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Sökning: WFRF:(Carlson Joyce)

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1.
  • Zheng, Hou-Feng, et al. (författare)
  • Whole-genome sequencing identifies EN1 as a determinant of bone density and fracture
  • 2015
  • Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 526:7571, s. 112-
  • Tidskriftsartikel (refereegranskat)abstract
    • The extent to which low-frequency (minor allele frequency (MAF) between 1-5%) and rare (MAF <= 1%) variants contribute to complex traits and disease in the general population is mainly unknown. Bone mineral density (BMD) is highly heritable, a major predictor of osteoporotic fractures, and has been previously associated with common genetic variants(1-8), as well as rare, population specific, coding variants(9). Here we identify novel non-coding genetic variants with large effects on BMD (n(total) = 53,236) and fracture (n(total) = 508,253) in individuals of European ancestry from the general population. Associations for BMD were derived from whole-genome sequencing (n = 2,882 from UK10K (ref. 10); a population-based genome sequencing consortium), whole-exome sequencing (n = 3,549), deep imputation of genotyped samples using a combined UK10K/1000 Genomes reference panel (n = 26,534), and de novo replication genotyping (n = 20,271). We identified a low-frequency non-coding variant near a novel locus, EN1, with an effect size fourfold larger than the mean of previously reported common variants for lumbar spine BMD8 (rs11692564(T), MAF51.6%, replication effect size510.20 s.d., P-meta = 2 x 10(-14)), which was also associated with a decreased risk of fracture (odds ratio = 0.85; P = 2 x 10(-11); ncases = 98,742 and ncontrols = 409,511). Using an En1cre/flox mouse model, we observed that conditional loss of En1 results in low bone mass, probably as a consequence of high bone turnover. We also identified a novel low frequency non-coding variant with large effects on BMD near WNT16 (rs148771817(T), MAF = 1.2%, replication effect size +10.41 s.d., P-meta = 1 x 10(-11)). In general, there was an excess of association signals arising from deleterious coding and conserved non-coding variants. These findings provide evidence that low-frequency non-coding variants have large effects on BMD and fracture, thereby providing rationale for whole-genome sequencing and improved imputation reference panels to study the genetic architecture of complex traits and disease in the general population.
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2.
  • Astermark, Jan, et al. (författare)
  • Polymorphisms in the TNFA gene and the risk of inhibitor development in patients with hemophilia A.
  • 2006
  • Ingår i: Blood. - : American Society of Hematology. - 1528-0020 .- 0006-4971. ; 108:12, s. 3739-3745
  • Tidskriftsartikel (refereegranskat)abstract
    • The HLA class I/II alleles and the tumor necrosis factor alpha (TNFA) locus are closely linked in the MHC complex. We have characterized the causative factor VIII mutation, HLA alleles as well as 4 polymorphisms (-827C > T, -308G > A, -238A > G, and 670A > G) in the TNFA gene in 164 patients (124 severe, 26 moderate, and 14 mild) in 78 families with hemophilia A enrolled in the Malmo International Brother Study (MIBS). Inhibitors were identified in 77.8% of patients with a single haplotype (Hap 2) and 72.7% of the patients with the TNFA -308 A/A genotype within this haplotype compared with 39.70/6 for TNFA -308 G/G patients and 46.9% for TNFA -308 G/A heterozygotes (OR 4.0; 95% CI, 1.4-11.5; P = .008). The association between the -308 A/A genotype and inhibitors was enhanced in subgroups of patients with severe hemophilia (OR 19.2; 95% CI 2.4-156.5; P < .001) and with inversions (n = 75; OR, 11.8; 95% CI, 1.3-105.1; P = .013). Associations were found for the HLA A26 and B44 alleles, but these were not consistent in the subgroup analysis. Our data imply that the TNFA -308G > A polymorphism within Hap 2 is a useful marker and potential modulator of the immune response to replacement therapy in patients with hemophilia.
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3.
  • Björk, Jonas, et al. (författare)
  • Prediction of relative glomerular filtration rate in adults: New improved equations based on Swedish Caucasians and standardized plasma-creatinine assays.
  • 2007
  • Ingår i: Scandinavian Journal of Clinical & Laboratory Investigation. - : Informa UK Limited. - 1502-7686 .- 0036-5513. ; 67:7, s. 678-695
  • Tidskriftsartikel (refereegranskat)abstract
    • OBJECTIVE: To evaluate newly developed equations predicting relative glomerular filtration rate(GFR) in adult Swedish Caucasians and to compare with the Modification of Diet in Renal Disease(MDRD) and Mayo Clinic equations using enzymatic and zero-calibrated plasma creatinine assays. MATERIAL AND METHODS: GFR was measured with iohexol clearance adjusted to 1.73 m(2). One population sample (n=436/Lund) was used to derive an equation based on plasma-creatinine/age/gender, and a second with the addition of lean body mass (LBM). Both equations were validated in a separate sample (n=414/Malmö). The coefficients of the equations were eventually fine-tuned using all 850 patients and yielding Lund-Malmö equations without (LM) and with LBM-term (LM(LBM)).Their performance was compared with the MDRD(CC) (conventional creatinine calibration), MDRD(IDMS) (isotope dilution mass spectroscopy traceable calibration) and Mayo Clinic equations. RESULTS: The Lund equations performed similarly in both samples. In the combined set, the Mayo Clinic/MDRD(CC) resulted in +19.0/+10.2 % median bias, while bias for the other equations was < 10 %. LM(LBM) had the highest accuracy (86 % of estimates within 30 % of measured GFR), significantly (p < 0.001) better than for MDRD(IDMS) (80 %). In men with BMI < 20 kg/m(2), MDRD(IDMS)/LM had +46 %/+19 % median bias. MDRD(IDMS) also overestimated GFR by 22 %/14 % in men/women above 80 years of age. The LM(LBM) equation had < 10 % bias irrespective of BMI, age or GFR except for a 15 % negative bias at GFR > 90 mL/min/1.73 m(2). CONCLUSION: The newly developed Lund-Malmö equations for GFR estimation performed better than the MDRD(IDMS) and Mayo Clinic equations in a Swedish Caucasian sample. Inclusion of an LBM term improved performance markedly in certain subgroups.
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4.
  • Björkbacka, Harry, et al. (författare)
  • Weak associations between human leucocyte antigen genotype and acute myocardial infarction
  • 2010
  • Ingår i: Journal of Internal Medicine. - : Blackwell Publishing Ltd. - 0954-6820 .- 1365-2796. ; 268:1, s. 50-58
  • Tidskriftsartikel (refereegranskat)abstract
    • Objectives: Human leucocyte antigens (HLAs) are polymorphic molecules involved in antigen presentation. Associations between HLA type and autoimmune diseases, such as type 1 diabetes and rheumatoid arthritis, are well established but the potential association of genetic variation affecting antigen presentation with cardiovascular disease has not been systematically investigated in large cohorts. The importance of such studies is stressed by recent experimental findings of an involvement of autoimmunity in the atherosclerotic disease process. Results: An SSP-PCR method was used for HLA genotyping to determine associations of HLA-DRB1, -DQA1 and -DQB1 with cardiovascular disease in a population-based cohort of 1188 acute myocardial infarction (AMI) patients and 1191 matched healthy controls. The HLA-DRB1*0101 allele, as well as the HLA-DRB1*0101-DQA1*01-DQB1*05 haplotype, was found to be associated with increased risk for AMI (OR 1.24; 95% CI 1.00–1.54 for both). In contrast, the DRB1*07 and DQA*02 alleles (OR 0.78; 95% CI 0.65–0.95 for both), as well as the DRB1*07-DQA*02-DQB*02 haplotype, conferred protection (OR 0.79; 95% CI 0.63–0.98). An HLA risk score taking each individual’s both haplotypes into account was higher amongst cases (2.43 ± 0.92 vs. 2.29 ± 0.95, P = 0.001). The association between HLA risk score and AMI was independent of other cardiovascular riskfactors assessed. Conclusions: This study demonstrates that the associations between HLA-DRB1 and DQA1 loci and cardiovascular disease exists but that they are considerably weaker than those previously reported for other diseases with an established autoimmune aetiology such as type 1 diabetes, systemic lupus erythematosus and rheumatoid arthritis.
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5.
  • Butt, Salma, et al. (författare)
  • Genetic predisposition, parity, age at first childbirth and risk for breast cancer.
  • 2012
  • Ingår i: BMC Research Notes. - : Springer Science and Business Media LLC. - 1756-0500. ; 5
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: Recent studies have identified several single-nucleotide polymorphisms (SNPs) associated with the risk of breast cancer and parity and age at first childbirth are well established and important risk factors for breast cancer. The aim of the present study was to examine the interaction between these environmental factors and genetic variants on breast cancer risk.METHODS: The Malmö Diet and Cancer Study (MDCS) included 17 035 female participants, from which 728 incident breast cancer cases were matched to 1448 controls. The associations between 14 SNPs and breast cancer risk were investigated in different strata of parity and age at first childbirth. A logistic regression analysis for the per allele risk, adjusted for potential confounders yielded odds ratios (OR) with 95% confidence intervals (CI).RESULTS: Six of the previously identified SNPs showed a statistically significant association with breast cancer risk: rs2981582 (FGFR2), rs3803662 (TNRC9), rs12443621 (TNRC9), rs889312 (MAP3K1), rs3817198 (LSP1) and rs2107425 (H19). We could not find any statistically significant interaction between the effects of tested SNPs and parity/age at first childbirth on breast cancer risk after adjusting for multiple comparisons.CONCLUSIONS: The results of this study are in agreement with previous studies of null interactions between tested SNPs and parity/age at first childbirth with regard to breast cancer risk.
