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  • Barrett, Jennifer H., et al. (författare)
  • Fine mapping of genetic susceptibility loci for melanoma reveals a mixture of single variant and multiple variant regions
  • 2015
  • Ingår i: International Journal of Cancer. - : John Wiley and Sons Inc.. - 0020-7136 .- 1097-0215. ; 136:6, s. 1351-1360
  • Tidskriftsartikel (refereegranskat)abstract
    • At least 17 genomic regions are established as harboring melanoma susceptibility variants, in most instances with genome-wide levels of significance and replication in independent samples. Based on genome-wide single nucleotide polymorphism (SNP) data augmented by imputation to the 1,000 Genomes reference panel, we have fine mapped these regions in over 5,000 individuals with melanoma (mainly from the GenoMEL consortium) and over 7,000 ethnically matched controls. A penalized regression approach was used to discover those SNP markers that most parsimoniously explain the observed association in each genomic region. For the majority of the regions, the signal is best explained by a single SNP, which sometimes, as in the tyrosinase region, is a known functional variant. However in five regions the explanation is more complex. At the CDKN2A locus, for example, there is strong evidence that not only multiple SNPs but also multiple genes are involved. Our results illustrate the variability in the biology underlying genome-wide susceptibility loci and make steps toward accounting for some of the missing heritability. What's new? In genome-wide association studies, researchers identify genetic variants that frequently associate with a particular disease, though the variants identified may not contribute to the molecular cause of the disease. This study took a closer look at 17 regions associated with melanoma, fine mapping the regions both in people with melanoma and in healthy controls. Though single SNPs account for the association in some regions, they found that in a few regions, several SNPs - and possibly multiple genes - contributed to the association signal. These findings illustrate the importance of not overlooking the interaction between multiple genetic markers when conducting such studies.
  • Barrett, Jennifer H., et al. (författare)
  • Genome-wide association study identifies three new melanoma susceptibility loci
  • 2011
  • Ingår i: Nature Genetics. - : Nature Publishing Group. - 1546-1718. ; 43:11, s. 1108-1113
  • Tidskriftsartikel (refereegranskat)abstract
    • We report a genome-wide association study for melanoma that was conducted by the GenoMEL Consortium. Our discovery phase included 2,981 individuals with melanoma and 1,982 study-specific control individuals of European ancestry, as well as an additional 6,426 control subjects from French or British populations, all of whom were genotyped for 317,000 or 610,000 single-nucleotide polymorphisms (SNPs). Our analysis replicated previously known melanoma susceptibility loci. Seven new regions with at least one SNP with P < 10(-5) and further local imputed or genotyped support were selected for replication using two other genome-wide studies (from Australia and Texas, USA). Additional replication came from case-control series from the UK and The Netherlands. Variants at three of the seven loci replicated at P < 10(-3): an SNP in ATM (rs1801516, overall P = 3.4 x 10(-9)), an SNP in MX2 (rs45430, P = 2.9 x 10-9) and an SNP adjacent to CASP8 (rs13016963, P = 8.6 x 10(-10)). A fourth locus near CCND1 remains of potential interest, showing suggestive but inconclusive evidence of replication (rs1485993, overall P = 4.6 x 10(-7) under a fixed-effects model and P = 1.2 x 10(-3) under a random-effects model). These newly associated variants showed no association with nevus or pigmentation phenotypes in a large British case-control series.
