627 results on '"Daly, M. J."'
Search Results
2. Accumulation of Mn(II) in Deinococcus radiodurans Facilitates Gamma-Radiation Resistance
- Author
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Daly, M. J., Gaidamakova, E. K., Matrosova, V. Y., Vasilenko, A., Zhai, M., Venkateswaran, A., Hess, M., Omelchenko, M. V., Kostandarithes, H. M., Makarova, K. S., Wackett, L. P., Fredrickson, J. K., and Ghosal, D.
- Published
- 2004
3. Proteinuria Is Associated with Persistence of Antibody to Streptococcal M Protein in Aboriginal Australians
- Author
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Goodfellow, A. M., Hoy, W. E., Sriprakash, K. S., Daly, M. J., Reeve, M. P., and Mathews, J. D.
- Published
- 1999
4. The iPSYCH2012 case–cohort sample: new directions for unravelling genetic and environmental architectures of severe mental disorders
- Author
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Pedersen, C B, Bybjerg-Grauholm, J, Pedersen, M G, Grove, J, Agerbo, E, Bækvad-Hansen, M, Poulsen, J B, Hansen, C S, McGrath, J J, Als, T D, Goldstein, J I, Neale, B M, Daly, M J, Hougaard, D M, Mors, O, Nordentoft, M, Børglum, A D, Werge, T, and Mortensen, P B
- Published
- 2018
- Full Text
- View/download PDF
5. Author Correction: Somatic mosaicism and common genetic variation contribute to the risk of very-early-onset inflammatory bowel disease (Nature Communications, (2020), 11, 1, (995), 10.1038/s41467-019-14275-y)
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Serra E. G., Schwerd T., Moutsianas L., Cavounidis A., Fachal L., Pandey S., Kammermeier J., Croft N. M., Posovszky C., Rodrigues A., Russell R. K., Barakat F., Auth M. K. H., Heuschkel R., Zilbauer M., Fyderek K., Braegger C., Travis S. P., Satsangi J., Parkes M., Thapar N., Ferry H., Matte J. C., Gilmour K. C., Wedrychowicz A., Sullivan P., Moore C., Sambrook J., Ouwehand W., Roberts D., Danesh J., Baeumler T. A., Fulga T. A., Carrami E. M., Ahmed A., Wilson R., Barrett J. C., Elkadri A., Griffiths A. M., Zurek M., Strisciuglio C., Elawad M., Lo B., Arancibia-Carcamo C., Bailey A., Barnes E., Bird-Lieberman E. L., Brain O., Braden B., Collier J., East J., Howarth L., Keshav S., Klenerman P., Leedham S., Palmer R., Powrie F., Simmons A., Walker M., Tolkien Z., Kaptoge S., Allen D., Mehenny S., Mant J., Di Angelantonio E., Thompson S. G., Yilmaz B., Juillerat P., Geuking M., Wiest R., Macpherson A. J., Bravo F. D., Brugger L., Carstens O., Bigler U. G., Heimgartner B., Rusticeanu M., Schmid-Uebelhart S., Strebel B., Tatu A., Tutuian R., Oyas O., Ramon C., Stelling J., Franc Y., Fournier N., Pittet V. E. H., Burnand B., Egger M., Golay D., Marot A., Musso L., Rossel J. -B., Seematter V., Sommer J., Vulliamy R., Michetti P., Maillard M. H., Keller C., Nydegger A., Schoepfe A., Archanioti E., Ezri J., Fraga M., Schoepfer A., Muller C., Rogler G., Biedermann L., Blattmann M., Burk S., Dora B., Fried M., Misselwitz B., Mullhaupt B., Obialo N., Pohl D., Raschle N., Scharl M., Vavricka S., Von Kanel R., Zeitz J., Abdelrahman K., Ademi G., Borovicka J., Brand S., Frei R., Haarer J., Knellwolf-Grieger C., Krieger-Grubel C., Kunzler P., Meyenberger C., Meyer P., Rohrich N., Sawatzki M., Schelling M., Semadeni G. -M., Sulz M., Zimmermann D., Aepli P., Criblez D. H., Hess C., Richterich J. -P., Spalinger J., Staudenmann D., Stulz A., Wohrle S., Thomas A., Anderegg C., Kohler H., Kusche R., Antonino A. -T., Arrigoni E., Bengoa J. M., Cunningham S., de Saussure P., Girard L., de Jong D. B., Basturk P., Brunner S., Degen L., Hruz P., Bakker C. K. -D., Niess J., Balsiger B., Haldemann J., Saner G., Seibold F., Bauerfeind P., Becocci A., Belli D., Binek J., Hengstler P., Boehm S., Boldanov T., Buhr P., Koller R., Rueger V., Senning A., Burri E., Buyse S., Cao D. -T., D'Angelo F., Delarive J., Doerig C., Hessler R., Preissler C., Rentsch R., Risti B., Ritz M. A., Steuerwald M., Vogtlin J., Sagmeister M., Sauter B., Schibli S., Sokollik C., Schlauri H., Schnegg J. -F., Seirafi M., Spangenberger H., Stadler P., Staub P., Stenz V., Tempia-Caliera M., Thorens J., Truninger K., Urfer P., Viani F., Vouillamoz D., Zander S., Wyli T., Jostins L., Kennedy N. A., Ahmad T., Lamb C. A., Edwards C., Hart A., Hawkey C., Mansfield J. C., Mowat C., Newman W. G., Tremelling M., Lee J. C., Prescott N. J., Mathew C. G., Lees C. W., McGovern D. P. B., Targan S. R., Botwin G., Mengesha E., Fleshner P., Landers C., Li D., Rioux J. D., Bitton A., Cote-Daigneault J., Daly M. J., Xavier R., Morris K., Boucher G., Cho J. H., Abraham C., Merad M., Sands B., Peter I., Hao K., Itan Y., Duerr R. H., Konnikova L., Schwartz M. B., Proksell S., Johnston E., Miladinova V., Chen W., Brant S. R., Datta L., Silverberg M. S., Schumm L. P., Birch S., Giri M., Gettler K., Sharma Y., Stevens C., Lazarev M., Haritunians T., Snapper S. B., Shah N., Muise A. M., Wilson D. C., Uhlig H. H., Anderson C. A., Serra, E. G., Schwerd, T., Moutsianas, L., Cavounidis, A., Fachal, L., Pandey, S., Kammermeier, J., Croft, N. M., Posovszky, C., Rodrigues, A., Russell, R. K., Barakat, F., Auth, M. K. H., Heuschkel, R., Zilbauer, M., Fyderek, K., Braegger, C., Travis, S. P., Satsangi, J., Parkes, M., Thapar, N., Ferry, H., Matte, J. C., Gilmour, K. C., Wedrychowicz, A., Sullivan, P., Moore, C., Sambrook, J., Ouwehand, W., Roberts, D., Danesh, J., Baeumler, T. A., Fulga, T. A., Carrami, E. M., Ahmed, A., Wilson, R., Barrett, J. C., Elkadri, A., Griffiths, A. M., Zurek, M., Strisciuglio, C., Elawad, M., Lo, B., Arancibia-Carcamo, C., Bailey, A., Barnes, E., Bird-Lieberman, E. L., Brain, O., Braden, B., Collier, J., East, J., Howarth, L., Keshav, S., Klenerman, P., Leedham, S., Palmer, R., Powrie, F., Simmons, A., Walker, M., Tolkien, Z., Kaptoge, S., Allen, D., Mehenny, S., Mant, J., Di Angelantonio, E., Thompson, S. G., Yilmaz, B., Juillerat, P., Geuking, M., Wiest, R., Macpherson, A. J., Bravo, F. D., Brugger, L., Carstens, O., Bigler, U. G., Heimgartner, B., Rusticeanu, M., Schmid-Uebelhart, S., Strebel, B., Tatu, A., Tutuian, R., Oyas, O., Ramon, C., Stelling, J., Franc, Y., Fournier, N., Pittet, V. E. H., Burnand, B., Egger, M., Golay, D., Marot, A., Musso, L., Rossel, J. -B., Seematter, V., Sommer, J., Vulliamy, R., Michetti, P., Maillard, M. H., Keller, C., Nydegger, A., Schoepfe, A., Archanioti, E., Ezri, J., Fraga, M., Schoepfer, A., Muller, C., Rogler, G., Biedermann, L., Blattmann, M., Burk, S., Dora, B., Fried, M., Misselwitz, B., Mullhaupt, B., Obialo, N., Pohl, D., Raschle, N., Scharl, M., Vavricka, S., Von Kanel, R., Zeitz, J., Abdelrahman, K., Ademi, G., Borovicka, J., Brand, S., Frei, R., Haarer, J., Knellwolf-Grieger, C., Krieger-Grubel, C., Kunzler, P., Meyenberger, C., Meyer, P., Rohrich, N., Sawatzki, M., Schelling, M., Semadeni, G. -M., Sulz, M., Zimmermann, D., Aepli, P., Criblez, D. H., Hess, C., Richterich, J. -P., Spalinger, J., Staudenmann, D., Stulz, A., Wohrle, S., Thomas, A., Anderegg, C., Kohler, H., Kusche, R., Antonino, A. -T., Arrigoni, E., Bengoa, J. M., Cunningham, S., de Saussure, P., Girard, L., de Jong, D. B., Basturk, P., Brunner, S., Degen, L., Hruz, P., Bakker, C. K. -D., Niess, J., Balsiger, B., Haldemann, J., Saner, G., Seibold, F., Bauerfeind, P., Becocci, A., Belli, D., Binek, J., Hengstler, P., Boehm, S., Boldanov, T., Buhr, P., Koller, R., Rueger, V., Senning, A., Burri, E., Buyse, S., Cao, D. -T., D'Angelo, F., Delarive, J., Doerig, C., Hessler, R., Preissler, C., Rentsch, R., Risti, B., Ritz, M. A., Steuerwald, M., Vogtlin, J., Sagmeister, M., Sauter, B., Schibli, S., Sokollik, C., Schlauri, H., Schnegg, J. -F., Seirafi, M., Spangenberger, H., Stadler, P., Staub, P., Stenz, V., Tempia-Caliera, M., Thorens, J., Truninger, K., Urfer, P., Viani, F., Vouillamoz, D., Zander, S., Wyli, T., Jostins, L., Kennedy, N. A., Ahmad, T., Lamb, C. A., Edwards, C., Hart, A., Hawkey, C., Mansfield, J. C., Mowat, C., Newman, W. G., Tremelling, M., Lee, J. C., Prescott, N. J., Mathew, C. G., Lees, C. W., Mcgovern, D. P. B., Targan, S. R., Botwin, G., Mengesha, E., Fleshner, P., Landers, C., Li, D., Rioux, J. D., Bitton, A., Cote-Daigneault, J., Daly, M. J., Xavier, R., Morris, K., Boucher, G., Cho, J. H., Abraham, C., Merad, M., Sands, B., Peter, I., Hao, K., Itan, Y., Duerr, R. H., Konnikova, L., Schwartz, M. B., Proksell, S., Johnston, E., Miladinova, V., Chen, W., Brant, S. R., Datta, L., Silverberg, M. S., Schumm, L. P., Birch, S., Giri, M., Gettler, K., Sharma, Y., Stevens, C., Lazarev, M., Haritunians, T., Snapper, S. B., Shah, N., Muise, A. M., Wilson, D. C., Uhlig, H. H., and Anderson, C. A.
