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  • 1
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    Testicular germ cell tumor susceptibility associated with the UCK2 locus on chromosome 1q23 (2013)
    Oxford University Press
    Details
    Publication Date: 2013-06-07
    Description: Genome-wide association studies (GWASs) have identified multiple common genetic variants associated with an increased risk of testicular germ cell tumors (TGCTs). A previous GWAS reported a possible TGCT susceptibility locus on chromosome 1q23 in the UCK2 gene, but failed to reach genome-wide significance following replication. We interrogated this region by conducting a meta-analysis of two independent GWASs including a total of 940 TGCT cases and 1559 controls for 122 single-nucleotide polymorphisms (SNPs) on chromosome 1q23 and followed up the most significant SNPs in an additional 2202 TGCT cases and 2386 controls from four case–control studies. We observed genome-wide significant associations for several UCK2 markers, the most significant of which was for rs3790665 ( P Combined = 6.0 x 10 –9 ). Additional support is provided from an independent familial study of TGCT where a significant over-transmission for rs3790665 with TGCT risk was observed ( P FBAT = 2.3 x 10 –3 ). Here, we provide substantial evidence for the association between UCK2 genetic variation and TGCT risk.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 2
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    A meta-analysis of genome-wide association studies of breast cancer identifies two novel susceptibility loci at 6q14 and 20q11 (2012)
    Siddiq, A., Couch, F. J., Chen, G. K., Lindstrom, S., Eccles, D., Millikan, R. C., Michailidou, K., Stram, D. O., Beckmann, L., Rhie, S. K., Ambrosone, C. B., Aittomaki, K., Amiano, P., Apicella, C., Australian Breast Cancer Tissue Bank Investigators, Baglietto, L., Bandera, E. V., Beckmann, M. W., Berg, C. D., Bernstein, L., Blomqvist, C., Brauch, H., Brinton, L., Bui, Q. M., Buring, J. E., Buys, S. S., Campa, D., Carpenter, J. E., Chasman, D. I., Chang-Claude, J., Chen, C., Clavel-Chapelon, F., Cox, A., Cross, S. S., Czene, K., Deming, S. L., Diasio, R. B., Diver, W. R., Dunning, A. M., Durcan, L., Ekici, A. B., Fasching, P. A., Familial Breast Cancer Study, Feigelson, H. S., Fejerman, L., Figueroa, J. D., Fletcher, O., Flesch-Janys, D., Gaudet, M. M., The GENICA Consortium, Gerty, S. M., Rodriguez-Gil, J. L., Giles, G. G., van Gils, C. H., Godwin, A. K., Graham, N., Greco, D., Hall, P., Hankinson, S. E., Hartmann, A., Hein, R., Heinz, J., Hoover, R. N., Hopper, J. L., Hu, J. J., Huntsman, S., Ingles, S. A., Irwanto, A., Isaacs, C., Jacobs, K. B., John, E. M., Justenhoven, C., Kaaks, R., Kolonel, L. N., Coetzee, G. A., Lathrop, M., Le Marchand, L., Lee, A. M., Lee, I.-M., Lesnick, T., Lichtner, P., Liu, J., Lund, E., Makalic, E., Martin, N. G., McLean, C. A., Meijers-Heijboer, H., Meindl, A., Miron, P., Monroe, K. R., Montgomery, G. W., Muller-Myhsok, B., Nickels, S., Nyante, S. J., Olswold, C., Overvad, K., Palli, D., Park, D. J., Palmer, J. R., Pathak, H., Peto, J., Pharoah, P., Rahman, N., Rivadeneira, F., Schmidt, D. F., Schmutzler, R. K., Slager, S., Southey, M. C., Stevens, K. N., Sinn, H.-P., Press, M. F., Ross, E., Riboli, E., Ridker, P. M., Schumacher, F. R., Severi, G., dos Santos Silva, I., Stone, J., Sund, M., Tapper, W. J., Thun, M. J., Travis, R. C., Turnbull, C., Uitterlinden, A. G., Waisfisz, Q., Wang, X., Wang, Z., Weaver, J., Schulz-Wendtland, R., Wilkens, L. R., Van Den Berg, D., Zheng, W., Ziegler, R. G., Ziv, E., Nevanlinna, H., Easton, D. F., Hunter, D. J., Henderson, B. E., Chanock, S. J., Garcia-Closas, M., Kraft, P., Haiman, C. A., Vachon, C. M.
