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- Ferreira, MA, et al.
(författare)
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Genome-wide association and transcriptome studies identify target genes and risk loci for breast cancer
- 2019
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1, s. 1741-
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWAS) have identified more than 170 breast cancer susceptibility loci. Here we hypothesize that some risk-associated variants might act in non-breast tissues, specifically adipose tissue and immune cells from blood and spleen. Using expression quantitative trait loci (eQTL) reported in these tissues, we identify 26 previously unreported, likely target genes of overall breast cancer risk variants, and 17 for estrogen receptor (ER)-negative breast cancer, several with a known immune function. We determine the directional effect of gene expression on disease risk measured based on single and multiple eQTL. In addition, using a gene-based test of association that considers eQTL from multiple tissues, we identify seven (and four) regions with variants associated with overall (and ER-negative) breast cancer risk, which were not reported in previous GWAS. Further investigation of the function of the implicated genes in breast and immune cells may provide insights into the etiology of breast cancer.
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- Barnes, DR, et al.
(författare)
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Breast and Prostate Cancer Risks for Male BRCA1 and BRCA2 Pathogenic Variant Carriers Using Polygenic Risk Scores
- 2022
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Ingår i: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 1460-2105 .- 0027-8874. ; 114:1, s. 109-122
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundRecent population-based female breast cancer and prostate cancer polygenic risk scores (PRS) have been developed. We assessed the associations of these PRS with breast and prostate cancer risks for male BRCA1 and BRCA2 pathogenic variant carriers.Methods483 BRCA1 and 1318 BRCA2 European ancestry male carriers were available from the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). A 147-single nucleotide polymorphism (SNP) prostate cancer PRS (PRSPC) and a 313-SNP breast cancer PRS were evaluated. There were 3 versions of the breast cancer PRS, optimized to predict overall (PRSBC), estrogen receptor (ER)–negative (PRSER-), or ER-positive (PRSER+) breast cancer risk.ResultsPRSER+ yielded the strongest association with breast cancer risk. The odds ratios (ORs) per PRSER+ standard deviation estimates were 1.40 (95% confidence interval [CI] =1.07 to 1.83) for BRCA1 and 1.33 (95% CI = 1.16 to 1.52) for BRCA2 carriers. PRSPC was associated with prostate cancer risk for BRCA1 (OR = 1.73, 95% CI = 1.28 to 2.33) and BRCA2 (OR = 1.60, 95% CI = 1.34 to 1.91) carriers. The estimated breast cancer odds ratios were larger after adjusting for female relative breast cancer family history. By age 85 years, for BRCA2 carriers, the breast cancer risk varied from 7.7% to 18.4% and prostate cancer risk from 34.1% to 87.6% between the 5th and 95th percentiles of the PRS distributions.ConclusionsPopulation-based prostate and female breast cancer PRS are associated with a wide range of absolute breast and prostate cancer risks for male BRCA1 and BRCA2 carriers. These findings warrant further investigation aimed at providing personalized cancer risks for male carriers and informing clinical management.
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- Coignard, J, et al.
(författare)
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A case-only study to identify genetic modifiers of breast cancer risk for BRCA1/BRCA2 mutation carriers
- 2021
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12:1, s. 1078-
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Tidskriftsartikel (refereegranskat)abstract
- Breast cancer (BC) risk for BRCA1 and BRCA2 mutation carriers varies by genetic and familial factors. About 50 common variants have been shown to modify BC risk for mutation carriers. All but three, were identified in general population studies. Other mutation carrier-specific susceptibility variants may exist but studies of mutation carriers have so far been underpowered. We conduct a novel case-only genome-wide association study comparing genotype frequencies between 60,212 general population BC cases and 13,007 cases with BRCA1 or BRCA2 mutations. We identify robust novel associations for 2 variants with BC for BRCA1 and 3 for BRCA2 mutation carriers, P < 10−8, at 5 loci, which are not associated with risk in the general population. They include rs60882887 at 11p11.2 where MADD, SP11 and EIF1, genes previously implicated in BC biology, are predicted as potential targets. These findings will contribute towards customising BC polygenic risk scores for BRCA1 and BRCA2 mutation carriers.