- Published
- 2022
6. Genome-wide common and rare variant analysis provides novel insights into clozapine-associated neutropenia
- Author
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Legge, S E, Hamshere, M L, Ripke, S, Pardinas, A F, Goldstein, J I, Rees, E, Richards, A L, Leonenko, G, Jorskog, L F, Consortium, Clozapine-Induced Agranulocytosis, Chambert, K D, Collier, D A, Genovese, G, Giegling, I, Holmans, P, Jonasdottir, A, Kirov, G, McCarroll, S A, MacCabe, J H, Mantripragada, K, Moran, J L, Neale, B M, Stefansson, H, Rujescu, D, Daly, M J, Sullivan, P F, Owen, M J, OʼDonovan, M C, and Walters, J TR
- Published
- 2018
- Full Text
- View/download PDF
7. Whole-genome sequencing reveals host factors underlying critical COVID-19
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Kousathanas, A, Pairo-Castineira, E, Rawlik, K, Stuckey, A, Odhams, C, Walker, S, Russell, C, Malinauskas, T, Wu, Y, Millar, J, Shen, X, Elliott, K, Griffiths, F, Oosthuyzen, W, Morrice, K, Keating, S, Wang, B, Rhodes, D, Klaric, L, Zechner, M, Parkinson, N, Siddiq, A, Goddard, P, Donovan, S, Maslove, D, Nichol, A, Semple, M, Zainy, T, Maleady-Crowe, F, Todd, L, Salehi, S, Knight, J, Elgar, G, Chan, G, Arumugam, P, Patch, C, Rendon, A, Bentley, D, Kingsley, C, Kosmicki, J, Horowitz, J, Baras, A, Abecasis, G, Ferreira, M, Justice, A, Mirshahi, T, Oetjens, M, Rader, D, Ritchie, M, Verma, A, Fowler, T, Shankar-Hari, M, Summers, C, Hinds, C, Horby, P, Ling, L, Mcauley, D, Montgomery, H, Openshaw, P, Elliott, P, Walsh, T, Tenesa, A, Shelton, J, Shastri, A, Ye, C, Weldon, C, Filshtein-Sonmez, T, Coker, D, Symons, A, Esparza-Gordillo, J, Aslibekyan, S, Auton, A, Pathak, G, Karjalainen, J, Stevens, C, Andrews, S, Kanai, M, Cordioli, M, Polimanti, R, Pirinen, M, Harerimana, N, Veerapen, K, Wolford, B, Nguyen, H, Solomonson, M, Liao, R, Chwialkowska, K, Trankiem, A, Balaconis, M, Hayward, C, Richmond, A, Campbell, A, Morris, M, Fawns-Ritchie, C, Glessner, J, Shaw, D, Chang, X, Polikowski, H, Petty, L, Chen, H, Wanying, Z, Hakonarson, H, Porteous, D, Below, J, North, K, Mccormick, J, Timmers, P, Wilson, J, D'Mellow, K, Kerr, S, Niemi, M, Nkambul, L, von Hohenstaufen, K, Sobh, A, Eltoukhy, M, Yassen, A, Hegazy, M, Okasha, K, Eid, M, Moahmed, H, Shahin, D, El-Sherbiny, Y, Elhadidy, T, Abd Elghafar, M, El-Jawhari, J, Mohamed, A, Elnagdy, M, Samir, A, Abdel-Aziz, M, Khafaga, W, El-Lawaty, W, Torky, M, El-shanshory, M, Batini, C, Lee, P, Shrine, N, Williams, A, Tobin, M, Guyatt, A, John, C, Packer, R, Ali, A, Free, R, Wang, X, Wain, L, Hollox, E, Venn, L, Bee, C, Adams, E, Niavarani, A, Sharififard, B, Aliannejad, R, Amirsavadkouhi, A, Naderpour, Z, Tadi, H, Aleagha, A, Ahmadi, S, Moghaddam, S, Adamsara, A, Saeedi, M, Abdollahi, H, Hosseini, A, Chariyavilaskul, P, Chamnanphon, M, Suttichet, T, Shotelersuk, V, Pongpanich, M, Phokaew, C, Chetruengchai, W, Jantarabenjakul, W, Putchareon, O, Torvorapanit, P, Puthanakit, T, Suchartlikitwong, P, Hirankarn, N, Nilaratanakul, V, Sodsai, P, Brumpton, B, Hveem, K, Willer, C, Zhou, W, Rogne, T, Solligard, E, Asvold, B, Abedalthagafi, M, Alaamery, M, Alqahtani, S, Barakeh, D, Al Harthi, F, Alsolm, E, Safieh, L, Alowayn, A, Alqubaishi, F, Al Mutairi, A, Mangul, S, Alshareef, A, Sawaji, M, Almutairi, M, Aljawini, N, Albesher, N, Arabi, Y, Mahmoud, E, Khattab, A, Halawani, R, Alahmadey, Z, Albakri, J, Felemban, W, Suliman, B, Hasanato, R, Al-Awdah, L, Alghamdi, J, Alzahrani, D, Aljohani, S, Al-Afghani, H, Alrashed, M, Aldhawi, N, Albardis, H, Alkwai, S, Alswailm, M, Almalki, F, Albeladi, M, Almohammed, I, Barhoush, E, Albader, A, Massadeh, S, Almalik, A, Alotaibi, S, Alghamdi, B, Jung, J, Fawzy, M, Lee, Y, Magnus, P, Trogstad, L, Helgeland, O, Harris, J, Mangino, M, Spector, T, Duncan, E, Smieszek, S, Przychodzen, B, Polymeropoulos, C, Polymeropoulos, V, Polymeropoulos, M, Fernandez-Cadenas, I, Perez-Tur, J, Llucia-Carol, L, Cullell, N, Muino, E, Carcel-Marquez, J, Dediego, M, Iglesias, L, Planas, A, Soriano, A, Rico, V, Aguero, D, Bedini, J, Lozano, F, Domingo, C, Robles, V, Ruiz-Jaen, F, Marquez, L, Gomez, J, Coto, E, Albaiceta, G, Garcia-Clemente, M, Dalmau, D, Arranz, M, Dietl, B, Serra-Llovich, A, Soler, P, Colobran, R, Martin-Nalda, A, Martinez, A, Bernardo, D, Rojo, S, Fiz-Lopez, A, Arribas, E, de la Cal-Sabater, P, Segura, T, Gonzalez-Villa, E, Serrano-Heras, G, Marti-Fabregas, J, Jimenez-Xarrie, E, de Felipe Mimbrera, A, Masjuan, J, Garcia-Madrona, S, Dominguez-Mayoral, A, Villalonga, J, Menendez-Valladares, P, Chasman, D, Buring, J, Ridker, P, Franco, G, Sesso, H, Manson, J, Medina-Gomez, C, Uitterlinden, A, Ikram, M, Kristiansson, K, Koskelainen, S, Perola, M, Donner, K, Kivinen, K, Palotie, A, Ripatti, S, Ruotsalainen, S, Kaunisto, M, Nakanishi, T, Butler-Laporte, G, Forgetta, V, Morrison, D, Ghosh, B, Laurent, L, Belisle, A, Henry, D, Abdullah, T, Adeleye, O, Mamlouk, N, Kimchi, N, Afrasiabi, Z, Rezk, N, Vulesevic, B, Bouab, M, Guzman, C, Petitjean, L, Tselios, C, Xue, X, Schurr, E, Afilalo, J, Afilalo, M, Oliveira, M, Brenner, B, Lepage, P, Ragoussis, J, Auld, D, Brassard, N, Durand, M, Chasse, M, Kaufmann, D, Lathrop, G, Mooser, V, Richards, J, Li, R, Adra, D, Rahmouni, S, Georges, M, Moutschen, M, Misset, B, Darcis, G, Guiot, J, Guntz, J, Azarzar, S, Gofflot, S, Beguin, Y, Claassen, S, Malaise, O, Huynen, P, Meuris, C, Thys, M, Jacques, J, Leonard, P, Frippiat, F, Giot, J, Sauvage, A, von Frenckell, C, Belhaj, Y, Lambermont, B, Pigazzini, S, Nkambule, L, Daya, M, Shortt, J, Rafaels, N, Wicks, S, Crooks, K, Barnes, K, Gignoux, C, Chavan, S, Laisk, T, Lall, K, Lepamets, M, Magi, R, Esko, T, Reimann, E, Milani, L, Alavere, H, Metsalu, K, Puusepp, M, Metspalu, A, Naaber, P, Laane, E, Pesukova, J, Peterson, P, Kisand, K, Tabri, J, Allos, R, Hensen, K, Starkopf, J, Ringmets, I, Tamm, A, Kallaste, A, Bochud, P, Rivolta, C, Bibert, S, Quinodoz, M, Kamdar, D, Boillat, N, Nussle, S, Albrich, W, Suh, N, Neofytos, D, Erard, V, Voide, C, de Cid, R, Galvan-Femenia, I, Blay, N, Carreras, A, Cortes, B, Farre, X, Sumoy, L, Moreno, V, Mercader, J, Guindo-Martinez, M, Torrents, D, Kogevinas, M, Garcia-Aymerich, J, Castano-Vinyals, G, Dobano, C, Renieri, A, Mari, F, Fallerini, C, Daga, S, Benetti, E, Baldassarri, M, Fava, F, Frullanti, E, Valentino, F, Doddato, G, Giliberti, A, Tita, R, Amitrano, S, Bruttini, M, Croci, S, Meloni, I, Mencarelli, M, Rizzo, C, Pinto, A, Beligni, G, Tommasi, A, Di Sarno, L, Palmieri, M, Carriero, M, Alaverdian, D, Busani, S, Bruno, R, Vecchia, M, Belli, M, Picchiotti, N, Sanarico, M, Gori, M, Furini, S, Mantovani, S, Ludovisi, S, Mondelli, M, Castelli, F, Quiros-Roldan, E, Antoni, M, Zanella, I, Vaghi, M, Rusconi, S, Siano, M, Montagnani, F, Emiliozzi, A, Fabbiani, M, Rossetti, B, Bargagli, E, Bergantini, L, D'Alessandro, M, Cameli, P, Bennett, D, Anedda, F, Marcantonio, S, Scolletta, S, Franchi, F, Mazzei, M, Guerrini, S, Conticini, E, Cantarini, L, Frediani, B, Tacconi, D, Spertilli, C, Feri, M, Donati, A, Scala, R, Guidelli, L, Spargi, G, Corridi, M, Nencioni, C, Croci, L, Bandini, M, Caldarelli, G, Piacentini, P, Desanctis, E, Cappelli, S, Canaccini, A, Verzuri, A, Anemoli, V, Ognibene, A, Pancrazzi, A, Lorubbio, M, D'Arminio Monforte, A, Miraglia, F, Girardis, M, Venturelli, S, Cossarizza, A, Antinori, A, Vergori, A, Gabrieli, A, Riva, A, Francisci, D, Schiaroli, E, Paciosi, F, Scotton, P, Andretta, F, Panese, S, Scaggiante, R, Gatti, F, Parisi, S, Baratti, S, Della Monica, M, Piscopo, C, Capasso, M, Russo, R, Andolfo, I, Iolascon, A, Fiorentino, G, Carella, M, Castori, M, Merla, G, Squeo, G, Aucella, F, Raggi, P, Marciano, C, Perna, R, Bassetti, M, Di Biagio, A, Sanguinetti, M, Masucci, L, Valente, S, Mandala, M, Giorli, A, Salerni, L, Zucchi, P, Parravicini, P, Menatti, E, Trotta, T, Giannattasio, F, Coiro, G, Lena, F, Coviello, D, Mussini, C, Martinelli, E, Mancarella, S, Tavecchia, L, Crotti, L, Gabbi, C, Rizzi, M, Maggiolo, F, Ripamonti, D, Bachetti, T, La Rovere, M, Sarzi-Braga, S, Bussotti, M, Ceri, S, Pinoli, P, Raimondi, F, Biscarini, F, Stella, A, Zguro, K, Capitani, K, Suardi, C, Dei, S, Parati, G, Ravaglia, S, Artuso, R, Botta, G, Di Domenico, P, Rancan, I, Perrella, A, Bianchi, F, Romani, D, Bergomi, P, Catena, E, Colombo, R, Tanfoni, M, Vincenti, A, Ferri, C, Grassi, D, Pessina, G, Tumbarello, M, Di Pietro, M, Sabrina, R, Luchi, S, Barbieri, C, Acquilini, D, Andreucci, E, Segala, F, Tiseo, G, Falcone, M, Lista, M, Poscente, M, De Vivo, O, Petrocelli, P, Guarnaccia, A, Baroni, S, Smith, A, Boughton, A, Li, K, Lefaive, J, Annis, A, Chittoor, G, Josyula, N, Leader, J, Carey, D, Gass, M, Cantor, M, Yadav, A, van Heel, D, Hunt, K, Mason, D, Huang, Q, Finer, S, Trivedi, B, Griffiths, C, Martin, H, Wright, J, Trembath, R, Soranzo, N, Zhao, J, Butterworth, A, Danesh, J, Di Angelantonio, E, Franke, L, Boezen, M, Deelen, P, Claringbould, A, Lopera, E, Warmerdam, R, Vonk, J, van Blokland, I, Lanting, P, Ori, A, Zollner, S, Wang, J, Beck, A, Peloso, G, Ho, Y, Sun, Y, Huffman, J, O'Donnell, C, Cho, K, Tsao, P, Gaziano, J, Nivard, M, de Geus, E, Bartels, M, Jan Hottenga, J, Weiss, S, Karlson, E, Smoller, J, Green, R, Feng, Y, Murphy, S, Meigs, J, Woolley, A, Perez, E, Li, B, Verma, S, Lucas, A, Bradford, Y, Zeberg, H, Frithiof, R, Hultstrom, M, Lipcsey, M, Tardif, N, Rooyackers, O, Grip, J, Maricic, T, Karczewski, K, Atkinson, E, Tsuo, K, Baya, N, Turley, P, Gupta, R, Callier, S, Walters, R, Palmer, D, Sarma, G, Cheng, N, Lu, W, Bryant, S, Churchhouse, C, Cusick, C, Goldstein, J, King, D, Seed, C, Finucane, H, Martin, A, Satterstrom, F, Wilson, D, Armstrong, J, Rudkin, J, Band, G, Earle, S, Lin, S, Arning, N, Crook, D, Wyllie, D, O'Connell, A, Spencer, C, Koelling, N, Caulfield, M, Scott, R, Moutsianas, L, Pasko, D, Ball, C, Hong, E, Rand, K, Girshick, A, 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- Abstract
Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2–4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease.
