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4.
  • Fergelot, Patricia, et al. (författare)
  • Phenotype and genotype in 52 patients with Rubinstein–Taybi syndrome caused by EP300 mutations
  • Ingår i: American Journal of Medical Genetics. Part A. - : John Wiley and Sons. - 1552-4825 .- 1552-4833. ; 170:12, s. 3069-3082
  • Tidskriftsartikel (refereegranskat)abstract
    • Rubinstein–Taybi syndrome (RSTS) is a developmental disorder characterized by a typical face and distal limbs abnormalities, intellectual disability, and a vast number of other features. Two genes are known to cause RSTS, CREBBP in 60% and EP300 in 8–10% of clinically diagnosed cases. Both paralogs act in chromatin remodeling and encode for transcriptional co-activators interacting with >400 proteins. Up to now 26 individuals with an EP300 mutation have been published. Here, we describe the phenotype and genotype of 42 unpublished RSTS patients carrying EP300 mutations and intragenic deletions and offer an update on another 10 patients. We compare the data to 308 individuals with CREBBP mutations. We demonstrate that EP300 mutations cause a phenotype that typically resembles the classical RSTS phenotype due to CREBBP mutations to a great extent, although most facial signs are less marked with the exception of a low-hanging columella. The limb anomalies are more similar to those in CREBBP mutated individuals except for angulation of thumbs and halluces which is very uncommon in EP300 mutated individuals. The intellectual disability is variable but typically less marked whereas the microcephaly is more common. All types of mutations occur but truncating mutations and small rearrangements are most common (86%). Missense mutations in the HAT domain are associated with a classical RSTS phenotype but otherwise no genotype–phenotype correlation is detected. Pre-eclampsia occurs in 12/52 mothers of EP300 mutated individuals versus in 2/59 mothers of CREBBP mutated individuals, making pregnancy with an EP300 mutated fetus the strongest known predictor for pre-eclampsia.
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5.
  • Bolte, S., et al. (författare)
  • The Roots of Autism and ADHD Twin Study in Sweden (RATSS)
  • 2014
  • Ingår i: Twin Research and Human Genetics. - Stockholm : Karolinska Institutet, Dept of Medical Epidemiology and Biostatistics. - 1832-4274. ; 17:3, s. 164-176
  • Tidskriftsartikel (refereegranskat)abstract
    • Neurodevelopmental disorders affect a substantial minority of the general population. Their origins are still largely unknown, but a complex interplay of genetic and environmental factors causing disturbances of the central nervous system's maturation and a variety of higher cognitive skills is presumed. Only limited research of rather small sample size and narrow scope has been conducted in neurodevelopmental disorders using a twin-differences design. The Roots of Autism and ADHD Twin Study in Sweden (RATSS) is an ongoing project targeting monozygotic twins discordant for categorical or dimensional autistic and inattentive/hyperactive-impulsive phenotypes as well as other neurodevelopmental disorders, and typically developing twin controls. Included pairs are 9 years of age or older, and comprehensively assessed for psychopathology, medical history, neuropsychology, and dysmorphology, as well as structural, functional, and molecular brain imaging. Specimens are collected for induced pluripotent (iPS) and neuroepithelial stem cells, genetic, gut bacteria, protein-/monoamine, and electron microscopy analyses. RATSS's objective is to generate a launch pad for novel surveys to understand the complexity of genotype-environment-phenotype interactions in autism spectrum disorder and attention-deficit hyperactivity disorder (ADHD). By October 2013, RATSS had collected data from 55 twin pairs, among them 10 monozygotic pairs discordant for autism spectrum disorder, seven for ADHD, and four for other neurodevelopmental disorders. This article describes the design, recruitment, data collection, measures, collected pairs' characteristics, as well as ongoing and planned analyses in RATSS. Potential gains of the study comprise the identification of environmentally mediated biomarkers, the emergence of candidates for drug development, translational modeling, and new leads for prevention of incapacitating outcomes.
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6.
  • Khodorkovskii, M. A., et al. (författare)
  • Electronic spectra of ArXe molecules in the region of Xe* (5d, 7s, 7p, 6p '), 80 300-89 500 cm(-1), using resonantly enhanced multiphoton ionization
  • 2010
  • Ingår i: Journal of Physics B. - 0953-4075 .- 1361-6455. ; 43:23, s. 235101-
  • Tidskriftsartikel (refereegranskat)abstract
    • The electronic spectra of ArXe molecules in the 80 300-89 500 cm(-1) region were recorded by (2 + n) and (3 + n) REMPI methods. The vibrational progressions attributed to transitions of molecules from the ground state to the bounded excited state and wide unstructured bands related to transitions to the continuous upper state were obtained. The molecular constants of ArXe* were calculated for all the observed progressions in the 80 300-87 000 cm(-1) region as an approximation of an anharmonic oscillator and the Morse potential. For different excited states the energy of harmonic oscillator and the dissociation energy are changed from 10 to 100 cm(-1) and from 70 to 750 cm(-1), respectively.
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7.