  • Bishop, D. Timothy, et al. (författare)
  • Genome-wide association study identifies three loci associated with melanoma risk
  • 2009
  • Ingår i: Nature Genetics. - : Nature Publishing Group. - 1546-1718. ; 41:8, s. 920-925
  • Tidskriftsartikel (refereegranskat)abstract
    • We report a genome-wide association study of melanoma conducted by the GenoMEL consortium based on 317K tagging SNPs for 1,650 selected cases and 4,336 controls, with replication in an additional two cohorts (1,149 selected cases and 964 controls from GenoMEL, and a population-based case-control study in Leeds of 1,163 cases and 903 controls). The genome-wide screen identified five loci with genotyped or imputed SNPs reaching P < 5 x 10(-7). Three of these loci were replicated: 16q24 encompassing MC1R (combined P = 2.54 x 10(-27) for rs258322), 11q14-q21 encompassing TYR (P = 2.41 x 10(-14) for rs1393350) and 9p21 adjacent to MTAP and flanking CDKN2A (P = 4.03 x 10(-7) for rs7023329). MC1R and TYR are associated with pigmentation, freckling and cutaneous sun sensitivity, well-recognized melanoma risk factors. Common variants within the 9p21 locus have not previously been associated with melanoma. Despite wide variation in allele frequency, these genetic variants show notable homogeneity of effect across populations of European ancestry living at different latitudes and show independent association to disease risk.
  • Iles, Mark M., et al. (författare)
  • A variant in FTO shows association with melanoma risk not due to BMI
  • 2013
  • Ingår i: Nature Genetics. - : Nature Publishing Group. - 1546-1718. ; 45:4, s. 428-432
  • Tidskriftsartikel (refereegranskat)abstract
    • We report the results of an association study of melanoma that is based on the genome-wide imputation of the genotypes of 1,353 cases and 3,566 controls of European origin conducted by the GenoMEL consortium. This revealed an association between several SNPs in intron 8 of the FTO gene, including rs16953002, which replicated using 12,313 cases and 55,667 controls of European ancestry from Europe, the USA and Australia (combined P = 3.6 x 10(-12), per-allele odds ratio for allele A = 1.16). In addition to identifying a new melanomasusceptibility locus, this is to our knowledge the first study to identify and replicate an association with SNPs in FTO not related to body mass index (BMI). These SNPs are not in intron 1 (the BMI-related region) and exhibit no association with BMI. This suggests FTO's function may be broader than the existing paradigm that FTO variants influence multiple traits only through their associations with BMI and obesity.
  • Iles, Mark M., et al. (författare)
  • The Effect on Melanoma Risk of Genes Previously Associated With Telomere Length
  • 2014
  • Ingår i: Journal of the National Cancer Institute. - : Oxford University Press. - 1460-2105. ; 106:10, s. 267-267
  • Tidskriftsartikel (refereegranskat)abstract
    • Telomere length has been associated with risk of many cancers, but results are inconsistent. Seven single nucleotide polymorphisms (SNPs) previously associated with mean leukocyte telomere length were either genotyped or well-imputed in 11 108 case patients and 13 933 control patients from Europe, Israel, the United States and Australia, four of the seven SNPs reached a P value under .05 (two-sided). A genetic score that predicts telomere length, derived from these seven SNPs, is strongly associated (P = 8.92x10(-9), two-sided) with melanoma risk. This demonstrates that the previously observed association between longer telomere length and increased melanoma risk is not attributable to confounding via shared environmental effects (such as ultraviolet exposure) or reverse causality. We provide the first proof that multiple germline genetic determinants of telomere length influence cancer risk.
  • Law, Matthew H, et al. (författare)
  • Genome-wide meta-analysis identifies five new susceptibility loci for cutaneous malignant melanoma.
  • 2015
  • Ingår i: Nature Genetics. - : Nature Publishing Group. - 1546-1718. ; 47:9, s. 987-995
  • Tidskriftsartikel (refereegranskat)abstract
    • Thirteen common susceptibility loci have been reproducibly associated with cutaneous malignant melanoma (CMM). We report the results of an international 2-stage meta-analysis of CMM genome-wide association studies (GWAS). This meta-analysis combines 11 GWAS (5 previously unpublished) and a further three stage 2 data sets, totaling 15,990 CMM cases and 26,409 controls. Five loci not previously associated with CMM risk reached genome-wide significance (P < 5 × 10(-8)), as did 2 previously reported but unreplicated loci and all 13 established loci. Newly associated SNPs fall within putative melanocyte regulatory elements, and bioinformatic and expression quantitative trait locus (eQTL) data highlight candidate genes in the associated regions, including one involved in telomere biology.
