| 1. |
- Turcot, Valerie, et al.
(författare)
-
Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity
- 2018
-
Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 50:1, s. 26-41
-
Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWAS) have identified >250 loci for body mass index (BMI), implicating pathways related to neuronal biology. Most GWAS loci represent clusters of common, noncoding variants from which pinpointing causal genes remains challenging. Here we combined data from 718,734 individuals to discover rare and low-frequency (minor allele frequency (MAF) < 5%) coding variants associated with BMI. We identified 14 coding variants in 13 genes, of which 8 variants were in genes (ZBTB7B, ACHE, RAPGEF3, RAB21, ZFHX3, ENTPD6, ZFR2 and ZNF169) newly implicated in human obesity, 2 variants were in genes (MC4R and KSR2) previously observed to be mutated in extreme obesity and 2 variants were in GIPR. The effect sizes of rare variants are similar to 10 times larger than those of common variants, with the largest effect observed in carriers of an MC4R mutation introducing a stop codon (p.Tyr35Ter, MAF = 0.01%), who weighed similar to 7 kg more than non-carriers. Pathway analyses based on the variants associated with BMI confirm enrichment of neuronal genes and provide new evidence for adipocyte and energy expenditure biology, widening the potential of genetically supported therapeutic targets in obesity.
|
|
| 2. |
- Gaulton, Kyle J, et al.
(författare)
-
Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci.
- 2015
-
Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 47:12, s. 1415-1415
-
Tidskriftsartikel (refereegranskat)abstract
- We performed fine mapping of 39 established type 2 diabetes (T2D) loci in 27,206 cases and 57,574 controls of European ancestry. We identified 49 distinct association signals at these loci, including five mapping in or near KCNQ1. 'Credible sets' of the variants most likely to drive each distinct signal mapped predominantly to noncoding sequence, implying that association with T2D is mediated through gene regulation. Credible set variants were enriched for overlap with FOXA2 chromatin immunoprecipitation binding sites in human islet and liver cells, including at MTNR1B, where fine mapping implicated rs10830963 as driving T2D association. We confirmed that the T2D risk allele for this SNP increases FOXA2-bound enhancer activity in islet- and liver-derived cells. We observed allele-specific differences in NEUROD1 binding in islet-derived cells, consistent with evidence that the T2D risk allele increases islet MTNR1B expression. Our study demonstrates how integration of genetic and genomic information can define molecular mechanisms through which variants underlying association signals exert their effects on disease.
|
|
| 3. |
- Scott, Robert A., et al.
(författare)
-
An Expanded Genome-Wide Association Study of Type 2 Diabetes in Europeans
- 2017
-
Ingår i: Diabetes. - : American Diabetes Association. - 0012-1797 .- 1939-327X. ; 66:11, s. 2888-2902
-
Tidskriftsartikel (refereegranskat)abstract
- To characterize type 2 diabetes (T2D)-associated variation across the allele frequency spectrum, we conducted a meta-analysis of genome-wide association data from 26,676 T2D case and 132,532 control subjects of European ancestry after imputation using the 1000 Genomes multiethnic reference panel. Promising association signals were followed up in additional data sets (of 14,545 or 7,397 T2D case and 38,994 or 71,604 control subjects). We identified 13 novel T2D-associated loci (P < 5 x 10(-8)), including variants near the GLP2R, GIP, and HLA-DQA1 genes. Our analysis brought the total number of independent T2D associations to 128 distinct signals at 113 loci. Despite substantially increased sample size and more complete coverage of low-frequency variation, all novel associations were driven by common single nucleotide variants. Credible sets of potentially causal variants were generally larger than those based on imputation with earlier reference panels, consistent with resolution of causal signals to common risk haplotypes. Stratification of T2D-associated loci based on T2D-related quantitative trait associations revealed tissue-specific enrichment of regulatory annotations in pancreatic islet enhancers for loci influencing insulin secretion and in adipocytes, monocytes, and hepatocytes for insulin action-associated loci. These findings highlight the predominant role played by common variants of modest effect and the diversity of biological mechanisms influencing T2D pathophysiology.
|
|
| 4. |
- Surakka, Ida, et al.
(författare)
-
The impact of low-frequency and rare variants on lipid levels.
- 2015
-
Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 47:6, s. 589-597
-
Tidskriftsartikel (refereegranskat)abstract
- Using a genome-wide screen of 9.6 million genetic variants achieved through 1000 Genomes Project imputation in 62,166 samples, we identify association to lipid traits in 93 loci, including 79 previously identified loci with new lead SNPs and 10 new loci, 15 loci with a low-frequency lead SNP and 10 loci with a missense lead SNP, and 2 loci with an accumulation of rare variants. In six loci, SNPs with established function in lipid genetics (CELSR2, GCKR, LIPC and APOE) or candidate missense mutations with predicted damaging function (CD300LG and TM6SF2) explained the locus associations. The low-frequency variants increased the proportion of variance explained, particularly for low-density lipoprotein cholesterol and total cholesterol. Altogether, our results highlight the impact of low-frequency variants in complex traits and show that imputation offers a cost-effective alternative to resequencing.
|
|
| 5. |
- Awchi, Mo, et al.
