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  • 1.
    Andiappan, Anand Kumar
    et al.
    Department of Biological Sciences, National University of Singapore.
    Nilsson, Daniel
    Högskolan Kristianstad, Sektionen för lärande och miljö, Avdelningen för Naturvetenskap. Högskolan Kristianstad, Forskningsmiljön Biomedicin.
    Halldén, Christer
    Högskolan Kristianstad, Sektionen för lärande och miljö, Avdelningen för Naturvetenskap. Högskolan Kristianstad, Forskningsmiljön Biomedicin.
    Yun, Wang De
    Department of Otolaryngology, National University of Singapore.
    Säll, Torbjörn
    Department of Cell and Organism Biology, Lund University.
    Cardell, Lars Olaf
    Division of ENT Diseases, CLINTEC, Karolinska Institutet.
    Tim, Chew Fook
    Department of Biological Sciences, National University of Singapore.
    Investigating highly replicated asthma genes as candidate genes for allergic rhinitis2013Inngår i: BMC Medical Genetics, ISSN 1471-2350, E-ISSN 1471-2350, Vol. 14, 51- s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    BACKGROUND: Asthma genetics has been extensively studied and many genes have been associated with the development or severity of this disease. In contrast, the genetic basis of allergic rhinitis (AR) has not been evaluated as extensively. It is well known that asthma is closely related with AR since a large proportion of individuals with asthma also present symptoms of AR, and patients with AR have a 5-6 fold increased risk of developing asthma. Thus, the relevance of asthma candidate genes as predisposing factors for AR is worth investigating. The present study was designed to investigate if SNPs in highly replicated asthma genes are associated with the occurrence of AR.

    METHODS: A total of 192 SNPs from 21 asthma candidate genes reported to be associated with asthma in 6 or more unrelated studies were genotyped in a Swedish population with 246 AR patients and 431 controls. Genotypes for 429 SNPs from the same set of genes were also extracted from a Singapore Chinese genome-wide dataset which consisted of 456 AR cases and 486 controls. All SNPs were subsequently analyzed for association with AR and their influence on allergic sensitization to common allergens.

    RESULTS: A limited number of potential associations were observed and the overall pattern of P-values corresponds well to the expectations in the absence of an effect. However, in the tests of allele effects in the Chinese population the number of significant P-values exceeds the expectations. The strongest signals were found for SNPs in NPSR1 and CTLA4. In these genes, a total of nine SNPs showed P-values <0.001 with corresponding Q-values <0.05. In the NPSR1 gene some P-values were lower than the Bonferroni correction level. Reanalysis after elimination of all patients with asthmatic symptoms excluded asthma as a confounding factor in our results. Weaker indications were found for IL13 and GSTP1 with respect to sensitization to birch pollen in the Swedish population.

    CONCLUSIONS: Genetic variation in the majority of the highly replicated asthma genes were not associated to AR in our populations which suggest that asthma and AR could have less in common than previously anticipated. However, NPSR1 and CTLA4 can be genetic links between AR and asthma and associations of polymorphisms in NPSR1 with AR have not been reported previously.

  • 2.
    Halldén, Christer
    et al.
    Högskolan Kristianstad, Sektionen för lärande och miljö, Avdelningen för Naturvetenskap. Högskolan Kristianstad, Forskningsmiljön Biomedicin.
    Mårtensson, A.
    Department of Paediatrics and Malmö Centre for Thrombosis and Haemostasis, Skåne University Hospital, Lund University, Malmö.
    Nilsson, Daniel
    Högskolan Kristianstad, Sektionen för lärande och miljö, Avdelningen för Naturvetenskap. Högskolan Kristianstad, Forskningsmiljön Biomedicin.
    Säll, T.
    Department of Biology, Lund University.
    Lind-Halldén, Christina
    Högskolan Kristianstad, Sektionen för lärande och miljö, Avdelningen för Naturvetenskap. Högskolan Kristianstad, Forskningsmiljön Biomedicin.
    Lidén, Annika C.
    Högskolan Kristianstad, Sektionen för lärande och miljö, Avdelningen för Naturvetenskap. Högskolan Kristianstad, Forskningsmiljön Biomedicin.
    Ljung, R.
    Department of Paediatrics and Malmö Centre for Thrombosis and Haemostasis, Skåne University Hospital, Lund University, Malmö.
    Origin of Swedish hemophilia B mutations2013Inngår i: Journal of Thrombosis and Haemostasis, ISSN 1538-7933, E-ISSN 1538-7836, Vol. 11, nr 11, 2001-2008 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    BACKGROUND: More than 1100 mutations that cause hemophilia B (HB) have been identified. At the same time, specific F9 mutations are present at high frequencies in certain populations, which raise questions about the origin of HB mutations.

    OBJECTIVES: To describe the mutation spectrum of all HB families in Sweden and investigate if mutations appearing in several families are due to independent recurrent mutations (RMs) or to a common mutation event (i.e. are identical by descent (IBD)).