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7.
  • Carlson, Joyce, et al. (författare)
  • Digestionsorganens sjukdomar
  • 2012. - 9
  • Ingår i: Laurells Klinisk kemi i praktisk medicin. - Lund. - 9789144047874 ; , s. 441-496
  • Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
    • Klinisk kemi i praktisk medicin används som kurslitteratur för läkare, biomedicinska analytiker och biomedicinare sedan 40 år tillbaka. Den finns på avdelningar, mottagningar och vårdcentraler - överallt där man behöver ta prover för kliniskt kemiska analyser och tolka deras resultat. Nu föreligger den i sin nionde upplaga efter omfattande revision och med nyskrivna kapitel. I denna upplaga har innehållet organiserats med tydlig anknytning till kliniska problemområden. Alla kapitel har grundligt reviderats. Avsnitten om tolkning av analysresultat, allergi och autoimmunitet, hjärtinfarkt och hjärtskademarkörer, digestionsorganens sjukdomar, graviditet, infertilitet och prenataldiagnostik samt läkemedel, förgiftningar och missbruk är helt nyskrivna. Boken kan användas både för att slå upp fakta om specifika analyser och för att förstå de sjukdomsmekanismer som är av betydelse för tolkningen av laboratorieresultat. Modern medicinsk praxis är patientcentrerad och har sitt fundament i ett nära samspel mellan klinik, laboratorier och patienter. Kunskapsfragment inom klinisk kemi är lättillgängliga för alla och envar på nätet, men ger sällan den helhetsbild som behövs för grundlig förståelse och därmed optimal användning av laboratorieanalyser. Denna bok ger sådan helhetsbild.
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8.
  • Carlson, Joyce, et al. (författare)
  • In Memoriam, Carl-Bertil Laurell
  • 2001
  • Ingår i: Clinical Chemistry and Laboratory Medicine. - 1434-6621. ; 39:11, s. 1019-1019
  • Tidskriftsartikel (refereegranskat)
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9.
  • Concannon, P, et al. (författare)
  • Type 1 Diabetes: Evidence for susceptibility loci from four genome-wide linkage scans in 1,435 multiplex families.
  • 2005
  • Ingår i: Diabetes. - 1939-327X. ; 54, s. 2995-3001
  • Tidskriftsartikel (refereegranskat)abstract
    • Type 1 diabetes is a common, multifactorial disease with strong familial clustering (genetic risk ratio [{lambda}S] ~ 15). Approximately 40% of the familial aggregation of type 1 diabetes can be attributed to allelic variation of HLA loci in the major histocompatibility complex on chromosome 6p21 (locus-specific {lambda}S ~ 3). Three other disease susceptibility loci have been clearly demonstrated based on their direct effect on risk, INS (chromosome 11p15, allelic odds ratio [OR] ~ 1.9), CTLA4 (chromosome 2q33, allelic OR ~ 1.2), and PTPN22 (chromosome 1p13, allelic OR ~ 1.7). However, a large proportion of type 1 diabetes clustering remains unexplained. We report here on a combined linkage analysis of four datasets, three previously published genome scans, and one new genome scan of 254 families, which were consolidated through an international consortium for type 1 diabetes genetic studies (www.t1dgc.org) and provided a total sample of 1,435 families with 1,636 affected sibpairs. In addition to the HLA region (nominal P = 2.0 x 10–52), nine non–HLA-linked regions showed some evidence of linkage to type 1 diabetes (nominal P < 0.01), including three at (or near) genome-wide significance (P < 0.05): 2q31-q33, 10p14-q11, and 16q22-q24. In addition, after taking into account the linkage at the 6p21 (HLA) region, there was evidence supporting linkage for the 6q21 region (empiric P < 10–4). More than 80% of the genome could be excluded as harboring type 1 diabetes susceptibility genes of modest effect ({lambda}S ≥ 1.3) that could be detected by linkage. This study represents one of the largest linkage studies ever performed for any common disease. The results demonstrate some consistency emerging for the existence of susceptibility loci on chromosomes 2q31-q33, 6q21, 10p14-q11, and 16q22-q24 but diminished support for some previously reported locations.
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10.
  • Dahlberg, Jonas, et al. (författare)
  • Genetic variants in serum and glucocortocoid regulated kinase 1, a regulator of the epithelial sodium channel, are associated with ischaemic stroke.
  • 2011
  • Ingår i: Journal of Hypertension. - 1473-5598. ; 29, s. 884-889
  • Tidskriftsartikel (refereegranskat)abstract
    • OBJECTIVE: Serum and glucocorticoid regulated kinase 1 (SGK1) expression is increased by aldosterone and is a key regulator of the amiloride-sensitive sodium channel (ENaC) in the distal nephron. We have previously shown that two SNPs in SGK1 (rs1057293 and rs1743966) are associated with blood pressure variation and blood pressure progression in the general population. Therefore, we tested the association of these variants with ischaemic stroke. METHODS: Using logistic regression, we analysed rs1057293 and rs1743966 for association with ischaemic stroke in two independent age-matched and sex-matched case-control groups from the twin cities of Lund (cases n = 1837 and controls n = 947) and Malmö (cases n = 888 and controls n = 893) in the Scania region of southern Sweden. RESULTS: In additive models adjusted for hypertension, smoking and diabetes, the major allele (G) of rs1057293 was associated (odds ratio, 95% confidence interval; P value) with ischaemic stroke with similar effect size in both studies; in Lund (1.35, 1.11-1.64; P = 0.002) and Malmö (1.30, 1.03-1.65; P = 0.027). When the two studies were pooled, the overall association was 1.32, 1.14-1.52; P < 0.001. The major allele of rs1743966 (A), which was in linkage disequilibrium with rs1057293, showed a similar trend as rs1057293 G-allele but with slightly weaker effect size and P value. CONCLUSION: In two independent but ethnically similar populations, we observed an association between genetic variants in SGK1 and ischaemic stroke. Interestingly, the association seems to be at least partially independent of blood pressure. This could imply that cerebrovascular ENaC or other SGK1-regulated proteins may be of importance for development of ischaemic stroke.
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11.
  • De Basso, Rachel, et al. (författare)
  • Increased carotid plaque burden in men with the fibrillin-1 2/3 genotype
  • 2014
  • Ingår i: Clinical and Experimental Pharmacology and Physiology. - : Wiley. - 1440-1681 .- 0305-1870. ; 41:9, s. 637-642
  • Tidskriftsartikel (refereegranskat)abstract
    • Fibrillin-1 (FBN1) is an important constituent of the vascular wall and earlier studies have indicated an effect of the FBN1 2/3 genotype on blood pressure as well as aortic stiffness in men. The aim of the present study was to determine whether the FBN1 2/3 genotype was associated with the presence of carotid plaque and incident cardiovascular morbidity and mortality in middle-aged subjects. The FBN1 genotype was characterized in 5765 subjects (2424 men, 3341 women; age 45-69years) recruited from the Malmo Diet and Cancer Study Cardiovascular Cohort, Sweden. Plaque occurrence and intima-media thickness (IMT) of the carotid artery were assessed by ultrasound. The incidence of first cardiovascular events (myocardial infarction and stroke) and cause-specific mortality were monitored over a mean follow-up period of 13.2years. The most common FBN1 genotypes were 2/2, 2/3 and 2/4, which accounted for 92.2% (n=5317) of subjects. There were no differences between the three genotypes regarding age, blood pressure, glucose, lipids, smoking habits, common carotid artery diameter and intima-media thickness in men and women. The presence of plaque in the carotid artery was higher in men with the 2/3 genotype compared with the 2/2 and 2/4 genotypes (55% vs 46% and 50%, respectively; P=0.007). No similar differences were observed in women. No significant relationship was observed between FBN1 genotypes and the incidence of cardiovascular disease or all-cause mortality. The increased prevalence of plaque in the carotid artery of middle-aged men with the FBN1 2/3 genotype indicates pathological arterial wall remodelling with a more pronounced atherosclerotic burden.
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12.
