| 1. |
- Stranneheim, Henrik, et al.
(författare)
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Rapid pulsed whole genome sequencing for comprehensive acute diagnostics of inborn errors of metabolism
- 2014
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 15, s. 1090-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Massively parallel DNA sequencing (MPS) has the potential to revolutionize diagnostics, in particular for monogenic disorders. Inborn errors of metabolism (IEM) constitute a large group of monogenic disorders with highly variable clinical presentation, often with acute, nonspecific initial symptoms. In many cases irreversible damage can be reduced by initiation of specific treatment, provided that a correct molecular diagnosis can be rapidly obtained. MPS thus has the potential to significantly improve both diagnostics and outcome for affected patients in this highly specialized area of medicine. Results: We have developed a conceptually novel approach for acute MPS, by analysing pulsed whole genome sequence data in real time, using automated analysis combined with data reduction and parallelization. We applied this novel methodology to an in-house developed customized work flow enabling clinical-grade analysis of all IEM with a known genetic basis, represented by a database containing 474 disease genes which is continuously updated. As proof-of-concept, two patients were retrospectively analysed in whom diagnostics had previously been performed by conventional methods. The correct disease-causing mutations were identified and presented to the clinical team after 15 and 18 hours from start of sequencing, respectively. With this information available, correct treatment would have been possible significantly sooner, likely improving outcome. Conclusions: We have adapted MPS to fit into the dynamic, multidisciplinary work-flow of acute metabolic medicine. As the extent of irreversible damage in patients with IEM often correlates with timing and accuracy of management in early, critical disease stages, our novel methodology is predicted to improve patient outcome. All procedures have been designed such that they can be implemented in any technical setting and to any genetic disease area. The strategy conforms to international guidelines for clinical MPS, as only validated disease genes are investigated and as clinical specialists take responsibility for translation of results. As follow-up in patients without any known IEM, filters can be lifted and the full genome investigated, after genetic counselling and informed consent.
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| 2. |
- Göngrich, Christina, et al.
(författare)
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First Year of TREC-Based National SCID Screening in Sweden.
- 2021
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Ingår i: International journal of neonatal screening. - : MDPI AG. - 2409-515X. ; 7:3
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Tidskriftsartikel (refereegranskat)abstract
- Screening for severe combined immunodeficiency (SCID) was introduced into the Swedish newborn screening program in August 2019 and here we report the results of the first year. T cell receptor excision circles (TRECs), kappa-deleting element excision circles (KRECs), and actin beta (ACTB) levels were quantitated by multiplex qPCR from dried blood spots (DBS) of 115,786 newborns and children up to two years of age, as an approximation of the number of recently formed T and B cells and sample quality, respectively. Based on low TREC levels, 73 children were referred for clinical assessment which led to the diagnosis of T cell lymphopenia in 21 children. Of these, three were diagnosed with SCID. The screening performance for SCID as the outcome was sensitivity 100%, specificity 99.94%, positive predictive value (PPV) 4.11%, and negative predictive value (NPV) 100%. For the outcome T cell lymphopenia, PPV was 28.77%, and specificity was 99.95%. Based on the first year of screening, the incidence of SCID in the Swedish population was estimated to be 1:38,500 newborns.
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| 3. |
- Lingman Framme, Jenny, 1977, et al.
(författare)
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Long-Term Follow-Up of Newborns with 22q11 Deletion Syndrome and Low TRECs
- 2022
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Ingår i: Journal of Clinical Immunology. - : Springer. - 0271-9142 .- 1573-2592. ; 42, s. 618-633
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Tidskriftsartikel (refereegranskat)abstract
- Background: Population-based neonatal screening using T-cell receptor excision circles (TRECs) identifies infants with profound T lymphopenia, as seen in cases of severe combined immunodeficiency, and in a subgroup of infants with 22q11 deletion syndrome (22q11DS).Purpose: To investigate the long-term prognostic value of low levels of TRECs in newborns with 22q11DS.Methods: Subjects with 22q11DS and low TRECs at birth (22q11Low, N=10), matched subjects with 22q11DS and normal TRECs (22q11Normal, N=10), and matched healthy controls (HC, N=10) were identified. At follow-up (median age 16 years), clinical and immunological characterizations, covering lymphocyte subsets, immunoglobulins, TRECs, T-cell receptor repertoires, and relative telomere length (RTL) measurements were performed.Results: At follow-up, the 22q11Low group had lower numbers of naïve T-helper cells, naïve T-regulatory cells, naïve cytotoxic T cells, and persistently lower TRECs compared to healthy controls. Receptor repertoires showed skewed V-gene usage for naïve T-helper cells, whereas for naïve cytotoxic T cells, shorter RTL and a trend towards higher clonality were found. Multivariate discriminant analysis revealed a clear distinction between the three groups and a skewing towards Th17 differentiation of T-helper cells, particularly in the 22q11Low individuals. Perturbations of B-cell subsets were found in both the 22q11Low and 22q11Normal group compared to the HC group, with larger proportions of naïve B cells and lower levels of memory B cells, including switched memory B cells.Conclusions: This long-term follow-up study shows that 22q11Low individuals have persistent immunologic aberrations and increased risk for immune dysregulation, indicating the necessity of lifelong monitoring.Clinical Implications: This study elucidates the natural history of childhood immune function in newborns with 22q11DS and low TRECs, which may facilitate the development of programs for long-term monitoring and therapeutic choices.
