| 1. |
- Dahlberg, Johan, et al.
(författare)
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Arteria : An automation system for a sequencing core facility
- 2019
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Ingår i: GigaScience. - : Oxford University Press (OUP). - 2047-217X. ; 8:12
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Tidskriftsartikel (refereegranskat)abstract
- Background: In recent years, nucleotide sequencing has become increasingly instrumental in both research and clinical settings. This has led to an explosive growth in sequencing data produced worldwide. As the amount of data increases, so does the need for automated solutions for data processing and analysis. The concept of workflows has gained favour in the bioinformatics community, but there is little in the scientific literature describing end-to-end automation systems. Arteria is an automation system that aims at providing a solution to the data-related operational challenges that face sequencing core facilities.Findings: Arteria is built on existing open source technologies, with a modular design allowing for a community-driven effort to create plug-and-play micro-services. In this article we describe the system, elaborate on the underlying conceptual framework, and present an example implementation. Arteria can be reduced to 3 conceptual levels: orchestration (using an event-based model of automation), process (the steps involved in processing sequencing data, modelled as workflows), and execution (using a series of RESTful micro-services). This creates a system that is both flexible and scalable. Arteria-based systems have been successfully deployed at 3 sequencing core facilities. The Arteria Project code, written largely in Python, is available as open source software, and more information can be found at https://arteria-project.github.io/.Conclusions: We describe the Arteria system and the underlying conceptual framework, demonstrating how this model can be used to automate data handling and analysis in the context of a sequencing core facility.
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| 2. |
- Gremyr, Ida, 1975, et al.
(författare)
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Småskaliga live case för att integrera livslångt lärande och arbetslivsanknytning
- 2023
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Ingår i: Proceedings Chalmers Conference on Teaching and Learning 2023. - 9789188041548 ; , s. 47-50
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Konferensbidrag (refereegranskat)abstract
- I detta projekt utvecklas en live-case-modell som stödjer utbildningssamverkan och arbetsintegrerat lärande inom ramen för existerande universitetsutbildning och kurser för livslångt lärande (LLL). I denna modell får ingenjörsstudenter och LLL-studenter från vården arbeta tillsammans med ett verkligt problem från LLL-studenternas organisation. Den småskaliga live-case-modellen är resurseffektiv eftersom den är starkt avgränsad i tid (varaktighet: en vecka), dessutom är den unik då den inte bara fokuserar ingenjörsstudenternas, utan även praktikernas (LLL-studenternas), lärande.
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| 3. |
- La Fleur, Linnea, et al.
(författare)
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Mutation patterns in a population-based non-small cell lung cancer cohort and prognostic impact of concomitant mutations in KRAS and TP53 or STK11
- 2019
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Ingår i: Lung Cancer. - : Elsevier BV. - 0169-5002 .- 1872-8332. ; 130, s. 50-58
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES: Non-small cell lung cancer (NSCLC) is a heterogeneous disease with unique combinations of somatic molecular alterations in individual patients, as well as significant differences in populations across the world with regard to mutation spectra and mutation frequencies. Here we aim to describe mutational patterns and linked clinical parameters in a population-based NSCLC cohort.MATERIALS AND METHODS: Using targeted resequencing the mutational status of 82 genes was evaluated in a consecutive Swedish surgical NSCLC cohort, consisting of 352 patient samples from either fresh frozen or formalin fixed paraffin embedded (FFPE) tissues. The panel covers all exons of the 82 genes and utilizes reduced target fragment length and two-strand capture making it compatible with degraded FFPE samples.RESULTS: We obtained a uniform sequencing coverage and mutation load across the fresh frozen and FFPE samples by adaption of sequencing depth and bioinformatic pipeline, thereby avoiding a technical bias between these two sample types. At large, the mutation frequencies resembled the frequencies seen in other western populations, except for a high frequency of KRAS hotspot mutations (43%) in adenocarcinoma patients. Worse overall survival was observed for adenocarcinoma patients with a mutation in either TP53, STK11 or SMARCA4. In the adenocarcinoma KRAS-mutated group poor survival appeared to be linked to concomitant TP53 or STK11 mutations, and not to KRAS mutation as a single aberration. Similar results were seen in the analysis of publicly available data from the cBioPortal. In squamous cell carcinoma a worse prognosis could be observed for patients with MLL2 mutations, while CSMD3 mutations were linked to a better prognosis.CONCLUSION: Here we have evaluated the mutational status of a NSCLC cohort. We could not confirm any survival impact of isolated driver mutations. Instead, concurrent mutations in TP53 and STK11 were shown to confer poor survival in the KRAS-positive adenocarcinoma subgroup.