    Oxford University Press
    Details
    Publication Date: 2012-12-01
    Description: Genome-wide association studies (GWAS) of breast cancer defined by hormone receptor status have revealed loci contributing to susceptibility of estrogen receptor (ER)-negative subtypes. To identify additional genetic variants for ER-negative breast cancer, we conducted the largest meta-analysis of ER-negative disease to date, comprising 4754 ER-negative cases and 31 663 controls from three GWAS: NCI Breast and Prostate Cancer Cohort Consortium (BPC3) (2188 ER-negative cases; 25 519 controls of European ancestry), Triple Negative Breast Cancer Consortium (TNBCC) (1562 triple negative cases; 3399 controls of European ancestry) and African American Breast Cancer Consortium (AABC) (1004 ER-negative cases; 2745 controls). We performed in silico replication of 86 SNPs at P ≤ 1 x 10 -5 in an additional 11 209 breast cancer cases (946 with ER-negative disease) and 16 057 controls of Japanese, Latino and European ancestry. We identified two novel loci for breast cancer at 20q11 and 6q14. SNP rs2284378 at 20q11 was associated with ER-negative breast cancer (combined two-stage OR = 1.16; P = 1.1 x 10 –8 ) but showed a weaker association with overall breast cancer (OR = 1.08, P = 1.3 x 10 –6 ) based on 17 869 cases and 43 745 controls and no association with ER-positive disease (OR = 1.01, P = 0.67) based on 9965 cases and 22 902 controls. Similarly, rs17530068 at 6q14 was associated with breast cancer (OR = 1.12; P = 1.1 x 10 –9 ), and with both ER-positive (OR = 1.09; P = 1.5 x 10 –5 ) and ER-negative (OR = 1.16, P = 2.5 x 10 –7 ) disease. We also confirmed three known loci associated with ER-negative (19p13) and both ER-negative and ER-positive breast cancer (6q25 and 12p11). Our results highlight the value of large-scale collaborative studies to identify novel breast cancer risk loci.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 3
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    Strong regional atmospheric 14C signature of respired CO2 observed from a tall tower over the mid-western United States (2016)
    Wiley
    Details
    Publication Date: 2016-08-11
    Description: Radiocarbon in CO 2 ( 14 CO 2 ) measurements can aid in discriminating between fast (〈1 year) and slower (〉5-10 years) cycling of C between the atmosphere and the terrestrial biosphere due to the 14 C disequilibrium between atmospheric and terrestrial C. However, 14 CO 2 in the atmosphere is typically much more strongly impacted by fossil fuel emissions of CO 2 , and, thus, observations often provide little additional constraints on respiratory flux estimates at regional scales. Here, we describe a dataset of 14 CO 2 observations from a tall tower in northern Wisconsin (USA) where fossil fuel influence is far enough removed that, during the summer months, the biospheric component of the 14 CO 2 budget dominates. We find that the terrestrial biosphere is responsible for a significant contribution to 14 CO 2 that is 2-3 times higher than predicted by the CASA terrestrial ecosystem model for observations made in 2010. This likely includes a substantial contribution from the North American Boreal ecoregion, but transported biospheric emissions from outside the model domain cannot be ruled out. The 14 CO 2 enhancement also appears somewhat decreased in observations made over subsequent years, suggesting that 2010 may be anomalous. With these caveats acknowledged, we discuss the implications of the observation/model comparison in terms of possible systematic biases in the model vs short-term anomalies in the observations. Going forward, this isotopic signal could be exploited as an important indicator to better constrain both the long-term carbon balance of terrestrial ecosystems and the short-term impact of disturbance-based loss of carbon to the atmosphere.
