| 1. |
- Andersson, Anna, et al.
(författare)
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Microarray-based classification of a consecutive series of 121 childhood acute leukemias: prediction of leukemic and genetic subtype as well as of minimal residual disease status.
- 2007
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Ingår i: Leukemia. - : Springer Science and Business Media LLC. - 1476-5551 .- 0887-6924. ; 21:6, s. 1198-1203
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Tidskriftsartikel (refereegranskat)abstract
- Gene expression analyses were performed on 121 consecutive childhood leukemias (87 B-lineage acute lymphoblastic leukemias (ALLs), 11 T-cell ALLs and 23 acute myeloid leukemias (AMLs)), investigated during an 8-year period at a single center. The supervised learning algorithm k-nearest neighbor was utilized to build gene expression predictors that could classify the ALLs/AMLs according to clinically important subtypes with high accuracy. Validation experiments in an independent data set verified the high prediction accuracies of our classifiers. B-lineage ALLs with uncharacteristic cytogenetic aberrations or with a normal karyotype displayed heterogeneous gene expression profiles, resulting in low prediction accuracies. Minimal residual disease status (MRD) in T-cell ALLs with a high (40.1%) MRD at day 29 could be classified with 100% accuracy already at the time of diagnosis. In pediatric leukemias with uncharacteristic cytogenetic aberrations or with a normal karyotype, unsupervised analysis identified two novel subgroups: one consisting mainly of cases remaining in complete remission (CR) and one containing a few patients in CR and all but one of the patients who relapsed. This study of a consecutive series of childhood leukemias confirms and extends further previous reports demonstrating that global gene expression profiling provides a valuable tool for genetic and clinical classification of childhood leukemias.
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| 2. |
- Berndt, Sonja I., et al.
(författare)
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Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:5, s. 501-U69
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Tidskriftsartikel (refereegranskat)abstract
- Approaches exploiting trait distribution extremes may be used to identify loci associated with common traits, but it is unknown whether these loci are generalizable to the broader population. In a genome-wide search for loci associated with the upper versus the lower 5th percentiles of body mass index, height and waist-to-hip ratio, as well as clinical classes of obesity, including up to 263,407 individuals of European ancestry, we identified 4 new loci (IGFBP4, H6PD, RSRC1 and PPP2R2A) influencing height detected in the distribution tails and 7 new loci (HNF4G, RPTOR, GNAT2, MRPS33P4, ADCY9, HS6ST3 and ZZZ3) for clinical classes of obesity. Further, we find a large overlap in genetic structure and the distribution of variants between traits based on extremes and the general population and little etiological heterogeneity between obesity subgroups.
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| 3. |
- Broadaway, K Alaine, et al.
(författare)
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Loci for insulin processing and secretion provide insight into type 2 diabetes risk.
- 2023
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Ingår i: American Journal of Human Genetics. - : Elsevier. - 0002-9297 .- 1537-6605. ; 110:2, s. 284-299
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Tidskriftsartikel (refereegranskat)abstract
- Insulin secretion is critical for glucose homeostasis, and increased levels of the precursor proinsulin relative to insulin indicate pancreatic islet beta-cell stress and insufficient insulin secretory capacity in the setting of insulin resistance. We conducted meta-analyses of genome-wide association results for fasting proinsulin from 16 European-ancestry studies in 45,861 individuals. We found 36 independent signals at 30 loci (p value < 5 × 10-8), which validated 12 previously reported loci for proinsulin and ten additional loci previously identified for another glycemic trait. Half of the alleles associated with higher proinsulin showed higher rather than lower effects on glucose levels, corresponding to different mechanisms. Proinsulin loci included genes that affect prohormone convertases, beta-cell dysfunction, vesicle trafficking, beta-cell transcriptional regulation, and lysosomes/autophagy processes. We colocalized 11 proinsulin signals with islet expression quantitative trait locus (eQTL) data, suggesting candidate genes, including ARSG, WIPI1, SLC7A14, and SIX3. The NKX6-3/ANK1 proinsulin signal colocalized with a T2D signal and an adipose ANK1 eQTL signal but not the islet NKX6-3 eQTL. Signals were enriched for islet enhancers, and we showed a plausible islet regulatory mechanism for the lead signal in the MADD locus. These results show how detailed genetic studies of an intermediate phenotype can elucidate mechanisms that may predispose one to disease.