  • Elzouki, Abdul-Nasser, et al. (författare)
  • Serine protease inhibitors in patients with chronic viral hepatitis
  • 1997
  • Ingår i: Journal of Hepatology. - 0168-8278. ; 27:1, s. 42-48
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND/AIMS: This study aimed to determine whether deficiency of the major serine protease inhibitors (alpha1-antitrypsin (AAT) or alpha1-antichymotrypsin (ACT)) is associated with increased risk for chronic hepatitis B or C virus (HBV or HCV) infection. METHODS: We studied 709 adults with chronic liver disease who had undergone liver biopsy during the 14-year period 1978-92. Anti-HCV testing was carried out with second-generation ELISA and immunoblot assays (RIBA 2). HBV markers were tested with commercially available radioimmunoassays. ACT and AAT concentrations in plasma were measured with electroimmunoassay and immune nephelometry. Plasma samples were screened for the AAT PiZ deficiency with ELISA technique and phenotyped by isoelectric focusing. The 229Pro-->Ala mutation for ACT deficiency was identified by PCR techniques. RESULTS: Of the 709 patients, 132 (18.6%) were positive for anti-HCV according to RIBA 2. PiZ AAT deficiency was found in 44 (6.2%) of patients (one PiZZ, 38 PiMZ, and PiSZ), while subnormal ACT levels were found in 33 (4.6%) patients, frequencies that were higher than expected in the general population (p=0.0375 and p<0.0001, respectively). Of the PiZ-carriers, 8/44 (18%) were found to be anti-HCV positive according to RIBA 2, as compared to 123/662 (19%) non-PiZ-carriers (p>0.05). One of these patients had cirrhosis, four chronic active hepatitis, and three chronic persistent hepatitis. In contrast, 17/33 (51.5%) of the patients with subnormal ACT were anti-HCV positive (OR=5.2, CI=2.6-10.6; p<0.0001). No relationship was found between HBV infection and AAT deficiency or subnormal ACT levels. Only one patient with subnormal ACT levels was heterozygous for the 229Pro-->Ala mutation of ACT deficiency. There was no significant difference in the histological findings when the patients with subnormal ACT levels or PiZ allele were subgrouped according to HCV status. CONCLUSIONS: There is no overrepresentation of chronic HBV or HCV in heterozygous AAT deficiency, although an association with more severe liver disease in such patients cannot be excluded. In contrast, low plasma levels of ACT that may be acquired or hereditary, due to mutations other than 229Pro-->Ala, are frequent in HCV infection.
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13.
  • Erichsen, Martina M, et al. (författare)
  • Clinical, Immunological, and Genetic Features of Autoimmune Primary Adrenal Insufficiency: Observations from a Norwegian Registry.
  • 2009
  • Ingår i: The Journal of clinical endocrinology and metabolism. - : The Endocrine Society. - 1945-7197 .- 0021-972X. ; 94, s. 4882-4890
  • Tidskriftsartikel (refereegranskat)abstract
    • Objective: Primary adrenal insufficiency [Addison's disease (AD)] is rare, and systematic studies are few, mostly conducted on small patient samples. We aimed to determine the clinical, immunological, and genetic features of a national registry-based cohort. Design: Patients with AD identified through a nationwide search of diagnosis registries were invited to participate in a survey of clinical features, health-related quality of life (HRQoL), autoantibody assays, and human leukocyte antigen (HLA) class II typing. Results: Of 664 registered patients, 64% participated in the study. The prevalence of autoimmune or idiopathic AD in Norway was 144 per million, and the incidence was 0.44 per 100,000 per year (1993-2007). Familial disease was reported by 10% and autoimmune comorbidity by 66%. Thyroid disease was most common (47%), followed by type 1 diabetes (12%), vitiligo (11%), vitamin B12 deficiency (10%), and premature ovarian insufficiency (6.6% of women). The mean daily treatment for AD was 40.5 mg cortisone acetate and 0.1 mg fludrocortisone. The mean Short Form 36 vitality scores were significantly diminished from the norm (51 vs. 60), especially among those with diabetes. Concomitant thyroid autoimmunity did not lower scores. Anti-21-hydroxylase antibodies were found in 86%. Particularly strong susceptibility for AD was found for the DR3-DQ2/ DRB1*0404-DQ8 genotype (odds ratio, 32; P = 4 x 10(-17)), which predicted early onset. Conclusions: AD is almost exclusively autoimmune, with high autoimmune comorbidity. Both anti-21-hydroxylase antibodies and HLA class II can be clinically relevant predictors of AD. HRQoL is reduced, especially among diabetes patients, whereas thyroid disease did not have an impact on HRQoL. Treatment modalities that improve HRQoL are needed.
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14.
  • Ericson, Ulrika, et al. (författare)
  • Folate intake, methylenetetrahydrofolate reductase polymorphisms, and breast cancer risk in women from the Malmö Diet and Cancer cohort.
  • 2009
  • Ingår i: Cancer Epidemiology Biomarkers & Prevention. - 1538-7755. ; 18:4, s. 1101-1110
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: Single nucleotide polymorphisms (SNP) of the folate-metabolizing enzyme methylenetetrahydrofolate reductase (MTHFR) may modify associations between folate intake and breast cancer. We examined if the association between tertiles of dietary folate equivalents (DFE) and breast cancer was different in subgroups according to genotypes of the MTHFR 677 C>T (rs1801133) and 1298A>C (rs1801131) SNPs and if the polymorphisms per se were associated with breast cancer. METHODS: This nested case-control study included 544 incident cases with invasive breast cancer and 1,088 controls matched on age and blood sampling date from the population-based Malmö Diet and Cancer cohort. Genotyping of the MTHFR SNPs was done with PCR-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Odds ratios (OR) were obtained by unconditional logistic regression. RESULTS: DFE was positively associated with breast cancer in MTHFR 677CT/TT-1298AA women (P for trend = 0.01) but inversely associated in compound heterozygous women (P for trend = 0.01). Interaction was observed between DFE and the 1298C allele (P = 0.03). The 677T allele was associated with increased breast cancer risk in women above 55 years [multivariate adjusted OR, 1.34; 95% confidence interval (95% CI), 1.01-1.76] and an interaction was observed between the T allele and age (P = 0.03). Homozygosis for the 1298C allele was associated with increased risk in women between 45 and 55 years (multivariate adjusted OR, 1.89; 95% CI, 1.09-3.29). CONCLUSION: In conclusion, a positive association between DFE and breast cancer was observed in MTHFR 677CT/TT-1298AA women but an inverse association was observed in 677CT-1298AC women. The 677T allele was associated with higher breast cancer risk in women above 55 years of age.
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15.
  • Ericson, Ulrika, et al. (författare)
  • Increased breast cancer risk at high plasma folate concentrations among women with the MTHFR 677T allele.
  • 2009
  • Ingår i: The American journal of clinical nutrition. - : Elsevier BV. - 1938-3207 .- 0002-9165. ; 90, s. 1380-1389
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: Folate is involved in DNA synthesis and methylation and may thereby influence carcinogenesis. OBJECTIVES: We examined plasma folate (P-folate) concentration in relation to genotypes of the folate-metabolizing enzyme methylenetetrahydrofolate reductase [MTHFR 677C<--T (rs1801133) and 1298A<--C (rs1801131)]. We also explored whether P-folate was associated with risk of postmenopausal breast cancer overall and in subgroups with genetic variants of the MTHFR single nucleotide polymorphisms (SNPs). DESIGN: This nested case-control study included 313 cases (age 55-73 y at baseline) with invasive breast cancer and 626 control subjects, matched on age and blood-sample date, from the population-based Malmö Diet and Cancer cohort. P-folate and MTHFR genotypes were determined for 310 cases and 611 controls. P-folate according to genotype was calculated by using analysis of variance. Odds ratios were obtained by using logistic regression. All tests were 2-sided. RESULTS: The variant 677T allele was associated with lower P-folate. In women with the 677T allele, a high P-folate concentration was associated with increased breast cancer risk (P for trend across P-folate tertiles = 0.03). Interaction was seen between the 677C<--T SNP and P-folate (P = 0.002). A positive association, which was seen between P-folate and breast cancer risk in 1298AA women (P = 0.01), was probably due to linkage between the 2 SNPs. Overall, and in women with other genotypes, no significant associations were observed. CONCLUSIONS: Our results suggest an association of high P-folate concentration with increased risk of postmenopausal breast cancer in carriers of the 677T allele. The findings underline the importance of genetic variation of MTHFR in the complex relation between folate and cancer.
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16.
  • Ericson, Ulrika, et al. (författare)
  • Plasma Folate Concentrations Are Positively Associated with Risk of Estrogen Receptor {beta} Negative Breast Cancer in a Swedish Nested Case Control Study.