- Published
- 2022
8. Leveraging global multi-ancestry meta-analysis in the study of idiopathic pulmonary fibrosis genetics
- Author
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Partanen, J. J. (Juulia J.), Häppölä, P. (Paavo), Zhou, W. (Wei), Lehisto, A. A. (Arto A.), Ainola, M. (Mari), Sutinen, E. (Eva), Allen, R. J. (Richard J.), Stockwell, A. D. (Amy D.), Leavy, O. C. (Olivia C.), Oldham, J. M. (Justin M.), Guillen-Guio, B. (Beatriz), Cox, N. J. (Nancy J.), Hirbo, J. B. (Jibril B.), Schwartz, D. A. (David A.), Fingerlin, T. E. (Tasha E.), Flores, C. (Carlos), Noth, I. (Imre), Yaspan, B. L. (Brian L.), Jenkins, R. G. (R. Gisli), Wain, L. V. (Louise V.), Ripatti, S. (Samuli), Pirinen, M. (Matti), I. I. (International IPF Genetics Consortium), G. B. (Global Biobank Meta-Analysis Initiative (GBMI)), Laitinen, T. (Tarja), Kaarteenaho, R. (Riitta), Myllärniemi, M. (Marjukka), Daly, M. J. (Mark J.), Koskela, J. T. (Jukka T.), Partanen, J. J. (Juulia J.), Häppölä, P. (Paavo), Zhou, W. (Wei), Lehisto, A. A. (Arto A.), Ainola, M. (Mari), Sutinen, E. (Eva), Allen, R. J. (Richard J.), Stockwell, A. D. (Amy D.), Leavy, O. C. (Olivia C.), Oldham, J. M. (Justin M.), Guillen-Guio, B. (Beatriz), Cox, N. J. (Nancy J.), Hirbo, J. B. (Jibril B.), Schwartz, D. A. (David A.), Fingerlin, T. E. (Tasha E.), Flores, C. (Carlos), Noth, I. (Imre), Yaspan, B. L. (Brian L.), Jenkins, R. G. (R. Gisli), Wain, L. V. (Louise V.), Ripatti, S. (Samuli), Pirinen, M. (Matti), I. I. (International IPF Genetics Consortium), G. B. (Global Biobank Meta-Analysis Initiative (GBMI)), Laitinen, T. (Tarja), Kaarteenaho, R. (Riitta), Myllärniemi, M. (Marjukka), Daly, M. J. (Mark J.), and Koskela, J. T. (Jukka T.)
- Abstract
Summary The research of rare and devastating orphan diseases, such as idiopathic pulmonary fibrosis (IPF) has been limited by the rarity of the disease itself. The prognosis is poor—the prevalence of IPF is only approximately four times the incidence, limiting the recruitment of patients to trials and studies of the underlying biology. Global biobanking efforts can dramatically alter the future of IPF research. We describe a large-scale meta-analysis of IPF, with 8,492 patients and 1,355,819 population controls from 13 biobanks around the globe. Finally, we combine this meta-analysis with the largest available meta-analysis of IPF, reaching 11,160 patients and 1,364,410 population controls. We identify seven novel genome-wide significant loci, only one of which would have been identified if the analysis had been limited to European ancestry individuals. We observe notable pleiotropy across IPF susceptibility and severe COVID-19 infection and note an unexplained sex-heterogeneity effect at the strongest IPF locus MUC5B.
- Published
- 2022
9. Whole-genome sequencing reveals host factors underlying critical COVID-19
- Author
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Kousathanas, A., Pairo-Castineira, E., Rawlik, K., Stuckey, A., Odhams, C. A., Walker, S., Russell, C. D., Malinauskas, T., Wu, Y., Millar, J., Shen, X., Elliott, K. S., Griffiths, F., Oosthuyzen, W., Morrice, K., Keating, S., Wang, B., Rhodes, D., Klaric, L., Zechner, M., Parkinson, N., Siddiq, A., Goddard, P., Donovan, S., Maslove, D., Nichol, A., Semple, M. G., Zainy, T., Maleady-Crowe, F., Todd, L., Salehi, S., Knight, J., Elgar, G., Chan, G., Arumugam, P., Patch, C., Rendon, A., Bentley, D., Kingsley, C., Kosmicki, J. A., Horowitz, J. E., Baras, A., Abecasis, G. R., Ferreira, M. A. R., Justice, A., Mirshahi, T., Oetjens, M., Rader, D. J., Ritchie, M. D., Verma, A., Fowler, T. A., Shankar-Hari, M., Summers, C., Hinds, C., Horby, P., Mcauley, D., Montgomery, H., Openshaw, P. J. M., Elliott, P., Walsh, T., Tenesa, A., Fawkes, A., Murphy, L., Rowan, K., Ponting, C. P., Vitart, V., Wilson, J. F., Yang, J., Bretherick, A. D., Scott, R. H., Hendry, S. C., Moutsianas, L., Law, A., Caulfield, M. J., Baillie, J. K., Begg, C., Ling, L., Pereira, A. C., Aravindan, L., Armstrong, R., Biggs, H., Boz, C., Brown, A., Clark, R., Coutts, A., Coyle, J., Cullum, L., Das, S., Day, N., Donnelly, L., Duncan, E., Finernan, P., Fourman, M. H., Furlong, A., Furniss, J., Gallagher, B., Gilchrist, T., Golightly, A., Hafezi, K., Hamilton, D., Hendry, R., Law, D., Law, R., Law, S., Lidstone-Scott, R., Macgillivray, L., Maclean, A., Mal, H., Mccafferty, S., Mcmaster, E., Meikle, J., Moore, S. C., Murphy, S., Hellen, M., Zheng, C., Chen, J., Paterson, T., Schon, K., Stenhouse, A., Das, M., Swets, M., Szoor-McElhinney, H., Taneski, F., Turtle, L., Wackett, T., Ward, M., Weaver, J., Wrobel, N., Arbane, G., Bociek, A., Campos, S., Grau, N., Jones, T. O., Lim, R., Marotti, M., Ostermann, M., Whitton, C., Alldis, Z., Astin-Chamberlain, R., Bibi, F., Biddle, J., Blow, S., Bolton, M., Borra, C., Bowles, R., Burton, M., Choudhury, Y., Collier, D., Cox, A., Easthope, A., Ebano, P., Fotiadis, S., Gurasashvili, J., Halls, R., Hartridge, P., Kallon, D., Kassam, J., Lancoma-Malcolm, I., Matharu, M., May, P., Mitchelmore, O., Newman, T., Patel, M., Pheby, J., Pinzuti, I., Prime, Z., Prysyazhna, O., Shiel, J., Taylor, M., Tierney, C., Wood, S., Zak, A., Zongo, O., Bonner, S., Hugill, K., Jones, J., Liggett, S., Headlam, E., Bandla, N., Gellamucho, M., Davies, M., Thompson, C., Abdelrazik, M., Bakthavatsalam, D., Elhassan, M., Ganesan, A., Haldeos, A., Moreno-Cuesta, J., Purohit, D., Vincent, R., Xavier, K., Kumar, R., Frater, Alessia, Saleem, M., Carter, D., Jenkins, S., Lamond, Z., Wall, A., Fernandez-Roman, J., Hamilton, D. O., Johnson, E., Johnston, B., Martinez Guzman, Maria Loreto, Mulla, S., Shaw, D., Waite, A. A. C., Waugh, V., Welters, I. D., Williams, K., Cavazza, A., Cockrell, M., Corcoran, E., Depante, M., Finney, C., Jerome, E., Mcphail, M., Nayak, M., Noble, H., O'Reilly, K., Pappa, E., Saha, R., Saha, S., Smith, Jenovia Amisti, Knighton, A., Antcliffe, D., Banach, D., Brett, S., Coghlan, P., Fernandez, Z., Gordon, A., Rojo, R., Arias, S. S., Templeton, M., Meredith, M., Morris, L., Ryan, L., Clark, A., Sampson, J., Peters, C., Dent, M., Langley, M., Ashraf, Sana, Wei, S., Andrew, A., Bashyal, A., Davidson, N., Hutton, P., Mckechnie, S., Wilson, J., Baptista, D., Crowe, R., Fernandes, R., Herdman-Grant, R., Joseph, A., O'Connor, D., Allen, M., Loveridge, A., Mckenley, I., Morino, E., Naranjo, A., Simms, R., Sollesta, K., Swain, A., Venkatesh, H., Khera, J., Fox, J., Andrew, G., Barclay, L., Callaghan, M., Campbell, R., Clark, S., Hope, D., Marshall, L., Mcculloch, C., Briton, K., Singleton, J., Birch, S., Brimfield, L., Daly, Z., Pogson, D., Rose, S., Nown, A., Battle, C., Brinkworth, E., Harford, R., Murphy, C., Newey, L., Rees, T., Williams, M., Arnold, S., Polgarova, P., Stroud, K., Meaney, E., Jones, M., Ng, A., Agrawal, S., Pathan, N., White, D., Daubney, E., Elston, K., Grauslyte, L., Hussain, M., Phull, M., Pogreban, T., Rosaroso, L., Salciute, E., Franke, G., Wong, J., George, A., de Gordoa, L. O. -R., Peasgood, E., Phillips, C., Bates, M., Dasgin, J., Gill, J., Nilsson, A., Scriven, J., Collins, A., Khaliq, W., Gude, E. T., Delgado, C. C., Dawson, D., Ding, L., Durrant, G., Ezeobu, O., Farnell-Ward, S., Harrison, A., Kanu, R., Leaver, S., Maccacari, E., Manna, S., Saluzzio, R. P., Queiroz, J., Samakomva, T., Sicat, C., Texeira, J., Da