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| 4. |
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| 5. |
- Do, Ron, et al.
(författare)
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Common variants associated with plasma triglycerides and risk for coronary artery disease
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:11, s. 1345-
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Tidskriftsartikel (refereegranskat)abstract
- Triglycerides are transported in plasma by specific triglyceride-rich lipoproteins; in epidemiological studies, increased triglyceride levels correlate with higher risk for coronary artery disease (CAD). However, it is unclear whether this association reflects causal processes. We used 185 common variants recently mapped for plasma lipids (P < 5 x 10(-8) for each) to examine the role of triglycerides in risk for CAD. First, we highlight loci associated with both low-density lipoprotein cholesterol (LDL-C) and triglyceride levels, and we show that the direction and magnitude of the associations with both traits are factors in determining CAD risk. Second, we consider loci with only a strong association with triglycerides and show that these loci are also associated with CAD. Finally, in a model accounting for effects on LDL-C and/or high-density lipoprotein cholesterol (HDL-C) levels, the strength of a polymorphism's effect on triglyceride levels is correlated with the magnitude of its effect on CAD risk. These results suggest that triglyceride-rich lipoproteins causally influence risk for CAD.
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| 6. |
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| 7. |
- Dumanski, Jan P., et al.
(författare)
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Smoking is associated with mosaic loss of chromosome Y
- 2015
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 347:6217, s. 81-83
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Tidskriftsartikel (refereegranskat)abstract
- Tobacco smoking is a risk factor for numerous disorders, including cancers affecting organs outside the respiratory tract. Epidemiological data suggest that smoking is a greater risk factor for these cancers in males compared to females. This observation, together with the fact that males have a higher incidence of and mortality from most non-sex-specific cancers, remains unexplained. Loss of chromosome Y (LOY) in blood cells is associated with increased risk of nonhematological tumors. We demonstrate here that smoking is associated with LOY in blood cells in three independent cohorts [TwinGene: odds ratio (OR) = 4.3, 95% CI = 2.8-6.7; ULSAM: OR = 2.4, 95% CI = 1.6-3.6; and PIVUS: OR = 3.5, 95% CI = 1.4-8.4] encompassing a total of 6014 men. The data also suggest that smoking has a transient and dose-dependent mutagenic effect on LOY status. The finding that smoking induces LOY thus links a preventable risk factor with the most common acquired human mutation.
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| 8. |
- Engström, Elisabet, et al.
(författare)
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Auditory event-related potentials and mismatch negativity in children with hearing loss using hearing aids or cochlear implants : A three-year follow-up study
- 2021
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Ingår i: International Journal of Pediatric Otorhinolaryngology. - : Elsevier. - 0165-5876 .- 1872-8464. ; 140
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: The primary aim was to examine how event-related potentials (ERPs) and mismatch negativity (MMN) change and develop over time among children with hearing loss (HL) using hearing aids (HAs) or cochlear implants (CIs). Children with normal hearing (NH) were tested as a reference group.Methods: This three-year follow-up study included 13 children with sensorineural HL (SNHL); 7 children using bilateral HAs and 6 children using CIs; and 10 children with NH as a reference group. ERPs were recorded at baseline and after three years. At time for the original study the children were approximately 5-8 years old and at the follow-up study 8-11 years old. ERP recordings and data processing were identical in both sessions. A standard stimulus alternated with five different deviants (gap, intensity, pitch, location and duration), presented in a pseudorandom sequence, thus following the multi-feature paradigm, Optimum-1. MMN was calculated from the average ERP of each deviant minus the standard stimuli. Repeated measures ANOVA was used for the statistical analyses and the results were based on samples within a specific time interval; 80-224 ms.Results: There was a statistically significant difference in the obligatory responses between the NH and HA groups at baseline, but this difference disappeared after three years in our follow-up study. The children with HA also showed a significant difference in mean ERP at baseline compared to follow-up, and significant differences between the deviants at follow-up but not at baseline. This suggests an improvement over time among the children with HAs. On the other hand, the children with CIs did not differ from the NH children at baseline, but after three years their mean ERP was significantly lower compared to both the children with HA and NH, indicating a reduced development of the central auditory system in this age span among the children with CIs. Regarding MMN, there was an interaction between the duration deviant and time for the children with HA, also indicating a possible improvement over time among the HA children.Conclusions: This three-year follow-up study shows neurophysiological differences between children with HL and children with NH. The results suggest a delay in the central auditory processing among the HA children compared to children with NH, but a possible catch-up, over time, and this potential may be worth to be utilized. Regarding the CI children, similar improvement in this age span is missing, meaning there are differences between the subgroups of children with HL, i.e. the children with HAs vs. CIs. The results highlight the importance of distinguishing between subgroups of children with HL in further research.
