| 1. |
- Flannick, Jason, et al.
(författare)
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Data Descriptor : Sequence data and association statistics from 12,940 type 2 diabetes cases and controls
- 2017
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Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 4
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Tidskriftsartikel (refereegranskat)abstract
- To investigate the genetic basis of type 2 diabetes (T2D) to high resolution, the GoT2D and T2D-GENES consortia catalogued variation from whole-genome sequencing of 2,657 European individuals and exome sequencing of 12,940 individuals of multiple ancestries. Over 27M SNPs, indels, and structural variants were identified, including 99% of low-frequency (minor allele frequency [MAF] 0.1-5%) non-coding variants in the whole-genome sequenced individuals and 99.7% of low-frequency coding variants in the whole-exome sequenced individuals. Each variant was tested for association with T2D in the sequenced individuals, and, to increase power, most were tested in larger numbers of individuals (> 80% of low-frequency coding variants in similar to ~82 K Europeans via the exome chip, and similar to ~90% of low-frequency non-coding variants in similar to ~44 K Europeans via genotype imputation). The variants, genotypes, and association statistics from these analyses provide the largest reference to date of human genetic information relevant to T2D, for use in activities such as T2D-focused genotype imputation, functional characterization of variants or genes, and other novel analyses to detect associations between sequence variation and T2D.
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| 2. |
- Fuchsberger, Christian, et al.
(författare)
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The genetic architecture of type 2 diabetes
- 2016
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 536:7614, s. 41-47
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Tidskriftsartikel (refereegranskat)abstract
- The genetic architecture of common traits, including the number, frequency, and effect sizes of inherited variants that contribute to individual risk, has been long debated. Genome-wide association studies have identified scores of common variants associated with type 2 diabetes, but in aggregate, these explain only a fraction of the heritability of this disease. Here, to test the hypothesis that lower-frequency variants explain much of the remainder, the GoT2D and T2D-GENES consortia performed whole-genome sequencing in 2,657 European individuals with and without diabetes, and exome sequencing in 12,940 individuals from five ancestry groups. To increase statistical power, we expanded the sample size via genotyping and imputation in a further 111,548 subjects. Variants associated with type 2 diabetes after sequencing were overwhelmingly common and most fell within regions previously identified by genome-wide association studies. Comprehensive enumeration of sequence variation is necessary to identify functional alleles that provide important clues to disease pathophysiology, but large-scale sequencing does not support the idea that lower-frequency variants have a major role in predisposition to type 2 diabetes.
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| 3. |
- Manning, Alisa, et al.
(författare)
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A Low-Frequency Inactivating AKT2 Variant Enriched in the Finnish Population Is Associated With Fasting Insulin Levels and Type 2 Diabetes Risk
- 2017
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Ingår i: Diabetes. - : AMER DIABETES ASSOC. - 0012-1797 .- 1939-327X. ; 66:7, s. 2019-2032
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Tidskriftsartikel (refereegranskat)abstract
- To identify novel coding association signals and facilitate characterization of mechanisms influencing glycemic traits and type 2 diabetes risk, we analyzed 109,215 variants derived from exome array genotyping together with an additional 390,225 variants from exome sequence in up to 39,339 normoglycemic individuals from five ancestry groups. We identified a novel association between the coding variant (p.Pro50Thr) in AKT2 and fasting plasma insulin (FI), a gene in which rare fully penetrant mutations are causal for monogenic glycemic disorders. The low-frequency allele is associated with a 12% increase in FI levels. This variant is present at 1.1% frequency in Finns but virtually absent in individuals from other ancestries. Carriers of the FI-increasing allele had increased 2-h insulin values, decreased insulin sensitivity, and increased risk of type 2 diabetes (odds ratio 1.05). In cellular studies, the AKT2-Thr50 protein exhibited a partial loss of function. We extend the allelic spectrum for coding variants in AKT2 associated with disorders of glucose homeostasis and demonstrate bidirectional effects of variants within the pleckstrin homology domain of AKT2.
