| 1. |
- Hilson, P., et al.
(författare)
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Versatile gene-specific sequence tags for Arabidopsis functional genomics : Trancript profiling and reverse genetics applications
- 2004
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Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 14:10B, s. 2176-2189
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Tidskriftsartikel (refereegranskat)abstract
- Microarray transcript profiling and RNA interference are two new technologies crucial for large-scale gene function studies in multicellular eukaryotes. Both rely on sequence-specific hybridization between complementary nucleic acid strands, inciting us to create a collection of gene-specific sequence tags (GSTs) representing at least 21,500 Arabidopsis genes and which are compatible with both approaches. The GSTs were carefully selected to ensure that each of them shared no significant similarity with any other region in the Arabidopsis genome. They were synthesized by PCR amplification from genomic DNA. Spotted microarrays fabricated from the GSTs show good dynamic range, specificity, and sensitivity in transcript profiling experiments. The GSTs have also been transferred to bacterial plasmid vectors via recombinational cloning protocols. These cloned GSTs constitute the ideal starting point for a variety of functional approaches, including reverse genetics. We have subcloned GSTs on a large scale into vectors designed for gene silencing in plant cells. We show that in planta expression of GST hairpin RNA results in the expected phenotypes in silenced Arabidopsis lines. These versatile GST resources provide novel and powerful tools for functional genomics.
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| 6. |
- Andersson, T., et al.
(författare)
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Novel candidate genes for atherosclerosis are identified by representational difference analysis-based transcript profiling of cholesterol-loaded macrophages
- 2001
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Ingår i: Pathobiology (Basel). - : S. Karger AG. - 1015-2008 .- 1423-0291. ; 69:6, s. 304-314
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: To analyze the early gene expression in macrophages accompanying the phenotypic changes into foam cells upon exposure to oxidized low-density lipoprotein. To identify candidate genes and markers for further studies into the pathogenesis of atherosclerosis. Methods: Cells of the monocytic cell line THP-1 were activated by PMA and exposed to oxidized low-density lipoprotein. Gene expression profiles were investigated after 24 h, using a solid phase cDNA representational difference analysis (RDA) method and shotgun sequencing. Results were verified by microarray hybridization, and analyzed in the virtual chip display of a novel software tool for transcript profile exploration. Results: By comparing transcript profiles of exposed/unexposed cells, 1,984 transcript sequences, representing a total of 921 genes with altered expression levels in response to oxidized low-density lipoprotein exposure, were identified. Genes that are central to cell cycle control and proliferation, inflammatory response, and of pathways not previously implicated in atherosclerosis were identified. The data obtained is also made available on-line at http:// biobase.biotech.kth.se/thp1a for further exploration. Conclusion: The identification of new candidate genes for atherosclerotic disease through RDA-based transcript profiling facilitates further functional genomic studies in coronary artery disease. Candidate genetic polymorphism markers of potential clinical relevance can be identified by filtering information in genome variation databases through the virtual chip analysis of the transcript profiles and subsequently tested in association studies.
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| 8. |
- Andersson, T., et al.
(författare)
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Shotgun sequencing and microarray analysis of RDA transcripts
- 2003
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Ingår i: Gene. - : Elsevier BV. - 0378-1119 .- 1879-0038. ; 310, s. 39-47
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Tidskriftsartikel (refereegranskat)abstract
- Monitoring of differential gene expression is an important step towards understanding of gene function. We describe a comparison of the representational difference analysis (RDA) subtraction process with corresponding microarray analysis. The subtraction steps are followed in a quantitative manner using a shotgun cloning and sequencing procedure that includes over 1900 gene sequences. In parallel, the enriched transcripts are spotted onto microarrays facilitating large scale hybridization analysis of the representations and the difference products. We show by the shotgun procedure that there is a high diversity of gene fragments represented in the iterative RDA products (92-67% singletons) with a low number of shared sequences (<9%) between subsequent subtraction cycles. A non redundant set of 1141 RDA clones were immobilized on glass slides and the majority of these clones (97%) gave repeated good fluorescent signals in a subsequent hybridization of the labelled and amplified original cDNA. We observed only a low number of false positives (<2%) and a more than twofold differential expression for 32% (363) of the immobilized RDA clones. In conclusion, we show that by random sequencing of the difference products we obtained an accurate transcript profile of the individual steps and that large-scale confirmation of the obtained transcripts can be achieved by microarray analysis.
