Search

Your search keyword '"Long, J.R."' showing total 320 results
Start Over Author "Long, J.R."

Refine your results

more »

more »

more »
320 results on '"Long, J.R."'

2. Functional annotation of the 2q35 breast cancer risk locus implicates a structural variant in influencing activity of a long-range enhancer element

Author

Baxter, J.S., Johnson, N., Tomczyk, K., Gillespie, A., Maguire, S., Brough, R., Fachal, L., Michailidou, K., Bolla, M.K., Wang, Q., Dennis, J., Ahearn, T.U., Andrulis, I.L., Anton-Culver, H., Antonenkova, N.N., Arndt, V., Aronson, K.J., Augustinsson, A., Becher, H., Beckmann, M.W., Behrens, S., Benitez, J., Bermisheva, M., Bogdanova, N.V., Bojesen, S.E., Brenner, H., Brucker, S.Y., Cai, Q.Y., Campa, D., Canzian, F., Castelao, J.E., Chan, T.L., Chang-Claude, J., Chanock, S.J., Chenevix-Trench, G., Choi, J.Y., Clarke, C.L., Collaborators, N., Colonna, S., Conroy, D.M., Couch, F.J., Cox, A., Cross, S.S., Czene, K., Daly, M.B., Devilee, P., Dork, T., Dossus, L., Dwek, M., Eccles, D.M., Ekici, A.B., Eliassen, A.H., Engel, C., Fasching, P.A., Figueroa, J., Flyger, H., Gago-Dominguez, M., Gao, C., Garcia-Closas, M., Garcia-Saenz, J.A., Ghoussaini, M., Giles, G.G., Goldberg, M.S., Gonzalez-Neira, A., Guenel, P., Gundert, M., Haeberle, L., Hahnen, E., Haiman, C.A., Hall, P., Hamann, U., Hartman, M., Hatse, S., Hauke, J., Hollestelle, A., Hoppe, R., Hopper, J.L., Hou, M.F., Ito, H., Iwasaki, M., Jager, A., Jakubowska, A., Janni, W., John, E.M., Joseph, V., Jung, A., Kaaks, R., Kang, D., Keeman, R., Khusnutdinova, E., Kim, S.W., Kosma, V.M., Kraft, P., Kristensen, V.N., Kubelka-Sabit, K., Kurian, A.W., Kwong, A., Lacey, J.V., Lambrechts, D., Larson, N.L., Larsson, S.C., Marchand, L. le, Lejbkowicz, F., Li, J.M., Long, J.R., Lophatananon, A., LubiNski, J., Mannermaa, A., Manoochehri, M., Manoukian, S., Margolin, S., Matsuo, K., Mavroudis, D., Mayes, R., Menon, U., Milne, R.L., Taib, N.A.M., Muir, K., Muranen, T.A., Murphy, R.A., Nevanlinna, H., O'Brien, K.M., Offit, K., Olson, J.E., Olsson, H., Park, S.K., Park-Simon, T.W., Patel, A.V., Peterlongo, P., Peto, J., Plaseska-Karanfilska, D., Presneau, N., Pylkas, K., Rack, B., Rennert, G., Romero, A., Ruebner, M., Rudiger, T., Saloustros, E., Sandler, D.P., Sawyer, E.J., Schmidt, M.K., Schmutzler, R.K., Schneeweiss, A., Schoemaker, M.J., Shah, M., Shen, C.Y., Shu, X.O., Simard, J., Southey, M.C., Stone, J., Surowy, H., Swerdlow, A.J., Tamimi, R.M., Tapper, W.J., Taylor, J.A., Teo, S.H., Teras, L.R., Terry, M.B., Toland, A.E., Tomlinson, I., Truong, T., Tseng, C.C., Untch, M., Vachon, C.M., Ouweland, A.M.W. van den, Wang, S.S., Weinberg, C.R., Wendt, C., Winham, S.J., Winqvist, R., Wolk, A., Wu, A.H., Yamaji, T., Zheng, W., Ziogas, A., Pharoah, P.D.P., Dunning, A.M., Easton, D.F., Pettitt, S.J., Lord, C.J., Haider, S., Orr, N., Fletcher, O., kConFab Investigators, ABCTB Investigators, Medical Oncology, Clinical Genetics, HUS Gynecology and Obstetrics, Department of Obstetrics and Gynecology, Biosciences, Dennis, Joe [0000-0003-4591-1214], Pharoah, Paul [0000-0001-8494-732X], Dunning, Alison [0000-0001-6651-7166], Easton, Douglas [0000-0003-2444-3247], and Apollo - University of Cambridge Repository

Subjects
Basic medicine, breast cancer risk, 0302 clinical medicine, Transcription (biology), Risk Factors, WIDE ASSOCIATION, TRANSCRIPTION, Promoter Regions, Genetic, Genetics (clinical), Sequence Deletion, Genetics, Genetics & Heredity, 0303 health sciences, Chromosome Mapping, 3. Good health, 030220 oncology & carcinogenesis, Chromosomes, Human, Pair 2, Pair 2, Female, Medical Genetics, Life Sciences & Biomedicine, Human, Tumor suppressor gene, SUSCEPTIBILITY LOCI, In silico, 3122 Cancers, Locus (genetics), Breast Neoplasms, Biology, Chromosomes, Article, Cell Line, RNAS, Promoter Regions, 03 medical and health sciences, functional annotation, risk locus, CRISPR-Cas Systems, Genetic Association Studies, Genetic Variation, Humans, Insulin-Like Growth Factor Binding Protein 5, Molecular Sequence Annotation, 11Q13, Genetic, SDG 3 - Good Health and Well-being, Enhancer, Transcription factor, 030304 developmental biology, Medicinsk genetik, Reporter gene, Science & Technology, IDENTIFICATION, Clinical medicine, Estrogen receptor alpha
Abstract

A combination of genetic and functional approaches has identified three independent breast cancer risk loci at 2q35. A recent fine-scale mapping analysis to refine these associations resulted in 1 (signal 1), 5 (signal 2), and 42 (signal 3) credible causal variants at these loci. We used publicly available in silico DNase I and ChIP-seq data with in vitro reporter gene and CRISPR assays to annotate signals 2 and 3. We identified putative regulatory elements that enhanced cell-type-specific transcription from the IGFBP5 promoter at both signals (30- to 40-fold increased expression by the putative regulatory element at signal 2, 2- to 3-fold by the putative regulatory element at signal 3). We further identified one of the five credible causal variants at signal 2, a 1.4 kb deletion (esv3594306), as the likely causal variant; the deletion allele of this variant was associated with an average additional increase in IGFBP5 expression of 1.3-fold (MCF-7) and 2.2-fold (T-47D). We propose a model in which the deletion allele of esv3594306 juxtaposes two transcription factor binding regions (annotated by estrogen receptor alpha ChIP-seq peaks) to generate a single extended regulatory element. This regulatory element increases cell-type-specific expression of the tumor suppressor gene IGFBP5 and, thereby, reduces risk of estrogen receptor-positive breast cancer (odds ratio = 0.77, 95% CI 0.74-0.81, p = 3.1 × 10-31). ispartof: AMERICAN JOURNAL OF HUMAN GENETICS vol:108 issue:7 pages:1190-1203 ispartof: location:United States status: published

Published
2021

3. Literatuuronderzoek chrysantenteelt zonder stomen : Kan een monocultuur in een stabiel microbieel evenwicht blijven?

Author

Blok, C., Eveleens, B., de Long, J.R., Raaphorst, M., Messelink, G., Streminska, M., Voogt, W., Kruidhof, M., Fradin, M., Leiss, K.A., van der Salm, C., Blok, C., Eveleens, B., de Long, J.R., Raaphorst, M., Messelink, G., Streminska, M., Voogt, W., Kruidhof, M., Fradin, M., Leiss, K.A., and van der Salm, C.

Abstract

Chrysanthemum are grown in a soil-based cultivation with 4-6 cultivation cycles per year. The build-up of diseases and pests in the soil is considerable. It is now common to steam the soil at least once a year. The related energy consumption is 4-6 m3 gas per m2 per year. The build-up of diseases is associated with hygiene, the cuttings, the press pots on which chrysanthemum cuttings are grown, the transition from propagation to cultivation medium, irrigation cycles and tilling root residues and press pots into the soil after cultivation. Major diseases and pests are Pythium, Fusarium, nematodes and Thrips. This literature study describes what is known about cultivation circumstances promoting diseases and pests. The aim was to assess the feasibility of a chrysanthemum crop without steaming based on adaptations of the current cultivation method., Chrysantenteelt is een grondgebonden teelt met 4-6 teeltcycli per jaar. De opbouw van ziekten en plagen in de bodem is aanzienlijk. Het is nu gebruikelijk de grond minstens eens per jaar te stomen. Het gerelateerde energieverbruik is 4-6 m3 gas per m2 per jaar. De ziektenopbouw wordt in verband gebracht met bedrijfshygiëne, de stekken, de perspotten waarop wordt opgekweekt, de overgang van opkweek naar teeltbodem, de watergiften en het onder frezen van wortelresten en perspotten. De belangrijke ziekten en plagen zijn Pythium, Fusarium, nematoden en Thrips. In dit literatuuronderzoek wordt beschreven wat bekend is over teeltomstandigheden die bevorderlijk zijn voor de ziekten en plagen. Doel was te komen tot een beoordeling van de haalbaarheid van een chrysantenteelt zonder stomen gebaseerd op aanpassingen van de huidige teeltmethode.

Published
2021

4. Biological control of Meloidogyne spp. In glasshouse-grown chrysanthemum

Author

De Long, J.R., Streminska, M.A., Persijn, A., Huisman, H.M.I., Van Der Salm, C., De Long, J.R., Streminska, M.A., Persijn, A., Huisman, H.M.I., and Van Der Salm, C.

Abstract

Root-knot nematodes (Meloidogyne spp.) are a major problem in soil-based glasshouse-grown chrysanthemums. To combat rootknot nematodes in the glasshouse, the soil is typically steamed every 5-6 production cycles. However, this method is expensive, environmentally unfriendly and reduces resistance and resilience of the soil against pathogens and pests. Here, we added biological pesticides/a basic substance and biostimulants both individually and in combination to determine individual or interactive effects against damage by root-knot nematodes in chrysanthemums. We found that the application of biological nematicides derived from garlic extract, the basic substance chitosan HCl and biostimulants comprised of sea minerals and plant oils correlated with reduced root-knot nematode damage. These effects may have been due to direct effects against the nematodes or through indirect effects such as increased resistance and resilience of the plants. Overall, the biostimulants increased the total number of free-living nematodes in the soil, which could lead to a beneficial increase in nutrient cycling in the soils. Our results demonstrate that biological reagents show promise in reducing root-knot nematode damage in glasshousegrown chrysanthemum and may lead to more resistance and resilient soils.

