| 1. |
- Ameur, Adam, et al.
(författare)
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SweGen : a whole-genome data resource of genetic variability in a cross-section of the Swedish population
- 2017
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Ingår i: European Journal of Human Genetics. - : NATURE PUBLISHING GROUP. - 1018-4813 .- 1476-5438. ; 25:11, s. 1253-1260
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Tidskriftsartikel (refereegranskat)abstract
- Here we describe the SweGen data set, a comprehensive map of genetic variation in the Swedish population. These data represent a basic resource for clinical genetics laboratories as well as for sequencing-based association studies by providing information on genetic variant frequencies in a cohort that is well matched to national patient cohorts. To select samples for this study, we first examined the genetic structure of the Swedish population using high-density SNP-array data from a nation-wide cohort of over 10 000 Swedish-born individuals included in the Swedish Twin Registry. A total of 1000 individuals, reflecting a cross-section of the population and capturing the main genetic structure, were selected for whole-genome sequencing. Analysis pipelines were developed for automated alignment, variant calling and quality control of the sequencing data. This resulted in a genome-wide collection of aggregated variant frequencies in the Swedish population that we have made available to the scientific community through the website https://swefreq.nbis.se. A total of 29.2 million single-nucleotide variants and 3.8 million indels were detected in the 1000 samples, with 9.9 million of these variants not present in current databases. Each sample contributed with an average of 7199 individual-specific variants. In addition, an average of 8645 larger structural variants (SVs) were detected per individual, and we demonstrate that the population frequencies of these SVs can be used for efficient filtering analyses. Finally, our results show that the genetic diversity within Sweden is substantial compared with the diversity among continental European populations, underscoring the relevance of establishing a local reference data set.
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| 2. |
- Jemt, Anders, 1985-, et al.
(författare)
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Evaluation of methods for whole genome and transcriptome sequencing from nanograms of FFPE samples
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The most widely used method for the preservation of clinical tissue specimens is formalin fixation and paraffin embedding (FFPE). Simultaneous analysis of RNA and DNA from samples preserved using this method have long proved problematic, primarily due to lack of material. Here, we describe an attempt to build a complete analysis package for RNA and DNA extracted from single tissue sections. The workflow includes quality control of the extracted material, library preparation and data analysis. We extract DNA with varying integrity from FFPE sections and subject them to whole genome sequencing using two library preparation methods, Illumina TruSeq Nano using the Illumina NeoPrep and Rubicon Genomics ThruPlex. We are able to obtain some usable data, albeit with high duplication rates, demonstrating both the possibilities and challenges of sequencing damaged DNA. Two different approaches to transcriptome sequencing are assessed, the TruSeq RNA Access library preparation kit from Illumina and the SMARTer Stranded Total RNA-Seq Kit - Pico Input from Clonetech. The sequence capture approach of the TruSeq kit is shown to be more robust to low integrity RNA compared to the SMARTer kit. However, the SMARTer kit needs much less starting material and is able to yield data about all transcripts, not just protein coding mRNA.
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| 3. |
- Akan, Pelin, et al.
(författare)
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Comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines
- 2012
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Ingår i: Genome Medicine. - : Springer Science and Business Media LLC. - 1756-994X .- 1756-994X. ; 4, s. 86-
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Tidskriftsartikel (refereegranskat)abstract
- We here present a comparative genome, transcriptome and functional network analysis of three human cancer cell lines (A431, U251MG and U2OS), and investigate their relation to protein expression. Gene copy numbers significantly influenced corresponding transcript levels; their effect on protein levels was less pronounced. We focused on genes with altered mRNA and/or protein levels to identify those active in tumor maintenance. We provide comprehensive information for the three genomes and demonstrate the advantage of integrative analysis for identifying tumor-related genes amidst numerous background mutations by relating genomic variation to expression/protein abundance data and use gene networks to reveal implicated pathways.
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| 4. |
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| 5. |
- Berglund, Leo, 1986-
(författare)
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Kritiskt tänkande som utbildningsmål : Från modernistisk filosofi till policy för högre utbildning
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The goal of critical thinking in higher education is paradoxical, since it implies a form of education that both directs the student towards a pre-defined goal, and commands the student to be autonomous. This paradox is studied in four contexts, as to investigate what pedagogical contradictions the goal of critical thinking generates, and how they transform pedagogical thinking. 1) In the 1930s, European logical positivists cooperated with American pragmatists to "unify science". For Dewey, the realisation of this ideal depended on individuals adopting a "scientific attitude", which could be cultivated in schools and universities. Dewey’s position influenced a pedagogical discourse of critical thinking as the spirit of rational and democratic citizenship. 2) In the 1980s, the Critical Thinking Movement (CTM) addressed the issue on how to make logical thinking applicable in everyday life. Understanding critical thinking as individuals’ problem-solving skills, the CTM essentially inverted the collectivist political orientation of Dewey and the neo-positivists. 3) In the Swedish 1968 governmental investigation of higher education (U 68), a sociologically informed conception of critical thinking, that involved the student in the project of social planning, was promoted. However, educational experts perceived critical thinking as a vague goal, which could not be operationalised. In the 1990s, critical thinking reappeared as part of the doctrine of learning, but only as a generic term used to signify advanced cognitive operations in relation to different subject matters. 4) In contemporary courses in critical thinking held at Swedish universities, radically diverse conceptions are being taught. An analysis of three courses identified three subjectivities "called" by the arrangements and bodies of literature in the courses: the critical thinker as reason, intellect, and moral consciousness. Each of the subjectivities, however, comprises inconsistencies and contradictions, since they are all to be both produced by and autonomous from the orders that the educational institution represents. The dissertation is concluded by a discussion on critical thinking as both a goal and a by-product of education.
