Karlsson M.K.,DiaGenic ASA |
Karlsson M.K.,Norwegian University of Life Sciences |
Lonneborg A.,DiaGenic ASA |
Saebo S.,Norwegian University of Life Sciences
Statistics in Medicine | Year: 2012
Recent discoveries and developments in the field of genomics have led to the commercialization of novel diagnostic devices for studying disease or estimating therapeutic outcomes in individual patients. With this emerging field, the emphasis is shifting to integration of clinical research into product development. Data acquisition is primary in the initial exploratory phase of product development, and during the process of sample collection and data generation in clinical microarray studies, great amounts of additional information, such as demographic, clinical, and study design variables associated with the data, are often accumulated and made available. Including additional information in classification has been addressed in many different ways. However, in previous studies, the additional information have consistently been treated as extra predictors, which can be a problem for future prediction if such information are not available or collectable for the new samples. We instead propose to adopt a method called canonical partial least squares, which for our purpose, only uses the additional information at the model building stage to stabilize the construction of a classifier for disease status from microarray data. The canonical partial least squares method is compared with regular partial least squares for the classification of Parkinson's disease from gene expression in peripheral blood samples and also through computer simulations. The present study showed that including clinical data in the model building produces simpler and more stable models for prediction of Parkinson's disease from gene expression data. © 2012 John Wiley & Sons, Ltd.
Aaroe J.,University of Oslo |
Lindahl T.,DiaGenic ASA |
Dumeaux V.,University of Tromsø |
Saebo S.,Norwegian University of Life Sciences |
And 6 more authors.
Breast Cancer Research | Year: 2010
Introduction: Early detection of breast cancer is key to successful treatment and patient survival. We have previously reported the potential use of gene expression profiling of peripheral blood cells for early detection of breast cancer. The aim of the present study was to refine these findings using a larger sample size and a commercially available microarray platform.Methods: Blood samples were collected from 121 females referred for diagnostic mammography following an initial suspicious screening mammogram. Diagnostic work-up revealed that 67 of these women had breast cancer while 54 had no malignant disease. Additionally, nine samples from six healthy female controls were included. Gene expression analyses were conducted using high density oligonucleotide microarrays. Partial Least Squares Regression (PLSR) was used for model building while a leave-one-out (LOO) double cross validation approach was used to identify predictors and estimate their prediction efficiency.Results: A set of 738 probes that discriminated breast cancer and non-breast cancer samples was identified. By cross validation we achieved an estimated prediction accuracy of 79.5% with a sensitivity of 80.6% and a specificity of 78.3%. The genes deregulated in blood of breast cancer patients are related to functional processes such as defense response, translation, and various metabolic processes, such as lipid- and steroid metabolism.Conclusions: We have identified a gene signature in whole blood that classifies breast cancer patients and healthy women with good accuracy supporting our previous findings. © 2010 Aarøe et al.; licensee BioMed Central Ltd.
Tenstad E.,Buskerud and Vestfold University College |
Tourovskaia A.,VisionGate |
Folch A.,University of Washington |
Myklebost O.,University of Oslo |
Rian E.,DiaGenic ASA
Lab on a Chip - Miniaturisation for Chemistry and Biology | Year: 2010
Microtechnology offers great prospects for cellular research by enabling controlled experimental conditions that cannot be achieved by traditional methods. This study demonstrates the use of a microfluidic platform for long-term cultivation (3 weeks) of human mesenchymal stem-like cells (MSCs), a cell population of high interest for tissue engineering. The typical high motility of the MSCs required a strategy for preventing cells from inhabiting the feeding channels and thus interfere with a steady perfusion of medium to the cell cultivation chamber. Hence, a straightforward and long-term patterning method was developed and implemented for reliable cell positioning within the device. This method was based on the modification of a polystyrene substrate into cell supportive and non-supportive regions by the use of selective oxygen plasma treatment and the triblock copolymer Pluronic. Also, a novel and size-effective "flip-chip" set-up for operating the devices was invented. Successful and reproducible adipogenic and osteogenic differentiation of MSCs in the device was demonstrated, verifying that an adequate long-term microfluidic cultivation environment was obtained. Strengths of the experimental protocol include ease of fabrication and maintenance (gravity driven), good cell performance (viability/differentiation), as well as the possibility of exposing the culture to heterogeneous laminar flow for experimental purposes. © The Royal Society of Chemistry 2010.
Almasbak H.,University of Oslo |
Rian E.,University of Oslo |
Rian E.,DiaGenic ASA |
Hoel H.J.,University of Oslo |
And 5 more authors.