Published
2021

9. TRY plant trait database – enhanced coverage and open access

Author

Kattge, J., Bönisch, G., Díaz, S., Lavorel, S., Prentice, I.C., Leadley, P., Tautenhahn, S., Werner, G.D.A., Aakala, T., Abedi, M., Acosta, A.T.R., Adamidis, G.C., Adamson, K., Aiba, M., Albert, C.H., Alcántara, J.M., Alcázar, C.C., Aleixo, I., Ali, H., Amiaud, B., Ammer, C., Amoroso, M.M., Anand, M., Anderson, C., Anten, N., Antos, J., Apgaua, D.M.G., Ashman, T‐L, Asmara, D.H., Asner, G.P., Aspinwall, M., Atkin, O., Aubin, I., Baastrup‐Spohr, L., Bahalkeh, K., Bahn, M., Baker, T., Baker, W.J., Bakker, J.P., Baldocchi, D., Baltzer, J., Banerjee, A., Baranger, A., Barlow, J., Barneche, D.R., Baruch, Z., Bastianelli, D., Battles, J., Bauerle, W., Bauters, M., Bazzato, E., Beckmann, M., Beeckman, H., Beierkuhnlein, C., Bekker, R., Belfry, G., Belluau, M., Beloiu, M., Benavides, R., Benomar, L., Berdugo‐Lattke, M.L., Berenguer, E., Bergamin, R., Bergmann, J., Bergmann Carlucci, M., Berner, L., Bernhardt‐Römermann, M., Bigler, C., Bjorkman, A.D., Blackman, C., Blanco, C., Blonder, B., Blumenthal, D., Bocanegra‐González, K.T., Boeckx, P., Bohlman, S., Böhning‐Gaese, K., Boisvert‐Marsh, L., Bond, W., Bond‐Lamberty, B., Boom, A., Boonman, C.C.F., Bordin, K., Boughton, E.H., Boukili, V., Bowman, D.M.J.S., Bravo, S., Brendel, M.R., Broadley, M.R., Brown, K.A., Bruelheide, H., Brumnich, F., Bruun, H.H., Bruy, D., Buchanan, S.W., Bucher, S.F., Buchmann, N., Buitenwerf, R., Bunker, D.E., Bürger, J., Burrascano, S., Burslem, D.F.R.P., Butterfield, B.J., Byun, C., Marques, M., Scalon, M.C., Caccianiga, M., Cadotte, M., Cailleret, M., Camac, J., Camarero, J.J., Campany, C., Campetella, G., Campos, J.A., Cano‐Arboleda, L., Canullo, R., Carbognani, M., Carvalho, F., Casanoves, F., Castagneyrol, B., Catford, J.A., Cavender‐Bares, J., Cerabolini, B.E.L., Cervellini, M., Chacón‐Madrigal, E., Chapin, K., Chapin, F.S., Chelli, S., Chen, S‐C, Chen, A., Cherubini, P., Chianucci, F., Choat, B., Chung, K‐S, Chytrý, M., Ciccarelli, D., Coll, L., Collins, C.G., Conti, L., Coomes, D., Cornelissen, J.H.C., Cornwell, W.K., Corona, P., Coyea, M., Craine, J., Craven, D., Cromsigt, J.P.G.M., Csecserits, A., Cufar, K., Cuntz, M., Silva, A.C., Dahlin, K.M., Dainese, M., Dalke, I., Dalle Fratte, M., Dang‐Le, A.T., Danihelka, J., Dannoura, M., Dawson, S., Beer, A.J., De Frutos, A., De Long, J.R., Dechant, B., Delagrange, S., Delpierre, N., Derroire, G., Dias, A.S., Diaz‐Toribio, M.H., Dimitrakopoulos, P.G., Dobrowolski, M., Doktor, D., Dřevojan, P., Dong, N., Dransfield, J., Dressler, S., Duarte, L., Ducouret, E., Dullinger, S., Durka, W., Duursma, R., Dymova, O., E‐Vojtkó, A., Eckstein, R.L., Ejtehadi, H., Elser, J., Emilio, T., Engemann, K., Erfanian, M.B., Erfmeier, A., Esquivel‐Muelbert, A., Esser, G., Estiarte, M., Domingues, T.F., Fagan, W.F., Fagúndez, J., Falster, D.S., Fan, Y., Fang, J., Farris, E., Fazlioglu, F., Feng, Y., Fernandez‐Mendez, F., Ferrara, C., Ferreira, J., Fidelis, A., Finegan, B., Firn, J., Flowers, T.J., Flynn, D.F.B., Fontana, V., Forey, E., Forgiarini, C., François, L., Frangipani, M., Frank, D., Frenette‐Dussault, C., Freschet, G.T., Fry, E.L., Fyllas, N.M., Mazzochini, G.G., Gachet, S., Gallagher, R., Ganade, G., Ganga, F., García‐Palacios, P., Gargaglione, V., Garnier, E., Garrido, J.L., Gasper, A.L., Gea‐Izquierdo, G., Gibson, D., Gillison, A.N., Giroldo, A., Glasenhardt, M‐C, Gleason, S., Gliesch, M., Goldberg, E., Göldel, B., Gonzalez‐Akre, E., Gonzalez‐Andujar, J.L., González‐Melo, A., González‐Robles, A., Graae, B.J., Granda, E., Graves, S., Green, W.A., Gregor, T., Gross, N., Guerin, G.R., Günther, A., Gutiérrez, A.G., Haddock, L., Haines, A., Hall, J., Hambuckers, A., Han, W., Harrison, S.P., Hattingh, W., Hawes, J.E., He, T., He, P., Heberling, J.M., Helm, A., Hempel, S., Hentschel, J., Hérault, B., Hereş, A‐M, Herz, K., Heuertz, M., Hickler, T., Hietz, P., Higuchi, P., Hipp, A.L., Hirons, A., Hock, M., Hogan, J.A., Holl, K., Honnay, O., Hornstein, D., Hou, E., Hough‐Snee, N., Hovstad, K.A., Ichie, T., Igić, B., Illa, E., Isaac, M., Ishihara, M., Ivanov, L., Ivanova, L., Iversen, C.M., Izquierdo, J., Jackson, R.B., Jackson, B., Jactel, H., Jagodzinski, A.M., Jandt, U., Jansen, S., Jenkins, T., Jentsch, A., Jespersen, J.R.P., Jiang, G‐F, Johansen, J.L., Johnson, D., Jokela, E.J., Joly, C.A., Jordan, G.J., Joseph, G.S., Junaedi, D., Junker, R.R., Justes, E., Kabzems, R., Kane, J., Kaplan, Z., Kattenborn, T., Kavelenova, L., Kearsley, E., Kempel, A., Kenzo, T., Kerkhoff, A., Khalil, M.I., Kinlock, N.L., Kissling, W.D., Kitajima, K., Kitzberger, T., Kjøller, R., Klein, T., Kleyer, M., Klimešová, J., Klipel, J., Kloeppel, B., Klotz, S., Knops, J.M.H., Kohyama, T., Koike, F., Kollmann, J., Komac, B., Komatsu, K., König, C., Kraft, N.J.B., Kramer, K.., Kreft, H., Kühn, I., Kumarathunge, D., Kuppler, J., Kurokawa, H., Kurosawa, Y., Kuyah, S., Laclau, J‐P, Lafleur, B., Lallai, E., Lamb, E., Lamprecht, A., Larkin, D.J., Laughlin, D., Le Bagousse‐Pinguet, Y., Maire, G., Roux, P.C., Roux, E., Lee, T., Lens, F., Lewis, S.L., Lhotsky, B., Li, Y., Li, X., Lichstein, J.W., Liebergesell, M., Lim, J.Y., Lin, Y‐S, Linares, J.C., Liu, C., Liu, D., Liu, U., Livingstone, S., Llusià, J., Lohbeck, M., López‐García, Á., Lopez‐Gonzalez, G., Lososová, Z., Louault, F., Lukács, B.A., Lukeš, P., Luo, Y.J., Lussu, M., Ma, S., Maciel Rabelo Pereira, C., Mack, M., Maire, V., Mäkelä, A., Mäkinen, H., Malhado, A.C.M., Mallik, A., Manning, P., Manzoni, S., Marchetti, Z., Marchino, L., Marcilio‐Silva, V., Marcon, E., Marignani, M., Markesteijn, L., Martin, A., Martínez‐Garza, C., Martínez‐Vilalta, J., Mašková, T., Mason, K., Mason, N., Massad, T.J., Masse, J., Mayrose, I., McCarthy, J., McCormack, M.L., McCulloh, K., McFadden, I.R., McGill, B.J., McPartland, M.Y., Medeiros, J.S., Medlyn, B., Meerts, P., Mehrabi, Z., Meir, P., Melo, F.P.L., Mencuccini, M., Meredieu, C., Messier, J., Mészáros, I., Metsaranta, J., Michaletz, S.T., Michelaki, C., Migalina, S., Milla, R., Miller, J.E.D., Minden, V., Ming, R., Mokany, K., Moles, A.T., Molnár, A., Molofsky, J., Molz, M., Montgomery, R.A., Monty, A., Moravcová, L., Moreno‐Martínez, A., Moretti, M., Mori, A.S., Mori, S., Morris, D., Morrison, J., Mucina, L., Mueller, S., Muir, C.D., Müller, S.C., Munoz, F., Myers‐Smith, I.H., Myster, R.W., Nagano, M., Naidu, S., Narayanan, A., Natesan, B., Negoita, L., Nelson, A.S., Neuschulz, E.L., Ni, J., Niedrist, G., Nieto, J., Niinemets, Ü., Nolan, R., Nottebrock, H., Nouvellon, Y., Novakovskiy, A., Nystuen, K.O., O'Grady, A., O'Hara, K., O'Reilly‐Nugent, A., Oakley, S., Oberhuber, W., Ohtsuka, T., Oliveira, R., Öllerer, K., Olson, M.E., Onipchenko, V., Onoda, Y., Onstein, R.E., Ordonez, J.C., Osada, N., Ostonen, I., Ottaviani, G., Otto, S., Overbeck, G.E., Ozinga, W.A., Pahl, A.T., Paine, C.E.T., Pakeman, R.J., Papageorgiou, A.C., Parfionova, E., Pärtel, M., Patacca, M., Paula, S., Paule, J., Pauli, H., Pausas, J.G., Peco, B., Penuelas, J., Perea, A., Peri, P.L., Petisco‐Souza, A.C., Petraglia, A., Petritan, A.M., Phillips, O.L., Pierce, S., Pillar, V.D., Pisek, J., Pomogaybin, A., Poorter, H., Portsmuth, A., Poschlod, P., Potvin, C., Pounds, D., Powell, A.S., Power, S.A., Prinzing, A., Puglielli, G., Pyšek, P., Raevel, V., Rammig, A., Ransijn, J., Ray, C.A., Reich, P.B., Reichstein, M., Reid, D.E. B., Réjou‐Méchain, M., Dios, V.R., Ribeiro, S., Richardson, S., Riibak, K., Rillig, M.C., Riviera, F., Robert, E.M.R., Roberts, S., Robroek, B., Roddy, A., Rodrigues, A.V., Rogers, A., Rollinson, E., Rolo, V., Römermann, C., Ronzhina, D., Roscher, C., Rosell, J.A., Rosenfield, M.F., Rossi, C., Roy, D.B., Royer‐Tardif, S., Rüger, N., Ruiz‐Peinado, R., Rumpf, S.B., Rusch, G.M., Ryo, M., Sack, L., Saldaña, A., Salgado‐Negret, B., Salguero‐Gomez, R., Santa‐Regina, I., Santacruz‐García, A.C., Santos, J., Sardans, J., Schamp, B., Scherer‐Lorenzen, M., Schleuning, M., Schmid, B., Schmidt, M., Schmitt, S., Schneider, J.V., Schowanek, S.D., Schrader, J., Schrodt, F., Schuldt, B., Schurr, F., Selaya Garvizu, G., Semchenko, M., Seymour, C., Sfair, J.C., Sharpe, J.M., Sheppard, C.S., Sheremetiev, S., Shiodera, S., Shipley, B., Shovon, T.A., Siebenkäs, A., Sierra, C., Silva, V., Silva, M., Sitzia, T., Sjöman, H., Slot, M., Smith, N.G., Sodhi, D., Soltis, P., Soltis, D., Somers, B., Sonnier, G., Sørensen, M.V., Sosinski, E.E., Soudzilovskaia, N.A., Souza, A.F., Spasojevic, M., Sperandii, M.G., Stan, A.B., Stegen, J., Steinbauer, K., Stephan, J.G., Sterck, F., Stojanovic, D.B., Strydom, T., Suarez, M.L., Svenning, J‐C, Svitková, I., Svitok, M., Svoboda, M., Swaine, E., Swenson, N., Tabarelli, M., Takagi, K., Tappeiner, U., Tarifa, R., Tauugourdeau, S., Tavsanoglu, C., Beest, M., Tedersoo, L., Thiffault, N., Thom, D., Thomas, E., Thompson, K., Thornton, P.E., Thuiller, W., Tichý, L., Tissue, D., Tjoelker, M.G., Tng, D.Y.P., Tobias, J., Török, P., Tarin, T., Torres‐Ruiz, J.M., Tóthmérész, B., Treurnicht, M., Trivellone, V., Trolliet, F., Trotsiuk, V., Tsakalos, J.L., Tsiripidis, I., Tysklind, N., Umehara, T., Usoltsev, V., Vadeboncoeur, M., Vaezi, J., Valladares, F., Vamosi, J., Bodegom, P.M., Breugel, M., Van Cleemput, E., Weg, M., Merwe, S., Plas, F., Sande, M.T., Kleunen, M., Van Meerbeek, K., Vanderwel, M., Vanselow, K.A., Vårhammar, A., Varone, L., Vasquez