  • 2010
  • Ingår i: Journal of Nutrition. - : Elsevier BV. - 1541-6100 .- 0022-3166. ; 140:9, s. 1661-1668
  • Tidskriftsartikel (refereegranskat)abstract
    • Folate's role in breast cancer development is controversial. Not only estrogen receptor (ER) alpha status, but also ERbeta status of tumors may have confounded results from previous epidemiological studies. We aimed to examine associations between plasma folate concentration and postmenopausal breast cancer defined by ER status. This nested case-control study, within the Malmö diet and cancer cohort, included 204 incident breast cancer cases with information on ERalpha and ERbeta status determined by immunochemistry on tissue micro-array sections. Plasma folate concentration was analyzed for the cases and 408 controls (matched on age and blood sample date). Odds ratios (OR) for ER-defined breast cancers in tertiles of plasma folate concentration were calculated with unconditional logistic regression. All tests were 2-sided. Women in the third tertile of plasma folate concentration (>12 nmol/L) had higher incidence of ERbeta- breast cancer than women in the first tertile (OR: 2.67; 95% CI: 1.44-4.92; P-trend = 0.001). We did not observe significant associations between plasma folate concentration and other breast cancer subgroups defined by ER status. We observed a difference between risks for ERbeta+ and ERbeta- cancer (P-heterogeneity = 0.003). Our findings, which indicate a positive association between plasma folate and ERbeta- breast cancer, highlight the importance of taking ERbeta status into consideration in studies of folate and breast cancer. The study contributes knowledge concerning folate's multifaceted role in cancer development. If replicated in other populations, the observations may have implications for public health, particularly regarding folic acid fortification.
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18.
  • Erlich, Henry, et al. (författare)
  • HLA DR-DQ haplotypes and genotypes and type 1 diabetes risk: Analysis of the Type 1 Diabetes Genetics Consortium families
  • 2008
  • Ingår i: Diabetes. - : American Diabetes Association. - 1939-327X .- 0012-1797. ; 57:4, s. 1084-1092
  • Tidskriftsartikel (refereegranskat)abstract
    • OBJECTIVE-The Type 1 Diabetes Genetics Consortium has collected type 1 diabetic families worldwide for genetic analysis. The major genetic determinants of type 1 diabetes are alleles at the HLA-DRB1 and DQB1 loci, with both susceptible and protective DR-DQ haplotypes present in all human populations. The aim of this study is to estimate the risk conferred by specific DR-DQ haplotypes and genotypes. RESEARCH DESIGN AND METHODS:-Six hundred and seven Caucasian families and 38 Asian families were typed at high resolution for the DRB1, DQA1, and DQB1 loci. The association analysis was performed by comparing the frequency of DR-DQ haplotypes among the chromosomes transmitted to an affected child with the frequency of chromosomes not transmitted to any affected child. RESULTS-A number of susceptible, neutral, and protective DR-DQ haplotypes have been identified, and a statistically significant hierarchy of type 1 diabetes risk has been established. The most susceptible haplotypes are the DRB1*0301-DQA1*0501-DQB1*0201 (odds ratio [OR] 3.64) and the DRB1*0405-DQA1*0301-DQB1*0302, DRB1*0401-DQA1*0301-DQB*0302, and DRB1*0402-DQA1*0301-DQB1*0302 haplotypes (ORs 11.37, 8.39, and 3.63), followed by the DRB1*0404-DQA1*0301-DQB1*0302 (OR 1.59) and the DRB1*0801-DQB1*0401-DQB1*0402 (OR 1.25) haplotypes. The most protective haplotypes are DRB1*1501-DQA1*0102-DQB1*0602 (OR 0.03), DRB1*1401-DQA1*0101-DQB1*0503 (OR 0.02), and DRB1*0701-DQA1*0201-DQB1*0303 (OR 0.02). CONCLUSIONS-Specific combinations of alleles at the DRB1, DQA1, and DQB1 loci determine the extent of haplotypic risk. The comparison of closely related DR-DQ haplotype pairs with different type I diabetes risks allowed identification of specific amino acid positions critical in determining disease susceptibility. These data also indicate that the risk associated with specific HLA haplotypes can be influenced by the genotype context and that the trans-complementing heterodimer encoded by DQA1*0501 and DQB1*0302 confers very high risk.
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19.
  • Fredriksson, Jenny, et al. (författare)
  • Variation in GYS1 Interacts with Exercise and Gender to Predict Cardiovascular Mortality
  • 2007
  • Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 2:3
  • Tidskriftsartikel (refereegranskat)abstract
    • Background. The muscle glycogen synthase gene (GYS1) has been associated with type 2 diabetes (T2D), the metabolic syndrome (MetS), male myocardial infarction and a defective increase in muscle glycogen synthase protein in response to exercise. We addressed the questions whether polymorphism in GYS1 can predict cardiovascular (CV) mortality in a high-risk population, if this risk is influenced by gender or physical activity, and if the association is independent of genetic variation in nearby apolipoprotein E gene (APOE). Methodology/Principal Findings. Polymorphisms in GYS1 (XbaIC>T) and APOE (-219G>T, epsilon 2/epsilon 3/epsilon 4) were genotyped in 4,654 subjects participating in the Botnia T2D-family study and followed for a median of eight years. Mortality analyses were performed using Cox proportional-hazards regression. During the follow-up period, 749 individuals died, 409 due to CV causes. In males the GYS1 XbaI T-allele (hazard ratio (HR) 1.9 [1.2-2.9]), T2D (2.5 [1.7-3.8]), earlier CV events (1.7 [1.2-2.5]), physical inactivity (1.9 [1.2-2.9]) and smoking (1.5 [1.0-2.3]) predicted CV mortality. The GYS1 XbaI T-allele predicted CV mortality particularly in physically active males (HR 1.7 [1.3-2.0]). Association of GYS1 with CV mortality was independent of APOE (219TT/epsilon 4), which by its own exerted an effect on CV mortality risk in females (2.9 [1.9-4.4]). Other independent predictors of CV mortality in females were fasting plasma glucose (1.2 [1.1-1.2]), high body mass index (BMI) (1.0 [1.0-1.1]), hypertension (1.9 [1.2-3.1]), earlier CV events (1.9 [1.3-2.8]) and physical inactivity (1.9 [1.2-2.8]). Conclusions/Significance. Polymorphisms in GYS1 and APOE predict CV mortality in T2D families in a gender-specific fashion and independently of each other. Physical exercise seems to unmask the effect associated with the GYS1 polymorphism, rendering carriers of the variant allele less susceptible to the protective effect of exercise on the risk of CV death, which finding could be compatible with a previous demonstration of defective increase in the glycogen synthase protein in carriers of this polymorphism.
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20.
  • Gidlöf, Olof, et al. (författare)
  • A Common Missense Variant in the ATP Receptor P2X7 Is Associated with Reduced Risk of Cardiovascular Events
  • 2012
  • Ingår i: Plos One. - : Public Library of Science (PLoS). - 1932-6203. ; 7:5
  • Tidskriftsartikel (refereegranskat)abstract
    • Background and Purpose: Extracellular adenosine triphosphate (ATP) regulates inflammatory cells by activation of the P2X(7) receptor. We hypothesized that polymorphisms in P2RX7 influence the risk of ischemic heart disease (IHD), ischemic stroke (IS) and cardiovascular risk factors and tested this hypothesis using genetic association studies. Methods: Two loss-of-function SNPs in P2RX7 were genotyped in 1244 IHD cases and 2488 controls as well as 5969 individuals with cardiovascular risk factors. Eleven SNPs in a 250 kb region on chromosome 12 spanning P2RX7 as well as neighboring genes OASL, P2RX4 and CAMKK2 were genotyped in 4138 individuals with IS and 2528 controls. Association was examined using linear and logistic regression models with an additive genetic model. Results: The common loss-of-function variant rs3751143 was significantly associated with a decreased risk of IHD in smokers (P = 0.03) as well as decreased risk of IS (OR 0.89; 95% CI = 0.81-0.97; P = 0.012). In addition, an intronic SNP in CAMKK2, rs2686342, were associated with a decreased risk of IS (OR 0.89; 95% CI = 0.82-0.97; P = 0.011). In subgroup analyses, both SNPs were associated with decreased risk of IS in individuals with hypertension (P = 0.045 and 0.015, respectively). Conclusions: A common loss-of-function missense variant in the gene encoding the P2X7 receptor is associated with reduced risk of IS and with IHD in smokers. These findings might implicate a role of purinergic signaling in atherogenesis or atherothrombosis.
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21.
  • Hansson, Mats G, et al. (författare)
  • Should donors be allowed to give broad consent to future biobank research?
  • 2006
  • Ingår i: The Lancet Oncology. - 1474-5488 .- 1470-2045. ; 7:3, s. 266-9
  • Tidskriftsartikel (refereegranskat)abstract
    • Large international biobank studies can make substantial contributions to scientific research by validation of the biological importance of previous research and by identification of previously unknown causes of disease. However, regulations for patient consent that are too strict and discrepancies in national policies on informed consent might hinder progress. Therefore, establishment of common ground for ethical review of biobank research is essential. in this essay, broad consent is defined on a scale between strictly specified (eg, for a specific study) and blanket consent (ie, with no restrictions regarding the purpose of the research). Future research includes that which might not be planned or even conceptualised when consent is obtained. In conclusion, broad consent and consent for future research are valid ethically and should be recommended for biobank research provided that: personal information related to research is handled safely; donors of biological samples are granted the right to withdraw consent; and new research studies or changes to the legal or ethical authority of a biobank are approved by an ethics-review board.
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22.