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| 6. |
- Borgström, Erik, et al.
(författare)
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Large Scale Library Generation for High Throughput Sequencing Authors and Affiliations
- 2011
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 6:4, s. e19119-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Large efforts have recently been made to automatethe sample preparation protocols for massively parallel sequencing in order to match the increasing instrument throughput. Still, the size selection through agarose gel electrophoresis separation is a labor-intensive bottleneck of these protocols. Methodology/Principal Findings: In this study a method for automatic library preparation and size selection on a liquid handling robot is presented. The method utilizes selective precipitation of certain sizes of DNA molecules on to paramagnetic beads for cleanup and selection after standard enzymatic reactions. Conclusions/Significance: The method is used to generate libraries for de novo and re-sequencing on the Illumina HiSeq 2000 instrument with a throughput of 12 samples per instrument in approximately 4 hours. The resulting output data show quality scores and pass filter rates comparable to manually prepared samples. The sample size distribution can be adjusted for each application, and are suitable for all high throughput DNA processing protocols seeking to control size intervals.
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| 7. |
- Borgström, Erik, et al.
(författare)
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Phasing of single DNA molecules by massively parallel barcoding
- 2015
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- High-throughput sequencing platforms mainly produce short-read data, resulting in a loss of phasing information for many of the genetic variants analysed. For certain applications, it is vital to know which variant alleles are connected to each individual DNA molecule. Here we demonstrate a method for massively parallel barcoding and phasing of single DNA molecules. First, a primer library with millions of uniquely barcoded beads is generated. When compartmentalized with single DNA molecules, the beads can be used to amplify and tag any target sequences of interest, enabling coupling of the biological information from multiple loci. We apply the assay to bacterial 16S sequencing and up to 94% of the hypothesized phasing events are shown to originate from single molecules. The method enables use of widely available short-read-sequencing platforms to study long single molecules within a complex sample, without losing phase information.
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| 8. |
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| 9. |
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Den förnekade kunskapen. En introduktion till Robert Pfallers filosofi
- 2019
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Samlingsverk (redaktörskap) (övrigt vetenskapligt/konstnärligt)abstract
- Robert Pfaller är en österrikisk filosof och kulturteoretiker med intressen som sträcker sig från epistemologi och psykoanalys, via konst och populärkultur, till ideologikritik och politik. Han ägnar sig åt frågan om ”trons form” – det vill säga inte vad vi tror på, utan hur vi tror. Pfaller kan hjälpa oss förstå sambandet mellan två aktuella tendenser i det moderna samhället: å ena sidan den av nyliberalismen pådrivna nedmonteringen av välfärdssystemen, vilken förändrar vårt samhälle och våra livsvillkor i grunden till det sämre; å andra sidan den tilltagande moralismen inom det politiska området, som fäster sig vid sådant som rökning, plastpåsar, musik på hög volym, könsstereotyper och köttätande. Pfaller gör det möjligt att i båda dessa tendenser identifiera ett narcissistiskt ”ansvarstagande” som är mer upptaget av att framställa sig själv som moraliskt högtstående, än att bereda väg för ett gott liv. Det är denna fråga – om det goda livet, och om lyckan, som Pfaller vill ge plats i den politiska debatten och i den filosofiska diskussionen. Föreliggande volym är en introduktion till Pfallers filosofi med bidrag som visar dess relevans inom områden som psykoanalys, sociologi, teologi, pedagogik och socialt arbete.
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| 10. |
- Dodillet, Susanne, 1977, et al.
(författare)
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Constructing professionalism in teacher education. Analytical tools from a comparative study.
- 2019
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Ingår i: Education Inquiry. - : Informa UK Limited. - 2000-4508. ; 10:3, s. 208-225
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Tidskriftsartikel (refereegranskat)abstract
- This article studies the meaning of professionalism in current attempts to professionalise teachers by means of education. The point of departure for our analysis is a small-scale survey among Swedish and German student teachers on their perception of the meaning of professionalism with regard to teachers’ work. The article presents two contrasting ideal types of professionalism identified in this data: the concept of science-based professionalism is characterised by an ambition to develop theories that can be translated into more or less direct prescriptions for the efficient exercise of the profession; the concept of pedagogic professionalism, in contrast, originates in basic mistrust of this ambition concerning teachers’ work and instead aims to develop a thorough understanding of the paradoxes and antinomies of education. The article outlines the theoretical foundations of these ideal types and shows how they can shed light on the aims of educational research in different contexts, as well as help explain the rationale behind structural differences in the design of teacher education programmes.
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