNA-editing discovery in breast cancer
- 2019
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9:1, s. 5064-
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Tidskriftsartikel (refereegranskat)abstract
- Adenosine-to-Inosine (A-to-I) RNA editing is the most prevalent post-transcriptional modification of RNA molecules. Researchers have attempted to find reliable RNA editing using next generation sequencing (NGS) data. However, most of these attempts suffered from a high rate of false positives, and they did not consider the clinical relevance of the identified RNA editing, for example, in disease progression. We devised an effective RNA-editing discovery pipeline called CREDO, which includes novel statistical filtering modules based on integration of DNA- and RNA-seq data from matched tumor-normal tissues. CREDO was compared with three other RNA-editing discovery pipelines and found to give significantly fewer false positives. Application of CREDO to breast cancer data from the Cancer Genome Atlas (TCGA) project discovered highly confident RNA editing with clinical relevance to cancer progression in terms of patient survival. RNA-editing detection using DNA- and RNA-seq data from matched tumor-normal tissues should be more routinely performed as multiple omics data are becoming commonly available from each patient sample. We believe CREDO is an effective and reliable tool for this problem.
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| 11. |
- Lee, W, et al.
(författare)
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Sparse Canonical Covariance Analysis for High-throughput Data
- 2011
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Ingår i: STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY. - : Walter de Gruyter GmbH. - 2194-6302 .- 1544-6115. ; 10:1
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Canonical covariance analysis (CCA) has gained popularity as a method for the analysis of two sets of high-dimensional genomic data. However, it is often difficult to interpret the results because canonical vectors are linear combinations of all variables, and the coefficients are typically nonzero. Several sparse CCA methods have recently been proposed for reducing the number of nonzero coefficients, but these existing methods are not satisfactory because they still give too many nonzero coefficients. In this paper, we propose a new random-effect model approach for sparse CCA; the proposed algorithm can adapt arbitrary penalty functions to CCA without much computational demands. Through simulation studies, we compare various penalty functions in terms of the performance of correct model identification. We also develop an extension of sparse CCA to address more than two sets of variables on the same set of observations. We illustrate the method with an analysis of the NCI cancer dataset.
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| 15. |
- Pawitan, Y, et al.
(författare)
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Confidence as Likelihood
- 2021
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Ingår i: STATISTICAL SCIENCE. - 0883-4237. ; 36:4, s. 509-517
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 17. |
- Pawitan, Y, et al.
(författare)
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Rejoinder: Confidence as Likelihood
- 2022
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Ingår i: STATISTICAL SCIENCE. - 0883-4237. ; 37:4, s. 628-629
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 20. |
- Penney, K. L., et al.
(författare)
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mRNA expression signature of Gleason grade predicts lethal prostate cancer
- 2011
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Ingår i: Journal of Clinical Oncology. - : American Society of Clinical Oncology. - 0732-183X .- 1527-7755. ; 29:17, s. 2391-2396
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Tidskriftsartikel (refereegranskat)abstract
- PURPOSE: Prostate-specific antigen screening has led to enormous overtreatment of prostate cancer because of the inability to distinguish potentially lethal disease at diagnosis. We reasoned that by identifying an mRNA signature of Gleason grade, the best predictor of prognosis, we could improve prediction of lethal disease among men with moderate Gleason 7 tumors, the most common grade, and the most indeterminate in terms of prognosis.PATIENTS AND METHODS: Using the complementary DNA-mediated annealing, selection, extension, and ligation assay, we measured the mRNA expression of 6,100 genes in prostate tumor tissue in the Swedish Watchful Waiting cohort (n = 358) and Physicians' Health Study (PHS; n = 109). We developed an mRNA signature of Gleason grade comparing individuals with Gleason ≤ 6 to those with Gleason ≥ 8 tumors and applied the model among patients with Gleason 7 to discriminate lethal cases.RESULTS: We built a 157-gene signature using the Swedish data that predicted Gleason with low misclassification (area under the curve [AUC] = 0.91); when this signature was tested in the PHS, the discriminatory ability remained high (AUC = 0.94). In men with Gleason 7 tumors, who were excluded from the model building, the signature significantly improved the prediction of lethal disease beyond knowing whether the Gleason score was 4 + 3 or 3 + 4 (P = .006).CONCLUSION: Our expression signature and the genes identified may improve our understanding of the de-differentiation process of prostate tumors. Additionally, the signature may have clinical applications among men with Gleason 7, by further estimating their risk of lethal prostate cancer and thereby guiding therapy decisions to improve outcomes and reduce overtreatment.
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| 38. |
- Dahlqwist, E, et al.
(författare)
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Regression standardization and attributable fraction estimation with between-within frailty models for clustered survival data
- 2019
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Ingår i: Statistical methods in medical research. - : SAGE Publications. - 1477-0334 .- 0962-2802. ; 28:2, s. 462-485
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Tidskriftsartikel (refereegranskat)abstract
- The between-within frailty model has been proposed as a viable analysis tool for clustered survival time outcomes. Previous research has shown that this model gives consistent estimates of the exposure–outcome hazard ratio in the presence of unmeasured cluster-constant confounding, which the ordinary frailty model does not, and that estimates obtained from the between-within frailty model are often more efficient than estimates obtained from the stratified Cox proportional hazards model. In this paper, we derive novel estimation techniques for regression standardization with between-within frailty models. We also show how between-within frailty models can be used to estimate the attributable fraction function, which is a generalization of the attributable fraction for survival time outcomes. We illustrate the proposed methods by analyzing a large cohort on preterm birth and attention deficit hyperactivity disorder. To facilitate use of the proposed methods, we provide R code for all analyses.