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| 9. |
- Geale, Kirk, et al.
(författare)
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Persistence of biologic treatment in psoriatic arthritis : a population-based study in Sweden
- 2020
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Ingår i: Annals of the Rheumatic Diseases. - : BMJ Publishing Group Ltd. - 0003-4967 .- 1468-2060. ; 79, s. 37-38
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Psoriatic arthritis (PsA) is a chronic, heterogeneous, immune-mediated seronegative arthritis characterized by joint inflammation in people with skin psoriasis (PsO). In recent years several effective biologic treatments such as tumour necrosis factor inhibitors (TNFi), interleukin (IL) 12 and 23 inhibitors (IL-12/23i), and IL 17 inhibitors (IL-17i) have been introduced for PsA. Discontinuation (non-persistence) of therapy is usually a consequence of lack of effect and intolerability.Objectives:Compare time to discontinuation of TNFi (adalimumab, ADA), IL-17i (secukinumab, SEC), and IL-12/23i (ustekinumab, UST) treatment exposures and the association with previous biologic treatment experience.Methods:Population-based national health data from the Swedish Patient Registry, Prescribed Drug Registry and Cause of Death Registry were linked at the patient level and used to identify treatment exposures in PsA patients initiating ADA, SEC, or UST between January 2008 and September 2018. Discontinuation was defined as a treatment switch to any other PsA-indicated biologic, or failure to re-dispense treatment within a grace period following end of drug supplied. The grace period, defined as the number of days between end of drug supply and re-dispensation during which a patient is considered to be on active treatment, was set dynamically to the number of days of drug supplied in the primary analysis. As a sensitivity analysis, a fixed 90-day grace period was used. Supply was calculated as total milligrams dispensed divided by maintenance dose posology, where the following assumptions were made due to the limitations of the administrative data used: UST patients’ weight corresponded to the amount of drug dispensed (both 45mg and 90mg dispensations last 84 days), SEC patients with prior TNFi experience consumed 300mg/28 days and all others consumed 150mg/28 days, and ADA patients consumed 40mg/14 days. Adjusted hazard ratios (HR) for time to discontinuation were calculated using a Cox proportional hazards model. Covariates for age, marital status, and previous biologic treatment experience were assessed at the initiation of treatment exposure, while comorbidity including skin PsO was assessed during the two years prior. Exposures without discontinuation events were censored at death or end of follow-up. The study was approved by the Stockholm Regional Ethical Review Board.Results:3,620 discontinuation events were observed in the main analysis across 4,649 treatment exposures (ADA: 3,255; SEC: 887; UST: 507) (Figure 1, unadjusted). 3,162 events were observed in the sensitivity analysis. Average age at treatment initiation was 50, 54% were female, 47% were biologic treatment naïve, and 39% had skin PsO. In the multivariate main analysis, UST exhibited lower discontinuation rates vs ADA (HR=0.56, 95% CI: 0.49-0.64) while there was no significant difference between SEC and ADA (HR=1.01, 95% CI: 0.88-1.15). In the multivariate sensitivity analysis, both UST (HR=0.81, 95% CI: 0.70-0.94) and SEC (HR=0.82, 95% CI: 0.70-0.95) were associated with significantly lower discontinuation rates ratio relative to ADA. Overall, patients with more biologic treatment experience were statistically significantly (p<0.05) associated with higher risk of treatment discontinuation.Figure 1.Unadjusted Kaplan-Meier curves of time to treatment discontinuation (main analysis, dynamic grace period)Conclusion:UST exhibits a favourable treatment persistency profile relative to ADA, regardless of the grace period definition. The relative risk of discontinuing SEC vs ADA is sensitive to the grace period. Treatment discontinuation was higher in treatment exposures with more biologic experience.Disclosure of Interests:Kirk Geale Consultant of: Quantify Research, Speakers bureau: Indirectly as a consultant, Ingrid Lindberg Consultant of: Quantify Research, Emma Paulsson Consultant of: Quantify Research, Christina Wennerström Employee of: Janssen-Cilag Sweden AB, Anna Tjärnlund Employee of: Janssen-Cilag Sweden AB, Virginia Taliadouros Shareholder of: JnJ, Employee of: Janssen Pharmaceuticals NV, Wim Noel Employee of: Janssen Pharmaceuticals NV, Dana Enkusson Employee of: Janssen-Cilag AB, Elke Theander Employee of: Janssen-Cilag Sweden AB, Sara Bruce Wirta Employee of: Janssen-Cilag Sweden AB
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| 17. |
- Nilsson, D., et al.