  • Harlid, Sophia, 1978-, et al. (författare)
  • A candidate CpG SNP approach identifies a breast cancer associated ESR1-SNP
  • 2011
  • Ingår i: International Journal of Cancer. - : Wiley-Blackwell. - 0020-7136 .- 1097-0215. ; 129:7, s. 1689-1698
  • Tidskriftsartikel (refereegranskat)abstract
    • Altered DNA methylation is often seen in malignant cells, potentially contributing to carcinogenesis by suppressing gene expression. We hypothesized that heritable methylation potential might be a risk factor for breast cancer and evaluated possible association with breast cancer for single nucleotide polymorphisms (SNPs) either involving CpG sequences in extended 5'-regulatory regions of candidate genes (ESR1, ESR2, PGR, and SHBG) or CpG and missense coding SNPs in genes involved in methylation (MBD1, MECP2, DNMT1, MGMT, MTHFR, MTR, MTRR, MTHFD1, MTHFD2, BHMT, DCTD, and SLC19A1). Genome-wide searches for genetic risk factors for breast cancers have in general not investigated these SNPs, because of low minor allele frequency or weak haplotype associations. Genotyping was performed using Mass spectrometry-Maldi-Tof in a screening panel of 538 cases and 1,067 controls. Potential association to breast cancer was identified for 15 SNPs and one of these SNPs (rs7766585 in ESR1) was found to associate strongly with breast cancer, OR 1.30 (95% CI 1.17-1.45; p-value 2.1 × 10(-6) ), when tested in a verification panel consisting of 3,211 unique breast cancer cases and 4,223 unique controls from five European biobank cohorts. In conclusion, a candidate gene search strategy focusing on methylation-related SNPs did identify a SNP that associated with breast cancer at high significance.
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23.
  • Harlid, Sophia, 1978-, et al. (författare)
  • Combined effect of low-penetrant SNPs on breast cancer risk
  • 2012
  • Ingår i: British Journal of Cancer. - London : Nature Publishing Group. - 0007-0920 .- 1532-1827. ; 106:2, s. 389-396
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: Although many low-penetrant genetic risk factors for breast cancer have been discovered, knowledge about the effect of multiple risk alleles is limited, especially in women <50 years. We therefore investigated the association between multiple risk alleles and breast cancer risk as well as individual effects according to age-approximated pre- and post-menopausal status.METHODS: Ten previously described breast cancer-associated single-nucleotide polymorphisms (SNPs) were analysed in a joint European biobank-based study comprising 3584 breast cancer cases and 5063 cancer-free controls. Genotyping was performed using MALDI-TOF mass spectrometry, and odds ratios were estimated using logistic regression.RESULTS: Significant associations with breast cancer were confirmed for 7 of the 10 SNPs. Analysis of the joint effect of the original 10 as well as the statistically significant 7 SNPs (rs2981582, rs3803662, rs889312, rs13387042, rs13281615, rs3817198 and rs981782) found a highly significant trend for increasing breast cancer risk with increasing number of risk alleles (P-trend 5.6 x 10(-20) and 1.5 x 10(-25), respectively). Odds ratio for breast cancer of 1.84 (95% confidence interval (CI): 1.59-2.14; 10 SNPs) and 2.12 (95% CI: 1.80-2.50; 7 SNPs) was seen for the maximum vs the minimum number of risk alleles. Additionally, one of the examined SNPs (rs981782 in HCN1) had a protective effect that was significantly stronger in premenopausal women (P-value: 7.9 x 10(-4)).CONCLUSION: The strongly increasing risk seen when combining many low-penetrant risk alleles supports the polygenic inheritance model of breast cancer. British Journal of Cancer (2012) 106, 389-396. doi:10.1038/bjc.2011.461 www.bjcancer.com Published online 1 November 2011 (C) 2012 Cancer Research UK
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24.
  • Harlid, Sophia, 1978-, et al. (författare)
  • Interactive effect of genetic susceptibility with height, body mass index, and hormone replacement therapy on the risk of breast cancer.
  • 2012
  • Ingår i: BMC Women's Health. - : Springer Science and Business Media LLC. - 1472-6874. ; 12
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: Breast cancer today has many established risk factors, both genetic and environmental, but these risk factors by themselves explain only part of the total cancer incidence. We have investigated potential interactions between certain known genetic and phenotypic risk factors, specifically nine single nucleotide polymorphisms (SNPs) and height, body mass index (BMI) and hormone replacement therapy (HRT).METHODS: We analyzed samples from three different study populations: two prospectively followed Swedish cohorts and one Icelandic case-control study. Totally 2884 invasive breast cancer cases and 4508 controls were analysed in the study. Genotypes were determined using Mass spectrometry-Maldi-TOF and phenotypic variables were derived from measurements and/or questionnaires. Odds Ratios and 95% confidence intervals were calculated using unconditional logistic regression with the inclusion of an interaction term in the logistic regression model.RESULTS: One SNP (rs851987 in ESR1) tended to interact with height, with an increasingly protective effect of the major allele in taller women (p = 0.007) and rs13281615 (on 8q24) tended to confer risk only in non users of HRT (p-for interaction = 0.03). There were no significant interactions after correction for multiple testing.CONCLUSIONS: We conclude that much larger sample sets would be necessary to demonstrate interactions between low-risk genetic polymorphisms and the phenotypic variables height, BMI and HRT on the risk for breast cancer. However the present hypothesis-generating study has identified tendencies that would be of interest to evaluate for gene-environment interactions in independent materials.
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25.
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26.
  • Ivarsson, Malin, et al. (författare)
  • Extraction, quantitation, and evaluation of function DNA from various sample types.
  • 2011
  • Ingår i: Methods in Molecular Biology. - Totowa, NJ : Humana Press. - 1940-6029. ; 675, s. 261-277
  • Tidskriftsartikel (refereegranskat)abstract
    • Two vital pre-requisites for genetic epidemiology have been fullfiled during the past decade and have led to a virtual explosion of knowledge concerning disease risks. Reliable databases over genetic variation derived from, e.g. the HUGO and HapMap projects, coupled with technological advances make large-scale genetic analyses and downstream bioinformatics suddenly affordable. Although recent prospective population-based biobanks have included DNA collection and purification in their planning, it is the older projects that currently are of greatest value due to the numbers of accumulated disease endpoints. In this chapter, methods to purify and use DNA derived from a variety of archival materials, including whole blood, formalin-fixed paraffin-embedded (FFPE) tissues, sera, dried blood spots (DBS), cervical cell suspensions, and mouthwash are presented and evaluated in a context of quality control guidelines to provide objective measure of the usefulness of various sample types for genetic epidemiology.
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27.
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28.
  • Johansson, Björn, et al. (författare)
  • Alpha-1-antitrypsin is present in the specific granules of human eosinophilic granulocytes
  • 2001
  • Ingår i: Clinical and Experimental Allergy. - : Wiley. - 1365-2222 .- 0954-7894. ; 31:3, s. 379-386
  • Tidskriftsartikel (refereegranskat)abstract
    • Eosinophils may be found at sites of inflammation, for example in asthma, allergy and helminthic infestation, but their role in human inflammatory disease is unclear. In the present study, we investigated the presence of alpha-1-antitrypsin (AAT), a serine proteinase inhibitor, in human eosinophils. When lysates of highly purified eosinophils were subjected to Western blotting, with a chemiluminescent substrate, immunoreactive bands were seen. An ELISA was developed to measure the AAT content, which was found to be about 100 ng/5 x 106 eosinophils, about 50 ng/5 x 106 neutrophils, and about 25 ng/5 x 106 monocytes. Immunoelectron microscopy showed localization of AAT to the specific granules of eosinophils. During prolonged incubation of eosinophils, no significant increase in the total amount of AAT could be detected by ELISA. However, there was an increased level of AAT in the medium, in parallel with a decrease in the intracellular AAT content, suggesting release of preformed AAT. Apparent complex formation between iodinated elastase and AAT in eosinophil lysates provided evidence that the AAT is functionally active. On the basis of these findings it is suggested that by releasing AAT, eosinophils may, in a microenvironment, play a role in counteracting the tissue damage caused by serine proteinases released by neutrophils in inflammatory conditions.
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29.
  • Jonsson, Magnus, et al. (författare)
  • Computer-supported detection of M-components and evaluation of immunoglobulins after capillary electrophoresis
  • 2001
  • Ingår i: Clinical Chemistry. - 0009-9147. ; 47:1, s. 110-117
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: Electrophoresis of serum samples allows detection of monoclonal gammopathies indicative of multiple myeloma, Waldenstrom macroglobulinemia, monoclonal gammopathy of undetermined significance, and amyloidosis. Present methods of high-resolution agarose gel electrophoresis (HRAGE) and immunofixation electrophoresis (IFE) are manual and labor-intensive. Capillary zone electrophoresis (CZE) allows rapid automated protein separation and produces digital absorbance data, appropriate as input for a computerized decision support system. METHODS: Using the Beckman Paragon CZE 2000 instrument, we analyzed 711 routine clinical samples, including 95 monoclonal components (MCs) and 9 cases of Bence Jones myeloma, in both the CZE and HRAGE systems. Mathematical algorithms developed for the detection of monoclonal immunoglobulins (MCs) in the gamma- and ss-regions of the electropherogram were tested on the entire material. Additional algorithms evaluating oligoclonality and polyclonal concentrations of immunoglobulins were also tested. RESULTS: CZE electropherograms corresponded well with HRAGE. Only one IgG MC of 1 g/L, visible on HRAGE, was not visible after CZE. Algorithms detected 94 of 95 MCs (98.9%) and 100% of those visible after CZE. Of 607 samples lacking an MC on HRAGE, only 3 were identified by the algorithms (specificity, 99%). Algorithms evaluating total gammaglobulinemia and oligoclonality also identified several cases of Bence Jones myeloma. CONCLUSIONS: The use of capillary electrophoresis provides a modern, rapid, and cost-effective method of analyzing serum proteins. The additional option of computerized decision support, which provides rapid and standardized interpretations, should increase the clinical availability and usefulness of protein analyses in the future.