    Print ISSN: 0148-0227
    Topics: Biology , Geosciences
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 4
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    Linking emissions of fossil fuel CO2 and other anthropogenic trace gases using atmospheric 14CO2 (2012)
    Wiley
    Details
    Publication Date: 2012-04-19
    Description: Atmospheric CO2 gradients are usually dominated by the signal from net terrestrial biological fluxes, despite the fact that fossil fuel combustion fluxes are larger in the annual mean. Here, we use a six year long series of 14CO2 and CO2 measurements obtained from vertical profiles at two northeast U.S. aircraft sampling sites to partition lower troposphere CO2 enhancements (and depletions) into terrestrial biological and fossil fuel components (Cbio and Cff). Mean Cff is 1.5 ppm, and 2.4 ppm when we consider only planetary boundary layer samples. However, we find that the contribution of Cbio to CO2 enhancements is large throughout the year, and averages 60% in winter. Paired observations of Cff and the lower troposphere enhancements (Δgas) of 22 other anthropogenic gases (CH4, CO, halo- and hydrocarbons and others) measured in the same samples are used to determine apparent emission ratios for each gas. We then scale these ratios by the well known U.S. fossil fuel CO2 emissions to provide observationally based estimates of national emissions for each gas and compare these to “bottom up” estimates from inventories. Correlations of Δgas with Cff for almost all gases are statistically significant with median r2 for winter, summer and the entire year of 0.59, 0.45, and 0.42, respectively. Many gases exhibit statistically significant winter:summer differences in ratios that indicate seasonality of emissions or chemical destruction. The variability of ratios in a given season is not readily attributable to meteorological or geographic variables and instead most likely reflects real, short-term spatiotemporal variability of emissions.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 5
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    Diurnal patterns of water use in Eucalyptus victrix indicate pronounced desiccation-rehydration cycles despite unlimited water supply (2011)
    Oxford University Press
    Details
    Publication Date: 2011-11-24
    Description: Knowledge about nocturnal transpiration ( E night ) of trees is increasing and its impact on regional water and carbon balance has been recognized. Most of this knowledge has been generated in temperate or equatorial regions. Yet, little is known about E night and tree water use ( Q ) in semi-arid regions. We investigated the influence of atmospheric conditions on daytime ( Q day ) and nighttime water transport ( Q night ) of Eucalyptus victrix L.A.S. Johnson & K.D. Hill growing over shallow groundwater (not 〉1.5 m in depth) in semi-arid tropical Australia. We recorded Q day and Q night at different tree heights in conjunction with measurements of stomatal conductance ( g s ) and partitioned E night from refilling processes. Q of average-sized trees (200–400 mm diameter) was 1000–3000 l month –1 , but increased exponentially with diameter such that large trees (〉500 mm diameter) used up to 8000 l month –1 . Q was remarkably stable across seasons. Water flux densities ( J s ) varied significantly at different tree heights during day and night. We show that g s remained significantly different from zero and E night was always greater than zero due to vapor pressure deficits ( D ) that remained 〉1.5 kPa at night throughout the year. Q night reached a maximum of 50% of Q day and was 〉0.03 mm h –1 averaged across seasons. Refilling began during afternoon hours and continued well into the night. Q night eventually stabilized and closely tracked D night . Coupling of Q night and D night was particularly strong during the wet season ( R 2 = 0.95). We suggest that these trees have developed the capacity to withstand a pronounced desiccation–rehydration cycle in a semi-arid environment. Such a cycle has important implications for local and regional hydrological budgets of semi-arid landscapes, as large nighttime water fluxes must be included in any accounting.