  • Khodorkovskii, M. A., et al. (författare)
  • Electronic spectra of ArXe molecules in the region of Xe* (6s ', 6p, 5d), 77 000-80 200 cm(-1), using resonantly enhanced multiphoton ionization
  • 2010
  • Ingår i: Journal of Physics B. - 0953-4075 .- 1361-6455. ; 43:15, s. 155101-
  • Tidskriftsartikel (refereegranskat)abstract
    • The excited electronic states of ArXe molecules in the region 77 000-80 200 cm(-1) were studied using the (2+1) and (3+1) resonance-enhanced multiphoton ionization methods. The use of different methods of multi-photon excitation and Ar+ ion registration allowed us to obtain some new data. Molecular constants were obtained for previously unknown excited states of molecules with the following dissociation limits: ArXe* -> (ArS0)-S-1+Xe*6p[5/2](3) with Omega = 2, 3 symmetry; (ArS0)-S-1+Xe*6p[3/2](2) with Omega = 1, 2 symmetry; (XeS1)-S-0 -> Xe*6s'[1/2](1)(0) with Omega = 0(+) symmetry.
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8.
  • Khodorkovskii, M. A., et al. (författare)
  • Electronic spectra of XeNe molecules in the range 77100-90100 cm(-1) near Xe* (6p, 5d, 6p', 7s, 7p, 6d) obtained by the (3+1) REMPI and (2+1) REMPI methods
  • 2010
  • Ingår i: Optics and Spectroscopy. - 0030-400X .- 1562-6911. ; 108:6, s. 899-914
  • Tidskriftsartikel (refereegranskat)abstract
    • The electronic spectra of XeNe molecules in the range of 77100-90100 cm(-1) are measured by the method of laser resonance multiphoton ionization in a supersonic jet. The photoionization spectra are obtained upon two- and three-photon excitations of molecules and their ionization by the next photon. In the range of 80300-90100 cm(-1) near Xe*(5d, 6p', 6d, 7s, and 7p), the spectra are obtained for the first time. A whole number of vibrational systems are measured in this range. The majority of vibrational systems near Xe* (5d, 6d, 7p, and 7s) are located in the red range with respect to their dissociation limits. In the blue range with respect to the dissociation limits, continua corresponding to transitions of molecules from the ground state to repulsive potential curves of excited states are detected. For a number of excited states of XeNe molecules, the vibrational analysis is performed and molecular constants are estimated.
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9.
  • Lindstrand, Anna, et al. (författare)
  • From cytogenetics to cytogenomics : whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability
  • 2019
  • Ingår i: Genome Medicine. - : BMC. - 1756-994X .- 1756-994X. ; 11:1
  • Tidskriftsartikel (refereegranskat)abstract
    • BackgroundSince different types of genetic variants, from single nucleotide variants (SNVs) to large chromosomal rearrangements, underlie intellectual disability, we evaluated the use of whole-genome sequencing (WGS) rather than chromosomal microarray analysis (CMA) as a first-line genetic diagnostic test.MethodsWe analyzed three cohorts with short-read WGS: (i) a retrospective cohort with validated copy number variants (CNVs) (cohort 1, n=68), (ii) individuals referred for monogenic multi-gene panels (cohort 2, n=156), and (iii) 100 prospective, consecutive cases referred to our center for CMA (cohort 3). Bioinformatic tools developed include FindSV, SVDB, Rhocall, Rhoviz, and vcf2cytosure.ResultsFirst, we validated our structural variant (SV)-calling pipeline on cohort 1, consisting of three trisomies and 79 deletions and duplications with a median size of 850kb (min 500bp, max 155Mb). All variants were detected. Second, we utilized the same pipeline in cohort 2 and analyzed with monogenic WGS panels, increasing the diagnostic yield to 8%. Next, cohort 3 was analyzed by both CMA and WGS. The WGS data was processed for large (>10kb) SVs genome-wide and for exonic SVs and SNVs in a panel of 887 genes linked to intellectual disability as well as genes matched to patient-specific Human Phenotype Ontology (HPO) phenotypes. This yielded a total of 25 pathogenic variants (SNVs or SVs), of which 12 were detected by CMA as well. We also applied short tandem repeat (STR) expansion detection and discovered one pathologic expansion in ATXN7. Finally, a case of Prader-Willi syndrome with uniparental disomy (UPD) was validated in the WGS data.Important positional information was obtained in all cohorts. Remarkably, 7% of the analyzed cases harbored complex structural variants, as exemplified by a ring chromosome and two duplications found to be an insertional translocation and part of a cryptic unbalanced translocation, respectively.ConclusionThe overall diagnostic rate of 27% was more than doubled compared to clinical microarray (12%). Using WGS, we detected a wide range of SVs with high accuracy. Since the WGS data also allowed for analysis of SNVs, UPD, and STRs, it represents a powerful comprehensive genetic test in a clinical diagnostic laboratory setting.
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10.
  • Nilsson, D., et al. (författare)
  • 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
  • Ingår i: Human Mutation. - : John Wiley & Sons. - 1059-7794 .- 1098-1004. ; 38:2, s. 180-192
  • 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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