Cytotherapy | Year: 2011
Background aims. T cells can be redirected to reject cancer by retroviral transduction with a chimeric antigen receptor (CAR) or by administration of a bispecific T cell engager (BiTE). We demonstrate that transfection of T cells with messenger (m) RNA coding for CAR is an alternative strategy. Methods. We describe the pre-clinical evaluation of a method based on transient modification of expanded T cells with a CD19 CAR directed against B-cell malignancies. CAR mRNA was generated under cell-free conditions in a scalable process using recombinant RNA polymerase. Efficient and non-toxic square-wave electroporation was used to load the mRNA into the cytoplasm of T cells with no risk of insertional mutagenesis. Results. After transfection >80% of T cells were viable, with 94% CAR expression. Transfected T cells were cytolytic to CD19 + targets and produced interferon (IFN)-γ? in response. Killing of CD19+ target cells was demonstrated even at day 8 with undetectable CAR expression. Increasing the concentration of mRNA resulted in higher surface CAR expression, better killing and more IFN-γ? release but at the expense of increased activation-induced cell death. Finally, we demonstrated that a second transgene could be introduced by co-electroporation of CXCR4 or CCR7 with CAR to also modify chemotactic responses. Conclusions. We advocate the transient redirection approach as well suited to meet safety aspects for early phase studies, prior to trials using stably transduced cells once CAR has been proven safe. The simplicity of this methodology also facilitates rapid screening of candidate targets and novel receptors in pre-clinical studies. © 2011 Informa Healthcare.
Diagenic As | Date: 2013-01-07
The present invention relates to oligonucleotide probes, for use in assessing gene transcript levels in a cell, which may be used in analytical techniques, particularly diagnosis techniques and kits containing the same.
Diagenic As | Date: 2012-01-05
The present invention provides sets of oligonucleotides corresponding to genes encoding proteins involved in protein synthesis and/or stability or genes encoding proteins involved in the regulation of defense and/or chromatin remodeling for use in preparing transcript patterns particularly for cancer diagnosis. The invention also extends to such sets and kits containing such sets as well as related method reliant on analysis of marker polypeptides encoded by the genes to develop characteristic expression profiles.
Diagenic Asa | Date: 2011-01-14
The invention provides a set of oligonucleotide probes specific to cancer, preferably breast cancer, kits containing them and their use in preparing standard and test patterns and methods of diagnosis of cancer, preferably breast cancer.
Agency: European Commission | Branch: FP7 | Program: CP-IP | Phase: HEALTH-2007-1.2-5 | Award Amount: 13.82M | Year: 2008
In vitro diagnostics have allowed a great deal of progress in medicine but are limited by two factors: (a) the lack of guidelines in collection, handling, stabilisation and storage of biosamples which limits the reproducibility of subsequent diagnoses, and (b) its scale is restrained to the cellular level. To address this first point, this IP, SPIDIA, built of clinicians, academics, tool and assay developers, aims to develop quality guidelines for molecular in vitro diagnostics and to standardize the pre-analytical workflow in related procedures. Regarding the second point, SPIDIA aims to develop modern pre-analytical tools for diagnostics improving the stabilisation, handling and study of free biomolecules within blood, plasma, serum, tissues and tumours. Recent discoveries have revealed that RNA, DNA or proteins, released from pathological sites, like tumour cells or Alzheimers disease (AD) brain lesions, into the blood or as a secondary blood based response to the disease can serve as biomarkers for early and reliable molecular diagnosis of such debilitating diseases. Further discoveries have shown that the cellular profiles of these molecules and structures in clinical samples can change during transport and storage thus making clinical assay results and pharmaceutical research unreliable or even impossible. It will therefore be a decisive prerequisite for future and current diagnostic assays to develop standards and new technologies, tools and devices that eliminate the human error in the pre-analytical steps of in vitro diagnostics. At this crucial moment in the development of molecular diagnostics, SPIDIA proposes an IP that reunites 7 private research companies (including 4 SMEs), 1 private research institute, 6 public research organisms, including universities, hospitals and biobanks, one management SME and an official European Standards Organisation. This strong consortium is balanced and empowered to maximise the impacts of in vitro diagnostics on human health.
Diagenic As | Date: 2013-07-01
A method for preparing a gene transcript pattern probe kit characteristic of a disease or condition or a stage thereof in a prokaryotic or eukaryotic organism using mRNA which is differentially expressed in the disease or condition or stage as probes, methods of diagnosis using the method and kits for performing the same are disclosed.
Diagenic Asa | Date: 2011-12-29
Oligonucleotide probes for use in assessing gene transcript levels in a sample, which may be used in analytical techniques, particularly diagnostic techniques, are disclosed. Conveniently the probes are provided in kit form. Different sets of probes may be used in techniques to prepare gene expression patterns and identify, diagnose or monitor neurodegenerative diseases or conditions and their progression.