Gloria, E. F., Lisboa, A., Rawlins, J., Mathew, J., Kinch, A., Hurt, W. J., Shah, N., Clark, V., Thanasi, M., Yun, N., Patel, K., Bennett, S., Goodwin, E., Jackson, M., Kent, A., Tibke, C., Woodyatt, W., Zaki, A., Abraheem, A., Bamford, P., Cawley, K., Dunmore, C., Faulkner, M., Girach, R., Jeffrey, H., Jones, R., London, E., Nagra, I., Nasir, F., Sainsbury, H., Smedley, C., Patel, T., Smith, M., Chukkambotla, S., Kazi, A., Hartley, J., Dykes, J., Hijazi, M., Keith, S., Khan, M., Ryan-Smith, J., Springle, P., Thomas, J., Truman, N., Saad, S., Coleman, D., Fine, C., Matt, R., Gay, B., Dalziel, J., Ali, S., Goodchild, D., Harling, R., Bhatterjee, R., Goddard, W., Davison, C., Duberly, S., Hargreaves, J., Bolton, R., Davey, M., Golden, D., Seaman, R., Cherian, S., Cutler, S., Heron, A. E., Roynon-Reed, A., Szakmany, T., Williams, G., Richards, O., Cheema, Y., Brooke, H., Buckley, S., Suarez, J. C., Charlesworth, R., Hansson, K., Norris, J., Poole, A., Rose, A., Sandhu, R., Sloan, B., Smithson, E., Thirumaran, M., Wagstaff, V., Metcalfe, A., Brunton, M., Caterson, J., Coles, H., Frise, M., Rai, S. G., Jacques, N., Keating, L., Tilney, E., Bartley, S., Bhuie, P., Gibson, S., Lyle, A., Mcneela, F., Radhakrishnan, J., Hughes, A., Yates, B., Reynolds, J., Campbell, H., Thompsom, M., Dodds, S., Duffy, S., Greer, S., Shuker, K., Tridente, A., Khade, R., Sundar, A., Tsinaslanidis, G., Birkinshaw, I., Carter, J., Howard, K., Ingham, J., Joy, R., Pearson, H., Roche, S., Scott, Z., Bancroft, H., Bellamy, M., Carmody, M., Daglish, J., Moore, F., Rhodes, J., Sangombe, M., Kadiri, S., Croft, M., White, I., Frost, V., Aquino, M., Jha, R., Krishnamurthy, V., Lim, L., Combes, E., Joefield, T., Monnery, S., Beech, V., Trotman, S., Christine, Almaden-Boyle, Austin, P., Cabrelli, L., Cole, S., Casey, M., Chapman, S., Whyte, C., Baird, Y., Butler, A., Chadbourn, I., Folkes, L., Fox, H., Gardner, A., Gomez, R., Hobden, G., Hodgson, L., King, K., Margarson, M., Martindale, T., Meadows, E., Raynard, D., Thirlwall, Y., Helm, D., Margalef, J., Criste, K., Cusack, R., Golder, K., Golding, H., Jones, O., Leggett, S., Male, M., Marani, M., Prager, K., Williams, T., Roberts, B., Salmon, K., Anderson, P., Archer, K., Austin, K., Davis, C., Durie, A., Kelsall, O., Thrush, J., Vigurs, C., Wild, L., Wood, H. -L., Tranter, H., Cowley, N., Mcalindon, M., Burtenshaw, A., Digby, S., Low, E., Morgan, A., Cother, N., Rankin, T., Clayton, S., Mccurdy, A., Ahmed, C., Baines, B., Clamp, S., Colley, J., Haq, R., Hayes, A., Hulme, J., Hussain, S., Joseph, S., Maqsood, Z., Purewal, M., Benham, L., Bradshaw, Z., Brown, J., Caswell, M., Cupitt, J., Melling, S., Preston, S., Slawson, N., Stoddard, E., Warden, S., Deacon, B., Lynch, C., Pothecary, C., Roche, L., Howe, G. S., Singh, Jaywant, Turner, K., Ellis, H., Stroud, N., Hunt, J., Dearden, J., Dobson, E., Drummond, A., Mulcahy, M., Munt, S., O'Connor, G., Philbin, J., Rishton, C., Tully, R., Winnard, S., Cathcart, S., Duffy, K., Puxty, A., Puxty, K., Turner, L., Ireland, J., Semple, G., Long, K., Whiteley, S., Wilby, E., Ogg, B., Cowton, A., Kay, Abigail, Kent, M., Potts, K., Wilkinson, A., Campbell, S., Brown, E., Melville, J., Naisbitt, J., Joseph, R., Lazo, M., Walton, O., Neal, A., Alexander, P., Allen, S., Bradley-Potts, J., Brantwood, C., Egan, J., Felton, T., Padden, G., Ward, L., Moss, S., Glasgow, S., Abel, L., Brett, M., Digby, B., Gemmell, L., Hornsby, J., Macgoey, P., O'Neil, P., Price, R., Rodden, N., Rooney, K., Sundaram, R., Thomson, N., Hopkins, B., Thrasyvoulou, L., Willis, H., Clark, M., Coulding, M., Jude, E., Mccormick, J., Mercer, O., Potla, D., Rehman, H., Savill, H., Turner, V., Downes, C., Holding, K., Riches, K., Hilton, M., Hayman, M., Subramanian, D., Daniel, P., Adanini, O., Bhatia, N., Msiska, M., Collins, R., Clement, I., Patel, B., Gulati, A., Hays, C., Webster, K., Hudson, A., Webster, A., Stephenson, E., Mccormack, L., Slater, V., Nixon, R., Hanson, H., Fearby, M., Kelly, S., Bridgett, V., Robinson, P., Camsooksai, J., Humphrey, C., Reschreiter, H., Wadams, B., Death, Y., Bastion, V., Clarke, D., David, B., Kent, H., Lorusso, Riccardo, Lubimbi, G., Murdoch, S., Penacerrada, M., Thomas, A., Valentine, J., Vochin, A., Wulandari, R., Djeugam, B., Bell, G., English, K., Katary, A., Wilcox, L., Bruce, M., Connolly, K., Duncan, T., Michael, H. T., Lindergard, G., Hey, S., Fox, C., Alfonso, J., Durrans, L. J., Guerin, J., Blackledge, B., Harris, J., Hruska, M., Eltayeb, A., Lamb, T., Hodgkiss, T., Cooper, L., Rothwell, J., Allan, A., Anderson, F., Kaye, C., Liew, J., Medhora, J., Scott, T., Trumper, E., Botello, A., Lankester, L., Nikitas, N., Wells, C., Stowe, B., Spencer, K., Brandwood, C., Smith, L., Birchall, K., Kolakaluri, L., Baines, D., Sukumaran, A., Apetri, E., Basikolo, C., Catlow, L., Charles, B., Dark, P., Doonan, R., Harvey, A., Horner, D., Knowles, K., Lee, S., Lomas, D., Lyons, C., Marsden, T., Mclaughlan, D., Mcmorrow, L., Pendlebury, J., Perez, J., Poulaka, M., Proudfoot, N., Slaughter, M., Slevin, K., Thomas, V., Walker, D., Michael, A., Collis, M., Cosier, T., Millen, G., Richardson, N., Schumacher, N., Weston, H., Rand, J., Baxter, N., Henderson, S., Kennedy-Hay, S., Mcparland, C., Rooney, L., Sim, M., Mccreath, G., Akeroyd, L., Bano, S., Bromley, M., Gurr, L., Lawton, T., Morgan, J., Sellick, K., Warren, D., Wilkinson, B., Mcgowan, J., Ledgard, C., Stacey, A., Pye, K., Bellwood, R., Bentley, M., Bewley, J., Garland, Z., Grimmer, L., Gumbrill, B., Johnson, R., Sweet, K., Webster, D., Efford, G., Convery, K., Fottrell-Gould, D., Hudig, L., Keshet-Price, J., Randell, G., Stammers, K., Bokhari, M., Linnett, V., Lucas, R., Mccormick, W., Ritzema, J., Sanderson, A., Wild, H., Rostron, A., Roy, A., Woods, L., Cornell, S., Wakinshaw, F., Rogerson, K., Jarmain, J., Parker, R., Reddy, A., Turner-Bone, I., Harding, P., Abernathy, C., Foster, L., Gratrix, A., Martinson, V., Parkinson, P., Stones, E., Carbral-Ortega, L., Bercades, G., Brealey, D., Hass, I., Maccallum, N., Martir, G., Raith, E., Reyes, A., Smyth, D., Zitter, L., Benyon, S., Marriott, S., Park, L., Keenan, S., Gordon, E., Quinn, H., Baines, K., Cagova, L., Fofano, A., Garner, L., Holcombe, H., Mepham, S., Mitchell, A. M., Mwaura, L., Praman, K., Vuylsteke, A., Zamikula, J., Purewal, B., Rivers, V., Bell, S., Blakemore, H., Borislavova, B., Faulkner, B., Gendall, E., Goff, E., Hayes, K., Thomas, M., Worner, R., Smith, K., Stephens, D., Mew, L., Mwaura, E., Stewart, R., Williams, F., Wren, L., Sutherland, S. -B., Bevan, E., Martin, J., Trodd, D., Watson, G., Brown, C. W., Akinkugbe, O., Bamford, A., Beech, E., Belfield, H., Bell, M., Davies, C., Jones, G. A. L., Mchugh, T., Meghari, H., O'Neill, L., Peters, M. J., Ray, S., Tomas, A. L., Burn, I., Hambrook, G., Manso, K., Penn, R., Shanmugasundaram, P., Tebbutt, J., Thornton, D., Cole, J., Davies, R., Duffin, D., Hill, H., Player, B., Thomas, E., Williams, A., Griffin, D., Muchenje, N., Mupudzi, M., Partridge, R., Conyngham, J. -A., Thomas, R., Wright, M., Corral, M. A., Jacob, R., Jones, C., Denmade, C., Beavis, S., Dale, K., Gascoyne, R., Hawes, J., Pritchard, K., Stevenson, L., Whileman, A., Doble, P., Hutter, J., Pawley, C., Shovelton, C., Vaida, M., Butcher, D., O'Sullivan, S., Butterworth-Cowin, N., Ahmad, N., Barker, J., Bauchmuller, K., Bird, S., Cawthron, K., Harrington, K., Jackson, Y., Kibutu, F., Lenagh, B., Masuko, S., Mills, G. 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J., Kanai, M., Cordioli, M., Polimanti, R., Pirinen, M., Harerimana, N., Veerapen, K., Wolford, B., Nguyen, H., Solomonson, M., Liao, R. G., Chwialkowska, K., Trankiem, A., Balaconis, M. K., Hayward, C., Richmond, A., Morris, M., Fawns-Ritchie, C., Glessner, J. T., Shaw, D. M., Chang, X., Polikowski, H., Petty, L. E., Chen, H. -H., Wanying, Z., Porteous, D. J., Below, J., North, K., Mccormick, J. B., Timmers, P. H. J., D'Mellow, K., Kerr, S. M., Niemi, M. E. K., Nkambul, L., von Hohenstaufen, K. A., Sobh, A., Eltoukhy, M. M., Yassen, A. M., Hegazy, M. A. F., Okasha, K., Eid, M. A., Moahmed, H. S., Shahin, D., El-Sherbiny, Y. M., Elhadidy, T. A., Abd Elghafar, M. S., El-Jawhari, J. J., Mohamed, A. A. S., Elnagdy, M. H., Samir, A., Abdel-Aziz, M., Khafaga, W. T., El-Lawaty, W. A., Torky, M. S., El-shanshory, M. R., Batini, C., Lee, P. H., Shrine, N., Williams, A. T., Tobin, M. D., Guyatt, A. L., John, C., Packer, R. J., Free, R. C., Wang, X., Wain, L. V., Hollox, E. J., Venn, L. D., Bee, C. E., Adams, Mary