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30.
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31.
  • Kristensson, Malin, et al. (författare)
  • Design of recombinant antibody microarrays for urinary proteomics.
  • 2012
  • Ingår i: Proteomics Clinical Applications. - : Wiley. - 1862-8354 .- 1862-8346. ; 6:5-6, s. 291-296
  • Tidskriftsartikel (refereegranskat)abstract
    • PURPOSE: Urinary proteomics has become a key discipline within clinical proteomics for noninvasive diagnosis and monitoring of disease, and biomarker discovery. In order to decipher complex proteomes, high demands will, however, be placed upon the methodology applied. The purpose of this study was to develop a recombinant antibody microarray platform for urinary proteomics. EXPERIMENTAL DESIGN: We adopted our previously in-house developed recombinant antibody microarray set-up and redesigned the platform for urinary proteomics. In this process, the key antibody array assay parameters, such as sample handling, sample labeling protocol, and assay conditions, etc, reflecting the unique properties of urine as sample format, were addressed and reoptimized in a step-by-step procedure. RESULTS: In this proof-of-concept study, we have designed the first generation of a recombinant antibody microarray technology platform for urinary proteomics. The results showed that multiplexed, sensitive (pg/mL range), and reproducible urine protein expression profiling could be performed targeting directly labeled, nonfractionated urine. CONCLUSION AND CLINICAL RELEVANCE: We have demonstrated that crude, directly labeled urine samples could be profiled in a rapid, reproducible, sensitive, and multiplexed manner after minimal sample prehandling. These findings could potentially pave the way for enhanced urinary proteomics and understanding of renal physiology with implications in both health and disease.
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32.
  • Lavant, Ewa, et al. (författare)
  • A new automated human leukocyte antigen genotyping strategy to identify DR-DQ risk alleles for celiac disease and type 1 diabetes mellitus
  • 2009
  • Ingår i: Clinical Chemistry and Laboratory Medicine. - : Walter de Gruyter. - 1434-6621 .- 1437-4331. ; 47:12, s. 1489-1489
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: The risk for type 1 diabetes mellitus (T1DM) and celiac disease (CD) is related to human leukocyte antigen (HLA) DQA1, DQB1 and DRB1 loci. Unfortunately, HLA typing has been too difficult and costly for frequent use. Automated genotyping focused on risk alleles could provide access to HLA typing in diagnostic evaluations, epidemiological screening and contribute to preventive strategies. METHODS: A sequence specific primer amplification method requiring a total of four PCR reactions, one restriction enzyme digestion and a single electrophoretic step provides low to medium resolution typing of DQA1, DQB1 and DRB1 using Applied Biosystems 3730 DNA analyzer. The method was validated using 261 samples with genotypes determined using a reference method. RESULTS: Specific fluorescent DQA1, DQB1 and DRB1 amplicons were of expected size. Concordance with the reference method was 100% for DQA1 and DQB1 alleles and 99.8% for DRB1 alleles. CONCLUSIONS: We have developed a high throughput HLA typing method that accurately distinguishes risk alleles for T1DM and CD. This method allows screening of several thousand samples per week, consuming 32 ng of DNA template, low reagent volumes and minimal time for data review.
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33.
  • Lavant, Eva, et al. (författare)
  • A new PCR-SSP method for HLA DR-DQ risk assessment for celiac disease
  • 2011
  • Ingår i: Clinica Chimica Acta. - : Elsevier. - 0009-8981 .- 1873-3492. ; 412:9-10, s. 782-784
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Susceptibility to celiac disease is essentially restricted to carriers of specific HLA DQA1 and DQB1 alleles. We have developed a semi-automated sequence specific primer (SSP) PCR method for clinical HLA typing and compared the test results with those from a commercial method. Methods: Primers for each DQA1 and DQB1 allele group were included in our PCR-SSP reaction to allow differentiation of homozygous from heterozygous carriers of risk alleles. Primers detecting the tightly linked DRB1*04, *03, *07 and *09 alleles were included to resolve potentially ambiguous results. Fluorescently labeled PCR products of 119 clinical samples were analyzed by capillary electrophoresis, and results were compared to those previously obtained from the DELFIA® Type 1 Diabetes Genetic Predisposition assay. Results: The risk assessment derived from the two methods was 100% concordant. One previously unreported haplotype was detected and haplotype assignments in two of the 119 samples were improved from previous reports. Conclusions: The use of three PCR reactions and a single electrophoretic step for DQA1, DQB1 and DRB1 typing provides distinction of celiac disease associated alleles and their homo- or heterozygous status. This multiplex analysis reduces reagent costs, personnel and instrument time, while enabling improved allelic assignment through HLA-DR-DQ haplotype association.
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34.
  • Lavant, Ewa H., et al. (författare)
  • HLA DR-DQ genotyping by capillary electrophoresis for risk assessment for celiac disease.
  • 2013
  • Ingår i: Clinical Applications of Capillary Electrophoresis. - Totowa, NJ : Humana Press. - 9781627030281 - 9781627030298 ; 919, s. 297-307
  • Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
    • The risk for celiac disease (CD) is clearly related to specific HLA DQA1 and DQB1 alleles, but HLA -typing is often considered too costly for frequent use.Here we present a method using sequence-specific primed PCR (PCR-SSP) for HLA-DR-DQ genotyping optimized for capillary electrophoresis on Applied Biosystems 3130xl Genetic Analyzer. Requiring a total of three PCR reactions and a single electrophoretic step, this method reduces the reagent expenses and technical time for directed HLA typing to distinguish risk alleles for CD, with a sufficient throughput for large-scale screening projects.
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35.
  • Lindqvist, P G, et al. (författare)
  • Family secrets to be disclosed.
  • 2006
  • Ingår i: Journal of Thrombosis and Haemostasis. - : Elsevier BV. - 1538-7933 .- 1538-7836. ; 4:10, s. 2180-2181
  • Tidskriftsartikel (refereegranskat)
  •  
36.
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37.
  • Martin, Joyce, et al. (författare)
  • Decisions Supported by the Core Ontology for Missions and Capabilities in Systems of Systems
  • 2024
  • Ingår i: SysCon 2024 - 18th Annual IEEE International Systems Conference, Proceedings. - : Institute of Electrical and Electronics Engineers (IEEE). - 9798350358803
  • Konferensbidrag (refereegranskat)abstract
    • This study explores how a core ontology for missions and capabilities in systems of systems supports basic and fundamental decisions related to development and operations of systems of systems. The study is based on a previously developed core ontology for mission and capability in the context of systems of systems. From the relationships in the core ontology concepts, this study extracts fundamental design and operational decisions. These decisions are compiled into a preliminary guideline aimed at assessing the feasibility of systems of systems. This compilation uses Kipling's six honest serving men's reasoning to support clustering of decisions based on their intended outcome. The study identifies categories of generic constraints that affect these decisions. The overall aim is that the clustered decisions and the constraint categories should trigger different points of views for designers and operators as they envision their systems of systems and constituent systems. The preliminary guideline developed is then used to illustrate a road paving system, and different ways of using the guideline are discussed. The tool demonstrates flexibility, therefore setting a good starting point for brainstorming and exploration of systems of systems design and operations.
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38.
  • Martin, Joyce, et al. (författare)
  • The Capability Concept in the Context of Systems of Systems : A Systematic Literature Review
  • 2022
  • Ingår i: ISSE 2022 - 2022 8th IEEE International Symposium on Systems Engineering, Conference Proceedings. - : Institute of Electrical and Electronics Engineers Inc.. - 9781665481823
  • Konferensbidrag (refereegranskat)abstract
    • Systems of systems (SoS) leverage dynamic configuration of independent systems to achieve a capability neither of the independent constituent systems can achieve on their own. Therefore, SoS engineering goes beyond addressing requirements to addressing capabilities. Due to the independence of the constituent systems, capability is formed by complex interdependence of legacy systems. It is also subject to uncertainty of the evolutionary development of the SoS, making it important to not only see the bigger picture but to plan for the changing capability patterns in the life of an SoS. This study looks at the body of knowledge surrounding definitions, support systems and practices around the concept of capability in the context of SoS. The results show; context dependent nature of the definition of capability, country-specific support systems, ongoing efforts to form more robust frameworks and dominant establishment of this theme in the defense sector.
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39.