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Oxford University Press
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  • 6
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    Atmospheric observations of carbon monoxide and fossil fuel CO2 emissions from East Asia (2011)
    Wiley
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    Publication Date: 2011-12-30
    Description: Flask samples from two sites in East Asia, Tae-Ahn Peninsula, Korea (TAP), and Shangdianzi, China (SDZ), were measured for trace gases including CO2, CO and fossil fuel CO2 (CO2ff, derived from Δ14CO2 observations). The five-year TAP record shows high CO2ff when local air comes from the Korean Peninsula. Most samples, however, reflect air masses from Northeastern China with lower CO2ff. Our small set of SDZ samples from winter 2009/2010 have strongly elevated CO2ff. Biospheric CO2 contributes substantially to total CO2 variability at both sites, even in winter when non-fossil CO2 sources (including photosynthesis, respiration, biomass burning and biofuel use) contribute 20–30% of the total CO2 enhancement. Carbon monoxide (CO) correlates strongly with CO2ff. The SDZ and TAP far-field (China influenced) samples have CO: CO2ff ratios (RCO:CO2ff) of 47 ± 2 and 44 ± 3 ppb/ppm respectively, consistent with recent bottom-up inventory estimates and other observational studies. Locally influenced TAP samples fall into two distinct data sets, ascribed to air sourced from South Korea and North Korea. The South Korea samples have low RCO:CO2ff of 13 ± 3 ppb/ppm, slightly higher than bottom-up inventories, but consistent with emission ratios for other developed nations. We compare our CO2ff observations with modeled CO2ff using the FLEXPART Lagrangian particle dispersion model convolved with a bottom-up CO2ff emission inventories. The modeled annual mean CO2ff mole fractions are consistent with our observations when the model inventory includes the reported 63% increase in Chinese emissions from 2004 to 2010, whereas a model version which holds Chinese emissions flat is unable to replicate the observations.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 7
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    Towards quantification and source sector identification of fossil fuel CO2 emissions from an urban area: Results from the INFLUX experiment (2014)
    Wiley
    Details
    Publication Date: 2014-12-10
    Description: The Indianapolis Flux Experiment (INFLUX) aims to develop and assess methods for quantifying urban greenhouse gas emissions. Here we use CO 2 , 14 CO 2 and CO measurements from tall towers around Indianapolis, USA to determine urban total CO 2 , the fossil fuel derived CO 2 component (CO 2 ff) and CO enhancements relative to background measurements. When a local background directly upwind of the urban area is used, the wintertime total CO 2 enhancement over Indianapolis can be entirely explained by urban CO 2 ff emissions. Conversely, when a continental background is used, CO 2 ff enhancements are larger and account for only half the total CO 2 enhancement, effectively representing the combined CO 2 ff enhancement from Indianapolis and the wider region. In summer, we find that diurnal variability in both background CO 2 mole fraction and co-varying vertical mixing make it difficult to use a simple upwind-downwind difference for a reliable determination of total CO 2 urban enhancement. We use characteristic CO 2 ff source sector CO:CO 2 ff emission ratios to examine the contribution of the CO 2 ff source sectors to total CO 2 ff emissions. This method is strongly sensitive to the mobile sector, which produces most CO. We show that the inventory-based emission product (“bottom-up”) and atmospheric observations (“top-down”) can be directly compared throughout the diurnal cycle using this ratio method. For Indianapolis, the top-down observations are consistent with the bottom-up Hestia data product emission sector patterns for most of the diurnal cycle, but disagree during the nighttime hours. Further examination of both the top-down and bottom-up assumptions is needed to assess the exact cause of the discrepancy.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 8