Valderrama, M.Y., Vassilev, K., Vellend, M., Veneklaas, E.J., Verbeeck, H., Verheyen, K., Vibrans, A., Vieira, I., Villacís, J., Violle, C., Vivek, P., Wagner, K., Waldram, M., Waldron, A., Walker, A.P., Waller, M., Walther, G., Wang, H., Wang, F., Wang, W., Watkins, H., Watkins, J., Weber, U., Weedon, J.T., Wei, L., Weigelt, P., Weiher, E., Wells, A.W., Wellstein, C., Wenk, E., Westoby, M., Westwood, A., White, P.J., Whitten, M., Williams, M., Winkler, D.E., Winter, K., Womack, C., Wright, I.J., Wright, S.J., Wright, J., Pinho, B.X., Ximenes, F., Yamada, T., Yamaji, K., Yanai, R., Yankov, N., Yguel, B., Zanini, K.J., Zanne, A.E., Zelený, D., Zhao, Y‐P, Zheng, J., Ziemińska, K., Zirbel, C.R., Zizka, G., Zo‐Bi, I.C., Zotz, G., Wirth, C., Kattge, J., Bönisch, G., Díaz, S., Lavorel, S., Prentice, I.C., Leadley, P., Tautenhahn, S., Werner, G.D.A., Aakala, T., Abedi, M., Acosta, A.T.R., Adamidis, G.C., Adamson, K., Aiba, M., Albert, C.H., Alcántara, J.M., Alcázar, C.C., Aleixo, I., Ali, H., Amiaud, B., Ammer, C., Amoroso, M.M., Anand, M., Anderson, C., Anten, N., Antos, J., Apgaua, D.M.G., Ashman, T‐L, Asmara, D.H., Asner, G.P., Aspinwall, M., Atkin, O., Aubin, I., Baastrup‐Spohr, L., Bahalkeh, K., Bahn, M., Baker, T., Baker, W.J., Bakker, J.P., Baldocchi, D., Baltzer, J., Banerjee, A., Baranger, A., Barlow, J., Barneche, D.R., Baruch, Z., Bastianelli, D., Battles, J., Bauerle, W., Bauters, M., Bazzato, E., Beckmann, M., Beeckman, H., Beierkuhnlein, C., Bekker, R., Belfry, G., Belluau, M., Beloiu, M., Benavides, R., Benomar, L., Berdugo‐Lattke, M.L., Berenguer, E., Bergamin, R., Bergmann, J., Bergmann Carlucci, M., Berner, L., Bernhardt‐Römermann, M., Bigler, C., Bjorkman, A.D., Blackman, C., Blanco, C., Blonder, B., Blumenthal, D., Bocanegra‐González, K.T., Boeckx, P., Bohlman, S., Böhning‐Gaese, K., Boisvert‐Marsh, L., Bond, W., Bond‐Lamberty, B., Boom, A., Boonman, C.C.F., Bordin, K., Boughton, E.H., Boukili, V., Bowman, D.M.J.S., Bravo, S., Brendel, M.R., Broadley, M.R., Brown, K.A., Bruelheide, H., Brumnich, F., Bruun, H.H., Bruy, D., Buchanan, S.W., Bucher, S.F., Buchmann, N., Buitenwerf, R., Bunker, D.E., Bürger, J., Burrascano, S., Burslem, D.F.R.P., Butterfield, B.J., Byun, C., Marques, M., Scalon, M.C., Caccianiga, M., Cadotte, M., Cailleret, M., Camac, J., Camarero, J.J., Campany, C., Campetella, G., Campos, J.A., Cano‐Arboleda, L., Canullo, R., Carbognani, M., Carvalho, F., Casanoves, F., Castagneyrol, B., Catford, J.A., Cavender‐Bares, J., Cerabolini, B.E.L., Cervellini, M., Chacón‐Madrigal, E., Chapin, K., Chapin, F.S., Chelli, S., Chen, S‐C, Chen, A., Cherubini, P., Chianucci, F., Choat, B., Chung, K‐S, Chytrý, M., Ciccarelli, D., Coll, L., Collins, C.G., Conti, L., Coomes, D., Cornelissen, J.H.C., Cornwell, W.K., Corona, P., Coyea, M., Craine, J., Craven, D., Cromsigt, J.P.G.M., Csecserits, A., Cufar, K., Cuntz, M., Silva, A.C., Dahlin, K.M., Dainese, M., Dalke, I., Dalle Fratte, M., Dang‐Le, A.T., Danihelka, J., Dannoura, M., Dawson, S., Beer, A.J., De Frutos, A., De Long, J.R., Dechant, B., Delagrange, S., Delpierre, N., Derroire, G., Dias, A.S., Diaz‐Toribio, M.H., Dimitrakopoulos, P.G., Dobrowolski, M., Doktor, D., Dřevojan, P., Dong, N., Dransfield, J., Dressler, S., Duarte, L., Ducouret, E., Dullinger, S., Durka, W., Duursma, R., Dymova, O., E‐Vojtkó, A., Eckstein, R.L., Ejtehadi, H., Elser, J., Emilio, T., Engemann, K., Erfanian, M.B., Erfmeier, A., Esquivel‐Muelbert, A., Esser, G., Estiarte, M., Domingues, T.F., Fagan, W.F., Fagúndez, J., Falster, D.S., Fan, Y., Fang, J., Farris, E., Fazlioglu, F., Feng, Y., Fernandez‐Mendez, F., Ferrara, C., Ferreira, J., Fidelis, A., Finegan, B., Firn, J., Flowers, T.J., Flynn, D.F.B., Fontana, V., Forey, E., Forgiarini, C., François, L., Frangipani, M., Frank, D., Frenette‐Dussault, C., Freschet, G.T., Fry, E.L., Fyllas, N.M., Mazzochini, G.G., Gachet, S., Gallagher, R., Ganade, G., Ganga, F., García‐Palacios, P., Gargaglione, V., Garnier, E., Garrido, J.L., Gasper, A.L., Gea‐Izquierdo, G., Gibson, D., Gillison, A.N., Giroldo, A., Glasenhardt, M‐C, Gleason, S., Gliesch, M., Goldberg, E., Göldel, B., Gonzalez‐Akre, E., Gonzalez‐Andujar, J.L., González‐Melo, A., González‐Robles, A., Graae, B.J., Granda, E., Graves, S., Green, W.A., Gregor, T., Gross, N., Guerin, G.R., Günther, A., Gutiérrez, A.G., Haddock, L., Haines, A., Hall, J., Hambuckers, A., Han, W., Harrison, S.P., Hattingh, W., Hawes, J.E., He, T., He, P., Heberling, J.M., Helm, A., Hempel, S., Hentschel, J., Hérault, B., Hereş, A‐M, Herz, K., Heuertz, M., Hickler, T., Hietz, P., Higuchi, P., Hipp, A.L., Hirons, A., Hock, M., Hogan, J.A., Holl, K., Honnay, O., Hornstein, D., Hou, E., Hough‐Snee, N., Hovstad, K.A., Ichie, T., Igić, B., Illa, E., Isaac, M., Ishihara, M., Ivanov, L., Ivanova, L., Iversen, C.M., Izquierdo, J., Jackson, R.B., Jackson, B., Jactel, H., Jagodzinski, A.M., Jandt, U., Jansen, S., Jenkins, T., Jentsch, A., Jespersen, J.R.P., Jiang, G‐F, Johansen, J.L., Johnson, D., Jokela, E.J., Joly, C.A., Jordan, G.J., Joseph, G.S., Junaedi, D., Junker, R.R., Justes, E., Kabzems, R., Kane, J., Kaplan, Z., Kattenborn, T., Kavelenova, L., Kearsley, E., Kempel, A., Kenzo, T., Kerkhoff, A., Khalil, M.I., Kinlock, N.L., Kissling, W.D., Kitajima, K., Kitzberger, T., Kjøller, R., Klein, T., Kleyer, M., Klimešová, J., Klipel, J., Kloeppel, B., Klotz, S., Knops, J.M.H., Kohyama, T., Koike, F., Kollmann, J., Komac, B., Komatsu, K., König, C., Kraft, N.J.B., Kramer, K.., Kreft, H., Kühn, I., Kumarathunge, D., Kuppler, J., Kurokawa, H., Kurosawa, Y., Kuyah, S., Laclau, J‐P, Lafleur, B., Lallai, E., Lamb, E., Lamprecht, A., Larkin, D.J., Laughlin, D., Le Bagousse‐Pinguet, Y., Maire, G., Roux, P.C., Roux, E., Lee, T., Lens, F., Lewis, S.L., Lhotsky, B., Li, Y., Li, X., Lichstein, J.W., Liebergesell, M., Lim, J.Y., Lin, Y‐S, Linares, J.C., Liu, C., Liu, D., Liu, U., Livingstone, S., Llusià, J., Lohbeck, M., López‐García, Á., Lopez‐Gonzalez, G., Lososová, Z., Louault, F., Lukács, B.A., Lukeš, P., Luo, Y.J., Lussu, M., Ma, S., Maciel Rabelo Pereira, C., Mack, M., Maire, V., Mäkelä, A., Mäkinen, H., Malhado, A.C.M., Mallik, A., Manning, P., Manzoni, S., Marchetti, Z., Marchino, L., Marcilio‐Silva, V., Marcon, E., Marignani, M., Markesteijn, L., Martin, A., Martínez‐Garza, C., Martínez‐Vilalta, J., Mašková, T., Mason, K., Mason, N., Massad, T.J., Masse, J., Mayrose, I., McCarthy, J., McCormack, M.L., McCulloh, K., McFadden, I.R., McGill, B.J., McPartland, M.Y., Medeiros, J.S., Medlyn, B., Meerts, P., Mehrabi, Z., Meir, P., Melo, F.P.L., Mencuccini, M., Meredieu, C., Messier, J., Mészáros, I., Metsaranta, J., Michaletz, S.T., Michelaki, C., Migalina, S., Milla, R., Miller, J.E.D., Minden, V., Ming, R., Mokany, K., Moles, A.T., Molnár, A., Molofsky, J., Molz, M., Montgomery, R.A., Monty, A., Moravcová, L., Moreno‐Martínez, A., Moretti, M., Mori, A.S., Mori, S., Morris, D., Morrison, J., Mucina, L., Mueller, S., Muir, C.D., Müller, S.C., Munoz, F., Myers‐Smith, I.H., Myster, R.W., Nagano, M., Naidu, S., Narayanan, A., Natesan, B., Negoita, L., Nelson, A.S., Neuschulz, E.L., Ni, J., Niedrist, G., Nieto, J., Niinemets, Ü., Nolan, R., Nottebrock, H., Nouvellon, Y., Novakovskiy, A., Nystuen, K.O., O'Grady, A., O'Hara, K., O'Reilly‐Nugent, A., Oakley, S., Oberhuber, W., Ohtsuka, T., Oliveira, R., Öllerer, K., Olson, M.E., Onipchenko, V., Onoda, Y., Onstein, R.E., Ordonez, J.C., Osada, N., Ostonen, I., Ottaviani, G., Otto, S., Overbeck, G.E., Ozinga, W.A., Pahl, A.T., Paine, C.E.T., Pakeman, R.J., Papageorgiou, A.C., Parfionova, E., Pärtel, M., Patacca, M., Paula, S., Paule, J., Pauli, H., Pausas, J.G., Peco, B., Penuelas, J., Perea, A., Peri, P.L., Petisco‐Souza, A.C., Petraglia, A., Petritan, A.M., Phillips, O.L., Pierce, S., Pillar, V.D., Pisek, J., Pomogaybin, A., Poorter, H., Portsmuth, A., Poschlod, P., Potvin, C., Pounds, D., Powell, A.S., Power, S.A., Prinzing, A., Puglielli, G., Pyšek, P., Raevel, V., Rammig, A., Ransijn, J., Ray, C.A., Reich, P.B., Reichstein, M., Reid, D.E. B., Réjou‐Méchain, M., Dios, V.R., Ribeiro, S., Richardson, S., Riibak, K., Rillig, M.C., Riviera, F., Robert, E.M.R., Roberts, S., Robroek, B., Roddy, A., Rodrigues, A.V., Rogers, A., Rollinson, E., Rolo, V., Römermann, C., Ronzhina, D., Roscher, C., Rosell, J.A., Rosenfield, M.F., Rossi, C., Roy, D.B., Royer‐Tardif, S., Rüger, N., Ruiz‐Peinado, R., Rumpf, S.B., Rusch, G.M., Ryo, M., Sack, L., Saldaña, A., Salgado‐Negret, B., Salguero‐Gomez, R., Santa‐Regina, I., Santacruz‐García, A.C., Santos, J., Sardans, J., Schamp, B., Scherer‐Lorenzen, M., Schleuning, M., Schmid, B., Schmidt, M., Schmitt, S., Schneider, J.V., Schowanek, S.D., Schrader, J., Schrodt, F., Schuldt, B., Schurr, F., Selaya Garvizu, G., Semchenko, M., Seymour, C., Sfair, J.C., Sharpe, J.M., Sheppard, C.S., Sheremetiev, S., Shiodera, S., Shipley, B., Shovon, T.A., Siebenkäs, A., Sierra, C., Silva, V., Silva, M., Sitzia, T., Sjöman, H., Slot, M., Smith, N.G., Sodhi, D., Soltis, P., Soltis, D., Somers, B., Sonnier, G., Sørensen, M.V., Sosinski, E.E., Soudzilovskaia, N.A., Souza, A.F., Spasojevic, M., Sperandii, M.G., Stan, A.B., Stegen, J., Steinbauer, K., Stephan, J.G., Sterck, F., Stojanovic, D.B., Strydom, T., Suarez, M.L., Svenning, J‐C, Svitková, I., Svitok, M., Svoboda, M., Swaine, E., Swenson, N., Tabarelli, M., Takagi, K., Tappeiner, U., Tarifa, R., Tauugourdeau, S., Tavsanoglu, C., Beest, M., Tedersoo, L., Thiffault, N., Thom, D., Thomas, E., Thompson, K., Thornton, P.E., Thuiller, W., Tichý, L., Tissue, D., Tjoelker, M.G., Tng, D.Y.P., Tobias, J., Török, P., Tarin, T., Torres‐Ruiz, J.M., Tóthmérész, B., Treurnicht, M., Trivellone, V., Trolliet, F., Trotsiuk, V., Tsakalos, J.L., Tsiripidis, I., Tysklind, N., Umehara, T., Usoltsev, V., Vadeboncoeur, M., Vaezi, J., Valladares, F., Vamosi, J., Bodegom, P.M., Breugel, M., Van Cleemput, E., Weg, M., Merwe, S., Plas, F., Sande, M.T., Kleunen, M., Van Meerbeek, K., Vanderwel, M., Vanselow, K.A., Vårhammar, A., Varone, L., Vasquez Valderrama, M.Y., Vassilev, K., Vellend, M., Veneklaas, E.J., Verbeeck, H., Verheyen, K., Vibrans, A., Vieira, I., Villacís, J., Violle, C., Vivek, P., Wagner, K., Waldram, M., Waldron, A., Walker, A.P., Waller, M., Walther, G., Wang, H., Wang, F., Wang, W., Watkins, H., Watkins, J., Weber, U., Weedon, J.T., Wei, L., Weigelt, P., Weiher, E., Wells, A.W., Wellstein, C., Wenk, E., Westoby, M., Westwood, A., White, P.J., Whitten, M., Williams, M., Winkler, D.E., Winter, K., Womack, C., Wright, I.J., Wright, S.J., Wright, J., Pinho, B.X., Ximenes, F., Yamada, T., Yamaji, K., Yanai, R., Yankov, N., Yguel, B., Zanini, K.J., Zanne, A.E., Zelený, D., Zhao, Y‐P, Zheng, J., Ziemińska, K., Zirbel, C.R., Zizka, G., Zo‐Bi, I.C., Zotz, G., and Wirth, C.