(författare)
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Whole-Genome Sequencing of Cytogenetically Balanced Chromosome Translocations Identifies Potentially Pathological Gene Disruptions and Highlights the Importance of Microhomology in the Mechanism of Formation
- 2017
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Ingår i: Human Mutation. - : John Wiley & Sons. - 1059-7794 .- 1098-1004. ; 38:2, s. 180-192
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Tidskriftsartikel (refereegranskat)abstract
- Most balanced translocations are thought to result mechanistically from nonhomologous end joining or, in rare cases of recurrent events, by nonallelic homologous recombination. Here, we use low-coverage mate pair whole-genome sequencing to fine map rearrangement breakpoint junctions in both phenotypically normal and affected translocation carriers. In total, 46 junctions from 22 carriers of balanced translocations were characterized. Genes were disrupted in 48% of the breakpoints; recessive genes in four normal carriers and known dominant intellectual disability genes in three affected carriers. Finally, seven candidate disease genes were disrupted in five carriers with neurocognitive disabilities (SVOPL, SUSD1, TOX, NCALD, SLC4A10) and one XX-male carrier with Tourette syndrome (LYPD6, GPC5). Breakpoint junction analyses revealed microhomology and small templated insertions in a substantive fraction of the analyzed translocations (17.4%; n = 4); an observation that was substantiated by reanalysis of 37 previously published translocation junctions. Microhomology associated with templated insertions is a characteristic seen in the breakpoint junctions of rearrangements mediated by error-prone replication-based repair mechanisms. Our data implicate that a mechanism involving template switching might contribute to the formation of at least 15% of the interchromosomal translocation events.
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| 18. |
- Nystedt, B., et al.
(författare)
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Sarek : A portable workflow for whole-genome sequencing analysis of germline and somatic variants
- 2020
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Ingår i: F1000 Research. - : F1000 Research Ltd. - 2046-1402. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Whole-genome sequencing (WGS) is a fundamental technology for research to advance precision medicine, but the limited availability of portable and user-friendly workflows for WGS analyses poses a major challenge for many research groups and hampers scientific progress. Here we present Sarek, an open-source workflow to detect germline variants and somatic mutations based on sequencing data from WGS, whole-exome sequencing (WES), or gene panels. Sarek features (i) easy installation, (ii) robust portability across different computer environments, (iii) comprehensive documentation, (iv) transparent and easy-to-read code, and (v) extensive quality metrics reporting. Sarek is implemented in the Nextflow workflow language and supports both Docker and Singularity containers as well as Conda environments, making it ideal for easy deployment on any POSIX-compatible computers and cloud compute environments. Sarek follows the GATK best-practice recommendations for read alignment and pre-processing, and includes a wide range of software for the identification and annotation of germline and somatic single-nucleotide variants, insertion and deletion variants, structural variants, tumour sample purity, and variations in ploidy and copy number. Sarek offers easy, efficient, and reproducible WGS analyses, and can readily be used both as a production workflow at sequencing facilities and as a powerful stand-alone tool for individual research groups. The Sarek source code, documentation and installation instructions are freely available at https://github.com/nf-core/sarek and at https://nf-co.re/sarek/.
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| 23. |
- Rodin, S., et al.