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| 4. |
- Kumar, Varun, et al.
(författare)
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Highly time-resolved chemical speciation and source apportionment of organic aerosol components in Delhi, India, using extractive electrospray ionization mass spectrometry
- 2022
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Ingår i: Atmospheric Chemistry And Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 22:11, s. 7739-7761
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Tidskriftsartikel (refereegranskat)abstract
- In recent years, the Indian capital city of Delhi has been impacted by very high levels of air pollution, especially during winter. Comprehensive knowledge of the composition and sources of the organic aerosol (OA), which constitutes a substantial fraction of total particulate mass (PM) in Delhi, is central to formulating effective public health policies. Previous source apportionment studies in Delhi identified key sources of primary OA (POA) and showed that secondary OA (SOA) played a major role but were unable to resolve specific SOA sources. We address the latter through the first field deployment of an extractive electrospray ionization time-of-flight mass spectrometer (EESI-TOF) in Delhi, together with a high-resolution aerosol mass spectrometer (AMS). Measurements were conducted during the winter of 2018/19, and positive matrix factorization (PMF) was used separately on AMS and EESI-TOF datasets to apportion the sources of OA. AMS PMF analysis yielded three primary and two secondary factors which were attributed to hydrocarbon-like OA (HOA), biomass burning OA (BBOA-1 and BBOA-2), more oxidized oxygenated OA (MO-OOA), and less oxidized oxygenated OA (LO-OOA). On average, 40 % of the total OA mass was apportioned to the secondary factors. The SOA contribution to total OA mass varied greatly between the daytime (76.8 %, 10:00–16:00 local time (LT)) and nighttime (31.0 %, 21:00–04:00 LT). The higher chemical resolution of EESI-TOF data allowed identification of individual SOA sources. The EESI-TOF PMF analysis in total yielded six factors, two of which were primary factors (primary biomass burning and cooking-related OA). The remaining four factors were predominantly of secondary origin: aromatic SOA, biogenic SOA, aged biomass burning SOA, and mixed urban SOA. Due to the uncertainties in the EESI-TOF ion sensitivities, mass concentrations of EESI-TOF SOA-dominated factors were related to the total AMS SOA (i.e. MO-OOA + LO-OOA) by multiple linear regression (MLR). Aromatic SOA was the major SOA component during the daytime, with a 55.2 % contribution to total SOA mass (42.4 % contribution to total OA). Its contribution to total SOA, however, decreased to 25.4 % (7.9 % of total OA) during the nighttime. This factor was attributed to the oxidation of light aromatic compounds emitted mostly from traffic. Biogenic SOA accounted for 18.4 % of total SOA mass (14.2 % of total OA) during the daytime and 36.1 % of total SOA mass (11.2 % of total OA) during the nighttime. Aged biomass burning and mixed urban SOA accounted for 15.2 % and 11.0 % of total SOA mass (11.7 % and 8.5 % of total OA mass), respectively, during the daytime and 15.4 % and 22.9 % of total SOA mass (4.8 % and 7.1 % of total OA mass), respectively, during the nighttime. A simple dilution–partitioning model was applied on all EESI-TOF factors to estimate the fraction of observed daytime concentrations resulting from local photochemical production (SOA) or emissions (POA). Aromatic SOA, aged biomass burning, and mixed urban SOA were all found to be dominated by local photochemical production, likely from the oxidation of locally emitted volatile organic compounds (VOCs). In contrast, biogenic SOA was related to the oxidation of diffuse regional emissions of isoprene and monoterpenes. The findings of this study show that in Delhi, the nighttime high concentrations are caused by POA emissions led by traffic and biomass burning and the daytime OA is dominated by SOA, with aromatic SOA accounting for the largest fraction. Because aromatic SOA is possibly more toxic than biogenic SOA and primary OA, its dominance during the daytime suggests an increased OA toxicity and health-related consequences for the general public.
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