Elizabeth, Niavarani, A., Sharififard, B., Aliannejad, R., Amirsavadkouhi, A., Naderpour, Z., Tadi, H. A., Aleagha, A. E., Ahmadi, S., Moghaddam, S. B. M., Adamsara, A., Saeedi, M., Abdollahi, H., Hosseini, A., Chariyavilaskul, P., Chamnanphon, M., Suttichet, T. B., Shotelersuk, V., Pongpanich, M., Phokaew, C., Chetruengchai, W., Jantarabenjakul, W., Putchareon, O., Torvorapanit, P., Puthanakit, T., Suchartlikitwong, P., Hirankarn, N., Nilaratanakul, V., Sodsai, P., Brumpton, B. M., Hveem, K., Willer, C., Zhou, W., Rogne, T., Solligard, E., Asvold, B. O., Abedalthagafi, M., Alaamery, M., Alqahtani, S., Barakeh, D., Harthi, F. A., Alsolm, E., Safieh, L. A., Alowayn, A. M., Alqubaishi, F., Mutairi, A. A., Mangul, S., Alshareef, A., Sawaji, M., Almutairi, M., Aljawini, N., Albesher, N., Arabi, Y. M., Mahmoud, E. S., Khattab, A. K., Halawani, R. T., Alahmadey, Z. Z., Albakri, J. K., Felemban, W. A., Suliman, B. A., Hasanato, R., Al-Awdah, L., Alghamdi, J., Alzahrani, D., Aljohani, S., Al-Afghani, H., Alrashed, M., Aldhawi, N., Albardis, H., Alkwai, S., Alswailm, M., Almalki, F., Albeladi, M., Almohammed, I., Barhoush, E., Albader, A., Massadeh, S., Almalik, A., Alotaibi, S., Alghamdi, B., Jung, J., Fawzy, M. S., Lee, Y., Magnus, P., Trogstad, L. -I. S., Helgeland, O., Harris, J. R., Mangino, M., Spector, T. D., Smieszek, S. P., Przychodzen, B. P., Polymeropoulos, C., Polymeropoulos, V., Polymeropoulos, M. H., Fernandez-Cadenas, I., Perez-Tur, J., Llucia-Carol, L., Cullell, N., Muino, E., Carcel-Marquez, J., Dediego, M. L., Iglesias, L. L., Planas, A. M., Soriano, A., Rico, V., Aguero, D., Bedini, J. L., Lozano, F., Domingo, C., Robles, V., Ruiz-Jaen, F., Marquez, L., Gomez, J., Coto, E., Albaiceta, G. M., Garcia-Clemente, M., Dalmau, D., Arranz, M. J., Dietl, B., Serra-Llovich, A., Soler, P., Colobran, R., Martin-Nalda, A., Martinez, A. P., Bernardo, D., Rojo, S., Fiz-Lopez, A., Arribas, E., de la Cal-Sabater, P., Segura, T., Gonzalez-Villa, E., Serrano-Heras, G., Marti-Fabregas, J., Jimenez-Xarrie, E., Mimbrera, A. F., Masjuan, J., Garcia-Madrona, S., Dominguez-Mayoral, A., Villalonga, J. M., Menendez-Valladares, P., Chasman, D. I., Buring, J. E., Ridker, P. M., Franco, G., Sesso, H. D., Manson, J. E., Glessner, J. R., Hakonarson, H., Medina-Gomez, C., Uitterlinden, A. G., Ikram, M. A., Kristiansson, K., Koskelainen, S., Perola, M., Donner, K., Kivinen, K., Palotie, A., Ripatti, S., Ruotsalainen, S., Kaunisto, M., Nakanishi, T., Butler-Laporte, G., Forgetta, V., Morrison, D. R., Ghosh, B., Laurent, L., Belisle, A., Henry, D., Abdullah, T., Adeleye, O., Mamlouk, N., Kimchi, N., Afrasiabi, Z., Rezk, N., Vulesevic, B., Bouab, M., Guzman, C., Petitjean, L., Tselios, C., Xue, X., Schurr, E., Afilalo, J., Afilalo, M., Oliveira, M., Brenner, B., Lepage, P., Ragoussis, J., Auld, D., Brassard, N., Durand, M., Chasse, M., Kaufmann, D. E., Lathrop, G. M., Mooser, V., Richards, J. B., Li, R., Adra, D., Rahmouni, S., Georges, M., Moutschen, M., Misset, B., Darcis, G., Guiot, J., Guntz, J., Azarzar, S., Gofflot, S., Beguin, Y., Claassen, S., Malaise, O., Huynen, P., Meuris, C., Thys, M., Jacques, J., Leonar, P., Frippiat, F., Giot, J. -B., Sauvage, A. -S., von Frenckell, C., Belhaj, Y., Lambermont, B., Pigazzini, S., Daya, M., Shortt, J., Rafaels, N., Wicks, S. J., Crooks, K., Barnes, K. C., Gignoux, C. R., Chavan, S., Laisk, T., Lall, K., Lepamets, M., Magi, R., Esko, T., Reimann, E., Milani, Luca, Alavere, H., Metsalu, K., Puusepp, M., Metspalu, A., Naaber, P., Laane, E., Pesukova, J., Peterson, P., Kisand, K., Tabri, J., Allos, R., Hensen, K., Starkopf, J., Ringmets, I., Tamm, A., Kallaste, A., Bochud, P. -Y., Rivolta, C., Bibert, S., Quinodoz, M., Kamdar, D., Boillat, N., Nussle, S. G., Albrich, W., Suh, N., Neofytos, D., Erard, V., Voide, C., de Cid, R., Galvan-Femenia, I., Blay, N., Carreras, A., Cortes, B., Farre, X., Sumoy, L., Moreno, V., Mercader, J. M., Guindo-Martinez, M., Torrents, D., Kogevinas, M., Garcia-Aymerich, J., Castano-Vinyals, G., Dobano, C., Renieri, A., Mari, F., Fallerini, C., Daga, S., Benetti, E., Baldassarri, M., Fava, F., Frullanti, E., Valentino, Francesca, Doddato, G., Giliberti, A., Tita, R., Amitrano, S., Bruttini, M., Croci, S., Meloni, I., Mencarelli, Marta, Rizzo, C. L., Pinto, A. M., Beligni, G., Tommasi, A., Sarno, L. D., Palmieri, Marco, Carriero, M. L., Alaverdian, D., Busani, S., Bruno, R., Vecchia, M., Belli, M. A., Picchiotti, N., Sanarico, M., Gori, Mario, Furini, S., Mantovani, Susanna, Ludovisi, S., Mondelli, M. U., Castelli, F., Quiros-Roldan, E., Antoni, M. D., Zanella, I., Vaghi, M., Rusconi, S., Siano, M., Montagnani, F., Emiliozzi, A., Fabbiani, M., Rossetti, Barbara, Bargagli, E., Bergantini, L., D'Alessandro, Michele, Cameli, P., Bennett, D., Anedda, F., Marcantonio, S., Scolletta, S., Franchi, Francesca, Mazzei, M. A., Guerrini, S., Conticini, E., Cantarini, L., Frediani, B., Tacconi, D., Spertilli, C., Feri, M., Donati, Andrea, Scala, R., Guidelli, L., Spargi, G., Corridi, M., Nencioni, C., Croci, L., Bandini, M., Caldarelli, G. P., Piacentini, P., Desanctis, E., Cappelli, S., Canaccini, A., Verzuri, A., Anemoli, V., Ognibene, A., Pancrazzi, A., Lorubbio, M., Monforte, A. D., Miraglia, F. G., Girardis, M., Venturelli, S., Cossarizza, A., Antinori, Armando, Vergori, A., Gabrieli, A., Riva, A., Francisci, D., Schiaroli, E., Paciosi, F., Scotton, P. G., Andretta, F., Panese, S., Scaggiante, R., Gatti, F., Parisi, S. G., Baratti, S., Monica, M. D., Piscopo, C., Capasso, Monica, Russo, R., Andolfo, I., Iolascon, A., Fiorentino, Giuseppe, Carella, M., Castori, M., Merla, G., Squeo, G. M., Aucella, F., Raggi, P., Marciano, C., Perna, Raffaella, Bassetti, M., Biagio, A. D., Sanguinetti, Maurizio, Masucci, Luca, Valente, S., Mandala, M., Giorli, A., Salerni, L., Zucchi, P., Parravicini, P., Menatti, E., Trotta, T., Giannattasio, F., Coiro, G., Lena, Francesco, Coviello, D. A., Mussini, C., Martinelli, E., Mancarella, S., Tavecchia, L., Crotti, L., Gabbi, Chiara, Rizzi, M., Maggiolo, F., Ripamonti, D., Bachetti, T., Rovere, M. T. L., Sarzi-Braga, S., Bussotti, M., Ceri, S., Pinoli, P., Raimondi, F., Biscarini, F., Stella, A., Zguro, K., Capitani, K., Suardi, C., Dei, S., Parati, G., Ravaglia, S., Artuso, R., Botta, Giovanni, Di Domenico, Pasqualina, Rancan, I., Perrella, A., Bianchi, F., Romani, D., Bergomi, P., Catena, E., Colombo, R., Tanfoni, M., Vincenti, A., Ferri, C., Grassi, D., Pessina, Gloria, Tumbarello, Mario, Di Pietro, Maria Luisa, Sabrina, R., Luchi, S., Barbieri, Cristiano, Acquilini, D., Andreucci, E., Segala, F. V., Tiseo, G., Falcone, M., Lista, Maddalena, Poscente, M., De Vivo, O., Petrocelli, Paolo, Guarnaccia, A., Baroni, S., Smith, A. V., Boughton, A. P., Li, K. W., Lefaive, J., Annis, A., Chittoor, G., Josyula, N. S., Leader, J. B., Carey, D. J., Gass, M. C., Cantor, M. N., Yadav, A., van Heel, D. A., Hunt, K. A., Mason, D., Huang, Q. Q., Finer, S., Trivedi, B., Griffiths, C. J., Martin, H. C., Wright, J., Trembath, R. C., Soranzo, N., Zhao, J. H., Butterworth, A. S., Danesh, J., Di Angelantonio, E., Franke, L., Boezen, M., Deelen, P., Claringbould, A., Lopera, E., Warmerdam, R., Vonk, J. M., van Blokland, I., Lanting, P., Ori, A. P. S., Zollner, S., Wang, J., Beck, A., Peloso, G., Ho, Y. -L., Sun, Y. V., Huffman, J. E., O'Donnell, C. J., Cho, K., Tsao, P., Gaziano, J. M., Nivard, M., de Geus, E., Bartels, M., Hottenga, J. J., Weiss, S. T., Karlson, E. W., Smoller, J. W., Green, R. C., Feng, Y. -C. A., Mercader, J., Murphy, S. N., Meigs, J. B., Woolley, A. E., Perez, E. F., Rader, D., Li, B., Verma, S. S., Lucas, A., Bradford, Y., Zeberg, H., Frithiof, R., Hultstrom, M., Lipcsey, M., Tardif, N., Rooyackers, O., Grip, J., Maricic, T., Karczewski, K. J., Atkinson, E. G., Tsuo, K., Baya, N., Turley, P., Gupta, R., Callier, S., Walters, R. K., Palmer, D. S., Sarma, G., Cheng, N., Lu, W., Bryant, S., Churchhouse, C., Cusick, C., Goldstein, J. I., King, D., Seed, C., Finucane, H., Martin, A. R., Satterstrom, F. K., Wilson, D. 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J., Neale, B. M., Ganna, A., Frater A., Martinez M. L., Smith J., Ashraf S., Singh J., Kay A., Lorusso R., Ali A., Williams H., Barberis L., Wood D. (ORCID:0000-0001-8588-8931), Latif M., Finn S., Taylor A., Tucci A., Adams E. L., Milani L. (ORCID:0000-0003-0218-458X), Valentino F., Mencarelli M. A., Palmieri M. (ORCID:0000-0001-8263-336X), Gori M., Mantovani S., Rossetti B., D'Alessandro M., Franchi F., Donati A., Antinori A. (ORCID:0000-0002-6019-2417), Capasso M., Fiorentino G., Perna R., Sanguinetti M. (ORCID:0000-0002-9780-7059), Masucci L. (ORCID:0000-0002-8358-6726), Lena F. (ORCID:0000-0001-5528-319X), Gabbi C., Botta G., Di Domenico P., Pessina G., Tumbarello M. (ORCID:0000-0002-9519-8552), Di Pietro M. (ORCID:0000-0002-3893-8788), Barbieri C., Lista M., and Petrocelli P.
- Abstract
Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2–4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease.