(författare)
-
Development, validation, and application of a new method for the quantitative determination of monohydrogen-substituted perfluoroalkyl carboxylic acids (H-PFCAs) in surface water
- 2022
-
Ingår i: Chemosphere. - : Elsevier BV. - 0045-6535 .- 1879-1298. ; 287
-
Tidskriftsartikel (refereegranskat)abstract
- Per- and polyfluoroalkyl substances (PFASs) are a large and diverse class of chemicals. While some have been phased out internationally due to concerns over their human and environmental health risks, novel alternative PFASs continue to be manufactured and detected in environmental samples. The occurrence and fate of these alternatives remain poorly understood. The present study investigated the occurrence of an emerging class of PFAS alternative, the monohydrogen-substituted perfluoroalkyl carboxylic acids (H-PFCAs), in conjunction with the more well-known PFCAs. A weak anion exchange solid phase extraction-liquid chromatography tandem mass spectrometry method for quantitative determination of H-PFCAs in surface water was developed, validated, and applied on samples collected from the Netherlands. To improve chromatography, especially for short-chain (H-) PFCAs, an ion-pairing agent, tetrabutylammonium hydrogen sulphate, was used. The method was validated for linearity (R2 > 0.99), instrumental detection limits (0.01-0.09 ng/mL), method detection limits (0.03-0.75 ng/ mL), matrix effects (<20%), percent absolute- and relative recovery (57-121%), trueness (130-80%), repeatability (<20%), and within-lab reproducibility (<20%). Eleven out of fourteen PFASs showed acceptable results. Application of the newly validated method to surface water throughout the Netherlands revealed trace levels of H-PFCAs (including two new H-PFCAs) and high concentrations of PFCAs.
|
|
| 6. |
- van Leeuwen, Stefan P. J., et al.
(författare)
-
Struggle for quality in determination of perfluorinated contaminants in environmental and human samples
- 2006
-
Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 40:24, s. 7854-7860
-
Tidskriftsartikel (refereegranskat)abstract
- The first worldwide interlaboratory study on the analyses of 13 perfluorinated compounds (PFCs) in three environmental and two human samples indicates a varying degree of accuracy in relation to the matrix or analyte determined. The ability of 38 participating laboratories from 13 countries to determine the analytes in the various matrices was evaluated by calculation of z-scores according to the Cofino model. The PFCs which were reported most frequently by the laboratories, and assessed with the most satisfactory agreement, were perfluorooctane sulfonate (PFOS) and perfluorooctanoic acid (PFOA). In general, the level of agreement between the participating laboratories decreased in the following order: PFC standard solution (76% satisfactory z-scores of <[2]1 for PFOS) < human blood (67%) < human plasma (63%) < fish liver extract (55%) < water (31%) < fish tissue (17%). This shows that relative good agreement between laboratories was obtained for the study of standard and human matrices. For the fish extract, most laboratories underestimated the actual PFOS concentration due to matrix effects. The results for the fish tissue and water are also poor, indicating that the extraction and cleanup steps require further improvement. It was concluded that the PFC determinations in various matrices are not yet fully mastered.
|
|
| 7. |
- Berger, Urs, et al.
(författare)
-
Recent developments in trace analysis of poly- and perfluoroalkyl substances
- 2011
-
Ingår i: Analytical and Bioanalytical Chemistry. - : Springer Science and Business Media LLC. - 1618-2642 .- 1618-2650. ; 400:6, s. 1625-1635
-
Tidskriftsartikel (refereegranskat)abstract
- Recent developments, improvements, and trends in the ultra-trace determination of per- and polyfluoroalkyl substances (PFASs) in environmental and human samples are highlighted and the remaining challenges and uncertainties are outlined and discussed. Understanding the analytical implications of such things as adsorption of PFASs to surfaces, effects of differing matrices, varying PFAS isomer response factors, potential bias effects of sampling, sample preparation, and analysis is critical to measuring highly fluorinated compounds at trace levels. These intricate analytical issues and the potential consequences of ignoring to deal with them correctly are discussed and documented with examples. Isomer-specific analysis and the development of robust multi-chemical methods are identified as topical trends in method development for an ever-increasing number of PFASs of environmental and human interest. Ultimately, the state-of-the-art of current analytical method accuracy is discussed on the basis of results from interlaboratory comparison studies.
|
|
| 8. |
- Weiss, Jana M, et al.
(författare)
-
Competitive Binding of Poly- and Perfluorinated Compounds to the Thyroid Hormone Transport Protein Transthyretin
- 2009
-
Ingår i: Toxicological sciences : an official journal of the Society of Toxicology. - : Oxford University Press of the Society of Toxicology. - 1096-0929. ; 109:2, s. 206-16
-
Tidskriftsartikel (refereegranskat)abstract
- Due to their unique surfactant properties, poly- and perfluorinated compounds (PFCs) have been extensively used, and can be found all over the environment.. Concern about their environmental fate and toxicological properties have initiated several research projects. In the present study, we investigated if PFCs can compete with thyroxin (T4, i.e. the transport form of thyroid hormone) for binding to the human thyroid hormone transport protein transthyretin (TTR). Such competitive capacity may lead to decreased thyroid hormone levels as previously reported for animals exposed to PFCs. Twenty four PFCs, together with six structurally similar natural fatty acids, were tested for binding capacity in a radioligand binding assay. The binding potency decreased in the order: PFHxS>PFOS/PFOA>PFHpA>L-PFOSi>PFNA, with TTR binding potencies 12.5-50 times lower than the natural ligand thyroxine (T4). Some lower molecular weight compounds with structural similarity to these PFCs were >100 times less potent than T4. Simple descriptors based on the two dimensional molecular structures of the compounds were used to visualize the chemical variation and to model the structure-activity relationship for the competitive potencies of the TTR-binding compounds. The models indicated the dependence on molecular size and functional group(s), but demanded a more detailed description of the chemical properties and data for validation and further QSAR development. Competitive binding of PFCs to TTR as observed for human TTR in the present study, may explain altered thyroid hormone levels described for PFC-exposed rats and monkeys. Median human blood levels of the most potent TTR-binding PFCs are 1-2 orders of magnitude lower than IC50-values determined in the present study. In addition, this study contributes to the understanding of the bioaccumulation of PFCs in man and possibly in other wildlife species.
|
|