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- Hakkaart, C, et al.
(författare)
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Copy number variants as modifiers of breast cancer risk for BRCA1/BRCA2 pathogenic variant carriers
- 2022
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Ingår i: Communications biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 5:1, s. 1061-
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Tidskriftsartikel (refereegranskat)abstract
- The contribution of germline copy number variants (CNVs) to risk of developing cancer in individuals with pathogenic BRCA1 or BRCA2 variants remains relatively unknown. We conducted the largest genome-wide analysis of CNVs in 15,342 BRCA1 and 10,740 BRCA2 pathogenic variant carriers. We used these results to prioritise a candidate breast cancer risk-modifier gene for laboratory analysis and biological validation. Notably, the HR for deletions in BRCA1 suggested an elevated breast cancer risk estimate (hazard ratio (HR) = 1.21), 95% confidence interval (95% CI = 1.09–1.35) compared with non-CNV pathogenic variants. In contrast, deletions overlapping SULT1A1 suggested a decreased breast cancer risk (HR = 0.73, 95% CI 0.59-0.91) in BRCA1 pathogenic variant carriers. Functional analyses of SULT1A1 showed that reduced mRNA expression in pathogenic BRCA1 variant cells was associated with reduced cellular proliferation and reduced DNA damage after treatment with DNA damaging agents. These data provide evidence that deleterious variants in BRCA1 plus SULT1A1 deletions contribute to variable breast cancer risk in BRCA1 carriers.
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| 20. |
- Menkveld, Albert J., et al.
(författare)
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Nonstandard Errors
- 2024
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Ingår i: JOURNAL OF FINANCE. - : Wiley-Blackwell. - 0022-1082 .- 1540-6261. ; 79:3, s. 2339-2390
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Tidskriftsartikel (refereegranskat)abstract
- In statistics, samples are drawn from a population in a data-generating process (DGP). Standard errors measure the uncertainty in estimates of population parameters. In science, evidence is generated to test hypotheses in an evidence-generating process (EGP). We claim that EGP variation across researchers adds uncertainty-nonstandard errors (NSEs). We study NSEs by letting 164 teams test the same hypotheses on the same data. NSEs turn out to be sizable, but smaller for more reproducible or higher rated research. Adding peer-review stages reduces NSEs. We further find that this type of uncertainty is underestimated by participants.
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- Putaud, J. -P, et al.
(författare)
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A European aerosol phenomenology-3 : Physical and chemical characteristics of particulate matter from 60 rural, urban, and kerbside sites across Europe
- 2010
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Ingår i: Atmospheric Environment. - : Elsevier BV. - 1352-2310 .- 1873-2844. ; 44:10, s. 1308-1320
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Tidskriftsartikel (refereegranskat)abstract
- This paper synthesizes data on aerosol (particulate matter, PM) physical and chemical characteristics, which were obtained over the past decade in aerosol research and monitoring activities at more than 60 natural background, rural, near-city, urban, and kerbside sites across Europe. The data include simultaneously measured PM10 and/or PM2.5 mass on the one hand, and aerosol particle number concentrations or PM chemistry on the other hand. The aerosol data presented in our previous works (Van Dingenen et al., 2004; Putaud et al., 2004) were updated and merged to those collected in the framework of the EU supported European Cooperation in the field of Scientific and Technical action COST633 (Particulate matter: Properties related to health effects). A number of conclusions from our previous studies were confirmed. There is no single ratio between PM2.5 and PM10 mass concentrations valid for all sites, although fairly constant ratios ranging from 0.5 to 0.9 are observed at most individual sites. There is no general correlation between PM mass and particle number concentrations, although particle number concentrations increase with PM2.5 levels at most sites. The main constituents of both PM10 and PM2.5 are generally organic matter, sulfate and nitrate. Mineral dust can also be a major constituent of PM10 at kerbside sites and in Southern Europe. There is a clear decreasing gradient in SO42- and NO3- contribution to PM10 when moving from rural to urban to kerbside sites. In contrast, the total carbon/PM10 ratio increases from rural to kerbside sites. Some new conclusions were also drawn from this work: the ratio between ultrafine particle and total particle number concentration decreases with PM2.5 concentration at all sites but one, and significant gradients in PM chemistry are observed when moving from Northwestern, to Southern to Central Europe. Compiling an even larger number of data sets would have further increased the significance of our conclusions, but collecting all the aerosol data sets obtained also through research projects remains a tedious task.