  • Lucas, R. W., et al. (författare)
  • A meta-analysis of the effects of nitrogen additions on base cations : Implications for plants, soils, and streams
  • 2011
  • Ingår i: Forest Ecology and Management. - : Elsevier. - 0378-1127 .- 1872-7042. ; 262:2, s. 95-104
  • Forskningsöversikt (refereegranskat)abstract
    • The dominant base cations (BC: i.e., Ca(2+), Mg(2+), K(+), and Na(+)) are important in buffering soil and water acidity in both terrestrial and aquatic ecosystems. Ca(2+)., Mg(2+), and K(+) are also important in many plant physiological functions. Because BC availability is affected by changes in the nitrogen (N) cycle, we conducted a meta-analysis of previously published data to determine if N fertilization alters the availability of BC in terrestrial and stream ecosystems across biomes. We include data from 107 independent studies published in 62 different articles, taking a holistic perspective on BC by examining their responses to added N in plant foliage, bulk soil, soil solution, and stream water. Our results suggest N fertilization may accelerate BC loss from terrestrial ecosystems over time periods less than five years. We found that N additions resulted in an overall 24% decrease in the availability of exchangeable Ca(2+), Mg(2+), and K(+) in the bulk soil of boreal forest, temperate forest, and grassland biomes. Collectively, responses of BC in boreal forest, temperate forest, tropical forest, and grassland biomes increased following N fertilization by about 71% in soil solution and 48% in stream waters. Additionally, BC responses in foliage decreased in boreal forest and temperate forest biomes following N additions over time periods less than five years, but there were no significant changes over longer time periods. Despite large short-term shifts in BC responses following N additions, we did not find evidence of widespread negative impacts on ecosystems over time periods greater than five years. This analysis suggests effects of N addition on the availability of exchangeable BC may diminish over time. Although the effects on BC can be substantial over periods less than five years, there is little available evidence that N fertilization has had large-scale detrimental effects on the availability of BC needed for plant growth within terrestrial or aquatic ecosystems.
  • Lyon, S. W., et al. (författare)
  • Controls on snowmelt water mean transit times in northern boreal catchments
  • 2010
  • Ingår i: Hydrological Processes. - : Wiley: 12 months. - 0885-6087 .- 1099-1085. ; 24:12, s. 1672-1684
  • Tidskriftsartikel (refereegranskat)abstract
    • Catchment-scale transit times for water are increasingly being recognized as an important control on geochemical processes. In this study, snowmelt water mean transit times (MTTs) were estimated for the 15 Krycklan research catchments in northern boreal Sweden. The snowmelt water MTTs were assumed to be representative of the catchment-scale hydrologic response during the spring thaw period and, as such, may be considered to be a component of the catchment's overall MTT. These snowmelt water MTTs were empirically related to catchment characteristics and landscape structure represented by using different indices of soil cover, topography and catchment similarity. Mire wetlands were shown to be significantly correlated to snowmelt MTTs for the studied catchments. In these wetlands, shallow ice layers form that have been shown to serve as impervious boundaries to vertical infiltration during snowmelt periods and, thus, alter the flow pathways of water in the landscape. Using a simple thought experiment, we could estimate the potential effect of thawing of ice layers on snowmelt hydrologic response using the empirical relationship between landscape structure (represented using a catchment-scale Pe number) and hydrologic response. The result of this thought experiment was that there could be a potential increase of 20-45% in catchment snowmelt water MTTs for the Krycklan experimental catchments. It is therefore possible that climatic changes present competing influences on the hydrologic response of northern boreal catchments that need to be considered. For example, MTTs may tend to decrease during some times of the year due to an acceleration in the hydrologic cycle, while they tend to increase MTTs during other times of the year due to shifts in hydrologic flow pathways. The balance between the competing influences on a catchment's MTT has consequences on climatic feedbacks as it could influence hydrological and biogeochemical cycles at the catchment scale for northern latitude boreal catchments. Copyright (C) 2010 John Wiley & Sons, Ltd.