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| 9. |
- Engström, Elisabet, et al.
(författare)
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Computer-assisted reading intervention for children with hearing impairment using cochlear implants : Effects on auditory event-related potentials and mismatch negativity
- 2020
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Ingår i: International Journal of Pediatric Otorhinolaryngology. - : Elsevier. - 0165-5876 .- 1872-8464. ; 137
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES: The primary aim was to find out whether a computer-assisted reading intervention program with a phonic approach can affect event-related (ERPs) and mismatch negativity (MMN) in hearing impaired (HI) children using cochlear implants (CIs).METHODS: This study involved a test group of 15 HI children with CIs and a control group of 14 normal hearing (NH) children. The children were 4 years and 10 months to 8 years and 1 month old. ERPs were recorded immediately before and after 4 weeks of training with a computer-assisted reading intervention, GraphoGame. A multi-feature paradigm, Optimum-1, was used, i.e. a standard stimulus alternated with five different deviants: gap intensity, pitch, location and duration. MMN was calculated from the mean amplitude ERP of each deviant minus the standard stimulus response in a specific time interval, 80 - 224 ms. Repeated measures ANOVA was used for the statistical analysis.RESULTS: The results did not show any significant changes with the computerassisted training in the ERPs and MMNs among the HI children with CIs. The presence of both MMN and a positive mismatch response (pMMR), which might reflect an immaturity, complicates interpreting the results in this age group. Individually, there was a mix of MMNs and pMMRs among all participants, pre and post training, and the change of each deviant after intervention was not predictable.CONCLUSIONS: There are no significant changes in ERP or MMN after intervention, however lack of significances must be interpreted with caution. Besides the presence of both MMNs and pMMRs, only modest changes are to be expected on an individual basis and small samples hinder making statistical conclusions regarding the training's effects. The study contributes to some more descriptive pieces of ERPs and MMNs among the HI children with CIs. The issues of MMN and pMMR are highlighted.
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| 10. |
- Engström, Elisabet, et al.
(författare)
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Computer-assisted reading intervention for children with sensorineural hearing loss using hearing aids : Effects on auditory event-related potentials and mismatch negativity
- 2019
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Ingår i: International Journal of Pediatric Otorhinolaryngology. - : Elsevier. - 0165-5876 .- 1872-8464. ; 117, s. 17-25
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES: The primary aim was to investigate whether computer-assisted reading intervention somehow can affect event-related potentials (ERP) and mismatch negativity (MMN) in hearing impaired (HI) children with hearing aids (HAs) and normal hearing (NH) children.METHODS: The study included 15 HI children with sensorineural hearing loss (SNHL) using bilateral HAs and 14 NH children as a reference group; all children between the ages of 5 and 8. A multi-feature MMN-paradigm, Optimum-1, with a standard stimulus alternating with 5 different deviants was used. ERPs were recorded pre and post intervention, i.e. one month of repeatedly computer-assisted training (GraphoGame). MMN was calculated from the average ERP of each deviant minus standard. Data were based on samples within a specific time interval, 80-224 ms, and repeated measures ANOVA was used to analyze possible interactions.RESULTS: There was a significant difference between groups before training, though, the mean obligatory responses or MMN was not statistically significantly different before versus after training, neither among the NH nor the HI children. Further, the HI children did generally achieve lower levels in GraphoGame compared to the NH children. Altogether, our findings indicate differences between the groups and that training may affect the neurophysiological processing in the brain, gaining the HI children. Both MMN and positive mismatch response (pMMR) were seen among both the HA and NH children, irrespective to deviant type. Individually, changes of the MMN and pMMR after training seem unpredictable.CONCLUSION: There are statistically significant differences in both the obligatory responses in ERP and the MMNs between the NH and HI groups before the computer-assisted training. Though, these differences disappear after the intervention. This suggests possible training effects regarding the central auditory processing among the HI children.
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