| 1. |
- Thompson, B.A., et al.
(författare)
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Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database
- 2014
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 46:2, s. 107-115
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Tidskriftsartikel (refereegranskat)abstract
- The clinical classification of hereditary sequence variants identified in disease-related genes directly affects clinical management of patients and their relatives. The International Society for Gastrointestinal Hereditary Tumours (InSiGHT) undertook a collaborative effort to develop, test and apply a standardized classification scheme to constitutional variants in the Lynch syndrome-associated genes MLH1, MSH2, MSH6 and PMS2. Unpublished data submission was encouraged to assist in variant classification and was recognized through microattribution. The scheme was refined by multidisciplinary expert committee review of the clinical and functional data available for variants, applied to 2,360 sequence alterations, and disseminated online. Assessment using validated criteria altered classifications for 66% of 12,006 database entries. Clinical recommendations based on transparent evaluation are now possible for 1,370 variants that were not obviously protein truncating from nomenclature. This large-scale endeavor will facilitate the consistent management of families suspected to have Lynch syndrome and demonstrates the value of multidisciplinary collaboration in the curation and classification of variants in public locus-specific databases. © 2014 Nature America, Inc.
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| 2. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 3. |
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| 6. |
- Lynch, I, et al.
(författare)
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Can an InChI for Nano Address the Need for a Simplified Representation of Complex Nanomaterials across Experimental and Nanoinformatics Studies?
- 2020
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Ingår i: Nanomaterials (Basel, Switzerland). - : MDPI AG. - 2079-4991. ; 10:12
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Tidskriftsartikel (refereegranskat)abstract
- Chemoinformatics has developed efficient ways of representing chemical structures for small molecules as simple text strings, simplified molecular-input line-entry system (SMILES) and the IUPAC International Chemical Identifier (InChI), which are machine-readable. In particular, InChIs have been extended to encode formalized representations of mixtures and reactions, and work is ongoing to represent polymers and other macromolecules in this way. The next frontier is encoding the multi-component structures of nanomaterials (NMs) in a machine-readable format to enable linking of datasets for nanoinformatics and regulatory applications. A workshop organized by the H2020 research infrastructure NanoCommons and the nanoinformatics project NanoSolveIT analyzed issues involved in developing an InChI for NMs (NInChI). The layers needed to capture NM structures include but are not limited to: core composition (possibly multi-layered); surface topography; surface coatings or functionalization; doping with other chemicals; and representation of impurities. NM distributions (size, shape, composition, surface properties, etc.), types of chemical linkages connecting surface functionalization and coating molecules to the core, and various crystallographic forms exhibited by NMs also need to be considered. Six case studies were conducted to elucidate requirements for unambiguous description of NMs. The suggested NInChI layers are intended to stimulate further analysis that will lead to the first version of a “nano” extension to the InChI standard.
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| 7. |
- Colbourne, JK, et al.
(författare)
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The Precision Toxicology initiative
- 2023
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Ingår i: Toxicology letters. - 1879-3169. ; 383, s. 33-42
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 8. |
- Federico, A, et al.
(författare)
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Transcriptomics in Toxicogenomics, Part II: Preprocessing and Differential Expression Analysis for High Quality Data
- 2020
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Ingår i: Nanomaterials (Basel, Switzerland). - : MDPI AG. - 2079-4991. ; 10:5
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Tidskriftsartikel (refereegranskat)abstract
- Preprocessing of transcriptomics data plays a pivotal role in the development of toxicogenomics-driven tools for chemical toxicity assessment. The generation and exploitation of large volumes of molecular profiles, following an appropriate experimental design, allows the employment of toxicogenomics (TGx) approaches for a thorough characterisation of the mechanism of action (MOA) of different compounds. To date, a plethora of data preprocessing methodologies have been suggested. However, in most cases, building the optimal analytical workflow is not straightforward. A careful selection of the right tools must be carried out, since it will affect the downstream analyses and modelling approaches. Transcriptomics data preprocessing spans across multiple steps such as quality check, filtering, normalization, batch effect detection and correction. Currently, there is a lack of standard guidelines for data preprocessing in the TGx field. Defining the optimal tools and procedures to be employed in the transcriptomics data preprocessing will lead to the generation of homogeneous and unbiased data, allowing the development of more reliable, robust and accurate predictive models. In this review, we outline methods for the preprocessing of three main transcriptomic technologies including microarray, bulk RNA-Sequencing (RNA-Seq), and single cell RNA-Sequencing (scRNA-Seq). Moreover, we discuss the most common methods for the identification of differentially expressed genes and to perform a functional enrichment analysis. This review is the second part of a three-article series on Transcriptomics in Toxicogenomics.
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| 9. |
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| 10. |
- Jeliazkova, N, et al.
(författare)
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Towards FAIR nanosafety data
- 2021
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Ingår i: Nature nanotechnology. - : Springer Science and Business Media LLC. - 1748-3395 .- 1748-3387. ; 16:86, s. 644-
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Tidskriftsartikel (refereegranskat)
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