- Published
- 2022
10. Genome-wide common and rare variant analysis provides novel insights into clozapine-associated neutropenia
- Author
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Legge, S E, Hamshere, M L, Ripke, S, Pardinas, A F, Goldstein, J I, Rees, E, Richards, A L, Leonenko, G, Jorskog, L F, Chambert, K D, Collier, D A, Genovese, G, Giegling, I, Holmans, P, Jonasdottir, A, Kirov, G, McCarroll, S A, MacCabe, J H, Mantripragada, K, Moran, J L, Neale, B M, Stefansson, H, Rujescu, D, Daly, M J, Sullivan, P F, Owen, M J, OʼDonovan, M C, and Walters, J TR
- Published
- 2017
- Full Text
- View/download PDF
11. The genetic architecture of pediatric cognitive abilities in the Philadelphia Neurodevelopmental Cohort
- Author
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Robinson, E B, Kirby, A, Ruparel, K, Yang, J, McGrath, L, Anttila, V, Neale, B M, Merikangas, K, Lehner, T, Sleiman, P M A, Daly, M J, Gur, R, Gur, R, and Hakonarson, H
- Published
- 2015
- Full Text
- View/download PDF
12. Rare coding variation provides insight into the genetic architecture and phenotypic context of autism
- Author
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J. M., Fu, Satterstrom, F. K., Peng, M., Brand, H., Collins, R. L., Dong, S., Wamsley, B., Klei, L., Wang, L., Hao, S. P., Stevens, C. R., Cusick, C., Babadi, M., Banks, E., Collins, B., Dodge, S., Gabriel, S. B., Gauthier, L., Lee, S. K., Liang, L., Ljungdahl, A., Mahjani, B., Sloofman, L., Smirnov, A. N., Barbosa, M., Betancur, C., Brusco, A., Chung, B. H. Y., Cook, E. H., Cuccaro, M. L., Domenici, E., Ferrero, G. B., Gargus, J. J., Herman, G. E., Hertz-Picciotto, I., Maciel, P., Manoach, D. S., Passos-Bueno, M. R., Persico, A., Renieri, A., Sutcliffe, J. S., Tassone, F., Trabetti, E., Campos, G., Cardaropoli, S., Carli, D., Chan, M. C. Y., Fallerini, C., Giorgio, E., Girardi, A. C., Hansen-Kiss, E., Lee, S. L., Lintas, C., Ludena, Y., Nguyen, R., Pavinato, L., Pericak-Vance, M., Pessah, I. N., Schmidt, R. J., Smith, M., Costa, C. I. S., Trajkova, S., Wang, J. Y. T., M. H. C., Yu, Aleksic, B., Artomov, M., Benetti, E., Biscaldi-Schafer, M., Borglum, A. D., Carracedo, A., Chiocchetti, A. G., Coon, H., Doan, R. N., Fernandez-Prieto, M., Freitag, C. M., Gerges, S., Guter, S., Hougaard, D. M., Hultman, C. M., Jacob, S., Kaartinen, M., Kolevzon, A., Kushima, I., Lehtimaki, T., Rizzo, C. L., Maltman, N., Manara, M., Meiri, G., Menashe, I., Miller, J., Minshew, N., Mosconi, M., Ozaki, N., Palotie, A., Parellada, M., Puura, K., Reichenberg, A., Sandin, S., Scherer, S. W., Schlitt, S., Schmitt, L., Schneider-Momm, K., Siper, P. M., Suren, P., Sweeney, J. A., Teufel, K., del Pilar Trelles, M., Weiss, L. A., Yuen, R., Cutler, D. J., De Rubeis, S., Buxbaum, J. D., Daly, M. J., Devlin, B., Roeder, K., Sanders, S. J., Talkowski, M. E., Massachusetts General Hospital [Boston], Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Carnegie Mellon University [Pittsburgh] (CMU), Harvard Medical School [Boston] (HMS), University of California [San Francisco] (UC San Francisco), University of California (UC), University of California [Los Angeles] (UCLA), University of Pittsburgh School of Medicine, Pennsylvania Commonwealth System of Higher Education (PCSHE), Icahn School of Medicine at Mount Sinai [New York] (MSSM), Neuroscience Paris Seine (NPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Università degli studi di Torino = University of Turin (UNITO), Azienda Ospedalerio - Universitaria Città della Salute e della Scienza di Torino = University Hospital Città della Salute e della Scienza di Torino, The University of Hong Kong (HKU), University of Illinois [Chicago] (UIC), University of Illinois System, University of Miami Leonard M. Miller School of Medicine (UMMSM), University of Trento [Trento], University of California [Irvine] (UC Irvine), Nationwide Children's Hospital, University of California [Davis] (UC Davis), Universidade do Minho = University of Minho [Braga], Massachusetts General Hospital [Boston, MA, USA], Escola Politecnica da Universidade de Sao Paulo [Sao Paulo], Università degli Studi di Messina = University of Messina (UniMe), Università degli Studi di Siena = University of Siena (UNISI), Azienda Ospedaliera Universitaria Senese, Vanderbilt University [Nashville], Vanderbilt University School of Medicine [Nashville], Università degli studi di Verona = University of Verona (UNIVR), University of Texas Health Science Center, The University of Texas Health Science Center at Houston (UTHealth), Università Campus Bio-Medico di Roma / University Campus Bio-Medico of Rome ( UCBM), Emory University School of Medicine, Emory University [Atlanta, GA], Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Autism Sequencing Consortium (ASC), Broad Institute Center for Common Disease Genomics (Broad-CCDG), iPSYCH-BROAD Consortium : Branko Aleksic, Mykyta Artomov, Elisa Benetti, Monica Biscaldi-Schafer, Anders D Børglum, Angel Carracedo, Andreas G Chiocchetti, Hilary Coon, Ryan N Doan, Montserrat Fernández-Prieto, Christine M Freitag, Sherif Gerges, Stephen Guter, David M Hougaard, Christina M Hultman, Suma Jacob, Miia Kaartinen, Alexander Kolevzon, Itaru Kushima, Terho Lehtimäki, Caterina Lo Rizzo, Nell Maltman, Marianna Manara, Gal Meiri, Idan Menashe, Judith Miller, Nancy Minshew, Matthew Mosconi, Norio Ozaki, Aarno Palotie, Mara Parellada, Kaija Puura, Abraham Reichenberg, Sven Sandin, Stephen W Scherer, Sabine Schlitt, Lauren Schmitt, Katja Schneider-Momm, Paige M Siper, Pål Suren, John A Sweeney, Karoline Teufel, Maria Del Pilar Trelles, Lauren A Weiss, Ryan Yuen., and Betancur, Catalina
- Subjects
Broad Institute Center for Common Disease Genomics ,Autism Sequencing Consortium ,DNA Copy Number Variations ,Autism Spectrum Disorder ,[SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology ,Autism ,Intellectual and Developmental Disabilities (IDD) ,iPSYCH-BROAD Consortium ,autism spectrum disorders ,disease gene ,copy number variants ,neuropsychiatric disorders ,[SDV.GEN.GH] Life Sciences [q-bio]/Genetics/Human genetics ,GENOMAS ,Medical and Health Sciences ,Article ,Clinical Research ,Genetics ,Humans ,2.1 Biological and endogenous factors ,Genetic Predisposition to Disease ,Autistic Disorder ,Aetiology ,Genetic association study ,Pediatric ,Human Genome ,Neurodevelopmental disorders ,[SDV.NEU.NB] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology ,Biological Sciences ,Autism spectrum disorders ,Brain Disorders ,Mental Health ,[SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics ,Mutation ,Gene expression ,Biotechnology ,Developmental Biology - Abstract
International audience; Some individuals with autism spectrum disorder (ASD) carry functional mutations rarely observed in the general population. We explored the genes disrupted by these variants from joint analysis of protein-truncating variants (PTVs), missense variants and copy number variants (CNVs) in a cohort of 63,237 individuals. We discovered 72 genes associated with ASD at false discovery rate (FDR) ≤ 0.001 (185 at FDR ≤ 0.05). De novo PTVs, damaging missense variants and CNVs represented 57.5%, 21.1% and 8.44% of association evidence, while CNVs conferred greatest relative risk. Meta-analysis with cohorts ascertained for developmental delay (DD) (n = 91,605) yielded 373 genes associated with ASD/DD at FDR ≤ 0.001 (664 at FDR ≤ 0.05), some of which differed in relative frequency of mutation between ASD and DD cohorts. The DD-associated genes were enriched in transcriptomes of progenitor and immature neuronal cells, whereas genes showing stronger evidence in ASD were more enriched in maturing neurons and overlapped with schizophrenia-associated genes, emphasizing that these neuropsychiatric disorders may share common pathways to risk.
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- 2022
13. Particulate Stack Emissions from Coal Fired Power Stations
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Clark, I., Daly, M. J., Gradstein, F. M., editor, and Soares, Amilcar, editor
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- 1993
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14. Myocardial Ischaemia: An Overview
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Nayler, W. G., Gu, Xin Hua, Daly, M. J., Brittnell, S. L., Lichtlen, P. R., editor, and Reale, A., editor
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- 1991
- Full Text
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15. Clinical and genetic markers of prehypertension in North-Western Russian population
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Erina, A, primary, Usoltsev, U, additional, Kolosov, N, additional, Solntsev, V, additional, Kostareva, A, additional, Palotie, A, additional, Daly, M J, additional, Konradi, A, additional, Rotar, O, additional, and Artomov, M, additional
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- 2021
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16. Hematopoietic mosaic chromosomal alterations increase the risk for diverse types of infection
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Zekavat, S. M. (Seyedeh M.), Lin, S.-H. (Shu-Hong), Bick, A. G. (Alexander G.), Liu, A. (Aoxing), Paruchuri, K. (Kaavya), Wang, C. (Chen), Uddin, M. M. (Md Mesbah), Ye, Y. (Yixuan), Yu, Z. (Zhaolong), Liu, X. (Xiaoxi), Kamatani, Y. (Yoichiro), Bhattacharya, R. (Romit), Pirruccello, J. P. (James P.), Pampana, A. (Akhil), Loh, P.-R. (Po-Ru), Kohli, P. (Puja), McCarroll, S. A. (Steven A.), Kiryluk, K. (Krzysztof), Neale, B. (Benjamin), Ionita-Laza, I. (Iuliana), Engels, E. A. (Eric A.), Brown, D. W. (Derek W.), Smoller, J. W. (Jordan W.), Green, R. (Robert), Karlson, E. W. (Elizabeth W.), Lebo, M. (Matthew), Ellinor, P. T. (Patrick T.), Weiss, S. T. (Scott T.), Daly, M. J. (Mark J.), T. B. (The Biobank Japan Project), F. C. (FinnGen Consortium), Terao, C. (Chikashi), Zhao, H. (Hongyu), Ebert, B. L. (Benjamin L.), Reilly, M. P. (Muredach P.), Ganna, A. (Andrea), Machiela, M. J. (Mitchell J.), Genovese, G. (Giulio), and Natarajan, P. (Pradeep)
- Abstract
Age is the dominant risk factor for infectious diseases, but the mechanisms linking age to infectious disease risk are incompletely understood. Age–related mosaic chromosomal alterations (mCAs) detected from genotyping of blood–derived DNA, are structural somatic variants indicative of clonal hematopoiesis, and are associated with aberrant leukocyte cell counts, hematological malignancy, and mortality. Here, we show that mCAs predispose to diverse types of infections. We analyzed mCAs from 768,762 individuals without hematological cancer at the time of DNA acquisition across five biobanks. Expanded autosomal mCAs were associated with diverse incident infections (hazard ratio (HR) 1.25; 95% confidence interval (CI) = 1.15–1.36; P = 1.8 x 10-7), including sepsis (HR 2.68; 95% CI = 2.25–3.19; P = 3.1 x 10-28), pneumonia (HR 1.76; 95% CI = 1.53–2.03; P = 2.3 x 10-15), digestive system infections (HR 1.51; 95% CI = 1.32–1.73; P = 2.2 x 10-9) and genitourinary infections (HR 1.25; 95% CI = 1.11–1.41; P = 3.7 x 10-4). A genome–wide association study of expanded mCAs identified 63 loci, which were enriched at transcriptional regulatory sites for immune cells. These results suggest that mCAs are a marker of impaired immunity and confer increased predisposition to infections.