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    Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-04-03
    Description: Copy number variants (CNVs) account for a major proportion of human genetic polymorphism and have been predicted to have an important role in genetic susceptibility to common disease. To address this we undertook a large, direct genome-wide study of association between CNVs and eight common human diseases. Using a purpose-designed array we typed approximately 19,000 individuals into distinct copy-number classes at 3,432 polymorphic CNVs, including an estimated approximately 50% of all common CNVs larger than 500 base pairs. We identified several biological artefacts that lead to false-positive associations, including systematic CNV differences between DNAs derived from blood and cell lines. Association testing and follow-up replication analyses confirmed three loci where CNVs were associated with disease-IRGM for Crohn's disease, HLA for Crohn's disease, rheumatoid arthritis and type 1 diabetes, and TSPAN8 for type 2 diabetes-although in each case the locus had previously been identified in single nucleotide polymorphism (SNP)-based studies, reflecting our observation that most common CNVs that are well-typed on our array are well tagged by SNPs and so have been indirectly explored through SNP studies. We conclude that common CNVs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2892339/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2892339/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wellcome Trust Case Control Consortium -- Craddock, Nick -- Hurles, Matthew E -- Cardin, Niall -- Pearson, Richard D -- Plagnol, Vincent -- Robson, Samuel -- Vukcevic, Damjan -- Barnes, Chris -- Conrad, Donald F -- Giannoulatou, Eleni -- Holmes, Chris -- Marchini, Jonathan L -- Stirrups, Kathy -- Tobin, Martin D -- Wain, Louise V -- Yau, Chris -- Aerts, Jan -- Ahmad, Tariq -- Andrews, T Daniel -- Arbury, Hazel -- Attwood, Anthony -- Auton, Adam -- Ball, Stephen G -- Balmforth, Anthony J -- Barrett, Jeffrey C -- Barroso, Ines -- Barton, Anne -- Bennett, Amanda J -- Bhaskar, Sanjeev -- Blaszczyk, Katarzyna -- Bowes, John -- Brand, Oliver J -- Braund, Peter S -- Bredin, Francesca -- Breen, Gerome -- Brown, Morris J -- Bruce, Ian N -- Bull, Jaswinder -- Burren, Oliver S -- Burton, John -- Byrnes, Jake -- Caesar, Sian -- Clee, Chris M -- Coffey, Alison J -- Connell, John M C -- Cooper, Jason D -- Dominiczak, Anna F -- Downes, Kate -- Drummond, Hazel E -- Dudakia, Darshna -- Dunham, Andrew -- Ebbs, Bernadette -- Eccles, Diana -- Edkins, Sarah -- Edwards, Cathryn -- Elliot, Anna -- Emery, Paul -- Evans, David M -- Evans, Gareth -- Eyre, Steve -- Farmer, Anne -- Ferrier, I Nicol -- Feuk, Lars -- Fitzgerald, Tomas -- Flynn, Edward -- Forbes, Alistair -- Forty, Liz -- Franklyn, Jayne A -- Freathy, Rachel M -- Gibbs, Polly -- Gilbert, Paul -- Gokumen, Omer -- Gordon-Smith, Katherine -- Gray, Emma -- Green, Elaine -- Groves, Chris J -- Grozeva, Detelina -- Gwilliam, Rhian -- Hall, Anita -- Hammond, Naomi -- Hardy, Matt -- Harrison, Pile -- Hassanali, Neelam -- Hebaishi, Husam -- Hines, Sarah -- Hinks, Anne -- Hitman, Graham A -- Hocking, Lynne -- Howard, Eleanor -- Howard, Philip -- Howson, Joanna M M -- Hughes, Debbie -- Hunt, Sarah -- Isaacs, John D -- Jain, Mahim -- Jewell, Derek P -- Johnson, Toby -- Jolley, Jennifer D -- Jones, Ian R -- Jones, Lisa A -- Kirov, George -- Langford, Cordelia F -- Lango-Allen, Hana -- Lathrop, G Mark -- Lee, James -- Lee, Kate L -- Lees, Charlie -- Lewis, Kevin -- Lindgren, Cecilia M -- Maisuria-Armer, Meeta -- Maller, Julian -- Mansfield, John -- Martin, Paul -- Massey, Dunecan C O -- McArdle, Wendy L -- McGuffin, Peter -- McLay, Kirsten E -- Mentzer, Alex -- Mimmack, Michael L -- Morgan, Ann E -- Morris, Andrew P -- Mowat, Craig -- Myers, Simon -- Newman, William -- Nimmo, Elaine R -- O'Donovan, Michael C -- Onipinla, Abiodun -- Onyiah, Ifejinelo -- Ovington, Nigel R -- Owen, Michael J -- Palin, Kimmo -- Parnell, Kirstie -- Pernet, David -- Perry, John R B -- Phillips, Anne -- Pinto, Dalila -- Prescott, Natalie J -- Prokopenko, Inga -- Quail, Michael A -- Rafelt, Suzanne -- Rayner, Nigel W -- Redon, Richard -- Reid, David M -- Renwick -- Ring, Susan M -- Robertson, Neil -- Russell, Ellie -- St Clair, David -- Sambrook, Jennifer G -- Sanderson, Jeremy D -- Schuilenburg, Helen -- Scott, Carol E -- Scott, Richard -- Seal, Sheila -- Shaw-Hawkins, Sue -- Shields, Beverley M -- Simmonds, Matthew J -- Smyth, Debbie J -- Somaskantharajah, Elilan -- Spanova, Katarina -- Steer, Sophia -- Stephens, Jonathan -- Stevens, Helen E -- Stone, Millicent A -- Su, Zhan -- Symmons, Deborah P M -- Thompson, John R -- Thomson, Wendy -- Travers, Mary E -- Turnbull, Clare -- Valsesia, Armand -- Walker, Mark -- Walker, Neil M -- Wallace, Chris -- Warren-Perry, Margaret -- Watkins, Nicholas A -- Webster, John -- Weedon, Michael N -- Wilson, Anthony G -- Woodburn, Matthew -- Wordsworth, B Paul -- Young, Allan H -- Zeggini, Eleftheria -- Carter, Nigel P -- Frayling, Timothy M -- Lee, Charles -- McVean, Gil -- Munroe, Patricia B -- Palotie, Aarno -- Sawcer, Stephen J -- Scherer, Stephen W -- Strachan, David P -- Tyler-Smith, Chris -- Brown, Matthew A -- Burton, Paul R -- Caulfield, Mark J -- Compston, Alastair -- Farrall, Martin -- Gough, Stephen C L -- Hall, Alistair S -- Hattersley, Andrew T -- Hill, Adrian V S -- Mathew, Christopher G -- Pembrey, Marcus -- Satsangi, Jack -- Stratton, Michael R -- Worthington, Jane -- Deloukas, Panos -- Duncanson, Audrey -- Kwiatkowski, Dominic P -- McCarthy, Mark I -- Ouwehand, Willem -- Parkes, Miles -- Rahman, Nazneen -- Todd, John A -- Samani, Nilesh J -- Donnelly, Peter -- 061858/Wellcome Trust/United Kingdom -- 083948/Wellcome Trust/United Kingdom -- 089989/Wellcome Trust/United Kingdom -- 090532/Wellcome Trust/United Kingdom -- 17552/Arthritis Research UK/United Kingdom -- CZB/4/540/Chief Scientist Office/United Kingdom -- ETM/137/Chief Scientist Office/United Kingdom -- ETM/75/Chief Scientist Office/United Kingdom -- G0000934/Medical Research Council/United Kingdom -- G0400874/Medical Research Council/United Kingdom -- G0500115/Medical Research Council/United Kingdom -- G0501942/Medical Research Council/United Kingdom -- G0600329/Medical Research Council/United Kingdom -- G0600705/Medical Research Council/United Kingdom -- G0700491/Medical Research Council/United Kingdom -- G0701003/Medical Research Council/United Kingdom -- G0701420/Medical Research Council/United Kingdom -- G0701810/Medical Research Council/United Kingdom -- G0701810(85517)/Medical Research Council/United Kingdom -- G0800383/Medical Research Council/United Kingdom -- G0800509/Medical Research Council/United Kingdom -- G0800759/Medical Research Council/United Kingdom -- G19/9/Medical Research Council/United Kingdom -- G90/106/Medical Research Council/United Kingdom -- G9521010/Medical Research Council/United Kingdom -- MC_UP_A390_1107/Medical Research Council/United Kingdom -- RG/09/012/28096/British Heart Foundation/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2010 Apr 1;464(7289):713-20. doi: 10.1038/nature08979.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20360734" target="_blank"〉PubMed〈/a〉