  • Martin, Joyce, et al. (författare)
  • Towards a Core Ontology for Missions and Capabilities in Systems of Systems
  • 2023
  • Ingår i: 2023 18th Annual System of Systems Engineering Conference, SoSe 2023. - : Institute of Electrical and Electronics Engineers Inc.. - 9798350327236
  • Konferensbidrag (refereegranskat)abstract
    • This study presents a core ontology for missions and capabilities in systems of systems. The aim of the study is to create artifacts that facilitate precise understanding of fundamental concepts of SoS. An ontological approach proposes and develops taxonomic homogeneity and structural knowledge of SoS. The ontology development process involved workshop sessions with industry experts and meta modelling of the different concepts and their relationships. The ontology includes thirteen concepts of types physical things, people, information and mixed. These concepts are defined and their relations are briefly described. The developed ontology is further illustrated using a wildfire scenario case study.
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40.
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41.
  • Mychaleckyj, Josyf C., et al. (författare)
  • HLA genotyping in the international Type 1 Diabetes Genetics Consortium
  • 2010
  • Ingår i: Clinical Trials. - : SAGE Publications. - 1740-7753 .- 1740-7745. ; 7:1 suppl., s. 75-87
  • Tidskriftsartikel (refereegranskat)abstract
    • Background Although human leukocyte antigen (HLA) DQ and DR loci appear to confer the strongest genetic risk for type 1 diabetes, more detailed information is required for other loci within the HLA region to understand causality and stratify additional risk factors. The Type 1 Diabetes Genetics Consortium (T1DGC) study design included high-resolution genotyping of HLA-A, B, C, DRB1, DQ, and DP loci in all affected sibling pair and trio families, and cases and controls, recruited from four networks worldwide, for analysis with clinical phenotypes and immunological markers. Purpose In this article, we present the operational strategy of training, classification, reporting, and quality control of HLA genotyping in four laboratories on three continents over nearly 5 years. Methods Methods to standardize HLA genotyping at eight loci included: central training and initial certification testing; the use of uniform reagents, protocols, instrumentation, and software versions; an automated data transfer; and the use of standardized nomenclature and allele databases. We implemented a rigorous and consistent quality control process, reinforced by repeated workshops, yearly meetings, and telephone conferences. Results A total of 15,246 samples have been HLA genotyped at eight loci to four-digit resolution; an additional 6797 samples have been HLA genotyped at two loci. The genotyping repeat rate decreased significantly over time, with an estimated unresolved Mendelian inconsistency rate of 0.21%. Annual quality control exercises tested 2192 genotypes (4384 alleles) and achieved 99.82% intra-laboratory and 99.68% inter-laboratory concordances. Limitations The chosen genotyping platform was unable to distinguish many allele combinations, which would require further multiple stepwise testing to resolve. For these combinations, a standard allele assignment was agreed upon, allowing further analysis if required. Conclusions High-resolution HLA genotyping can be performed in multiple laboratories using standard equipment, reagents, protocols, software, and communication to produce consistent and reproducible data with minimal systematic error. Many of the strategies used in this study are generally applicable to other large multi-center studies. Clinical Trials 2010; 7: S75-S87. http://ctj.sagepub.com.
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42.
  • Nelson, Dick, et al. (författare)
  • Semi-automated quantification of methylmalonic acid in human serum by LC-MS/MS
  • 2012
  • Ingår i: Scandinavian Journal of Clinical & Laboratory Investigation. - : Informa UK Limited. - 1502-7686 .- 0036-5513. ; 72:6, s. 441-446
  • Tidskriftsartikel (refereegranskat)abstract
    • Background. Methylmalonic acid (MMA), a sensitive biomarker of functional vitamin B12 deficiency, is commonly determined by gas chromatography-mass spectrometry (GC-MS) or liquid chromatography-tandem mass spectrometry (LC-MS/MS) methods using manual extraction and derivatization of MMA to reduce polarity prior to separation. Methods. In the present study we introduce a semi-automated extraction on a strong anion exchanger, HPLC separation on a BEH-amide column to separate serum MMA from its abundant isoform, succinic acid, followed by MS/MS detection and quantification. Results. The extraction of MMA plus internal standard provides full recovery and the method is linear between 0.03 mu mol/L and 20.0 mu mol/L (r(2) = 1.0) with intra-and inter-assay imprecision of 2.2%. Agreement with other laboratories has been demonstrated in external proficiency testing. Compared to both conventional GC-MS and LC-MS/MS methods, the correlation is r(2) > 0.99. Conclusions. The use of robotic pipetting, elimination of derivatization and improved separation by the BEH-amide column combined with HILIC chromatographic conditions significantly improve sample throughput compared to conventional methods. Using a single pipetting robot and LC-MS/MS instrument, this method is currently performing 180 analyses per day from 10 regional hospitals and several additional distant sites.
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43.
  • Noble, Janelle A., et al. (författare)
  • HLA Class I and Genetic Susceptibility to Type 1 Diabetes Results From the Type 1 Diabetes Genetics Consortium
  • 2010
  • Ingår i: Diabetes. - : American Diabetes Association. - 1939-327X .- 0012-1797. ; 59:11, s. 2972-2979
  • Tidskriftsartikel (refereegranskat)abstract
    • OBJECTIVE-We report here genotyping data and type 1 diabetes association analyses for HLA class I loci (A, B, and C) on 1,753 multiplex pedigrees from the Type 1 Diabetes Genetics Consortium (T1DGC), a large international collaborative study. RESEARCH DESIGN AND METHODS-Complete eight-locus HLA genotyping data were generated. Expected patient class I (HLA-A, -B, and -C) allele frequencies were calculated, based on linkage disequilibrium (LD) patterns with observed HLA class II DRB1-DQA1-DQB1 haplotype frequencies. Expected frequencies were compared to observed allele frequencies in patients. RESULTS-Significant type 1 diabetes associations were observed at all class I HLA loci. After accounting for LD with HLA class II, the most significantly type 1 diabetes-associated alleles were B*5701 (odds ratio 0.19; P = 4 x 10(-11)) and B*3906 (10.31; P = 4 X 10(-10)). Other significantly type 1 diabetes-associated alleles included A*2402, A*0201, B*1801, and C*0501 (predisposing) and A*1101, A*3201, A*6601, B*0702, B*4403, B*3502, C*1601, and C*0401 (protective). Some alleles, notably B*3906, appear to modulate the risk of all DRB1-DQA1-DQB1 haplotypes on which they reside, suggesting a class I effect that is independent of class H. Other class I type 1 diabetes associations appear to be specific to individual class H haplotypes. Some apparent associations (e.g., C*1601) could be attributed to strong LD to another class I susceptibility locus (B*4403). CONCLUSIONS-These data indicate that HLA class I alleles, in addition to and independently from HLA class H alleles, are associated with type 1 diabetes. Diabetes 59:2972-2979, 2010
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44.
  • Nyman, U., et al. (författare)
  • Standardization of p-creatinine assays and use of lean body mass allow improved prediction of calculated glomerular filtration rate in adults: A new equation
  • 2006
  • Ingår i: Scandinavian Journal of Clinical & Laboratory Investigation. - : Informa UK Limited. - 1502-7686 .- 0036-5513. ; 66:6, s. 451-468
  • Tidskriftsartikel (refereegranskat)abstract
    • Objective. To evaluate the Cockcroft - Gault (CG) equation, using various body weight expressions, and the Sawyer equation in predicting glomerular filtration rate (GFR) using an enzymatic and zero-calibrated Jaffe plasma-creatinine assay, and to derive a new robust equation in adults. Material and methods. The CG weight measures included total, ideal and adjusted body weight (ABW; lowest of total and ideal) and two lean body mass (LBM) expressions, while the Sawyer equation is based primarily on LBM. Iohexol clearance was used to measure GFR. One derivation set (n = 436; enzymatic assay) was used to evaluate and bias-adjust existing equations when indicated, and to derive a new equation based on plasma-creatinine, age, gender and the body weight measure yielding the best adjusted R-2. All equations were then validated in a separate set (n = 414; Jaffe assay). Results. The existing equations all performed similarly in both sets. Prediction errors of equations based on LBM showed no correlation with BMI. The CG(ABW) and Sawyer equations performed best. The new equation with LBM yielded the highest adjusted R-2. In the combined set (n = 850), its accuracy (86%/98% of estimates within 30%/50% of measured GFR) was significantly better than for the CGABW (79%/95%) and Sawyer equations (79%/93%) (p < 0.001) for each 30 mL/min GFR subgroup within +/- 30% and +/- 50%, except within +/- 30% > 120 mL/min. Prediction error did not correlate with BMI, age or gender. Conclusion. A new creatinine-based equation derived in a mainly Caucasian patient sample is a better predictor of GFR than CG-type equations irrespective of the body weight measure used or, if bias-adjusted, when using zero-calibrated creatinine assays.
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45.
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46.
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47.