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| 4. |
- Sörensen, Lene, et al.
(författare)
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Expanded Screening of One Million Swedish Babies with R4S and CLIR for Post-Analytical Evaluation of Data.
- 2020
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Ingår i: International journal of neonatal screening. - : MDPI AG. - 2409-515X. ; 6:2
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Tidskriftsartikel (refereegranskat)abstract
- Sweden has one neonatal screening laboratory, receiving 115 to 120 thousand samples per year. Among the one million babies screened by tandem mass spectrometry from November 2010 until July 2019, a total of 665 babies were recalled and 311 verified as having one of the diseases screened for with this methodology, giving a positive predictive value (PPV) of 47% and an incidence of 1:3200. The PPV was high (41%) already in the first year after start of screening, thanks to the availability of the collaborative project Region 4 Stork database. The PPV is presently 58%. This improvement was achieved by the implementation of second-tier analyses in the screening for methylmalonic aciduria, propionic aciduria, isovaleric aciduria, and homocystinuria, and the employment of various post analytical tools of the Region 4 Stork, and its successor the collaborative laboratory integrated reports.
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| 5. |
- Zetterström, Rolf H
(författare)
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On retinoid receptors, Nurr1 and related transcription factors in the CNS
- 1998
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- It has long been known that retinoids (vitamin A derivatives) are required for normal development and growth; in excess however metabolites such as all-trans retinoic acid are potent teratogens. Retinoids exert their effects through transcription factors known as the retinoic acid receptors (RARam -ß and -y) and retinoid X receptors (RXRa, -ß and -y). Intracellularly, two types of binding proteins also appear to be involved in retinoid homeostasis, cellular retinol binding protein I and II (CRBP I and II) and cellular retinoic acid binding protein I and II (CRABP I and II). RARs and RXRs belong to the nuclear receptor superfamily which also includes receptors for the steroid and thyroid hormones, vitamin D3 and several other small lipophilic molecules. Moreover, the superfamily includes a large group of receptors which lack identified ligands (termed "orphan receptors"). Nurr1, NGFI-B and Nor1 are closely related members of this latter group of proteins. This study was undertaken in order to explore the roles of retinoids and the Nurr1/NGFI-B/Norl subfamily of orphan receptors in the developing and adult CNS. The expression patterns of CRBPs and CRABPs and RARs and RXRs in the postnatal and adult CNS were investigated using immunocytochemistry and in situ hybridization histochemistry (ISH). In addition, an in vitro reporter assay was used to detect retinoids in striatal tissue. It was found that many of the retinoid binding proteins and receptors are present in the CNS. Striatum, a part of the basal ganglia, contains all necessary components for retinoid signaling. Both CRBP I and CRABP I as well as RARß RXRß and RXRy are highly expressed within this region. In addition, it has also been possible to detect retinoids in striatal tissue. The role of Nurr1, NGFI-B and Nor1 has been explored. In particular, these studies have emphasized the role of NuTrl. All three members have previously been shown to interact with DNA as monomers, but Nurr1 and NGFI-B have also been shown to heterodimerize with RXR, thereby defining a distinct pathway for retinoid signaling. The most recently cloned member, Nor1, was shown to lack the ability to heterodimerize with RXR. To begin to understand the function of these orphan receptors, ISH was used to localize the mRNA expression patterns in both developing and adult tissues. All three members are highly expressed in the CNS; a striking observation was that Nurr1 mRNA was present in the developing ventral midbrain as well as in the mature dopamine (DA) neurons of the substantia nigra pars compacta (SNc) and the ventral tegmental area (VTA). To further investigate the function of Nurr1, a targeted mutation was introduced into the Nurr1 locus. Mice lacking Nurr1 are born alive but die within the first two days after birth. The mice were found to completely lack DA neurons in the ventral midbrain as demonstrated by the absence of several markers, such as the rate limiting enzyme in DA synthesis, tyrosine hydroxylase, a postulated retinoic acid converting enzyme, AHD2, and the DA transporter in SNC, the VTA as well as in the retrorubral field. In addition, high-pressure liquid chromatography was used to demonstrate the absence of DA itself in the major target area for the DAergic midbrain neurons, striatum. The role of Nurrl during early development of the ventral midbrain has been further studied and the relation to other factors postulated to be important for DA cell generation such as sonic hedgehog explored. Since survival could not be prolonged by administration of either the DA precursor L-DOPA, the DA receptor agonist apomorphine or DA itself despite apparently normal DA receptor expression, it is hypothesized that the mice do not die from lack of DA. Interestingly, brains of newborn and two months old heterozygous, apparently healthy, mice contained less DA than wild type littermates, indicating a function for Nurr1 not only in the generation of the DA cells, but also for maturation and maintenance of a normal DAergic phenotype. These studies demonstrate that retinoids most likely are important signaling molecules in the postnatal and adult CNS and establish Nurr1 as a key component for proper development of DA midbrain neurons, known to degenerate in patients with Parkinson's disease.
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