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- Sikoparija, B., et al.
(författare)
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Spatial and temporal variations in airborne Ambrosia pollen in Europe
- 2017
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Ingår i: Aerobiologia. - : Springer Science and Business Media LLC. - 0393-5965 .- 1573-3025. ; 33, s. 181-189
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Tidskriftsartikel (refereegranskat)abstract
- © 2016, The Author(s). The European Commission Cooperation in Science and Technology (COST) Action FA1203 “SMARTER” aims to make recommendations for the sustainable management of Ambrosia across Europe and for monitoring its efficiency and cost-effectiveness. The goal of the present study is to provide a baseline for spatial and temporal variations in airborne Ambrosia pollen in Europe that can be used for the management and evaluation of this noxious plant. The study covers the full range of Ambrosia artemisiifolia L. distribution over Europe (39°N–60°N; 2°W–45°E). Airborne Ambrosia pollen data for the principal flowering period of Ambrosia (August–September) recorded during a 10-year period (2004–2013) were obtained from 242 monitoring sites. The mean sum of daily average airborne Ambrosia pollen and the number of days that Ambrosia pollen was recorded in the air were analysed. The mean and standard deviation (SD) were calculated regardless of the number of years included in the study period, while trends are based on those time series with 8 or more years of data. Trends were considered significant at p<0.05. There were few significant trends in the magnitude and frequency of atmospheric Ambrosia pollen (only 8% for the mean sum of daily average Ambrosia pollen concentrations and 14% for the mean number of days Ambrosia pollen were recorded in the air). The direction of any trends varied locally and reflected changes in sources of the pollen, either in size or in distance from the monitoring station. Pollen monitoring is important for providing an early warning of the expansion of this invasive and noxious plant.
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| 25. |
- Verstraeten, A., et al.
(författare)
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Effects of tree pollen on throughfall element fluxes in European forests
- 2023
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Ingår i: Biogeochemistry. - Göteborg : Springer. - 0168-2563 .- 1573-515X. ; 165:3, s. 311-325
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Tidskriftsartikel (refereegranskat)abstract
- The effects of tree pollen on precipitation chemistry are not fully understood and this can lead to misinterpretations of element deposition in European forests. We investigated the relationship between forest throughfall (TF) element fluxes and the Seasonal Pollen Integral (SPIn) using linear mixed-effects modelling (LME). TF was measured in 1990-2018 during the main pollen season (MPS, arbitrary two months) in 61 managed, mostly pure, even-aged Fagus, Quercus, Pinus, and Picea stands which are part of the ICP Forests Level II network. The SPIn for the dominant tree genus was observed at 56 aerobiological monitoring stations in nearby cities. The net contribution of pollen was estimated as the TF flux in the MPS minus the fluxes in the preceding and succeeding months. In stands of Fagus and Picea, two genera that do not form large amounts of flowers every year, TF fluxes of potassium (K+), ammonium-nitrogen (NH4+-N), dissolved organic carbon (DOC), and dissolved organic nitrogen (DON) showed a positive relationship with SPIn. However- for Fagus- a negative relationship was found between TF nitrate-nitrogen (NO3--N) fluxes and SPIn. For Quercus and Pinus, two genera producing many flowers each year, SPIn displayed limited variability and no clear association with TF element fluxes. Overall, pollen contributed on average 4.1-10.6% of the annual TF fluxes of K+ > DOC > DON > NH4+--N with the highest contribution in Quercus > Fagus > Pinus > Picea stands. Tree pollen appears to affect TF inorganic nitrogen fluxes both qualitatively and quantitatively, acting as a source of NH4+--N and a sink of NO3--N. Pollen appears to play a more complex role in nutrient cycling than previously thought.
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