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- 2021
17. Chromosome Xq23 is associated with lower atherogenic lipid concentrations and favorable cardiometabolic indices
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Natarajan, P. (Pradeep), Pampana, A. (Akhil), Graham, S. E. (Sarah E.), Ruotsalainen, S. E. (Sanni E.), Perry, J. A. (James A.), de Vries, P. S. (Paul S.), Broome, J. G. (Jai G.), Pirruccello, J. P. (James P.), Honigbere, M. C. (Michael C.), Aragam, K. (Krishna), Wolford, B. (Brooke), Brody, J. A. (Jennifer A.), Antonacci-Fulton, L. (Lucinda), Arden, M. (Moscati), Aslibekyan, S. (Stella), Assimes, T. L. (Themistocles L.), Ballantyne, C. M. (Christie M.), Bielak, L. F. (Lawrence F.), Bisl, J. C. (Joshua C.), Cade, B. E. (Brian E.), Do, R. (Ron), Doddapaneni, H. (Harsha), Emery, L. S. (Leslie S.), Hung, Y.-J. (Yi-Jen), Irvin, M. R. (Marguerite R.), Khan, A. T. (Alyna T.), Lange, L. (Leslie), Lee, J. (Jiwon), Lemaitre, R. N. (Rozenn N.), Martin, L. W. (Lisa W.), Metcalf, G. (Ginger), Montasser, M. E. (May E.), Moon, J.-Y. (Jee-Young), Muzny, D. (Donna), Connell, J. R. (Jeffrey R. O.), Palmer, N. D. (Nicholette D.), Peralta, J. M. (Juan M.), Peyser, P. A. (Patricia A.), Stilp, A. M. (Adrienne M.), Tsai, M. (Michael), Wang, F. F. (Fei Fei), Weeks, D. E. (Daniel E.), Yanek, L. R. (Lisa R.), Wilson, J. G. (James G.), Abecasis, G. (Goncalo), Arnett, D. K. (Donna K.), Becker, L. C. (Lewis C.), Blangercy, J. (John), Boerwinkle, E. (Eric), Bowden, D. W. (Donald W.), Chang, Y.-C. (Yi-Cheng), Chen, Y. I. (Yii-Der, I), Choi, W. J. (Won Jung), Correa, A. (Adolfo), Curran, J. E. (Joanne E.), Daly, M. J. (Mark J.), DutcherE, S. K. (Susan K.), Ellinor, P. T. (Patrick T.), Fornage, M. (Myriam), Freedman, B. I. (Barry, I), Gabriel, S. (Stacey), Germer, S. (Soren), Gibbs, R. A. (Richard A.), He, J. (Jiang), Hveem, K. (Kristian), Jarvik, G. P. (Gail P.), Kaplan, R. C. (Robert C.), Kardia, S. L. (Sharon L. R.), Kennyn, E. (Eimear), Kim, R. W. (Ryan W.), Kooperberg, C. (Charles), Laurie, C. C. (Cathy C.), Lee, S. (Seonwook), Lloyd-Jones, D. M. (Don M.), Loos, R. J. (Ruth J. F.), Lubitz, S. A. (Steven A.), Mathias, R. A. (Rasika A.), Martinez, K. A. (Karine A. Viaud), McGarvey, S. T. (Stephen T.), Mitche, B. D. (Braxton D.), Nickerson, D. A. (Deborah A.), North, K. E. (Kari E.), Palotie, A. (Aarno), Park, C. J. (Cheol Joo), Psat, B. M. (Bruce M. Y.), Rao, D. C. (D. C.), Redline, S. (Susan), Reiner, A. P. (Alexander P.), Seo, D. (Daekwan), Seo, J.-S. (Jeong-Sun), Smith, A. V. (Albert, V), Tracy, R. P. (Russell P.), Kathiresan, S. (Sekar), Cupples, L. A. (L. Adrienne), Rotten, J. I. (Jerome, I), Morrison, A. C. (Alanna C.), Rich, S. S. (Stephen S.), Ripatti, S. (Samuli), Wilier, C. (Cristen), Peloso, G. M. (Gina M.), Vasan, R. S. (Ramachandran S.), Abe, N. (Namiko), Albert, C. (Christine), Almasy, L. (Laura), Alonso, A. (Alvaro), Ament, S. (Seth), Anderson, P. (Peter), Applebaum-Bowden, D. (Deborah), Arking, D. (Dan), Ashley-Koch, A. (Allison), Auer, P. (Paul), Avramopoulos, D. (Dimitrios), Barnard, J. (John), Barnes, K. (Kathleen), Barr, R. G. (R. Graham), Barron-Casella, E. (Emily), Beaty, T. (Terri), Becker, D. (Diane), Beer, R. (Rebecca), Begum, F. (Ferdouse), Beitelshees, A. (Amber), Benjamin, E. (Emelia), Bezerra, M. (Marcos), Bielak, L. (Larry), Blackwel, T. (Thomas), Bowler, R. (Russell), Broecke, U. (Ulrich), Bunting, K. (Karen), Burchard, E. (Esteban), Buth, E. (Erin), Cardwel, J. (Jonathan), Carty, C. (Cara), Casaburi, R. (Richard), Casella, J. (James), Chaffin, M. (Mark), Chang, C. (Christy), Chasman, D. (Daniel), Chavan, S. (Sameer), Chen, B.-J. (Bo-Juen), Chen, W.-M. (Wei-Min), Chol, M. (Michael), Choi, S. H. (Seung Hoan), Chuang, L.-M. (Lee-Ming), Chung, M. (Mina), Conomos, M. P. (Matthew P.), Cornell, E. (Elaine), Crapo, J. (James), Curtis, J. (Jeffrey), Custer, B. (Brian), Damcott, C. (Coleen), Darbar, D. (Dawood), Das, S. (Sayantan), David, S. (Sean), Davis, C. (Colleen), Daya, M. (Michelle), de Andrade, M. (Mariza), DeBaunuo, M. (Michael), Duan, Q. (Qing), Devine, R. D. (Ranjan Deka Dawn DeMeo Scott), Duggirala, Q. R. (Qing Ravi), Durda, J. P. (Jon Peter), Dutcher, S. (Susan), Eaton, C. (Charles), Ekunwe, L. (Lynette), Farber, C. (Charles), Farnaml, L. (Leanna), Fingerlin, T. (Tasha), Flickinger, M. (Matthew), Franceschini, N. (Nora), Fu, M. (Mao), Fullerton, S. M. (Stephanie M.), Fulton, L. (Lucinda), Gan, W. (Weiniu), Gao, Y. (Yan), Gass, M. (Margery), Ge, B. (Bruce), Geng, X. P. (Xiaoqi Priscilla), Gignoux, C. (Chris), Gladwin, M. (Mark), Glahn, D. (David), Gogarten, S. (Stephanie), Gong, D.-W. (Da-Wei), Goring, H. (Harald), Gu, C. C. (C. Charles), Guan, Y. (Yue), Guo, X. (Xiuqing), Haessler, J. (Jeff), Hall, M. (Michael), Harris, D. (Daniel), Hawle, N. Y. (Nicola Y.), Heavner, B. (Ben), Heckbert, S. (Susan), Hernandez, R. (Ryan), Herrington, D. (David), Hersh, C. (Craig), Hidalgo, B. (Bertha), Hixson, J. (James), Hokanson, J. (John), Hong, E. (Elliott), Hoth, K. (Karin), Hsiung, C. A. (Chao Agnes), Huston, H. (Haley), Hwu, C. M. (Chii Min), Jackson, R. (Rebecca), Jain, D. (Deepti), Jaquish, C. (Cashell), Jhun, M. A. (Min A.), Johnsen, J. (Jill), Johnson, A. (Andrew), Johnson, C. (Craig), Johnston, R. (Rich), Jones, K. (Kimberly), Kang, H. M. (Hyun Min), Kaufman, L. (Laura), Kell, S. Y. (Shannon Y.), Kessler, M. (Michael), Kinney, G. (Greg), Konkle, B. (Barbara), Kramer, H. (Holly), Krauter, S. (Stephanie), Lange, C. (Christoph), Lange, E. (Ethan), Laurie, C. (Cecelia), LeBoff, M. (Meryl), Lee, S. S. (Seunggeun Shawn), Lee, W.-J. (Wen-Jane), LeFaive, J. (Jonathon), Levine, D. (David), Levy, D. (Dan), Lewis, J. (Joshua), Li, Y. (Yun), Lin, H. (Honghuang), Lin, K. H. (Keng Han), Lin, X. (Xihong), Liu, S. (Simin), Liu, Y. (Yongmei), Lunetta, K. (Kathryn), Luo, J. (James), Mahaney, M. (Michael), Make, B. (Barry), Manichaikul, A. (Ani), Mansonl, J. (JoAnn), Margolin, L. (Lauren), Mathai, S. (Susan), McArdle, P. (Patrick), Mcdonald, M.-L. (Merry-Lynn), McFarland, S. (Sean), McHugh, C. (Caitlin), Mei, H. (Hao), Meyers, D. A. (Deborah A.), Mikulla, J. (Julie), Min, N. (Nancy), Minear, M. (Mollie), Minster, R. L. (Ryan L.), Musani, S. (Solomon), Mwasongwe, S. (Stanford), Mychaleckyj, J. C. (Josyf C.), Nadkarni, G. (Girish), Naik, R. (Rakhi), Naseri, T. (Take), Nekhai, S. (Sergei), Nelson, S. C. (Sarah C.), Nickerson, D. (Deborah), Connell, J. O. (Jeff O.), Connor, T. O. (Tim O.), Ochs-Balcom, H. (Heather), Pankow, J. (James), Papanicolaou, G. (George), Parkerl, M. (Margaret), Parsa, A. (Afshin), Penchey, S. (Sara), Perez, M. (Marco), Peters, U. (Ulrike), Phillips, L. S. (Lawrence S.), Phillips, S. (Sam), Pollin, T. (Toni), Post, W. (Wendy), Becker, J. P. (Julia Powers), Boorgula, M. P. (Meher Preethi), Preuss, M. (Michael), Prokopenko, D. (Dmitry), Qasba, P. (Pankaj), Qiao, D. (Dandi), Rafaels, N. (Nicholas), Raffield, L. (Laura), Rasmussen-Torvik, L. (Laura), Ratan, A. (Aakrosh), Reed, R. (Robert), Reganl, E. (Elizabeth), Reupena, M. S. (Muagututi Sefuiva), Rice, K. (Ken), Roden, D. (Dan), Roselli, C. (Carolina), Ruczinski, I. (Ingo), Russel, P. (Pamela), Ruuska, S. (Sarah), Ryan, K. (Kathleen), Sabino, E. C. (Ester Cerdeira), Sakornsakolpatl, P. (Phuwanat), Salzberg, S. (Steven), Sandow, K. (Kevin), Sankaran, V. G. (Vijay G.), Scheller, C. (Christopher), Schmidt, E. (Ellen), Schwander, K. (Karen), Schwartz, D. (David), Sciurba, F. (Frank), Seidman, C. (Christine), Seidman, J. (Jonathan), Sheehan, V. (Vivien), Shetty, A. (Amol), Shetty, A. (Aniket), Sheu, W. H. (Wayne Hui-Heng), Shoemaker, M. B. (M. Benjamin), Silver, B. (Brian), Silvermanl, E. (Edwin), Smith, J. (Jennifer), Smith, J. (Josh), Smith, N. (Nicholas), Smith, T. (Tanja), Smoller, S. (Sylvia), Snively, B. (Beverly), Soferlm, T. (Tamar), Streeten, E. (Elizabeth), Su, J. L. (Jessica Lasky), Sung, Y. J. (Yun Ju), Sylvia, J. (Jody), Sztalryd, C. (Carole), Taliun, D. (Daniel), Tang, H. (Hua), Taub, M. (Margaret), Taylor, K. D. (Kent D.), Taylor, S. (Simeon), Telen, M. (Marilyn), Thornton, T. A. (Timothy A.), Tinker, L. (Lesley), Tirschwel, D. (David), Tiwari, H. (Hemant), Vaidya, D. (Dhananjay), VandeHaar, P. (Peter), Vrieze, S. (Scott), Walker, T. (Tarik), Wallace, R. (Robert), Waits, A. (Avram), Wan, E. (Emily), Wang, H. (Heming), Watson, K. (Karol), Weir, B. (Bruce), Weiss, S. (Scott), Weng, L.-C. (Lu-Chen), Williams, K. (Kayleen), Williams, L. K. (L. Keoki), Wilson, C. (Carla), Wong, Q. (Quenna), Xu, H. (Huichun), Yang, I. (Ivana), Yang, R. (Rongze), Zaghlou, N. (Norann), Zekavat, M. (Maryam), Zhang, Y. (Yingze), Zhao, S. X. (Snow Xueyan), Zhao, W. (Wei), Zni, D. (Degui), Zhou, X. (Xiang), Zhu, X. (Xiaofeng), Zody, M. (Michael), Zoellner, S. (Sebastian), Daly, M. (Mark), Jacob, H. (Howard), Matakidou, A. (Athena), Runz, H. (Heiko), John, S. (Sally), Plenge, R. (Robert), McCarthy, M. (Mark), Hunkapiller, J. (Julie), Ehm, M. (Meg), Waterworth, D. (Dawn), Fox, C. (Caroline), Malarstig, A. (Anders), Klinger, K. (Kathy), Call, K. (Kathy), Mkel, T. (Tomi), Kaprio, J. (Jaakko), Virolainen, P. (Petri), Pulkki, K. (Kari), Kilpi, T. (Terhi), Perola, M. (Markus), Partanen, J. (Jukka), Pitkranta, A. (Anne), Kaarteenaho, R. (Riitta), Vainio, S. (Seppo), Savinainen, K. (Kimmo), Kosma, V.