    PATIENTS/METHODS: The registered Swedish HB population consists of patients from 86 families. Mutations were identified by resequencing and identical haplotypes were defined using 74 markers and a control population of 285 individuals. The ages of IBD mutations were estimated using ESTIAGE.

    RESULTS: Out of 77 presumably unrelated patients with substitution mutations, 47 patients (61%) had mutations in common with other patients. Haplotyping of the 47 patients showed that 24 patients had IBD mutations (51%) with estimated ages of between two and 23 generations. A majority of these patients had mild disease. Eight of the 15 mutations observed in more than one family were C>T transitions in CpG sites and all eight were RMs.

    CONCLUSIONS: The association of IBD mutations with a mild phenotype is similar to what has been previously observed in hemophilia A. Noteworthy features of the mutations that are common to more than one family are the equal proportions of patients with RM and IBD mutations and the correlation between the occurrence of RMs and C>T transitions at CpG sites.

  • 3.
    Lindahl, Pernilla
    et al.
    Högskolan Kristianstad, Forskningsmiljön Biomedicin.
    Säll, Torbjörn
    Department of Biology, Lund University.
    Bjartell, Anders
    Department of Urology, Skåne University Hospital, Malmö.
    Johansson, Anna M
    Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala.
    Lilja, Hans
    Department of Laboratory Medicine, Division of Clinical Chemistry, Lund University, Skåne University Hospital, Malmö.
    Halldén, Christer
    Högskolan Kristianstad, Sektionen för lärande och miljö, Avdelningen för Naturvetenskap. Högskolan Kristianstad, Forskningsmiljön Biomedicin.
    Copy number variants in the kallikrein gene cluster2013Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, nr 7, e69097- s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The kallikrein gene family (KLK1-KLK15) is the largest contiguous group of protease genes within the human genome and is associated with both risk and outcome of cancer and other diseases. We searched for copy number variants in all KLK genes using quantitative PCR analysis and analysis of inheritance patterns of single nucleotide polymorphisms. Two deletions were identified: one 2235-bp deletion in KLK9 present in 1.2% of alleles, and one 3394-bp deletion in KLK15 present in 4.0% of alleles. Each deletion eliminated one complete exon and created out-of-frame coding that eliminated the catalytic triad of the resulting truncated gene product, which therefore likely is a non-functional protein. Deletion breakpoints identified by DNA sequencing located the KLK9 deletion breakpoint to a long interspersed element (LINE) repeated sequence, while the deletion in KLK15 is located in a single copy sequence. To search for an association between each deletion and risk of prostate cancer (PC), we analyzed a cohort of 667 biopsied men (266 PC cases and 401 men with no evidence of PC at biopsy) using short deletion-specific PCR assays. There was no association between evidence of PC in this cohort and the presence of either gene deletion. Haplotyping revealed a single origin of each deletion, with most recent common ancestor estimates of 3000-8000 and 6000-14 000 years for the deletions in KLK9 and KLK15, respectively. The presence of the deletions on the same haplotypes in 1000 Genomes data of both European and African populations indicate an early origin of both deletions. The old age in combination with homozygous presence of loss-of-function variants suggests that some kallikrein-related peptidases have non-essential functions.

  • 4.
    Nilsson, Daniel
    et al.
    Högskolan Kristianstad, Sektionen för lärande och miljö, Avdelningen för Naturvetenskap. Högskolan Kristianstad, Forskningsmiljön Biomedicin.
    Andiappan, Anand Kumar
    Department of Biological Sciences, National University of Singapore.
    Halldén, Christer
    Högskolan Kristianstad, Sektionen för lärande och miljö, Avdelningen för Naturvetenskap. Högskolan Kristianstad, Forskningsmiljön Biomedicin.
    Tim, Chew Fook
    Department of Biological Sciences, National University of Singapore.
    Säll, Torbjörn
    Department of Cell and Organism Biology, Lund University.
    Wang, De Yun
    Department of Otolaryngology, National University of Singapore.
    Cardell, Lars-Olaf
    Division of ENT Diseases, Department of Clinical Science, Intervention and Technology, Karolinska Institutet.
    Poor reproducibility of allergic rhinitis SNP associations2013Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, nr 1, e53975- s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Replication of reported associations is crucial to the investigation of complex disease. More than 100 SNPs have previously been reported as associated with allergic rhinitis (AR), but few of these have been replicated successfully. To investigate the general reproducibility of reported AR-associations in candidate gene studies, one Swedish (352 AR-cases, 709 controls) and one Singapore Chinese population (948 AR-cases, 580 controls) were analyzed using 49 AR-associated SNPs. The overall pattern of P-values indicated that very few of the investigated SNPs were associated with AR. Given published odds ratios (ORs) most SNPs showed high power to detect an association, but no correlations were found between the ORs of the two study populations or with published ORs. None of the association signals were in common to the two genome-wide association studies published in AR, indicating that the associations represent false positives or have much lower effect-sizes than reported.

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