  • Roulland, Sandrine, et al. (författare)
  • t(14;18) Translocation: A Predictive Blood Biomarker for Follicular Lymphoma
  • 2014
  • Ingår i: Journal of Clinical Oncology. - 1527-7755 .- 0732-183X. ; 32:13, s. 1347-1347
  • Tidskriftsartikel (refereegranskat)abstract
    • Purpose The (14;18) translocation constitutes both a genetic hallmark and critical early event in the natural history of follicular lymphoma (FL). However, t(14;18) is also detectable in the blood of otherwise healthy persons, and its relationship with progression to disease remains unclear. Here we sought to determine whether t(14;18)-positive cells in healthy individuals represent tumor precursors and whether their detection could be used as an early predictor for FL. Participants and Methods Among 520,000 healthy participants enrolled onto the EPIC (European Prospective Investigation Into Cancer and Nutrition) cohort, we identified 100 who developed FL 2 to 161 months after enrollment. Prediagnostic blood from these and 218 controls were screened for t(14;18) using sensitive polymerase chain reaction-based assays. Results were subsequently validated in an independent cohort (65 case participants; 128 controls). Clonal relationships between t(14;18) cells and FL were also assessed by molecular backtracking of paired prediagnostic blood and tumor samples. Results Clonal analysis of t(14;18) junctions in paired prediagnostic blood versus tumor samples demonstrated that progression to FL occurred from t(14;18)-positive committed precursors. Furthermore, healthy participants at enrollment who developed FL up to 15 years later showed a markedly higher t(14;18) prevalence and frequency than controls (P < .001). Altogether, we estimated a 23-fold higher risk of subsequent FL in blood samples associated with a frequency > 10(-4) (odds ratio, 23.17; 95% CI, 9.98 to 67.31; P < .001). Remarkably, risk estimates remained high and significant up to 15 years before diagnosis. Conclusion High t(14;18) frequency in blood from healthy individuals defines the first predictive biomarker for FL, effective years before diagnosis.
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48.
  • Rydén, Ingvar (författare)
  • Clinical studies on α1-acid glycoprotein glycosylation - with focus on fucose
  • 2002
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • α1-Acid glycoprotein (AGP, orosomucoid) is a heavily glycosylated protein found in blood plasma in all humans. AGP is one of the major acute phase proteins, and its concentration is frequently measured in clinical laboratories as a marker for inflammatory disease. For several years it has been known that the glycosylation of AGP is altered in different physiological and pathological conditions. However, methods for analysis of the glycosylation changes have been time-consuming and at best semi-quantitative. Consequently, clinical studies have been limited to small numbers of patients, and have not confirmed the usefulness of routine analysis of A GP glycosylation in clinical investigations. In the present study, two major issues were addressed: the need for new methods that would allow quantitative measurements of specific glycosylation changes, and the need for clinical studies with sufficient numbers of study subjects to evaluate the potential advantages and drawbacks of analyzing AGP glycosylation in a clinical laboratory.High-pH anion-exchange chromatography (HPAEC) separates oligosaccharides with high resolution and was used to study N-linked oligosaccharides (N-glycans) released from AGP obtained from patients with different inflannnatory conditions. We showed that HPAEC is a very reproducible and useful method for profiling of AGP N-glycans, providing infmmation on N-glycan sialylation and fucosylation simultaneously. In particular, we found a typical pattern with a sharp increase in fucosylated, tri-sialylated N-glycans in patients with rheumatoid arthritis (RA). The laborious preparation of samples prior to analysis is a drawback for the use ofHPAEC as a routine method in a clinical laboratory. However, HPAEC has a great potential as a tool for profiling AGP glycosylation in different pathologic conditions, and it was used as a reference for the development of other analytical methods. In order to analyze a larger number of patient samples, we developed a lectin immunoassay using a fucose specific lectin from the A!euria aurantia mushroom. The lectin immunoassay was well suited for use in a clinical laboratory and was used to study AGP fucosylation in patients with severe bmns, recent onset rheumatoid arthritis (RA), liver disease, and alcohol abuse. In a time study of 10 patients with severe bums, changes in AGP fucosylation showed a typical pattern, without con-elation to acute phase protein synthesis. This confirmed the results of previous studies indicating that glycosylation is regulated independently from protein synthesis in the acute phase response.We studied AGP fucosylation in 131 patients with recent onset RA. In these patients, AGP fucosy lation was increased, but the con elation with disease activity according to a clinical score (DAS28) was not superior to previously used biochemical markers of inflammation. However, in men with RA who had increased AGP fucosylation at the time of diagnosis, the degree of fucosylation conelated to disease progression during the first year following diagnosis. It remains to be confumed whether AGP fucosylation can provide prognostic information for this patient category.When we studied AGP fucosylation in 261 patients investigated for suspected liver disease, fucosylation was heavily increased in patients with histopathological signs of liver cirrhosis. In addition, AGP fucosylation coiTelated to the severity of disease. By calculating an AGP fucosylation index (AGP-Fl, AGP fucosylation/AGP serum concentration), a high diagnostic accuracy was found for liver cinhosis. Even in patients with cinhosis without any symptoms related to liver disease, AGP-FI was significantly higher than in patients with steatosis or chronic hepatitis. When compared with other biochemical markers of liver disease, AGP fucosylation was among the most specific in discriminating liver cin·hosis, and may be useful in clinical investigations of liver disease.We also studied AGP fucosylation in 21 patients with heavy alcohol abuse admitted to hospital for detoxification. fu the 16 male patients that were studied, AGP fucosylation was significantly increased compared to healthy controls. Furthermore, in these men there was a significant con·elation between AGP fucosylation and other biochemical markers previously used for detection of liver cirrhosis. This study should be extended with a larger number of patients, and histopathological examination following liver biopsy, in order to confirm the value of increased AGP fucosylation as an early marker for cirrhosis in this patient categmy.
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49.
  • Saxena, Richa, et al. (författare)
  • Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels
  • 2007
  • Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 316:5829, s. 1331-1336
  • Tidskriftsartikel (refereegranskat)abstract
    • New strategies for prevention and treatment of type 2 diabetes (T2D) require improved insight into disease etiology. We analyzed 386,731 common single-nucleotide polymorphisms (SNPs) in 1464 patients with T2D and 1467 matched controls, each characterized for measures of glucose metabolism, lipids, obesity, and blood pressure. With collaborators (FUSION and WTCCC/UKT2D), we identified and confirmed three loci associated with T2D - in a noncoding region near CDKN2A and CDKN2B, in an intron of IGF2BP2, and an intron of CDKAL1 - and replicated associations near HHEX and in SLC30A8 found by a recent whole-genome association study. We identified and confirmed association of a SNP in an intron of glucokinase regulatory protein (GCKR) with serum triglycerides. The discovery of associated variants in unsuspected genes and outside coding regions illustrates the ability of genome-wide association studies to provide potentially important clues to the pathogenesis of common diseases.
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50.
  • Shi, Hong, et al. (författare)
  • Single nucleotide polymorphisms in the 20q13 amplicon genes in relation to breast cancer risk and clinical outcome
  • 2011
  • Ingår i: Breast Cancer Research and Treatment. - New York : Springer-Verlag New York. - 0167-6806 .- 1573-7217. ; 130:3, s. 905-916
  • Tidskriftsartikel (refereegranskat)abstract
    • The 20q13 region is frequently amplified/overexpressed in breast tumours. However, the nature of this amplification/overexpression is unknown. Here, we investigated genetic variation in five 20q13 amplicon genes (MYBL2, AURKA, ZNF217, STK4 and PTPN1) and its impact on breast cancer (BC) susceptibility and clinical outcome. As a novel finding, four polymorphisms in STK4 (rs6017452, rs7271519) and AURKA (rs2273535, rs8173) associated with steroid hormone receptor status both in a Swedish population-based cohort of 783 BC cases and in a Polish familial/early onset cohort of 506 BC cases. In the joint analysis, the minor allele carriers of rs6017452 had more often hormone receptor positive tumours (OR 0.57, 95% CI 0.40-0.81), while homozygotes for the minor allele of rs7271519, rs2273535 and rs8173 had more often hormone receptor negative tumours (2.26, 1.30-3.39; 2.39, 1.14-5.01; 2.39, 1.19-4.80, respectively) than homozygotes for the common allele. BC-specific survival analysis of AURKA suggested that the Swedish carriers of the minor allele of rs16979877, rs2273535 and rs8173 might have a worse survival compared with the major homozygotes. The survival probabilities associated with the AURKA genotypes depended on the tumour phenotype. In the Swedish case-control study, associations with BC susceptibility were observed in a dominant model for three MYBL2 promoter polymorphisms (rs619289, P = 0.02; rs826943, P = 0.03 and rs826944, P = 0.02), two AURKA promoter polymorphisms (rs6064389, P = 0.04 and rs16979877, P = 0.02) and one 3'UTR polymorphism in ZNF217 (rs1056948, P = 0.01). In conclusion, our data confirmed the impact of the previously identified susceptibility locus and provided preliminary evidence for novel susceptibility variants in BC. We provided evidence for the first time that genetic variants at 20q13 may affect hormone receptor status in breast tumours and influence tumour aggressiveness and survival of the patients. Future studies are needed to confirm the prognostic value of our findings in the clinic.
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