Abstract

Plant traits—the morphological, anatomical, physiological, biochemical and phenological characteristics of plants—determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait‐based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits—almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.

Published
2020

13. Two truncating variants in FANCC and breast cancer risk

Author

Dork, T., Peterlongo, P., Mannermaa, A., Bolla, M.K., Wang, Q., Dennis, J., Ahearn, T., Andrulis, I.L., Anton-Culver, H., Arndt, V., Aronson, K.J., Augustinsson, A., Freeman, L.E.B., Beckmann, M.W., Beeghly-Fadiel, A., Behrens, S., Bermisheva, M., Blomqvist, C., Bogdanova, N., Bojesen, S.E., Brauch, H., Brenner, H., Burwinkel, B., Canzian, F., Chan, T.L., Chang-Claude, J., Chanock, S.J., Choi, J.Y., Christiansen, H., Clarke, C.L., Couch, F.J., Czene, K., Daly, M.B., dos-Santos-Silva, I., Dwek, M., Eccles, D.M., Ekici, A.B., Eriksson, M., Evans, D.G., Fasching, P.A., Figueroa, J., Flyger, H., Fritschisl, L., Gabrielson, M., Gago-Dominguez, M., Gao, C., Gapstur, S.M., Garcia-Closas, M., Garcia-Saenz, J.A., Gaudet, M.M., Giles, G.G., Goldberg, M.S., Goldgar, D.E., Guenel, P., Haeberle, L., Haiman, C.A., Hakansson, N., Hall, P., Hamann, U., Hartman, M., Hauke, J., Hein, A., Hillemanns, P., Hogervorst, F.B.L., Hooning, M.J., Hopper, J.L., Howell, T., Huo, D.Z., Ito, H., Iwasaki, M., Jakubowska, A., Janni, W., John, E.M., Jung, A., Kaaks, R., Kang, D., Kapoor, P.M., Khusnutdinova, E., Kim, S.W., Kitahara, C.M., Koutros, S., Kraft, P., Kristensen, V.N., Kwon, A., Lambrechts, D., Marchand, L. le, Li, J.M., Lindstrom, S., Linet, M., W.Y. lo, Long, J.R., Lophatananon, A., Lubinski, J., Manoochehri, M., Manoukian, S., Margolin, S., Martinez, E., Matsuo, K., Mavroudis, D., Meindl, A., Menon, U., Milne, R.L., Taib, N.A.M., Muir, K., Mulligan, A.M., Neuhausen, S.L., Nevanlinna, H., Neven, P., Newman, W.G., Offit, K., Olopade, O.I., Olshan, A.F., Olson, J.E., Olsson, H., Park, S.K., Park-Simon, T.W., Peto, J., Plaseska-Karanfilska, D., Pohl-Rescigno, E., Presneau, N., Rack, B., Radice, P., Rashid, M.U., Rennert, G., Rennert, H.S., Romero, A., Ruebner, M., Saloustros, E., Schmidt, M.K., Schmutzler, R.K., Schneider, M.O., Schoemaker, M.J., Scott, C., Shen, C.Y., Shu, X.O., Simard, J., Slager, S., Smichkoska, S., Southey, M.C., Spinelli, J.J., Stone, J., Surowy, H., Swerdlow, A.J., Tamimi, R.M., Tapper, W.J., Teo, S.H., Terry, M.B., Toland, A.E., Tollenaar, R.A.E.M., Torres, D., Torres-Mejia, G., Troester, M.A., Truong, T., Tsugane, S., Untch, M., Vachon, C.M., Ouweland, A.M.W. van den, Veen, E.M. van, Vijai, J., Wendt, C., Wolk, A., Yu, J.C., Zheng, W., Ziogas, A., Ziv, E., Dunning, A.M., Pharoah, P.D.P., Schindler, D., Devilee, P., Easton, D.F., Balleine, R., Baxter, R., Braye, S., Carpenter, J., Dahlstrom, J., Forbes, J., Lee, C.S., Marsh, D., Morey, A., Pathmanathan, N., Scott, R., Simpson, P., Spigelman, A., Wilcken, N., Yip, D., Zeps, N., Borresen-Dale, A.L., Alnaes, G.I.G., Sahlberg, K.K., Ottestad, L., Karesen, R., Schlichting, E., Holmen, M.M., Sauer, T., Haakensen, V., Engebraten, O., Naume, B., Fossa, A., Kiserud, C.E., Reinertsen, K.V., Helland, A., Riis, M., Geisler, J., ABCTB Investigators, NBCS Collaborators, Andrulis, Irene L [0000-0002-4226-6435], Arndt, Volker [0000-0001-9320-8684], Brauch, Hiltrud [0000-0001-7531-2736], Dwek, Miriam [0000-0001-7184-2932], Ekici, Arif B [0000-0001-6099-7066], Fasching, Peter A [0000-0003-4885-8471], Figueroa, Jonine [0000-0002-5100-623X], Hein, Alexander [0000-0003-2601-3398], Ito, Hidemi [0000-0002-8023-4581], Matsuo, Keitaro [0000-0003-1761-6314], Menon, Usha [0000-0003-3708-1732], Milne, Roger L [0000-0001-5764-7268], Muir, Kenneth [0000-0001-6429-988X], Nevanlinna, Heli [0000-0002-0916-2976], Newman, William G [0000-0002-6382-4678], Peto, Julian [0000-0002-1685-8912], Rennert, Gad [0000-0002-8512-068X], Romero, Atocha [0000-0002-1634-7397], Schmidt, Marjanka K [0000-0002-2228-429X], Scott, Christopher [0000-0003-1340-0647], Stone, Jennifer [0000-0001-5077-0124], Truong, Thérèse [0000-0002-2943-6786], Tsugane, Shoichiro [0000-0003-4105-2774], Ziogas, Argyrios [0000-0003-4529-3727], Dunning, Alison M [0000-0001-6651-7166], Pharoah, Paul DP [0000-0001-8494-732X], Devilee, Peter [0000-0002-8023-2009], Easton, Douglas F [0000-0003-2444-3247], Apollo - University of Cambridge Repository, Andrulis, Irene L. [0000-0002-4226-6435], Ekici, Arif B. [0000-0001-6099-7066], Fasching, Peter A. [0000-0003-4885-8471], Milne, Roger L. [0000-0001-5764-7268], Newman, William G. [0000-0002-6382-4678], Schmidt, Marjanka K. [0000-0002-2228-429X], Dunning, Alison M. [0000-0001-6651-7166], Pharoah, Paul D. P. [0000-0001-8494-732X], Easton, Douglas F. [0000-0003-2444-3247], HUS Comprehensive Cancer Center, Clinicum, University Management, Department of Oncology, University of Helsinki, Department of Obstetrics and Gynecology, HUS Gynecology and Obstetrics, Medical Oncology, and Clinical Genetics

Subjects
0301 basic medicine, Oncology, PROTEIN, lcsh:Medicine, 45/47, 0302 clinical medicine, Fanconi anemia, Genotype, lcsh:Science, Sequence Deletion, Multidisciplinary, BRCA1 Protein, Fanconi Anemia Complementation Group C Protein, 1184 Genetics, developmental biology, physiology, BRCA2 Protein, 3. Good health, BIALLELIC MUTATIONS, DNA-REPAIR, Female, 692/499, Medical Genetics, medicine.medical_specialty, PALB2, 3122 Cancers, ABCTB Investigators, Breast Neoplasms, FANCONIS ANEMIA, Article, 692/4028, NBCS Collaborators, 03 medical and health sciences, Breast cancer, SDG 3 - Good Health and Well-being, Internal medicine, medicine, Humans, NONSENSE MUTATION, Genetic Predisposition to Disease, Medicinsk genetik, 45, business.industry, Genetic heterogeneity, lcsh:R, Case-control study, Genetic Variation, Odds ratio, medicine.disease, GENE, Fanconi Anemia, 030104 developmental biology, Risk factors, Case-Control Studies, lcsh:Q, 3111 Biomedicine, business, 030217 neurology & neurosurgery
Abstract

Fanconi anemia (FA) is a genetically heterogeneous disorder with 22 disease-causing genes reported to date. In some FA genes, monoallelic mutations have been found to be associated with breast cancer risk, while the risk associations of others remain unknown. The gene for FA type C, FANCC, has been proposed as a breast cancer susceptibility gene based on epidemiological and sequencing studies. We used the Oncoarray project to genotype two truncating FANCC variants (p.R185X and p.R548X) in 64,760 breast cancer cases and 49,793 controls of European descent. FANCC mutations were observed in 25 cases (14 with p.R185X, 11 with p.R548X) and 26 controls (18 with p.R185X, 8 with p.R548X). There was no evidence of an association with the risk of breast cancer, neither overall (odds ratio 0.77, 95%CI 0.44–1.33, p = 0.4) nor by histology, hormone receptor status, age or family history. We conclude that the breast cancer risk association of these two FANCC variants, if any, is much smaller than for BRCA1, BRCA2 or PALB2 mutations. If this applies to all truncating variants in FANCC it would suggest there are differences between FA genes in their roles on breast cancer risk and demonstrates the merit of large consortia for clarifying risk associations of rare variants.

Published
2019

14. Drought soil legacy overrides maternal effects on plant growth

Author

De Long, J.R., Semchenko, M., Pritchard, W.J., Cordero, I., Fry, E.L., Jackson, B.G., Kurnosova, K., Ostle, N.J., Johnson, D., Baggs, E.M., Bardgett, R.D., De Long, J.R., Semchenko, M., Pritchard, W.J., Cordero, I., Fry, E.L., Jackson, B.G., Kurnosova, K., Ostle, N.J., Johnson, D., Baggs, E.M., and Bardgett, R.D.

Abstract

Maternal effects (i.e. trans‐generational plasticity) and soil legacies generated by drought and plant diversity can affect plant performance and alter nutrient cycling and plant community dynamics. However, the relative importance and combined effects of these factors on plant growth dynamics remain poorly understood. We used soil and seeds from an existing plant diversity and drought manipulation field experiment in temperate grassland to test maternal, soil drought and diversity legacy effects, and their interactions, on offspring plant performance of two grassland species (Alopecurus pratensis and Holcus lanatus) under contrasting glasshouse conditions. Our results showed that drought soil legacy effects eclipsed maternal effects on plant biomass. Drought soil legacy effects were attributed to changes in both abiotic (i.e. nutrient availability) and biotic soil properties (i.e. microbial carbon and enzyme activity), as well as plant root and shoot atom 15N excess. Further, plant tissue nutrient concentrations and soil microbial C:N responses to drought legacies varied between the two plant species and soils from high and low plant diversity treatments. However, these diversity effects did not affect plant root or shoot biomass. These findings demonstrate that while maternal effects resulting from drought occur in grasslands, their impacts on plant performance are likely minor relative to drought legacy effects on soil abiotic and biotic properties. This suggests that soil drought legacy effects could become increasingly important drivers of plant community dynamics and ecosystem functioning as extreme weather events become more frequent and intense with climate change.

Published
2019

15. Molecular dynamics and magic angle spinning NMR

Author

Long, J.R., Sun, B.Q., Bowen, A., and Griffin, R.G.

Subjects
Molecular dynamics -- Research, Nuclear magnetic resonance spectroscopy -- Research, Chemistry
Abstract

Deuterium NMR line shape experiments and molecular dynamics simulations help evaluate the influence of temperature on the rate of 3-fold hopping of the ammonium group in L-alanine. Theoretical studies and use of two techniques, continuous wave proton decoupling and multiple phase homonuclear decoupling, confirm that a decoupling field-induced coherent spin motion interferes with the incoherent hoping of the protons of the ammonium group. When the rate of 3-fold hopping is similar to the cycle time of the multiple pulse trains or the reciprocal of the decoupling field, the interference induces significant broadening of NMR lines.

Published
1994

16. Evidence that breast cancer risk at the 2q35 locus is mediated through IGFBP5 regulation (vol 5, 4999, 2014)

Author

Ghoussaini, M., Edwards, S.L., Michailidou, K., Nord, S., Lari, R.C.S., Desai, K., Kar, S., Hillman, K.M., Kaufmann, S., Glubb, D.M., Beesley, J., Dennis, J., Bolla, M.K., Wang, Q., Dicks, E., Guo, Q., Schmidt, M.K., Shah, M., Luben, R., Brown, J., Czene, K., Darabi, H., Eriksson, M., Klevebring, D., Bojesen, S.E., Nordestgaard, B.G., Nielsen, S.F., Flyger, H., Lambrechts, D., Thienpont, B., Neven, P., Wildiers, H., Broeks, A., Van't Veer, L.J., Rutgers, E.J.T., Couch, F.J., Olson, J.E., Hallberg, E., Vachon, C., Chang-Claude, J., Rudolph, A., Seibold, P., Flesch-Janys, D., Peto, J., dos-Santos-Silva, I., Gibson, L., Nevanlinna, H., Muranen, T.A., Aittomaki, K., Blomqvist, C., Hall, P., Li, J.M., Liu, J.J., Humphreys, K., Kang, D., Choi, J.Y., Park, S.K., Noh, D.Y., Matsuo, K., Ito, H., Iwata, H., Yatabe, Y., Guenel, P., Truong, T., Menegaux, F., Sanchez, M., Burwinkel, B., Marme, F., Schneeweiss, A., Sohn, C., Wu, A.H., Tseng, C.C., Berg, D. van den, Stram, D.O., Benitez, J., Zamora, M., Perez, J.I.A., Menendez, P., Shu, X.O., Lu, W., Gao, Y.T., Cai, Q.Y., Cox, A., Cross, S.S., Reed, M.W.R., Andrulis, I.L., Knight, J.A., Glendon, G., Tchatchou, S., Sawyer, E.J., Tomlinson, I., Kerin, M.J., Miller, N., Haiman, C.A., Henderson, B.E., Schumacher, F., Marchand, L. le, Lindblom, A., Margolin, S., Teo, S.H., Yip, C.H., Lee, D.S.C., Wong, T.Y., Hooning, M.J., Martens, J.W.M., Collee, J.M., Deurzen, C.H.M. van, Hopper, J.L., Southey, M.C., Tsimiklis, H., Kapuscinski, M.K., Shen, C.Y., Wu, P.E., Yu, J.C., Chen, S.T., Alnaes, G.G., Borresen-Dale, A.L., Giles, G.G., Milne, R.L., McLean, C., Muir, K., Lophatananon, A., Stewart-Brown, S., Siriwanarangsan, P., Hartman, M., Miao, H., Buhari, S.A.B.S., Teo, Y.Y., Fasching, P.A., Haeberle, L., Ekici, A.B., Beckmann, M.W., Brenner, H., Dieffenbach, A.K., Arndt, V., Stegmaier, C., Swerdlow, A., Ashworth, A., Orr, N., Schoemaker, M.J., Garcia-Closas, M., Figueroa, J., Chanock, S.J., Lissowska, J., Simard, J., Goldberg, M.S., Labreche, F., Dumont, M., Winqvist, R., Pylkas, K., Jukkola-Vuorinen, A., Brauch, H., Bruning, T., Koto, Y.D., Radice, P., Peterlongo, P., Bonanni, B., Volorio, S., Dork, T., Bogdanova, N.V., Helbig, S., Mannermaa, A., Kataja, V., Kosma, V.M., Hartikainen, J.M., Devilee, P., Tollenaar, R.A.E.M., Seynaeve, C., Asperen, C.J. van, Jakubowska, A., Lubinski, J., Jaworska-Bieniek, K., Durda, K., Slager, S., Toland, A.E., Ambrosone, C.B., Yannoukakos, D., Sangrajrang, S., Gaborieau, V., Brennan, P., Mckay, J., Hamann, U., Torres, D., Zheng, W., Long, J.R., Anton-Culver, H., Neuhausen, S.L., Luccarini, C., Baynes, C., Ahmed, S., Maranian, M., Healey, C.S., Gonzalez-Neira, A., Pita, G., Alonso, M.R., Alvarez, N., Herrero, D., Tessier, D.C., Vincent, D., Bacot, F., Santiago, I. de, Carroll, J., Caldas, C., Brown, M.A., Lupien, M., Kristensen, V.N., Pharoah, P.D.P., Chenevix-Trench, G., French, J.D., Easton, D.F., Dunning, A.M., and Australian Ovarian Canc Management

Published
2018

18. Fungal diversity regulates plant-soil feedbacks in temperate grassland

Author

Semchenko, M., Leff, J.W., Lozano, Y.M., Saar, S., Davison, J., Wilkinson, A., Jackson, B.G., Pritchard, W.J., De Long, J.R., Oakley, S., Mason, K.E., Ostle, N.J., Baggs, E.M., Johnson, D., Fierer, N., Bardgett, R.D., Semchenko, M., Leff, J.W., Lozano, Y.M., Saar, S., Davison, J., Wilkinson, A., Jackson, B.G., Pritchard, W.J., De Long, J.R., Oakley, S., Mason, K.E., Ostle, N.J., Baggs, E.M., Johnson, D., Fierer, N., and Bardgett, R.D.