(författare)
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Performance of a 70-mer oligonucleotide microarray for genotyping of Campylobacter jejuni
- 2008
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Ingår i: BMC Microbiology. - : Springer Science and Business Media LLC. - 1471-2180. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Campylobacter jejuni is widespread in the environment and is the major cause of bacterial gastroenteritis in humans. In the present study we use microarray-based comparative genomic hybridizations (CGH), pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) to analyze closely related C. jejuni isolates from chicken and human infection. RESULTS: With the exception of one isolate, the microarray data clusters the isolates according to the five groups determined by PFGE. In contrast, MLST defines only three genotypes among the isolates, indicating a lower resolution. All methods show that there is no inherit difference between isolates infecting humans and chicken, suggesting a common underlying population of C. jejuni. We further identify regions that frequently differ between isolates, including both previously described and novel regions. Finally, we show that genes that belong to certain functional groups differ between isolates more often than expected by chance. CONCLUSION: In this study we demonstrated the utility of 70-mer oligonucleotide microarrays for genotyping of Campylobacter jejuni isolates, with resolution outperforming MLST.
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| 26. |
- Wikstrom, G., et al.
(författare)
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Drug treatment patterns in patients newly diagnosed with heart failure : a retrospective population-based cohort study in Sweden
- 2017
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Ingår i: European Journal of Heart Failure. - : European Society of Cardiology. - 1388-9842 .- 1879-0844. ; 19:S1, s. 55-55
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Tidskriftsartikel (refereegranskat)abstract
- Background and purpose: Limited data are available on longitudinal drug treatment patterns in newly diagnosed patients with heart failure (HF) with preserved (HFpEF), reduced (HFrEF) and unknown ejection fraction (EF) in Sweden. We evaluated drug treatment patterns in these patients based on ESC 2012 guidelines, which recommend treatment with angiotensin-converting enzyme inhibitors (ACEis), angiotensin II receptor blockers (ARBs), ?-blockers (BBs) and mineralocorticoid receptor antagonists (MRAs) for HFrEF (ESC does not make recommendations for HFpEF or unknown EF).Methods: Patients were identified via electronic medical records from primary and/or secondary care in Västerbotten, linked via unique identifiers to the National Patient Register and Swedish Prescribed Drug Register. Local echocardiography data identified HFrEF (<50%) and HFpEF (≥50%). Patients aged ≥18 years with ≥2 diagnoses of HF between 01/01/2010 and 31/03/2015 and an ICD-10 diagnostic code of I50 (inclusive of all granular codes), I42.0, I42.6, I42.7, I42.9, I110, I130 or I132 in any position were included. The date of the first diagnosis was defined as the index date. A 10-year look-back period was used to exclude prevalent HF cases. ATC codes were identified from drug prescriptions. Patients with a 4-year look-back and 2 years of follow-up were included.Results: Overall, 4357 patients were included (mean± SD age, 76.6± 12.6 years; 27.7% aged ≥85 years; HFrEF, 24.6%; HFpEF, 12.9%; unknown EF, 62.5%). At the index date, 63.0% of patients were treated with an ACEi or an ARB, 62.3% with a BB and 16.0% with an MRA; 18.5% were not receiving treatment. The most common treatment groups (monotherapy or combinations) were: ACEi + BB (HFrEF, 20.5%; HFpEF, 21.0%; unknown EF, 23.5%); BB monotherapy (HFrEF, 12.1%; HFpEF, 14.0%; unknown EF, 15.6%); and ARB + BB (HFrEF, 8.5%; HFpEF, 12.3%; unknown EF, 12.3%) (Figure). The majority of patients receiving an ACEi or ARB at the index date continued to do so for the following 2 years (ACEi, 63.6%; ARB, 60.9%); most of these were receiving doses lower than those recommended by the ESC (70.8% and 88.9%, respectively). A small proportion of patients receiving an ACEi at the index date switched to an ARB over the 2-year period (4.1%) and vice versa (2.6%). Most patients were not receiving the recommended ESC dose before switching (ACEi, 81.8%; ARB, 77.8%). Similarly, most patients who discontinued an ACEi (37.3%) or ARB (39.1%) were not receiving the recommended dose before discontinuation (ACEi, 64.8%; ARB, 87.4%).Conclusions: A large proportion of patients with HF in Sweden do not receive drug combinations recommended by the ESC. Furthermore, few patients are prescribed ESC-recommended doses of HF drugs and few undergo up-titration of treatment before switching. These findings are remarkable for HFrEF, for which guidelines are established. These findings may be partly reflective of the high proportion of elderly patients studied.
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