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| 39. |
- Deng, WJ, et al.
(författare)
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Fusion Gene Detection Using Whole-Exome Sequencing Data in Cancer Patients
- 2022
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Ingår i: Frontiers in genetics. - : Frontiers Media SA. - 1664-8021. ; 13, s. 820493-
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Tidskriftsartikel (refereegranskat)abstract
- Several fusion genes are directly involved in the initiation and progression of cancers. Numerous bioinformatics tools have been developed to detect fusion events, but they are mainly based on RNA-seq data. The whole-exome sequencing (WES) represents a powerful technology that is widely used for disease-related DNA variant detection. In this study, we build a novel analysis pipeline called Fuseq-WES to detect fusion genes at DNA level based on the WES data. The same method applies also for targeted panel sequencing data. We assess the method to real datasets of acute myeloid leukemia (AML) and prostate cancer patients. The result shows that two of the main AML fusion genes discovered in RNA-seq data, PML-RARA and CBFB-MYH11, are detected in the WES data in 36 and 63% of the available samples, respectively. For the targeted deep-sequencing of prostate cancer patients, detection of the TMPRSS2-ERG fusion, which is the most frequent chimeric alteration in prostate cancer, is 91% concordant with a manually curated procedure based on four other methods. In summary, the overall results indicate that it is challenging to detect fusion genes in WES data with a standard coverage of ∼ 15–30x, where fusion candidates discovered in the RNA-seq data are often not detected in the WES data and vice versa. A subsampling study of the prostate data suggests that a coverage of at least 75x is necessary to achieve high accuracy.
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| 40. |
- Deng, W, et al.
(författare)
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Quantification of mutant-allele expression at isoform level in cancer from RNA-seq data
- 2022
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Ingår i: NAR genomics and bioinformatics. - : Oxford University Press (OUP). - 2631-9268. ; 4:3, s. lqac052-
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Tidskriftsartikel (refereegranskat)abstract
- Even though the role of DNA mutations in cancer is well recognized, current quantification of the RNA expression, performed either at gene or isoform level, typically ignores the mutation status. Standard methods for estimating allele-specific expression (ASE) consider gene-level expression, but the functional impact of a mutation is best assessed at isoform level. Hence our goal is to quantify the mutant–allele expression at isoform level. We have developed and implemented a method, named MAX, for quantifying mutant–allele expression given a list of mutations. For a gene of interest, a mutant reference is constructed by incorporating all possible mutant versions of the wild-type isoforms in the transcriptome annotation. The mutant reference is then used for the RNA-seq reads mapping, which in principle works similarly for any quantification tool. We apply an alternating EM algorithm to the read-count data from the mapping step. In a simulation study, MAX performs well against standard isoform-quantification methods. Also, MAX achieves higher accuracy than conventional gene-based ASE methods such as ASEP. An analysis of a real dataset of acute myeloid leukemia reveals a subgroup of NPM1-mutated patients responding well to a kinase inhibitor. Our findings indicate that quantification of mutant–allele expression at isoform level is feasible and has potential added values for assessing the functional impact of DNA mutations in cancers.
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| 46. |
- Fernberg, P., et al.
(författare)
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Time Trends in Risk and Risk Determinants of Non-Hodgkin Lymphoma in Solid Organ Transplant Recipients
- 2011
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Ingår i: American Journal of Transplantation. - : Elsevier BV. - 1600-6135 .- 1600-6143. ; 11:11, s. 2472-2482
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Tidskriftsartikel (refereegranskat)abstract
- Organ transplantation increases risk of non-Hodgkin lymphoma (NHL), but long-term risk and time trends have seldom been evaluated. Immunosuppressive drug load is an important risk determinant, but the details are unclear. We studied NHL risk in a nationwide Swedish cohort of 11 081 graft recipients transplanted 1970-2008. Relative risks (RRs) were estimated within the cohort and versus the general population by age, sex, follow-up time and calendar period. NHL risk was also assessed by cumulative and average doses of immunosuppressive treatments in a nested case-control design throughout 1997 using conditional logistic regression. We observed 153 NHL cases during 97 853 years of follow-up. Compared with the general population, NHL risk was eightfold increased (RR 7.9; 95% confidence interval [CI] 6.6-9.4), and increased risks persisted after >= 15 years of follow-up among kidney (6.1; 95% CI 3.5-10) and nonkidney recipients (44; 14-103). Among nonkidney recipients, NHL risk was lower in the 2000s compared with the 1990s (0.5; 95% CI 0.3-1.0; p = 0.04). A high average dose of antithymocyte immunoglobulin (ATG) conferred an eightfold increased risk of NHL (OR 8.5; 95% CI 1.9-38). To conclude, posttransplant NHL risk decreased during the last decade among nonkidney recipients, possibly because of a more careful use of ATG, the introduction of new drugs, or both.
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