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- 2019
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Tidskriftsartikel (refereegranskat)
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| 2. |
- Alvarez, Mariano J., et al.
(författare)
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A precision oncology approach to the pharmacological targeting of mechanistic dependencies in neuroendocrine tumors
- 2018
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 50:7, s. 979-989
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Tidskriftsartikel (refereegranskat)abstract
- We introduce and validate a new precision oncology framework for the systematic prioritization of drugs targeting mechanistic tumor dependencies in individual patients. Compounds are prioritized on the basis of their ability to invert the concerted activity of master regulator proteins that mechanistically regulate tumor cell state, as assessed from systematic drug perturbation assays. We validated the approach on a cohort of 212 gastroenteropancreatic neuroendocrine tumors (GEP-NETs), a rare malignancy originating in the pancreas and gastrointestinal tract. The analysis identified several master regulator proteins, including key regulators of neuroendocrine lineage progenitor state and immunoevasion, whose role as critical tumor dependencies was experimentally confirmed. Transcriptome analysis of GEP-NET-derived cells, perturbed with a library of 107 compounds, identified the HDAC class I inhibitor entinostat as a potent inhibitor of master regulator activity for 42% of metastatic GEP-NET patients, abrogating tumor growth in vivo. This approach may thus complement current efforts in precision oncology.
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| 3. |
- Altenhoff, Adrian M., et al.
(författare)
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Standardized benchmarking in the quest for orthologs
- 2016
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Ingår i: Nature Methods. - 1548-7091 .- 1548-7105. ; 13:5, s. 425-
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Tidskriftsartikel (refereegranskat)abstract
- Achieving high accuracy in orthology inference is essential for many comparative, evolutionary and functional genomic analyses, yet the true evolutionary history of genes is generally unknown and orthologs are used for very different applications across phyla, requiring different precision-recall trade-offs. As a result, it is difficult to assess the performance of orthology inference methods. Here, we present a community effort to establish standards and an automated web-based service to facilitate orthology benchmarking. Using this service, we characterize 15 well-established inference methods and resources on a battery of 20 different benchmarks. Standardized benchmarking provides a way for users to identify the most effective methods for the problem at hand, sets a minimum requirement for new tools and resources, and guides the development of more accurate orthology inference methods.
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| 4. |
- Dong, Yan, et al.
(författare)
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Atom Probe Tomography Interlaboratory Study on Clustering Analysis in Experimental Data Using the Maximum Separation Distance Approach
- 2019
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Ingår i: Microscopy and Microanalysis. - 1435-8115 .- 1431-9276. ; 25:2, s. 356-366
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Tidskriftsartikel (refereegranskat)abstract
- We summarize the findings from an interlaboratory study conducted between ten international research groups and investigate the use of the commonly used maximum separation distance and local concentration thresholding methods for solute clustering quantification. The study objectives are: to bring clarity to the range of applicability of the methods; identify existing and/or needed modifications; and interpretation of past published data. Participants collected experimental data from a proton-irradiated 304 stainless steel and analyzed Cu-rich and Ni-Si rich clusters. The datasets were also analyzed by one researcher to clarify variability originating from different operators. The Cu distribution fulfills the ideal requirements of the maximum separation method (MSM), namely a dilute matrix Cu concentration and concentrated Cu clusters. This enabled a relatively tight distribution of the cluster number density among the participants. By contrast, the group analysis of the Ni-Si rich clusters by the MSM was complicated by a high Ni matrix concentration and by the presence of Si-decorated dislocations, leading to larger variability among researchers. While local concentration filtering could, in principle, tighten the results, the cluster identification step inevitably maintained a high scatter. Recommendations regarding reporting, selection of analysis method, and expected variability when interpreting published data are discussed.
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| 5. |
- Marquis, Emmanuelle A., et al.
(författare)
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On the use of density-based algorithms for the analysis of solute clustering in atom probe tomography data
- 2019
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Ingår i: Minerals, Metals and Materials Series. - Cham : Springer International Publishing. - 2367-1696 .- 2367-1181. ; Part F11, s. 2097-2113
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Konferensbidrag (refereegranskat)abstract
- Because atom probe tomography (APT) provides three-dimensional reconstructions of small volumes by resolving atomic chemical identities and positions, it is uniquely suited to analyze solute clustering phenomena in materials. A number of approaches have been developed to extract clustering information from the 3D reconstructed dataset, and numerous reports can be found applying these methods to a wide variety of materials questions. However, results from clustering analyses can differ significantly from one report to another, even when performed on similar microstructures, raising questions about the reliability of APT to quantitatively describe solute clustering. In addition, analysis details are often not provided, preventing independent confirmation of the results. With the number of APT research groups growing quickly, the APT community recognizes the need for educating new users about common methods and artefacts, and for developing analysis and data reporting protocols that address issues of reproducibility, errors, and variability. To this end, a round robin experiment was organized among ten different international institutions. The goal is to provide a consistent framework for the analysis of irradiated stainless steels using APT. Through the development of more reliable and reproducible data analysis and through communication, this project also aims to advance the understanding between irradiated microstructure and materials performance by providing more complete quantitative microstructural input for modeling. The results, methods, and findings of this round robin will also apply to other clustering phenomena studied using APT, beyond the theme of radiation damage.
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| 6. |
- Satizabal, Claudia L., et al.
(författare)
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Genetic architecture of subcortical brain structures in 38,851 individuals
- 2019
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Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 51:11, s. 1624-
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Tidskriftsartikel (refereegranskat)abstract
- Subcortical brain structures are integral to motion, consciousness, emotions and learning. We identified common genetic variation related to the volumes of the nucleus accumbens, amygdala, brainstem, caudate nucleus, globus pallidus, putamen and thalamus, using genome-wide association analyses in almost 40,000 individuals from CHARGE, ENIGMA and UK Biobank. We show that variability in subcortical volumes is heritable, and identify 48 significantly associated loci (40 novel at the time of analysis). Annotation of these loci by utilizing gene expression, methylation and neuropathological data identified 199 genes putatively implicated in neurodevelopment, synaptic signaling, axonal transport, apoptosis, inflammation/infection and susceptibility to neurological disorders. This set of genes is significantly enriched for Drosophila orthologs associated with neurodevelopmental phenotypes, suggesting evolutionarily conserved mechanisms. Our findings uncover novel biology and potential drug targets underlying brain development and disease.
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