Abstract

Feedbacks between plants and soil microbial communities play an important role in vegetation dynamics, but the underlying mechanisms remain unresolved. Here, we show that the diversity of putative pathogenic, mycorrhizal, and saprotrophic fungi is a primary regulator of plant-soil feedbacks across a broad range of temperate grassland plant species. We show that plant species with resource-acquisitive traits, such as high shoot nitrogen concentrations and thin roots, attract diverse communities of putative fungal pathogens and specialist saprotrophs, and a lower diversity of mycorrhizal fungi, resulting in strong plant growth suppression on soil occupied by the same species. Moreover, soil properties modulate feedbacks with fertile soils, promoting antagonistic relationships between soil fungi and plants. This study advances our capacity to predict plant-soil feedbacks and vegetation dynamics by revealing fundamental links between soil properties, plant resource acquisition strategies, and the diversity of fungal guilds in soil. Copyright © 2018 The Authors, some rights reserved.

Published
2018

19. Genetic variation in mitotic regulatory pathway genes is associated with breast tumor grade

Author

Purrington, K.S., Slettedahl, S., Bolla, M.K., Michailidou, K., Czene, K., Nevanlinna, H., Bojesen, S.E., Andrulis, I.L., Cox, A., Hall, P., Carpenter, J., Yannoukakos, D., Haiman, C.A., Fasching, P.A., Mannermaa, A., Winqvist, R., Brenner, H., Lindblom, A., Chenevix-Trench, G., Benitez, J., Swerdlow, A., Kristensen, V., Guenel, P., Meindl, A., Darabi, H., Eriksson, M., Fagerholm, R., Aittomaki, K., Blomqvist, C., Nordestgaard, B.G., Nielsen, S.F., Flyger, H., Wang, X.S., Olswold, C., Olson, J.E., Mulligan, A.M., Knight, J.A., Tchatchou, S., Reed, M.W.R., Cross, S.S., Liu, J.J., Li, J.M., Humphreys, K., Clarke, C., Scott, R., Fostira, F., Fountzilas, G., Konstantopoulou, I., Henderson, B.E., Schumacher, F., Marchand, L. le, Ekici, A.B., Hartmann, A., Beckmann, M.W., Hartikainen, J.M., Kosma, V.M., Kataja, V., Jukkola-Vuorinen, A., Pylkas, K., Kauppila, S., Dieffenbach, A.K., Stegmaier, C., Arndt, V., Margolin, S., Balleine, R., Perez, J.I.A., Zamora, M.P., Menendez, P., Ashworth, A., Jones, M., Orr, N., Arveux, P., Kerbrat, P., Truong, T., Bugert, P., Toland, A.E., Ambrosone, C.B., Labreche, F., Goldberg, M.S., Dumont, M., Ziogas, A., Lee, E., Dite, G.S., Apicella, C., Southey, M.C., Long, J.R., Shrubsole, M., Deming-Halverson, S., Ficarazzi, F., Barile, M., Peterlongo, P., Durda, K., Jaworska-Bieniek, K., Tollenaar, R.A.E.M., Seynaeve, C., Bruning, T., Ko, Y.D., Deurzen, C.H.M. van, Martens, J.W.M., Kriege, M., Figueroa, J.D., Chanock, S.J., Lissowska, J., Tomlinson, I., Kerin, M.J., Miller, N., Schneeweiss, A., Tapper, W.J., Gerty, S.M., Durcan, L., Mclean, C., Milne, R.L., Baglietto, L., Silva, I.D., Fletcher, O., Johnson, N., Van'T Veer, L.J., Cornelissen, S., Forsti, A., Torres, D., Rudiger, T., Rudolph, A., Flesch-Janys, D., Nickels, S., Weltens, C., Floris, G., Moisse, M., Dennis, J., Wang, Q., Dunning, A.M., Shah, M., Brown, J., Simard, J., Anton-Culver, H., Neuhausen, S.L., Hopper, J.L., Bogdanova, N., Dork, T., Zheng, W., Radice, P., Jakubowska, A., Lubinski, J., Devillee, P., Brauch, H., Hooning, M., Garcia-Closas, M., Sawyer, E., Burwinkel, B., Marmee, F., Eccles, D.M., Giles, G.G., Peto, J., Schmidt, M., Broeks, A., Hamann, U., Chang-Claude, J., Lambrechts, D., Pharoah, P.D.P., Easton, D., Pankratz, V.S., Slager, S., Vachon, C.M., Couch, F.J., ABCTB Investigators, Australian Ovarian Canc Study Grp, kConFab Investigators, GENICA Network, Medical Oncology, Pathology, and Clinical Genetics

Subjects
Oncology, Candidate gene, Fibroblast Growth Factor, amplification, cancer susceptibility loci, Bioinformatics, medicine.disease_cause, Medical and Health Sciences, prostate-cancer, Prostate cancer, Risk Factors, Medizinische Fakultät, Genetics (clinical), Genetics & Heredity, tacc2, Association Studies Articles, Single Nucleotide, General Medicine, Biological Sciences, ddc, risk loci, cell-division, kConFab Investigators, Female, GENICA Network, Type 2, Receptor, Australian Ovarian Cancer Study Group, Breast Neoplasms, Carrier Proteins, Case-Control Studies, Haplotypes, Humans, Neoplasm Staging, Polymorphism, Single Nucleotide, Receptor, Fibroblast Growth Factor, Type 2, Tumor Suppressor Proteins, Genetic Variation, Molecular Biology, Genetics, medicine.medical_specialty, Mitotic index, ABCTB Investigators, Single-nucleotide polymorphism, Biology, Breast cancer, SDG 3 - Good Health and Well-being, Internal medicine, medicine, ddc:610, Polymorphism, Lung cancer, Odds ratio, medicine.disease, genome-wide association, lung-cancer, progression, Carcinogenesis
Abstract

Mitotic index is an important component of histologic grade and has an etiologic role in breast tumorigenesis. Several small candidate gene studies have reported associations between variation in mitotic genes and breast cancer risk. We measured associations between 2156 single nucleotide polymorphisms (SNPs) from 194 mitotic genes and breast cancer risk, overall and by histologic grade, in the Breast Cancer Association Consortium (BCAC) iCOGS study (n = 39 067 cases; n = 42 106 controls). SNPs in TACC2 [rs17550038: odds ratio (OR) = 1.24, 95% confidence interval (CI) 1.16-1.33, P = 4.2 × 10(-10)) and EIF3H (rs799890: OR = 1.07, 95% CI 1.04-1.11, P = 8.7 × 10(-6)) were significantly associated with risk of low-grade breast cancer. The TACC2 signal was retained (rs17550038: OR = 1.15, 95% CI 1.07-1.23, P = 7.9 × 10(-5)) after adjustment for breast cancer risk SNPs in the nearby FGFR2 gene, suggesting that TACC2 is a novel, independent genome-wide significant genetic risk locus for low-grade breast cancer. While no SNPs were individually associated with high-grade disease, a pathway-level gene set analysis showed that variation across the 194 mitotic genes was associated with high-grade breast cancer risk (P = 2.1 × 10(-3)). These observations will provide insight into the contribution of mitotic defects to histological grade and the etiology of breast cancer.

Published
2014

21. A test of the hierarchical model of litter decomposition

Author

Bradford, M.A., Veen, G.F., Bonis, A., Bradford, E.M., Classen, A. T., Cornelissen, J.H.C., Crowther, Thomas W., De Long, J.R., Freschet, G.T., Kardol, P., Manrubia, Marta, Maynard, Daniel S., Newman, G.S., Van Logtestijn, R., Viketoft, Maria, Wardle, David A., Wieder, W.R., Wood, S.A., van der Putten, W.H., Bradford, M.A., Veen, G.F., Bonis, A., Bradford, E.M., Classen, A. T., Cornelissen, J.H.C., Crowther, Thomas W., De Long, J.R., Freschet, G.T., Kardol, P., Manrubia, Marta, Maynard, Daniel S., Newman, G.S., Van Logtestijn, R., Viketoft, Maria, Wardle, David A., Wieder, W.R., Wood, S.A., and van der Putten, W.H.

Abstract

Our basic understanding of plant litter decomposition informs the assumptions underlying widely applied soil biogeochemical models, including those embedded in Earth system models. Confidence in projected carbon cycle–climate feedbacks therefore depends on accurate knowledge about the controls regulating the rate at which plant biomass is decomposed into products such as CO2. Here we test underlying assumptions of the dominant conceptual model of litter decomposition. The model posits that a primary control on the rate of decomposition at regional to global scales is climate (temperature and moisture), with the controlling effects of decomposers negligible at such broad spatial scales. Using a regional-scale litter decomposition experiment at six sites spanning from northern Sweden to southern France—and capturing both within and among site variation in putative controls—we find that contrary to predictions from the hierarchical model, decomposer (microbial) biomass strongly regulates decomposition at regional scales. Furthermore, the size of the microbial biomass dictates the absolute change in decomposition rates with changing climate variables. Our findings suggest the need for revision of the hierarchical model, with decomposers acting as both local- and broad-scale controls on litter decomposition rates, necessitating their explicit consideration in global biogeochemical models.

Published
2017

22. Fine-scale mapping of 8q24 locus identifies multiple independent risk variants for breast cancer

Author

Shi, J.J., Zhang, Y.F., Zheng, W., Michailidou, K., Ghoussaini, M., Bolla, M.K., Wang, Q., Dennis, J., Lush, M., Milne, R.L., Shu, X.O., Beesley, J., Kar, S., Andrulis, I.L., Anton-Culver, H., Arndt, V., Beckmann, M.W., Zhao, Z.G., Guo, X.Y., Benitez, J., Beeghly-Fadiel, A., Blot, W., Bogdanova, N.V., Bojesen, S.E., Brauch, H., Brenner, H., Brinton, L., Broeks, A., Bruening, T., Burwinkel, B., Cai, H., Canisius, S., Chang-Claude, J., Choi, J.Y., Couch, F.J., Cox, A., Cross, S.S., Czene, K., Darabi, H., Devilee, P., Droit, A., Dork, T., Fasching, P.A., Fletcher, O., Flyger, H., Fostira, F., Gaborieau, V., Garcia-Closas, M., Giles, G.G., Grip, M., Guenel, P., Haiman, C.A., Hamann, U., Hartman, M., Miao, H., Hollestelle, A., Hopper, J.L., Hsiung, C.N., Investigators, K., Ito, H., Jakubowska, A., Johnson, N., Torres, D., Kabisch, M., Kang, D., Khan, S., Knight, J.A., Kosma, V.M., Lambrechts, D., Li, J.M., Lindblom, A., Lophatananon, A., Lubinski, J., Mannermaa, A., Manoukian, S., Marchand, L. le, Margolin, S., Marme, F., Matsuo, K., McLean, C., Meindl, A., Muir, K., Neuhausen, S.L., Nevanlinna, H., Nord, S., Borresen-Dale, A.L., Olson, J.E., Orr, N., Ouweland, A.M.W. van den, Peterlongo, P., Putti, T.C., Rudolph, A., Sangrajrang, S., Sawyer, E.J., Schmidt, M.K., Schmutzler, R.K., Shen, C.Y., Hou, M.F., Shrubsole, M.J., Southey, M.C., Swerdlow, A., Teo, S.H., Thienpont, B., Toland, A.E., Tollenaar, R.A.E.M., Tomlinson, I., Truong, T., Tseng, C.C., Wen, W.Q., Winqvist, R., Wu, A.H., Yip, C.H., Zamora, P.M., Zheng, Y., Floris, G., Cheng, C.Y., Hooning, M.J., Martens, J.W.M., Seynaeve, C., Kristensen, V.N., Hall, P., Pharoah, P.D.P., Simard, J., Chenevix-Trench, G., Dunning, A.M., Antoniou, A.C., Easton, D.F., Cai, Q.Y., Long, J.R., Ghoussaini, Maya [0000-0002-2415-2143], Wang, Jean [0000-0002-9139-0627], Dennis, Joe [0000-0003-4591-1214], Pharoah, Paul [0000-0001-8494-732X], Dunning, Alison [0000-0001-6651-7166], Antoniou, Antonis [0000-0001-9223-3116], Easton, Douglas [0000-0003-2444-3247], and Apollo - University of Cambridge Repository

Subjects
breast cancer, fine-mapping, single nucleotide polymorphism, 8q24, genetic susceptibility
Abstract

Previous genome-wide association studies among women of European ancestry identified two independent breast cancer susceptibility loci represented by single nucleotide polymorphisms (SNPs) rs13281615 and rs11780156 at 8q24. A fine-mapping study across 2.06 Mb (chr8:127,561,724-129,624,067, hg19) in 55,540 breast cancer cases and 51,168 controls within the Breast Cancer Association Consortium was conducted. Three additional independent association signals in women of European ancestry, represented by rs35961416 (OR = 0.95, 95% CI = 0.93-0.97, conditional p = 5.8 × 10(-6) ), rs7815245 (OR = 0.94, 95% CI = 0.91-0.96, conditional p = 1.1 × 10(-6) ) and rs2033101 (OR = 1.05, 95% CI = 1.02-1.07, conditional p = 1.1 × 10(-4) ) were found. Integrative analysis using functional genomic data from the Roadmap Epigenomics, the Encyclopedia of DNA Elements project, the Cancer Genome Atlas and other public resources implied that SNPs rs7815245 in Signal 3, and rs1121948 in Signal 5 (in linkage disequilibrium with rs11780156, r(2) = 0.77), were putatively functional variants for two of the five independent association signals. The results highlighted multiple 8q24 variants associated with breast cancer susceptibility in women of European ancestry.