    Keywords: Arthritis, Rheumatoid/genetics ; Case-Control Studies ; Crohn Disease/genetics ; DNA Copy Number Variations/*genetics ; Diabetes Mellitus/genetics ; *Disease ; Gene Frequency/genetics ; Genetic Predisposition to Disease/*genetics ; *Genome-Wide Association Study ; Humans ; Nucleic Acid Hybridization ; Oligonucleotide Array Sequence Analysis ; Pilot Projects ; Polymorphism, Single Nucleotide/genetics ; Quality Control
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 9
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    Mosaic PPM1D mutations are associated with predisposition to breast and ovarian cancer (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-12-18
    Description: Improved sequencing technologies offer unprecedented opportunities for investigating the role of rare genetic variation in common disease. However, there are considerable challenges with respect to study design, data analysis and replication. Using pooled next-generation sequencing of 507 genes implicated in the repair of DNA in 1,150 samples, an analytical strategy focused on protein-truncating variants (PTVs) and a large-scale sequencing case-control replication experiment in 13,642 individuals, here we show that rare PTVs in the p53-inducible protein phosphatase PPM1D are associated with predisposition to breast cancer and ovarian cancer. PPM1D PTV mutations were present in 25 out of 7,781 cases versus 1 out of 5,861 controls (P = 1.12 x 10(-5)), including 18 mutations in 6,912 individuals with breast cancer (P = 2.42 x 10(-4)) and 12 mutations in 1,121 individuals with ovarian cancer (P = 3.10 x 10(-9)). Notably, all of the identified PPM1D PTVs were mosaic in lymphocyte DNA and clustered within a 370-base-pair region in the final exon of the gene, carboxy-terminal to the phosphatase catalytic domain. Functional studies demonstrate that the mutations result in enhanced suppression of p53 in response to ionizing radiation exposure, suggesting that the mutant alleles encode hyperactive PPM1D isoforms. Thus, although the mutations cause premature protein truncation, they do not result in the simple loss-of-function effect typically associated with this class of variant, but instead probably have a gain-of-function effect. Our results have implications for the detection and management of breast and ovarian cancer risk. More generally, these data provide new insights into the role of rare and of mosaic genetic variants in common conditions, and the use of sequencing in their identification.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3759028/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3759028/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ruark, Elise -- Snape, Katie -- Humburg, Peter -- Loveday, Chey -- Bajrami, Ilirjana -- Brough, Rachel -- Rodrigues, Daniel Nava -- Renwick, Anthony -- Seal, Sheila -- Ramsay, Emma -- Duarte, Silvana Del Vecchio -- Rivas, Manuel A -- Warren-Perry, Margaret -- Zachariou, Anna -- Campion-Flora, Adriana -- Hanks, Sandra -- Murray, Anne -- Ansari Pour, Naser -- Douglas, Jenny -- Gregory, Lorna -- Rimmer, Andrew -- Walker, Neil M -- Yang, Tsun-Po -- Adlard, Julian W -- Barwell, Julian -- Berg, Jonathan -- Brady, Angela F -- Brewer, Carole -- Brice, Glen -- Chapman, Cyril -- Cook, Jackie -- Davidson, Rosemarie -- Donaldson, Alan -- Douglas, Fiona -- Eccles, Diana -- Evans, D Gareth -- Greenhalgh, Lynn -- Henderson, Alex -- Izatt, Louise -- Kumar, Ajith -- Lalloo, Fiona -- Miedzybrodzka, Zosia -- Morrison, Patrick J -- Paterson, Joan -- Porteous, Mary -- Rogers, Mark T -- Shanley, Susan -- Walker, Lisa -- Gore, Martin -- Houlston, Richard -- Brown, Matthew A -- Caufield, Mark J -- Deloukas, Panagiotis -- McCarthy, Mark I -- Todd, John A -- Breast and Ovarian Cancer Susceptibility Collaboration -- Wellcome Trust Case Control Consortium -- Turnbull, Clare -- Reis-Filho, Jorge S -- Ashworth, Alan -- Antoniou, Antonis C -- Lord, Christopher J -- Donnelly, Peter -- Rahman, Nazneen -- 068545/Z/02/Wellcome Trust/United Kingdom -- 083948/Wellcome Trust/United Kingdom -- 090532/Wellcome Trust/United Kingdom -- 090532/Z/09/Z/Wellcome Trust/United Kingdom -- 091157/Wellcome Trust/United Kingdom -- 095552/Wellcome Trust/United Kingdom -- 098051/Wellcome Trust/United Kingdom -- 100140/Wellcome Trust/United Kingdom -- 11174/Cancer Research UK/United Kingdom -- C12292/A11174/Cancer Research UK/United Kingdom -- CZB/4/540/Chief Scientist Office/United Kingdom -- ETM/137/Chief Scientist Office/United Kingdom -- ETM/75/Chief Scientist Office/United Kingdom -- G0000934/Medical Research Council/United Kingdom -- G0600329/Medical Research Council/United Kingdom -- G0800759/Medical Research Council/United Kingdom -- G0900747 91070/Medical Research Council/United Kingdom -- G9521010/Medical Research Council/United Kingdom -- MR/K006584/1/Medical Research Council/United Kingdom -- England -- Nature. 2013 Jan 17;493(7432):406-10. doi: 10.1038/nature11725. Epub 2012 Dec 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton SM2 5NG, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23242139" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Breast Neoplasms/*genetics ; Cluster Analysis ; Exons ; Female ; Genetic Predisposition to Disease/*genetics ; Humans ; Isoenzymes/genetics ; Lymphocytes/metabolism ; *Mosaicism ; *Mutation ; Ovarian Neoplasms/*genetics ; Phosphoprotein Phosphatases/*genetics ; Sequence Analysis, DNA ; Tumor Suppressor Protein p53/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 10
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    FT protein movement contributes to long-distance signaling in floral induction of Arabidopsis (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-04-21
    Description: In plants, seasonal changes in day length are perceived in leaves, which initiate long-distance signaling that induces flowering at the shoot apex. The identity of the long-distance signal has yet to be determined. In Arabidopsis, activation of FLOWERING LOCUS T (FT) transcription in leaf vascular tissue (phloem) induces flowering. We found that FT messenger RNA is required only transiently in the leaf. In addition, FT fusion proteins expressed specifically in phloem cells move to the apex and move long distances between grafted plants. Finally, we provide evidence that FT does not activate an intermediate messenger in leaves. We conclude that FT protein acts as a long-distance signal that induces Arabidopsis flowering.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Corbesier, Laurent -- Vincent, Coral -- Jang, Seonghoe -- Fornara, Fabio -- Fan, Qingzhi -- Searle, Iain -- Giakountis, Antonis -- Farrona, Sara -- Gissot, Lionel -- Turnbull, Colin -- Coupland, George -- New York, N.Y. -- Science. 2007 May 18;316(5827):1030-3. Epub 2007 Apr 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute for Plant Breeding Research, Carl von Linne Weg 10, D-50829 Cologne, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17446353" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/genetics/metabolism/*physiology ; Arabidopsis Proteins/genetics/*metabolism ; DNA-Binding Proteins/genetics/metabolism ; Dexamethasone/pharmacology ; Flowers/*growth & development ; Gene Expression Regulation, Plant ; Green Fluorescent Proteins/genetics ; Membrane Transport Proteins/genetics ; Meristem/metabolism ; Models, Biological ; Phloem/metabolism ; Photoperiod ; Plant Leaves/metabolism ; Plant Proteins/genetics ; Plant Shoots/metabolism ; Plants, Genetically Modified ; Promoter Regions, Genetic ; RNA, Messenger/genetics/metabolism ; RNA, Plant/genetics/metabolism ; Recombinant Fusion Proteins/metabolism ; *Signal Transduction ; Transcription Factors/genetics/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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