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| 4. |
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| 5. |
- Smeds, Magdalena, Teknisk licentiat, 1990-, et al.
(författare)
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Helping a “sister” out : Bringing engineering students and healthcare practitioners together through live-cases
- 2023
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Konferensbidrag (refereegranskat)abstract
- Universities search for ways to prepare full-time students for real worklife challenges, but also for ways to offer practitioners life-long learning (LLL) opportunities. This paper presents a live-case model integrating full-time engineering students and LLL students from healthcare in a case model focusing learnings for both groups. The small-scale live-case model offers a resource-efficient learning activity for both traditional courses and LLL courses. The unique characteristics is that the model is strongly delineate in time (duration: one week), and that it focuses not only the students' but also the practitioners’ learning.
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| 6. |
- Smeds, Patrik, et al.
(författare)
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Hydra-genetics, a modular framework for bioinformatics pipeline development
- 2024
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Ingår i: European Journal of Human Genetics. - : Nature Portfolio. - 1018-4813 .- 1476-5438. ; 32:Suppl. 1, s. 675-676
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Background: Processing information from massively parallel sequencing/next-generation sequencing (NGS) data involves several steps that transform millions of rows of input data into more accessible genetic information. The combination of bioinformatics tools that extract all requested information for a particular clinical/research application, how they are tuned and the order in which they are executed constitute a bioinformatics pipeline. Software is often reused in several pipelines and regularly updated. For clinically validated NGS pipelines it may be challenging when individual components of several pipelines needs updating or when tools are replaced with new applications.Methods: The Hydra-genetics framework takes advantage of version controlled Snakemake modules. Pipeline steps are split into modules that can be configured and tested individually. The modules can be combined to build complete bioinformatics analyses, or be added to existing pipelines. All modules are subjected to extensive testing to ensure that new releases do not unexpectedly break existing pipelines or deviate from guidelines and best practices on how to write code.Results: Bioinformaticians from five Genomics Medicine Sweden centers used Hydra-genetics to develop the bioinformatics pipeline for the comprehensive solid tumor panel, GMS560. The pipeline analyses tumor DNA and/or RNA data and generates information on genetic variation including complex biomarkers such as tumor mutation burden and microsatellite instability. It is validated and in clinical use.Conclusions: The Hydra-genetics framework provides a platform for structured bioinformatics pipeline development and facilitates joint development projects involving multiple partners. It makes clinical pipeline development easier, faster and more structured.
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| 7. |
- Xu, Chunlin, et al.
(författare)
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Carboxymethylated spruce galactoglucomannans : preparation, characterisation, dispersion stability, water-in-oil emulsion stability, and sorption on cellulose surface
- 2011
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Ingår i: Nordic Pulp & Paper Research Journal. - : Walter de Gruyter GmbH. - 0283-2631 .- 2000-0669. ; 26:2, s. 167-178
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Tidskriftsartikel (refereegranskat)abstract
- Natively acetylated galactoglucomannans (GGMs) is the main hemicellulose type in most softwood species and can be utilised as, for example, bioactive polymers, hydrocolloids, papermaking chemicals, or coating polymers. In this study, carboxymethylated GGMs (CM-GGMs) were prepared and characterised by GC-MS, H-1 and C-13 NMR and FTIR spectroscopy, and SEC-MALLS. The thermal stability of the products was investigated by DSC-TGA. The accessibility of different C-positions in mannose and glucose was investigated. The emulsion stability of CM-GGMs in resin dispersion was studied and it was shown that CM-GGMs can stabilise the resin dispersion also in presence of CaCl2. The possibility of using CM-GGMs as emulsifiers in water-in-oil emulsions was assessed. A CM-GGM with a DS value of 0.25 at a concentration higher than 3% performed the best. Finally, the study of sorption of CM-GGM onto cellulose surface exhibited a decrease in binding ability with an increase in the degree of substitution (DS).
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