Published
2016

23. Identification and characterization of novel associations in the CASP8/ALS2CR12 region on chromosome 2 with breast cancer risk

Author

Lin, W.Y., Camp, N.J., Ghoussaini, M., Beesley, J., Michailidou, K., Hopper, J.L., Apicella, C., Southey, M.C., Stone, J., Schmidt, M.K., Broeks, A., Van't Veer, L.J., Rutgers, E.J.T., Muir, K., Lophatananon, A., Stewart-Brown, S., Siriwanarangsan, P., Fasching, P.A., Haeberle, L., Ekici, A.B., Beckmann, M.W., Peto, J., Dos-Santos-Silva, I., Fletcher, O., Johnson, N., Bolla, M.K., Wang, Q., Dennis, J., Sawyer, E.J., Cheng, T., Tomlinson, I., Kerin, M.J., Miller, N., Marme, F., Surowy, H.M., Burwinkel, B., Guenel, P., Truong, T., Menegaux, F., Mulot, C., Bojesen, S.E., Nordestgaard, B.G., Nielsen, S.F., Flyger, H., Benitez, J., Zamora, M.P., Perez, J.I.A., Menendez, P., Gonzalez-Neira, A., Pita, G., Alonso, M.R., Alvarez, N., Herrera, D., Anton-Culver, H., Brenner, H., Dieffenbach, A.K., Arndt, V., Stegmaier, C., Meindl, A., Lichtner, P., Schmutzler, R.K., Muller-Myhsok, B., Brauch, H., Bruning, T., Ko, Y.D., Tessier, D.C., Vincent, D., Bacot, F., Nevanlinna, H., Aittomaki, K., Blomqvist, C., Khan, S., Matsuo, K., Ito, H., Iwata, H., Horio, A., Bogdanova, N.V., Antonenkova, N.N., Dork, T., Lindblom, A., Margolin, S., Mannermaa, A., Kataja, V., Kosma, V.M., Hartikainen, J.M., Wu, A.H., Tseng, C.C., Berg, D. van den, Stram, D.O., Neven, P., Wauters, E., Wildiers, H., Lambrechts, D., Chang-Claude, J., Rudolph, A., Seibold, P., Flesch-Janys, D., Radice, P., Peterlongo, P., Manoukian, S., Bonanni, B., Couch, F.J., Wang, X.S., Vachon, C., Purrington, K., Giles, G.G., Milne, R.L., Mclean, C., Haiman, C.A., Henderson, B.E., Schumacher, F., Marchand, L. le, Simard, J., Goldberg, M.S., Labreche, F., Dumont, M., Teo, S.H., Yip, C.H., Hassan, N., Vithana, E.N., Kristensen, V., Zheng, W., Deming-Halverson, S., Shrubsole, M.J., Long, J.R., Winqvist, R., Pylkas, K., Jukkola-Vuorinen, A., Kauppila, S., Andrulis, I.L., Knight, J.A., Glendon, G., Tchatchou, S., Devilee, P., Tollenaar, R.A.E.M., Seynaeve, C., Asperen, C.J. van, Garcia-Closas, M., Figueroa, J., Lissowska, J., Brinton, L., Czene, K., Darabi, H., Eriksson, M., Brand, J.S., Hooning, M.J., Hollestelle, A., Ouweland, A.M.W. van den, Jager, A., Li, J.M., Liu, J.J., Humphreys, K., Shu, X.O., Lu, W., Gao, Y.T., Cai, H., Cross, S.S., Reed, M.W.R., Blot, W., Signorello, L.B., Cai, Q.Y., Pharoah, P.D.P., Perkins, B., Shah, M., Blows, F.M., Kang, D., Yoo, K.Y., Noh, D.Y., Hartman, M., Miao, H., Chia, K.S., Putti, T.C., Hamann, U., Luccarini, C., Baynes, C., Ahmed, S., Maranian, M., Healey, C.S., Jakubowska, A., Lubinski, J., Jaworska-Bieniek, K., Durda, K., Sangrajrang, S., Gaborieau, V., Brennan, P., Mckay, J., Slager, S., Toland, A.E., Yannoukakos, D., Shen, C.Y., Hsiung, C.N., Wu, P.E., Ding, S.L., Ashworth, A., Jones, M., Orr, N., Swerdlow, A.J., Tsimiklis, H., Makalic, E., Schmidt, D.F., Bui, Q.M., Chanock, S.J., Hunter, D.J., Hein, R., Dahmen, N., Beckmann, L., Aaltonen, K., Muranen, T.A., Heikkinen, T., Irwanto, A., Rahman, N., Turnbull, C.A., Waisfisz, Q., Meijers-Heijboer, H.E.J., Adank, M.A., Luijt, R.B. van der, Hall, P., Chenevix-Trench, G., Dunning, A., Easton, D.F., Cox, A., GENICA Network, kConFab Investigators, Australian Ovarian Canc Study Grp, Breast Ovarian Canc Susceptibility, Clinical Genetics, Obstetrics & Gynecology, Medical Oncology, Cardiothoracic Surgery, Cancer Center Amsterdam, Amsterdam Reproduction & Development (AR&D), Human Genetics, Human genetics, CCA - Oncogenesis, Ghoussaini, Maya [0000-0002-2415-2143], Wang, Jean [0000-0002-9139-0627], Dennis, Joe [0000-0003-4591-1214], Pharoah, Paul [0000-0001-8494-732X], Dunning, Alison [0000-0001-6651-7166], Easton, Douglas [0000-0003-2444-3247], and Apollo - University of Cambridge Repository

Subjects
Genotyping Techniques, Research Support, U.S. Gov't, P.H.S, CASP8 and FADD-Like Apoptosis Regulating Protein, Genome-wide association study, P.H.S, Medical and Health Sciences, Breast and Ovarian Cancer Susceptibility (BOCS) Study, Medizinische Fakultät, Genetics(clinical), Non-U.S. Gov't, Genetics (clinical), Genetics, Genetics & Heredity, variants, Caspase 8, Research Support, Non-U.S. Gov't, Association Studies Articles, General Medicine, Biological Sciences, ddc, Chromosomes, Human, Pair 2, kConFab Investigators, Female, GENICA Network, Australian Ovarian Cancer Study Group, European Continental Ancestry Group, Non-P.H.S, Single-nucleotide polymorphism, Breast Neoplasms, Biology, Research Support, Polymorphism, Single Nucleotide, White People, N.I.H, Breast cancer, Research Support, N.I.H., Extramural, SDG 3 - Good Health and Well-being, medicine, Journal Article, Humans, Genetic Predisposition to Disease, ddc:610, gene, Genotyping, Molecular Biology, Genetic association, disease, Extramural, Proteins, Odds ratio, medicine.disease, susceptibility loci, Minor allele frequency, Case-Control Studies, genome-wide association, enhancers, U.S. Gov't, casp8, Research Support, U.S. Gov't, Non-P.H.S, Genome-Wide Association Study
Abstract

Previous studies have suggested that polymorphisms in CASP8 on chromosome 2 are associated with breast cancer risk. To clarify the role of CASP8 in breast cancer susceptibility, we carried out dense genotyping of this region in the Breast Cancer Association Consortium (BCAC). Single-nucleotide polymorphisms (SNPs) spanning a 1 Mb region around CASP8 were genotyped in 46 450 breast cancer cases and 42 600 controls of European origin from 41 studies participating in the BCAC as part of a custom genotyping array experiment (iCOGS). Missing genotypes and SNPs were imputed and, after quality exclusions, 501 typed and 1232 imputed SNPs were included in logistic regressionmodels adjusting for study and ancestry principal components. The SNPs retained in the final model were investigated further in data from nine genome-wide association studies (GWAS) comprising in total 10 052 case and 12 575 control subjects. The most significant association signal observed in European subjects was for the imputed intronic SNP rs1830298 in ALS2CR12 (telomeric to CASP8), with per allele odds ratio and 95% confidence interval [OR (95% confidence interval, CI)] for the minor allele of 1.05 (1.03-1.07), P = 1 × 10-5. Three additional independent signals from intronic SNPs were identified, in CASP8 (rs36043647), ALS2CR11 (rs59278883) and CFLAR (rs7558475). The association with rs1830298 was replicated in the imputed results from the combined GWAS (P=3 × 10-6), yielding a combined OR (95% CI) of 1.06 (1.04-1.08), P = 1 × 10-9. Analyses of gene expression associations in peripheral blood and normal breast tissue indicate that CASP8might be the target gene, suggesting amechanism involving apoptosis.

Published
2016

24. Fine-mapping identifies two additional breast cancer susceptibility loci at 9q31.2

Author

Orr, N., Dudbridge, F., Dryden, N., Maguire, S., Novo, D., Perrakis, E., Johnson, N., Ghoussaini, M., Hopper, J.L., Southey, M.C., Apicella, C., Stone, J., Schmidt, M.K., Broeks, A., Van't Veer, L.J., Hogervorst, F.B., Fasching, P.A., Haeberle, L., Ekici, A.B., Beckmann, M.W., Gibson, L., Aitken, Z., Warren, H., Sawyer, E., Tomlinson, I., Kerin, M.J., Miller, N., Burwinkel, B., Marme, F., Schneeweiss, A., Sohn, C., Guenel, P., Truong, T., Cordina-Duverger, E., Sanchez, M., Bojesen, S.E., Nordestgaard, B.G., Nielsen, S.F., Flyger, H., Benitez, J., Zamora, M.P., Perez, J.I.A., Menendez, P., Anton-Culver, H., Neuhausen, S.L., Brenner, H., Dieffenbach, A.K., Arndt, V., Stegmaier, C., Hamann, U., Brauch, H., Justenhoven, C., Bruning, T., Ko, Y.D., Nevanlinna, H., Aittomaki, K., Blomqvist, C., Khan, S., Bogdanova, N., Dork, T., Lindblom, A., Margolin, S., Mannermaa, A., Kataja, V., Kosma, V.M., Hartikainen, J.M., Chenevix-Trench, G., Beesley, J., Lambrechts, D., Moisse, M., Floris, G., Beuselinck, B., Chang-Claude, J., Rudolph, A., Seibold, P., Flesch-Janys, D., Radice, P., Peterlongo, P., Peissel, B., Pensotti, V., Couch, F.J., Olson, J.E., Slettedahl, S., Vachon, C., Giles, G.G., Milne, R.L., McLean, C., Haiman, C.A., Henderson, B.E., Schumacher, F., Marchand, L. le, Simard, J., Goldberg, M.S., Labreche, F., Dumont, M., Kristensen, V., Alnaes, G.G., Nord, S., Borresen-Dale, A.L., Zheng, W., Deming-Halverson, S., Shrubsole, M., Long, J.R., Winqvist, R., Pylkas, K., Jukkola-Vuorinen, A., Grip, M., Andrulis, I.L., Knight, J.A., Glendon, G., Tchatchou, S., Devilee, P., Tollenaar, R.A.E.M., Seynaeve, C.M., Asperen, C.J. van, Garcia-Closas, M., Figueroa, J., Chanock, S.J., Lissowska, J., Czene, K., Darabi, H., Eriksson, M., Klevebring, D., Hooning, M.J., Hollestelle, A., Deurzen, C.H.M. van, Kriege, M., Hall, P., Li, J.M., Liu, J.J., Humphreys, K., Cox, A., Cross, S.S., Reed, M.W.R., Pharoah, P.D.P., Dunning, A.M., Shah, M., Perkins, B.J., Jakubowska, A., Lubinski, J., Jaworska-Bieniek, K., Durda, K., Ashworth, A., Swerdlow, A., Jones, M., Schoemaker, M.J., Meindl, A., Schmutzler, R.K., Olswold, C., Slager, S., Toland, A.E., Yannoukakos, D., Muir, K., Lophatananon, A., Stewart-Brown, S., Siriwanarangsan, P., Matsuo, K., Ito, H., Iwata, H., Ishiguro, J., Wu, A.H., Tseng, C.C., Berg, D. van den, Stram, D.O., Teo, S.H., Yip, C.H., Kang, P., Ikram, M.K., Shu, X.O., Lu, W., Gao, Y.T., Cai, H., Kang, D., Choi, J.Y., Park, S.K., Noh, D.Y., Hartman, M., Miao, H., Lim, W.Y., Lee, S.C., Sangrajrang, S., Gaborieau, V., Brennan, P., McKay, J., Wu, P.E., Hou, M.F., Yu, J.C., Shen, C.Y., Blot, W., Cai, Q.Y., Signorello, L.B., Luccarini, C., Bayes, C., Ahmed, S., Maranian, M., Healey, C.S., Gonzalez-Neira, A., Pita, G., Alonso, M.R., Alvarez, N., Herrero, D., Tessier, D.C., Vincent, D., Bacot, F., Hunter, D.J., Lindstrom, S., Dennis, J., Michailidou, K., Bolla, M.K., Easton, D.F., Silva, I.D., Fletcher, O., Peto, J., GENICA Network, kConFab Investigators, Australian Ovarian Canc Study Grp, Obstetrics & Gynecology, Medical Oncology, Pathology, Ophthalmology, Cardiothoracic Surgery, and Clinical Genetics

Subjects
Asian Continental Ancestry Group, Adult, Hepatocyte Nuclear Factor 3-alpha, Risk, binding, European Continental Ancestry Group, Kruppel-Like Transcription Factors, estrogen-receptor-alpha, Breast Neoplasms, GATA3 Transcription Factor, Polymorphism, Single Nucleotide, White People, Kruppel-Like Factor 4, Asian People, SDG 3 - Good Health and Well-being, Medizinische Fakultät, common variants, expression, Humans, Genetic Predisposition to Disease, ddc:610, Genetic Association Studies, Aged, Association Studies Articles, Estrogen Receptor alpha, Chromosome Mapping, foxa1, Middle Aged, confer susceptibility, analyses reveal, Enhancer Elements, Genetic, risk locus, Genetic Loci, functional variants, genome-wide association, Female, Chromosomes, Human, Pair 9
Abstract

We recently identified a novel susceptibility variant, rs865686, for estrogen-receptor positive breast cancer at 9q31.2. Here, we report a fine-mapping analysis of the 9q31.2 susceptibility locus using 43 160 cases and 42 600 controls of European ancestry ascertained from 52 studies and a further 5795 cases and 6624 controls of Asian ancestry from nine studies. Single nucleotide polymorphism (SNP) rs676256 was most strongly associated with risk in Europeans (odds ratios [OR] = 0.90 [0.88-0.92]; P-value = 1.58 × 10(-25)). This SNP is one of a cluster of highly correlated variants, including rs865686, that spans ∼14.5 kb. We identified two additional independent association signals demarcated by SNPs rs10816625 (OR = 1.12 [1.08-1.17]; P-value = 7.89 × 10(-09)) and rs13294895 (OR = 1.09 [1.06-1.12]; P-value = 2.97 × 10(-11)). SNP rs10816625, but not rs13294895, was also associated with risk of breast cancer in Asian individuals (OR = 1.12 [1.06-1.18]; P-value = 2.77 × 10(-05)). Functional genomic annotation using data derived from breast cancer cell-line models indicates that these SNPs localise to putative enhancer elements that bind known drivers of hormone-dependent breast cancer, including ER-α, FOXA1 and GATA-3. In vitro analyses indicate that rs10816625 and rs13294895 have allele-specific effects on enhancer activity and suggest chromatin interactions with the KLF4 gene locus. These results demonstrate the power of dense genotyping in large studies to identify independent susceptibility variants. Analysis of associations using subjects with different ancestry, combined with bioinformatic and genomic characterisation, can provide strong evidence for the likely causative alleles and their functional basis. ispartof: Human Molecular Genetics vol:24 issue:10 pages:2966-84 ispartof: location:England status: published

Published
2015

25. Wideband FM demodulation by injection-locked division of frequency deviation

Author

Visweswaran, A., Long, J.R., and Staszewski, R.B.