  • MacGregor, Stuart, et al. (författare)
  • Genome-wide association study identifies a new melanoma susceptibility locus at 1q21.3
  • 2011
  • Ingår i: Nature Genetics. - : Nature Publishing Group. - 1546-1718. ; 43:11, s. 1114-1118
  • Tidskriftsartikel (refereegranskat)abstract
    • We performed a genome-wide association study of melanoma in a discovery cohort of 2,168 Australian individuals with melanoma and 4,387 control individuals. In this discovery phase, we confirm several previously characterized melanoma-associated loci at MC1R, ASIP and MTAP-CDKN2A. We selected variants at nine loci for replication in three independent case-control studies (Europe: 2,804 subjects with melanoma, 7,618 control subjects; United States 1: 1,804 subjects with melanoma, 1,026 control subjects; United States 2: 585 subjects with melanoma, 6,500 control subjects). The combined meta-analysis of all case-control studies identified a new susceptibility locus at 1q21.3 (rs7412746, P = 9.0 x 10(-11), OR in combined replication cohorts of 0.89 (95% CI 0.85-0.95)). We also show evidence suggesting that melanoma associates with 1q42.12 (rs3219090, P = 9.3 x 10(-8)). The associated variants at the 1q21.3 locus span a region with ten genes, and plausible candidate genes for melanoma susceptibility include ARNT and SETDB1. Variants at the 1q21.3 locus do not seem to be associated with human pigmentation or measures of nevus density.
  • Erlandsson Lampa, Martin, et al. (författare)
  • Catchment export of base cations : Improved mineral dissolution kinetics influence the role of water transit time
  • 2020
  • Ingår i: Soil. - : Copernicus GmbH. - 2199-3971 .- 2199-398X. ; 6:1, s. 231-244
  • Tidskriftsartikel (refereegranskat)abstract
    • Soil mineral weathering is one of the major sources of base cations (BC), which play a dual role in forest ecosystems: they function as plant nutrients and buffer against the acidification of catchment runoff. On a long-term basis, soil weathering rates determine the highest sustainable forest productivity that does not cause acidification. It is believed that the hydrologic residence time plays a key role in determining the weathering rates at the landscape scale. The PROFILE weathering model has been used for almost 30 years to calculate weathering rates in the rooting zone of forest soils. However, the mineral dissolution equations in PROFILE are not adapted for the saturated zone, and employing these equations at the catchment scale results in a significant overprediction of base cation release rates to surface waters. In this study, we use a revised set of PROFILE equations which, among other features, include retardation due to silica concentrations. Relationships between the water transit time (WTT) and soil water concentrations were derived for each base cation, by simulating the soil water chemistry along a one-dimensional flow path, using the mineralogy from a glacial till soil. We show how the revised PROFILE equations are able to reproduce patterns in BC and silica concentrations as well as BC ratios (Ca2+/BC, Mg2+/BC and Na+/BC) that are observed in the soil water profiles and catchment runoff. In contrast to the original set of PROFILE equations, the revised set of equations could reproduce the fact that increasing WTT led to a decreasing Na+/BC ratio and increasing Ca2+/BC and Mg2+/BC ratios. Furthermore, the total release of base cations from a hillslope was calculated using a mixing model, where water with different WTTs was mixed according to an externally modeled WTT distribution. The revised set of equations gave a 50 % lower base cation release (0.23 eq m-2 yr-1) than the original PROFILE equations and are in better agreement with mass balance calculations of weathering rates. Thus, the results from this study demonstrate that the revised mineral dissolution equations for PROFILE are a major step forward in modeling weathering rates at the catchment scale.
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