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  • Ericsson, Olle, et al. (författare)
  • Clinical validation of a novel automated cell-free DNA screening assay for trisomies 21, 13, and 18 in maternal plasma.
  • 2019
  • Ingår i: Prenatal diagnosis. - 1097-0223. ; 39:11, s. 1011-1015
  • Tidskriftsartikel (refereegranskat)abstract
    • To evaluate clinical performance of a new automated cell-free (cf)DNA assay in maternal plasma screening for trisomies 21, 18, and 13, and to determine fetal sex.Maternal plasma samples from 1200 singleton pregnancies were analyzed with a new non-sequencing cfDNA method, which is based on imaging and counting specific chromosome targets. Reference outcomes were determined by either cytogenetic testing, of amniotic fluid or chorionic villi, or clinical examination of neonates.The samples examined included 158 fetal aneuploidies. Sensitivity was 100% (112/112) for trisomy 21, 89% (32/36) for trisomy 18, and 100% (10/10) for trisomy 13. The respective specificities were 100%, 99.5%, and 99.9%. There were five first pass failures (0.4%), all in unaffected pregnancies. Sex classification was performed on 979 of the samples and 99.6% (975/979) provided a concordant result.The new automated cfDNA assay has high sensitivity and specificity for trisomies 21, 18, and 13 and accurate classification of fetal sex, while maintaining a low failure rate. The study demonstrated that cfDNA testing can be simplified and automated to reduce cost and thereby enabling wider population-based screening.
  • Gustafsson, Harald, et al. (författare)
  • Den dubbla blicken. En inledning
  • 2007
  • Ingår i: Den dubbla blicken. Historia i de nordiska samhällena. - Sekel Bokförlag. - 978-91-85767-00-7 ; s. 7-26
  • Bokkapitel (övrigt vetenskapligt)
  • Nyberg, Lena K., et al. (författare)
  • A single-step competitive binding assay for mapping of single DNA molecules
  • 2012
  • Ingår i: Biochemical and Biophysical Research Communications. - 0006-291X. ; 417:1, s. 404-408
  • Tidskriftsartikel (refereegranskat)abstract
    • Optical mapping of genomic DNA is of relevance for a plethora of applications such as scaffolding for sequencing and detection of structural variations as well as identification cif pathogens like bacteria and viruses. For future clinical applications it is desirable to have a fast and robust mapping method based on as few steps as possible. We here demonstrate a single-step method to obtain a DNA barcode that is directly visualized using nanofluidic devices and fluorescence microscopy. Using a mixture of YOYO-1, a bright DNA dye, and netropsin, a natural antibiotic with very high AT specificity, we obtain a DNA map with a fluorescence intensity profile along the DNA that reflects the underlying sequence. The netropsin binds to AT-tetrads and blocks these binding sites from YOYO-1 binding which results in lower fluorescence intensity from AT-rich regions of the DNA. We thus obtain a DNA barcode that is dark in AT-rich regions and bright in GC-rich regions with kilobasepair resolution. We demonstrate the versatility of the method by obtaining a barcode on DNA from the phage T4 that captures its circular permutation and agrees well with its known sequence.
  • Persson, Fredrik, et al. (författare)
  • 2017
  • Ingår i: 2017 WINTER SIMULATION CONFERENCE (WSC). - IEEE. - 978-1-5386-3428-8 ; s. 3768-3779
  • Konferensbidrag (refereegranskat)abstract
    • Safety stock calculations are difficult for products with intermittent demand, long production lead times, and high monetary values. Theoretically, forecasts can be used to reduce the need for safety stocks. A high precision forecast minimizes the need for safety stock and forecast evaluation measurements can be used to calculate the safety stock level. However, a more realistic determination of safety stock levels can he obtained by simulation. In this paper, simulation is used to model and experiment on a case with three end products in order to determine the relationship between safety stock levels and service levels. Also, a comparison is made with theoretically calculated safety stocks to see how well basic theoretical models for safety stock calculations fulfill the requirements of service level. The result is that simulation can provide a much more accurate determination of safety stock levels for intermittent demands than theoretical calculations.