Abstract

A novel and useful wideband FM demodulator operating across an 8 GHz IF bandwidth for application in low-power, wideband heterodyne receivers. The demodulator includes an n-stage ring oscillator that is injection locked to a wideband input signal. Locking to the input frequency, it divides the FM deviation by n, thereby facilitating as well as reducing the energy required for wideband demodulation. The quadrature-phased output of the ring oscillator is auto correlated using a low-power folded CMOS mixer capable of detecting FM up to 400 Mb/s over a 2-10 GHz IF frequency range.

Published
2014

28. Common non-synonymous SNPs associated with breast cancer susceptibility: findings from the Breast Cancer Association Consortium

Author

Milne, R.L., Burwinkel, B., Michailidou, K., Arias-Perez, J.I., Zamora, M.P., Menendez-Rodriguez, P., Hardisson, D., Mendiola, M., Gonzalez-Neira, A., Pita, G., Alonso, M.R., Dennis, J., Wang, Q., Bolla, M.K., Swerdlow, A., Ashworth, A., Orr, N., Schoemaker, M., Ko, Y.D., Brauch, H., Hamann, U., Andrulis, I.L., Knight, J.A., Glendon, G., Tchatchou, S., Matsuo, K., Ito, H., Iwata, H., Tajima, K., Li, J.M., Brand, J.S., Brenner, H., Dieffenbach, A.K., Arndt, V., Stegmaier, C., Lambrechts, D., Peuteman, G., Christiaens, M.R., Smeets, A., Jakubowska, A., Lubinski, J., Jaworska-Bieniek, K., Durda, K., Hartman, M., Hui, M., Lim, W.Y., Chan, C.W., Marme, F., Yang, R.X., Bugert, P., Lindblom, A., Margolin, S., Garcia-Closas, M., Chanock, S.J., Lissowska, J., Figueroa, J.D., Bojesen, S.E., Nordestgaard, B.G., Flyger, H., Hooning, M.J., Kriege, M., Ouweland, A.M.W. van den, Koppert, L.B., Fletcher, O., Johnson, N., Dos-Santos-Silva, I., Peto, J., Zheng, W., Deming-Halverson, S., Shrubsole, M.J., Long, J.R., Chang-Claude, J., Rudolph, A., Seibold, P., Flesch-Janys, D., Winqvist, R., Pylkas, K., Jukkola-Vuorinen, A., Grip, M., Cox, A., Cross, S.S., Reed, M.W.R., Schmidt, M.K., Broeks, A., Cornelissen, S., Braaf, L., Kang, D., Choi, J.Y., Park, S.K., Noh, D.Y., Simard, J., Dumont, M., Goldberg, M.S., Labreche, F., Fasching, P.A., Hein, A., Ekici, A.B., Beckmann, M.W., Radice, P., Peterlongo, P., Azzollini, J., Barile, M., Sawyer, E., Tomlinson, I., Kerin, M., Miller, N., Hopper, J.L., Schmidt, D.F., Makalic, E., Southey, M.C., Teo, S.H., Yip, C.H., Sivanandan, K., Tay, W.T., Shen, C.Y., Hsiung, C.N., Yu, J.C., Hou, M.F., Guenel, P., Truong, T., Sanchez, M., Mulot, C., Blot, W., Cai, Q.Y., Nevanlinna, H., Muranen, T.A., Aittomaki, K., Blomqvist, C., Wu, A.H., Tseng, C.C., Berg, D. van den, Stram, D.O., Bogdanova, N., Dork, T., Muir, K., Lophatananon, A., Stewart-Brown, S., Siriwanarangsan, P., Mannermaa, A., Kataja, V., Kosma, V.M., Hartikainen, J.M., Shu, X.O., Lu, W., Gao, Y.T., Zhang, B., Couch, F.J., Toland, A.E., Yannoukakos, D., Sangrajrang, S., McKay, J., Wang, X.S., Olson, J.E., Vachon, C., Purrington, K., Severi, G., Baglietto, L., Haiman, C.A., Henderson, B.E., Schumacher, F., Marchand, L. le, Devilee, P., Tollenaar, R.A.E.M., Seynaeve, C., Czene, K., Eriksson, M., Humphreys, K., Darabi, H., Ahmed, S., Shah, M., Pharoah, P.D.P., Hall, P., Giles, G.G., Benitez, J., Dunning, A.M., Chenevix-Trench, G., Easton, D.F., GENICA Network, kConFab Investigators, Australian Ovarian Canc Study Grp, TNBCC, Dennis, Joe [0000-0003-4591-1214], Wang, Jean [0000-0002-9139-0627], Pharoah, Paul [0000-0001-8494-732X], Dunning, Alison [0000-0001-6651-7166], Easton, Douglas [0000-0003-2444-3247], and Apollo - University of Cambridge Repository

Subjects
Adult, Ataxin-7, A Kinase Anchor Proteins, Breast Neoplasms, Nerve Tissue Proteins, Middle Aged, Protein Serine-Threonine Kinases, Polymorphism, Single Nucleotide, Cytoskeletal Proteins, Case-Control Studies, Humans, NIMA-Related Kinases, Female, Genetic Predisposition to Disease, health care economics and organizations, Alleles, Genome-Wide Association Study
Abstract

Candidate variant association studies have been largely unsuccessful in identifying common breast cancer susceptibility\ud variants, although most studies have been underpowered to detect associations of a realistic magnitude.\ud We assessed 41 common non-synonymous single-nucleotide polymorphisms (nsSNPs) for which\ud evidence of association with breast cancer risk had been previously reported. Case-control data were combined\ud from 38 studies of white European women (46 450 cases and 42 600 controls) and analyzed using unconditional\ud logistic regression. Strong evidence of association was observed for three nsSNPs: ATXN7-K264R at 3p21\ud [rs1053338, per allele OR 5 1.07, 95% confidence interval (CI) 5 1.04–1.10, P 5 2.9 3 1026\ud ], AKAP9-M463I at\ud 7q21 (rs6964587, OR 5 1.05, 95% CI 5 1.03–1.07, P 5 1.7 3 1026\ud ) and NEK10-L513S at 3p24 (rs10510592,\ud OR 5 1.10, 95% CI 5 1.07 –1.12, P 5 5.1 3 10217). The first two associations reached genome-wide statistical\ud significance in a combined analysis of available data, including independent data from nine genome-wide association\ud studies (GWASs): for ATXN7-K264R, OR 5 1.07 (95% CI 5 1.05–1.10, P 5 1.0 3 1028\ud ); for AKAP9-M463I,\ud OR 5 1.05 (95% CI 5 1.04–1.07, P 5 2.0 3 10210). Further analysis of other common variants in these two\ud regions suggested that intronic SNPs nearby are more strongly associated with disease risk. We have thus identified\ud a novel susceptibility locus at 3p21, and confirmed previous suggestive evidence that rs6964587 at 7q21 is\ud associated with risk. The third locus, rs10510592, is located in an established breast cancer susceptibility\ud region; the association was substantially attenuated after adjustment for the known GWAS hit. Thus, each of\ud the associated nsSNPs is likely to be a marker for another, non-coding, variant causally related to breast\ud cancer risk. Further fine-mapping and functional studies are required to identify the underlying risk-modifying\ud variants and the genes through which they act.

Published
2014

29. High resolution millimeter wave digitally controlled oscillator with reconfigurable distributed metal capacitor passive resonators

Author

Wu, W., Long, J.R., and Staszewski, B.

Abstract

A novel and useful millimeter-wave digitally controlled oscillator (DCO) that achieve a tuning range greater than 10% and fine frequency resolution less than 1 MHz. Switched metal capacitors are distributed across a passive resonator for tuning the oscillation frequency. To obtain sub-MHz frequency resolution, tuning step attenuation techniques are used that exploit an inductor and a transformer. A 60-GHz fine-resolution inductor-based DCO (L-DCO) and a 60 GHz transformer-coupled DCO (T-DCO), both fabricated in 90 nm CMOS, are disclosed. The phase noise of both DCOs is lower than -90.5 dBc/Hz at 1 MHz offset across 56 to 62 GHz frequency range. The T-DCO achieves a fine frequency tuning step of 2.5 MHz, whereas the L-DCO tuning step is over one order of magnitude finer at 160 kHz.

Published
2014

30. A Wideband 2x13-bit All-Digital I/Q RF-DAC

Author

Alavi, S.M., Staszewski, R.B., De Vreede, L.C.N., and Long, J.R.

Subjects
Balun, transmitter (TX), digital power amplifier (DPA), digital predistortion (DPD), digital-to-RF-amplitude converter (DRAC), transformer, in-phase/quadrature-phase (I/Q) modulator, MOS switch, RF digital-to-analog converter (RF-DAC), class-E power amplifier
Abstract

This paper presents a wideband 2 13-bit in-phase/quadrature-phase (I/Q) RF digital-to-analog converter-based all-digital modulator realized in 65-nm CMOS. The isolation between I and Q paths is guaranteed employing 25% duty-cycle differential quadrature clocks. With a 1.3-V supply and an on-chip power combiner, the digital I/Q transmitter provides more than 21-dBm RF output power within a frequency range of 1.36–2.51 GHz. The peak RF output power, overall system, and drain efficiencies of the modulator are 22.8 dBm, 34%, and 42%, respectively. The measured static noise floor is below 160 dBc/Hz. The digital I/Q RF modulator demonstrates an IQ image rejection and local oscillator leakage of 65 and 68 dBc, respectively. It could be linearized using either of the two digital predistortion (DPD) approaches: a memoryless polynomial or a lookup table. Its linearity is examined using single-carrier 4/16/64/256/1024 quadrature amplitude modulation (QAM), as well as multi-carrier 256-QAM orthogonal frequency-division multiplexing baseband signals while their related modulation bandwidth can be as high as 154 MHz. Employing DPD improves the third-order intermodulation product (IM3) by more than 25 dB, while the measured error vector magnitude for a “single-carrier 22-MHz 64-QAM” signal is better than 28 dB.

Published
2014

31. Large-scale genotyping identifies 41 new loci associated with breast cancer risk

Author

Michailidou, K., Hall, P., Gonzalez-Neira, A., Ghoussaini, M., Dennis, J., Milne, R.L., Schmidt, M.K., Chang-Claude, J., Bojesen, S.E., Bolla, M.K., Wang, Q., Dicks, E., Lee, A., Turnbull, C., Rahman, N., Fletcher, O., Peto, J., Gibson, L., Silva, I.D., Nevanlinna, H., Muranen, T.A., Aittomaki, K., Blomqvist, C., Czene, K., Irwanto, A., Liu, J.J., Waisfisz, Q., Meijers-Heijboer, H., Adank, M., Luijt, R.B. van der, Hein, R., Dahmen, N., Beckman, L., Meindl, A., Schmutzler, R.K., Muller-Myhsok, B., Lichtner, P., Hopper, J.L., Southey, M.C., Makalic, E., Schmidt, D.F., Uitterlinden, A.G., Hofman, A., Hunter, D.J., Chanock, S.J., Vincent, D., Bacot, F., Tessier, D.C., Canisius, S., Wessels, L.F.A., Haiman, C.A., Shah, M., Luben, R., Brown, J., Luccarini, C., Schoof, N., Humphreys, K., Li, J.M., Nordestgaard, B.G., Nielsen, S.F., Flyger, H., Couch, F.J., Wang, X.S., Vachon, C., Stevens, K.N., Lambrechts, D., Moisse, M., Paridaens, R., Christiaens, M.R., Rudolph, A., Nickels, S., Flesch-Janys, D., Johnson, N., Aitken, Z., Aaltonen, K., Heikkinen, T., Broeks, A., Van't Veer, L.J., Schoot, C.E. van der, Guenel, P., Truong, T., Laurent-Puig, P., Menegaux, F., Marme, F., Schneeweiss, A., Sohn, C., Burwinke, B., Zamora, M.P., Perez, J.I.A., Pita, G., Alonso, M.R., Cox, A., Brock, I.W., Cross, S.S., Reed, M.W.R., Sawyer, E.J., Tomlinson, I., Kerin, M.J., Miller, N., Henderson, B.E., Schumacher, F., Marchand, L. le, Andrulis, I.L., Knight, J.A., Glendon, G., Mulligan, A.M., Lindblom, A., Margolin, S., Hooning, M.J., Hollestelle, A., Ouweland, A.M.W. van den, Jager, A., Bui, Q.M., Stone, J., Dite, G.S., Apicella, C., Tsimiklis, H., Giles, G.G., Severi, G., Baglietto, L., Fasching, P.A., Haeberle, L., Ekici, A.B., Beckmann, M.W., Brenner, H., Muller, H., Arndt, V., Stegmaier, C., Swerdlown, A., Ashworth, A., Orr, N., Jones, M., Figueroa, J., Lissowska, J., Brinton, L., Goldberg, M.S., Labreche, F., Dumont, M., Winqvist, R., Pylkas, K., Jukkola-Vuorinen, A., Grip, M., Brauch, H., Hamann, U., Bruning, T., Radice, P., Peterlongo, P., Manouldan, S., Bonanni, B., Devilee, P., Tollenaar, R.A.E.M., Seynaeve, C., Asperen, C.J. van, Jakubowska, A., Lubinski, J., Jaworska, K., Durda, K., Mannermaa, A., Kataja, V., Kosma, V.M., Hartikainen, J.M., Bogdanova, N.V., Antonenkova, N.N., Dork, T., Kristensen, V.N., Anton-Culver, H., Slager, S., Toland, A.E., Edge, S., Fostira, F., Kang, D., Yoo, K.Y., Noh, D.Y., Matsuo, K., Ito, H., Iwata, H., Sueta, A., Wu, A.H., Tseng, C.C., Berg, D. van den, Stram, D.O., Shu, X.O., Lu, W., Gao, Y.T., Cai, H., Teo, S.H., Yip, C.H., Phuah, S.Y., Cornes, B.K., Hartman, M., Miao, H., Lim, W.Y., Sng, J.H., Muir, K., Lophatananon, A., Stewart-Brown, S., Siriwanarangsan, P., Shen, C.Y., Hsiung, C.N., Wu, P.E., Ding, S.L., Sangrajrang, S., Gaborieau, V., Brennan, P., Mckay, J., Blot, W.J., Signorello, L.B., Cai, Q.Y., Zheng, W., Deming-Halverson, S., Shrubsole, M., Long, J.R., Simard, J., Garcia-Closas, M., Pharoah, P.D.P., Chenevix-Trench, G., Dunning, A.M., Benitez, J., Easton, D.F., Breast Ovarian Canc Susceptibility, Hereditary Breast Ovarian Canc Res, kConFab Investigators, Australian Ovarian Can Study Grp, GENICA Gene Environm Interaction B, CCA -Cancer Center Amsterdam, ARD - Amsterdam Reproduction and Development, Human Genetics, Landsteiner Laboratory, Clinical Haematology, Clinical Genetics, Internal Medicine, Epidemiology, Medical Oncology, Cardiothoracic Surgery, Human genetics, CCA - Oncogenesis, and ~

Subjects
signaling pathway, Genotyping, Genotype, Single-nucleotide polymorphism, Genome-wide association study, Breast Neoplasms, consortium, Biology, Case-Control Studies, Cooperative Behavior, Female, Gene-Environment Interaction, Genetic Loci, Genome-Wide Association Study, Humans, Meta-Analysis as Topic, Polymorphism, Single Nucleotide, Risk Factors, Genetic Predisposition to Disease, Genetics, Article, 03 medical and health sciences, 0302 clinical medicine, Breast cancer, SDG 3 - Good Health and Well-being, common variants, expression, medicine, Polymorphism, gene, hormone-related protein, 030304 developmental biology, Genetic association, 0303 health sciences, Breast cancer susceptibility, Cancer, Single Nucleotide, medicine.disease, confer susceptibility, susceptibility loci, 3. Good health, 14q24.1 rad51l1, TOX3, 030220 oncology & carcinogenesis, genome-wide association
Abstract

Journal article Breast cancer is the most common cancer among women. Common variants at 27 loci have been identified as associated with susceptibility to breast cancer, and these account for ~9% of the familial risk of the disease. We report here a meta-analysis of 9 genome-wide association studies, including 10,052 breast cancer cases and 12,575 controls of European ancestry, from which we selected 29,807 SNPs for further genotyping. These SNPs were genotyped in 45,290 cases and 41,880 controls of European ancestry from 41 studies in the Breast Cancer Association Consortium (BCAC). The SNPs were genotyped as part of a collaborative genotyping experiment involving four consortia (Collaborative Oncological Gene-environment Study, COGS) and used a custom Illumina iSelect genotyping array, iCOGS, comprising more than 200,000 SNPs. We identified SNPs at 41 new breast cancer susceptibility loci at genome-wide significance (P < 5 × 10!¿8). Further analyses suggest that more than 1,000 additional loci are involved in breast cancer susceptibility. European Community Seventh Framework Programme - grant agreement 223175 (HEALTH-F2-2009-223175) (COGS) peer-reviewed

Published
2013

32. Hydrocarbon separations in metal-organic frameworks

Author

Bloch, E.D., Herm, Z.R., Geier, S.J., Mason, J.A., Queen, W.L., Hudson, M.R., Wiers, B.M., Zadrozny, J.M., Brown, C.M., Krishna, R., Long, J.R., and Chemical Reactor engineering (HIMS, FNWI)

Abstract

Owing to their high surface areas, tunable pore dimensions, and adjustable surface functionality, metal-org. frameworks (MOFs) can offer advantages for a variety of gas storage and gas sepn. applications. In an effort to reduce the major energy requirements for the sepn. of mixts. of light hydrocarbons via cryogenic distn., we are developing new MOFs with a high capacity for the selective adsorption of unsatd. hydrocarbons at higher temps. In particular, the compds. M2(dobdc) (M = Mg, Mn, Fe, Co, Ni; dobdc4- = 2,5-dioxido-1,4-benzenedicarboxylate), featuring open M2+ cation sites, have been evaluated for their performance in the fractionation of mixts. of C1-C3 hydrocarbons at 45 °C. The results indicate that these materials have significant potential for applications in adsorption-based processes for natural gas purifn. and olefin/paraffin spearations. In addn., it will be shown that certain structural features possible within MOFs, but not in zeolites, can enable the fractionation of hexane isomers according to the degree of branching or octane no.c

Published
2013

34. High resolution millimeter wave digitally controlled oscillator with reconfigurable distributed metal capacitor passive resonators

Author

Wu, W. (author), Long, J.R. (author), Staszewski, B. (author), Wu, W. (author), Long, J.R. (author), and Staszewski, B. (author)

Abstract

A novel and useful millimeter-wave digitally controlled oscillator (DCO) that achieve a tuning range greater than 10% and fine frequency resolution less than 1 MHz. Switched metal capacitors are distributed across a passive resonator for tuning the oscillation frequency. To obtain sub-MHz frequency resolution, tuning step attenuation techniques are used that exploit an inductor and a transformer. A 60-GHz fine-resolution inductor-based DCO (L-DCO) and a 60 GHz transformer-coupled DCO (T-DCO), both fabricated in 90 nm CMOS, are disclosed. The phase noise of both DCOs is lower than -90.5 dBc/Hz at 1 MHz offset across 56 to 62 GHz frequency range. The T-DCO achieves a fine frequency tuning step of 2.5 MHz, whereas the L-DCO tuning step is over one order of magnitude finer at 160 kHz., Microelectronics, Electrical Engineering, Mathematics and Computer Science

Published
2014

35. Wideband FM demodulation by injection-locked division of frequency deviation

Author

Visweswaran, A. (author), Long, J.R. (author), Staszewski, R.B. (author), Visweswaran, A. (author), Long, J.R. (author), and Staszewski, R.B. (author)

Abstract

A novel and useful wideband FM demodulator operating across an 8 GHz IF bandwidth for application in low-power, wideband heterodyne receivers. The demodulator includes an n-stage ring oscillator that is injection locked to a wideband input signal. Locking to the input frequency, it divides the FM deviation by n, thereby facilitating as well as reducing the energy required for wideband demodulation. The quadrature-phased output of the ring oscillator is auto correlated using a low-power folded CMOS mixer capable of detecting FM up to 400 Mb/s over a 2-10 GHz IF frequency range., Microelectronics, Electrical Engineering, Mathematics and Computer Science

Published
2014

36. A Wideband 2x13-bit All-Digital I/Q RF-DAC

Author

Alavi, S.M. (author), Staszewski, R.B. (author), De Vreede, L.C.N. (author), Long, J.R. (author), Alavi, S.M. (author), Staszewski, R.B. (author), De Vreede, L.C.N. (author), and Long, J.R. (author)

Abstract

This paper presents a wideband 2 13-bit in-phase/quadrature-phase (I/Q) RF digital-to-analog converter-based all-digital modulator realized in 65-nm CMOS. The isolation between I and Q paths is guaranteed employing 25% duty-cycle differential quadrature clocks. With a 1.3-V supply and an on-chip power combiner, the digital I/Q transmitter provides more than 21-dBm RF output power within a frequency range of 1.36–2.51 GHz. The peak RF output power, overall system, and drain efficiencies of the modulator are 22.8 dBm, 34%, and 42%, respectively. The measured static noise floor is below 160 dBc/Hz. The digital I/Q RF modulator demonstrates an IQ image rejection and local oscillator leakage of 65 and 68 dBc, respectively. It could be linearized using either of the two digital predistortion (DPD) approaches: a memoryless polynomial or a lookup table. Its linearity is examined using single-carrier 4/16/64/256/1024 quadrature amplitude modulation (QAM), as well as multi-carrier 256-QAM orthogonal frequency-division multiplexing baseband signals while their related modulation bandwidth can be as high as 154 MHz. Employing DPD improves the third-order intermodulation product (IM3) by more than 25 dB, while the measured error vector magnitude for a “single-carrier 22-MHz 64-QAM” signal is better than 28 dB., Microelectronics & Computer Engineering, Electrical Engineering, Mathematics and Computer Science

Published
2014
Full Text
View/download PDF

37. A 56.4-to-63.4 GHz Multi-Rate All-Digital Fractional-N PLL for FMCW Radar Applications in 65 nm CMOS

Author

Wu, W. (author), Staszewski, R.B. (author), Long, J.R. (author), Wu, W. (author), Staszewski, R.B. (author), and Long, J.R. (author)

Abstract

A mm-wave digital transmitter based on a 60 GHz all-digital phase-locked loop (ADPLL) with wideband frequency modulation (FM) for FMCW radar applications is proposed. The fractional-N ADPLL employs a high-resolution 60 GHz digitally controlled oscillator (DCO) and is capable of multi-rate two-point FM. It achieves a measured rms jitter of 590.2 fs, while the loop settles within 3 ?s. The measured reference spur is only –74 dBc, the fractional spurs are below –62 dBc, with no other significant spurs. A closed-loop DCO gain linearization scheme realizes a GHz-level triangular chirp across multiple DCO tuning banks with a measured frequency error (i.e., nonlinearity) in the FMCW ramp of only 117 kHzrms for a 62 GHz carrier with 1.22 GHz bandwidth. The synthesizer is transformer-coupled to a 3-stage neutralized power amplifier (PA) that delivers +5 dBm to a 50 ? load. Implemented in 65 nm CMOS, the transmitter prototype (including PA) consumes 89 mW from a 1.2 V supply., Microelectronics & Computer Engineering, Electrical Engineering, Mathematics and Computer Science

Published
2014
Full Text
View/download PDF

44. Principles and Limitations of Ultra-Wideband FM Communications Systems

Author

Gerrits, J.F.M., Kouwenhoven, M.H.L., Van Der Meer, P.R., Farserotu, J.R., and Long, J.R.

Subjects
UWB, FM, WPAN, ComputerSystemsOrganization_COMPUTER-COMMUNICATIONNETWORKS, FDMA, multipath, subcarrier
Abstract

This paper presents a novel UWB communications system using double FM: a low-modulation index digital FSK followed by a high-modulation index analog FM to create a constant-envelope UWB signal. FDMA techniques at the subcarrier level are exploited to accommodate multiple users. The system is intended for low (110 kbps) and medium (1001000 kbps) bit rate, and short-range WPAN systems. A wideband delay-line FM demodulator that is not preceded by any limiting amplifier constitutes the key component of the UWBFM receiver. This unusual approach permits multiple users to share the same RF bandwidth. Multipath, however, may limit the useful subcarrier bandwidth to one octave. This paper addresses the performance with AWGN and multipath, the resistance to narrowband interference, as well as the simultaneous detection of multiple FM signals at the same carrier frequency. SPICE and Matlab simulation results illustrate the principles and limitations of this new technology. A hardware demonstrator has been realized and has allowed the confirmation of theory with practical results.

Published
2005

48. 17 GHz RF Front-Ends for Low-Power Wireless Sensor Networks

Author

Wu, W. (author), Sanduleanu, M.A.T. (author), Li, X. (author), Long, J.R. (author), Wu, W. (author), Sanduleanu, M.A.T. (author), Li, X. (author), and Long, J.R. (author)

Abstract

Microelectronics & Computer Engineering, Electrical Engineering, Mathematics and Computer Science

Published
2008

49. 17 GHz Front-Ends for Low-Power Wireless Sensor Networks

Author

Wu, Wanghua, Sanduleanu, M.A.T., Li, X., Long, J.R., Wu, Wanghua, Sanduleanu, M.A.T., Li, X., and Long, J.R.

Abstract

A 17 GHz low-power radio transceiver front-end implemented in a 0.25 mum SiGe:C BiCMOS technology is described. Operating at data rates up to 10 Mbit/s with a reduced transceiver turn-on time of 2 mus, gives an overall energy consumption of 1.75 nJ/bit for the receiver and 1.6 nJ/bit for the transmitter. The measured conversion gain of the receiver chain is 25-30 dB into a 50 Omega load at 10 MHz IF, and noise figure is 12 plusmn0.5 dB across the band from 10 to 200 MHz. The 1-dB compression point at the receiver input is -37 dBm and IIP3 is -25 dBm. The maximum saturated output power from the on-chip transmit amplifier is -1.4 dBm. Power consumption is 17.5 mW in receiver mode, and 16 mW in transmit mode, both operating from a 2.5 V supply. In standby, the transceiver supply current is less than 1 muA.

Published
2008

Catalog

Books, media, physical & digital resources
See catalog results