  • Alizadehheidari, Mohammadreza, et al. (författare)
  • Nanoconfined Circular and Linear DNA: Equilibrium Conformations and Unfolding Kinetics
  • 2015
  • Ingår i: Macromolecules. - The American Chemical Society (ACS). - 0024-9297. ; 48:3, s. 871-878
  • Tidskriftsartikel (refereegranskat)abstract
    • Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of confined DNA from the circular to linear configuration as a light-induced double-strand break occurs, characterize the dynamics, and compare the equilibrium conformational statistics of linear and circular configurations. This is important because it allows us to determine to what extent existing statistical theories describe the extension of confined circular DNA. We find that the ratio of the extensions of confined linear and circular DNA configurations increases as the buffer concentration decreases. The experimental results fall between theoretical predictions for the extended de Gennes regime at weaker confinement and the Odijk regime at stronger confinement. We show that it is possible to directly distinguish between circular and linear DNA molecules by measuring the emission intensity from the DNA. Finally, we determine the rate of unfolding and show that this rate is larger for more confined DNA, possibly reflecting the corresponding larger difference in entropy between the circular and linear configurations.
  • Alizadehheidari, Mohammadreza, et al. (författare)
  • Nanoconfined Circular DNA
  • 2014
  • Ingår i: Biophysical Journal. - 0006-3495 .- 1542-0086. ; 106:2, s. 274A-274A
  • Tidskriftsartikel (övrigt vetenskapligt)abstract
    • Nanofluidic channels have become a versatile tool to manipulate single DNA molecules. They allow investigation of confined single DNA molecules from a fundamental polymer physics perspective as well as for example in DNA barcoding techniques.
  • Alizadehheidari, Mohammadreza, et al. (författare)
  • Unfolding of nanoconfined circular DNA
  • 2015
  • Ingår i: BIOPHYSICAL JOURNAL. - 0006-3495. ; 108:2 Supplement 1, s. 231A-231A
  • Tidskriftsartikel (övrigt vetenskapligt)
  • Asp, Michaela, et al. (författare)
  • Spatial detection of fetal marker genes expressed at low level in adult human heart tissue
  • 2017
  • Ingår i: Scientific Reports. - NATURE PUBLISHING GROUP. - 2045-2322 .- 2045-2322. ; 7
  • Tidskriftsartikel (refereegranskat)abstract
    • Heart failure is a major health problem linked to poor quality of life and high mortality rates. Hence, novel biomarkers, such as fetal marker genes with low expression levels, could potentially differentiate disease states in order to improve therapy. In many studies on heart failure, cardiac biopsies have been analyzed as uniform pieces of tissue with bulk techniques, but this homogenization approach can mask medically relevant phenotypes occurring only in isolated parts of the tissue. This study examines such spatial variations within and between regions of cardiac biopsies. In contrast to standard RNA sequencing, this approach provides a spatially resolved transcriptome- and tissue-wide perspective of the adult human heart, and enables detection of fetal marker genes expressed by minor subpopulations of cells within the tissue. Analysis of patients with heart failure, with preserved ejection fraction, demonstrated spatially divergent expression of fetal genes in cardiac biopsies.
  • Enlund, Fredrik, 1968-, et al. (författare)
  • Molecular analyses of the candidate tumor suppressor gene, PLAGL1, in benign and malignant salivary gland tumors
  • 2004
  • Ingår i: EUROPEAN JOURNAL OF ORAL SCIENCES. - 0909-8836. ; 112:6, s. 545-547
  • Tidskriftsartikel (refereegranskat)abstract
    • Deletions affecting the long arm of chromosome 6 are a characteristic feature of all major subtypes of malignant salivary gland tumors. Moreover, a subgroup of adenoid cystic carcinomas have t(6;9)(q23-25;p21-24) translocations with breakpoints located within the commonly deleted region. Here we have examined the possible involvement of the candidate tumor suppressor gene, PLAGL1, in these deletions and translocations. Northern blot and fluorescence in situ hybridization (FISH) analyses of a series of 27 salivary gland tumors revealed no significant changes in the gene expression or rearrangements of PLAGL1. FISH analysis also demonstrated that the 6q translocation breakpoint in adenoid cystic carcinomas with t(6;9) is proximal to the PLAGL1 locus. Collectively, these results indicate that PLAGL1 is not likely to be the major target gene of the 6q rearrangements in salivary gland tumors.
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