-M. (Veli-Matti), Kujala, U. (Urho), Tuovila, O. (Outi), Hendolin, M. (Minna), Pakkanen, R. (Raimo), Waring, J. (Jeff), Riley-Gillis, B. (Bridget), Liu, J. (Jimmy), Biswas, S. (Shameek), Diogo, D. (Dorothee), Marshall, C. (Catherine), Hu, X. (Xinli), Gossel, M. (Matthias), Schleutker, J. (Johanna), Arvas, M. (Mikko), Hinttala, R. (Reetta), Kettunen, J. (Johannes), Laaksonen, R. (Reijo), Mannermaa, A. (Arto), Paloneva, J. (Juha), Soininen, H. (Hilkka), Julkunen, V. (Valtteri), Remes, A. (Anne), Klviinen, R. (Reetta), Hiltunen, M. (Mikko), Peltola, J. (Jukka), Tienari, P. (Pentti), Rinne, J. (Juha), Ziemann, A. (Adam), Waring, J. (Jeffrey), Esmaeeli, S. (Sahar), Smaoui, N. (Nizar), Lehtonen, A. (Anne), Eaton, S. (Susan), Landenper, S. (Sanni), Michon, J. (John), Kerchner, G. (Geoff), Bowers, N. (Natalie), Teng, E. (Edmond), Eicher, J. (John), Mehta, V. (Vinay), Gormle, P. Y. (Padhraig Y.), Linden, K. (Kari), Whelan, C. (Christopher), Xu, F. (Fanli), Pulford, D. (David), Frkkil, M. (Martti), Pikkarainen, S. (Sampsa), Jussila, A. (Airi), Blomster, T. (Timo), Kiviniemi, M. (Mikko), Voutilainen, M. (Markku), Georgantas, B. (Bob), Heap, G. (Graham), Rahimov, F. (Fedik), Usiskin, K. (Keith), Maranville, J. (Joseph), Lu, T. (Tim), Oh, D. (Danny), Kalpala, K. (Kirsi), Miller, M. (Melissa), McCarthy, L. (Linda), Eklund, K. (Kari), Palomki, A. (Antti), Isomki, P. (Pia), Piri, L. (Laura), Kaipiainen-Seppnen, O. (Oili), Lertratanaku, A. (Apinya), Bing, D. C. (David Close Marla Hochfeld Nan), Gordillo, J. E. (Jorge Esparza), Mars, N. (Nina), Laitinen, T. (Tarja), Pelkonen, M. (Margit), Kauppi, P. (Paula), Kankaanranta, H. (Hannu), Harju, T. (Terttu), Greenberg, S. (Steven), Chen, H. (Hubert), Betts, J. (Jo), Ghosh, S. (Soumitra), Salomaa, V. (Veikko), Niiranen, T. (Teemu), Juonala, M. (Markus), Metsrinne, K. (Kaj), Khnen, M. (Mika), Junttila, J. (Juhani), Laakso, M. (Markku), Pihlajamki, J. (Jussi), Sinisalo, J. (Juha), Taskinen, M.-R. (Marja-Riitta), Tuomi, T. (Tiinamaija), Laukkanen, J. (Jari), Challis, B. (Ben), Peterson, A. (Andrew), Chu, A. (Audrey), Parkkinen, J. (Jaakko), Muslin, A. (Anthony), Joensuu, H. (Heikki), Meretoja, T. (Tuomo), Aaltonen, L. (Lauri), Auranen, A. (Annika), Karihtala, P. (Peeter), Kauppila, S. (Saila), Auvinen, P. (Pivi), Elenius, K. (Klaus), Popovic, R. (Relja), Schutzman, J. (Jennifer), Loboda, A. (Andrey), Chhibber, A. (Aparna), Lehtonen, H. (Heli), McDonough, S. (Stefan), Crohns, M. (Marika), Kulkarni, D. (Diptee), Kaarniranta, K. (Kai), Turunen, J. (Joni), Ollila, T. (Terhi), Seitsonen, S. (Sanna), Uusitalo, H. (Hannu), Aaltonen, V. (Vesa), Uusitalo-Jrvinen, H. (Hannele), Luodonp, M. (Marja), Hautala, N. (Nina), Strauss, E. (Erich), Chen, H. (Hao), Podgornaia, A. (Anna), Hoffman, J. (Joshua), Tasanen, K. (Kaisa), Huilaja, L. (Laura), Hannula-Jouppi, K. (Katariina), Salmi, T. (Teea), Peltonen, S. (Sirkku), Koulu, L. (Leena), Harvima, I. (Ilkka), Wu, Y. (Ying), Choy, D. (David), Jalanko, A. (Anu), Kajanne, R. (Risto), Lyhs, U. (Ulrike), Kaunisto, M. (Mari), Davis, J. W. (Justin Wade), Quarless, D. (Danjuma), Petrovski, S. (Slav), Chen, C.-Y. (Chia-Yen), Bronson, P. (Paola), Yang, R. (Robert), Chang, D. (Diana), Bhangale, T. (Tushar), Holzinger, E. (Emily), Wang, X. (Xulong), Chen, X. (Xing), Auro, K. (Kirsi), Wang, C. (Clarence), Xu, E. (Ethan), Auge, F. (Franck), Chatelain, C. (Clement), Kurki, M. (Mitja), Karjalainen, J. (Juha), Havulinna, A. (Aki), Palin, K. (Kimmo), Palta, P. (Priit), Parolo, P. D. (Pietro Della Briotta), Zhou, W. (Wei), Lemmel, S. (Susanna), Rivas, M. (Manuel), Harju, J. (Jarmo), Lehisto, A. (Arto), Ganna, A. (Andrea), Llorens, V. (Vincent), Karlsson, A. (Antti), Kristiansson, K. (Kati), Hyvrinen, K. (Kati), Ritari, J. (Jarmo), Wahlfors, T. (Tiina), Koskinen, M. (Miika), Pylkäs, K. (Katri), Kalaoja, M. (Marita), Karjalainen, M. (Minna), Mantere, T. (Tuomo), Kangasniemi, E. (Eeva), Heikkinen, S. (Sami), Laakkonen, E. (Eija), Kononen, J. (Juha), Loukola, A. (Anu), Laiho, P. (Pivi), Sistonen, T. (Tuuli), Kaiharju, E. (Essi), Laukkanen, M. (Markku), Jrvensivu, E. (Elina), Lhteenmki, S. (Sini), Mnnikk, L. (Lotta), Wong, R. (Regis), Mattsson, H. (Hannele), Hiekkalinna, T. (Tero), Jimnez, M. G. (Manuel Gonzlez), Donner, K. (Kati), Prn, K. (KaIle), Nunez-Fontarnau, J. (Javier), Kilpelinen, E. (Elina), Sipi, T. P. (Timo P.), Brein, G. (Georg), Dada, A. (Alexander), Awaisa, G. (Ghazal), Shcherban, A. (Anastasia), Sipil, T. (Tuomas), Laivuori, H. (Hannele), Kiiskinen, T. (Tuomo), Siirtola, H. (Harri), Tabuenca, J. G. (Javier Gracia), Kallio, L. (Lila), Soini, S. (Sirpa), Pitknen, K. (Kimmo), and Kuopio, T. (Teijo)
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Cardiovascular genetics ,Genome-wide association studies - Abstract
Autosomal genetic analyses of blood lipids have yielded key insights for coronary heart disease (CHD). However, X chromosome genetic variation is understudied for blood lipids in large sample sizes. We now analyze genetic and blood lipid data in a high-coverage whole X chromosome sequencing study of 65,322 multi-ancestry participants and perform replication among 456,893 European participants. Common alleles on chromosome Xq23 are strongly associated with reduced total cholesterol, LDL cholesterol, and triglycerides (min P = 8.5 × 10−72), with similar effects for males and females. Chromosome Xq23 lipid-lowering alleles are associated with reduced odds for CHD among 42,545 cases and 591,247 controls (P = 1.7 × 10−4), and reduced odds for diabetes mellitus type 2 among 54,095 cases and 573,885 controls (P = 1.4 × 10−5). Although we observe an association with increased BMI, waist-to-hip ratio adjusted for BMI is reduced, bioimpedance analyses indicate increased gluteofemoral fat, and abdominal MRI analyses indicate reduced visceral adiposity. Co-localization analyses strongly correlate increased CHRDL1 gene expression, particularly in adipose tissue, with reduced concentrations of blood lipids.
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- 2021
18. Genome-wide association study of serious blistering skin rash caused by drugs
- Author
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Shen, Y, Nicoletti, P, Floratos, A, Pirmohamed, M, Molokhia, M, Geppetti, P, Benemei, S, Giomi, B, Schena, D, Vultaggio, A, Stern, R, Daly, M J, John, S, Nelson, M R, and Pe'er, I
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- 2012
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19. Common genetic variants differentially influence the transition from clinically defined states of fasting glucose metabolism
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Walford, G. A., Green, T., Neale, B., Isakova, T., Rotter, J. I., Grant, S. F. A., Fox, C. S., Pankow, J. S., Wilson, J. G., Meigs, J. B., Siscovick, D. S., Bowden, D. W., Daly, M. J., and Florez, J. C.
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- 2012
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20. Response to ‘Predicting the diagnosis of autism spectrum disorder using gene pathway analysis’
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Robinson, E B, Howrigan, D, Yang, J, Ripke, S, Anttila, V, Duncan, L E, Jostins, L, Barrett, J C, Medland, S E, MacArthur, D G, Breen, G, OʼDonovan, M C, Wray, N R, Devlin, B, Daly, M J, Visscher, P M, Sullivan, P F, and Neale, B M
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- 2014
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21. Guidelines for investigating causality of sequence variants in human disease
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MacArthur, D. G., Manolio, T. A., Dimmock, D. P., Rehm, H. L., Shendure, J., Abecasis, G. R., Adams, D. R., Altman, R. B., Antonarakis, S. E., Ashley, E. A., Barrett, J. C., Biesecker, L. G., Conrad, D. F., Cooper, G. M., Cox, N. J., Daly, M. J., Gerstein, M. B., Goldstein, D. B., Hirschhorn, J. N., Leal, S. M., Pennacchio, L. A., Stamatoyannopoulos, J. A., Sunyaev, S. R., Valle, D., Voight, B. F., Winckler, W., and Gunter, C.
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- 2014
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22. Multigenic control of tuberculosis resistance: analysis of a QTL on mouse chromosome 7 and its synergism with sst1
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Sissons, J, Yan, B-S, Pichugin, A V, Kirby, A, Daly, M J, and Kramnik, I
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- 2009
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23. Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data
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Romagnoni, A., Jegou, S., Van Steen, K., Wainrib, G., Hugot, J. -P., Peyrin-Biroulet, L., Chamaillard, M., Colombel, J. -F., Cottone, M., D'Amato, M., D'Inca, R., Halfvarson, J., Henderson, P., Karban, A., Kennedy, N. A., Khan, M. A., Lemann, M., Levine, A., Massey, D., Milla, M., S. M. E., Ng, Oikonomou, I., Peeters, H., Proctor, D. D., Rahier, J. -F., Rutgeerts, P., Seibold, F., Stronati, L., Taylor, K. M., Torkvist, L., Ublick, K., Van Limbergen, J., Van Gossum, A., Vatn, M. H., Zhang, H., Zhang, W., Andrews, J. M., Bampton, P. A., Barclay, M., Florin, T. H., Gearry, R., Krishnaprasad, K., Lawrance, I. C., Mahy, G., Montgomery, G. W., Radford-Smith, G., Roberts, R. L., Simms, L. A., Hanigan, K., Croft, A., Amininijad, L., Cleynen, I., Dewit, O., Franchimont, D., Georges, M., Laukens, D., Theatre, E., Vermeire, S., Aumais, G., Baidoo, L., Barrie, A. M., Beck, K., Bernard, E. -J., Binion, D. G., Bitton, A., Brant, S. R., Cho, J. H., Cohen, A., Croitoru, K., Daly, M. J., Datta, L. W., Deslandres, C., Duerr, R. H., Dutridge, D., Ferguson, J., Fultz, J., Goyette, P., Greenberg, G. R., Haritunians, T., Jobin, G., Katz, S., Lahaie, R. G., Mcgovern, D. P., Nelson, L., S. M., Ng, Ning, K., Pare, P., Regueiro, M. D., Rioux, J. D., Ruggiero, E., Schumm, L. P., Schwartz, M., Scott, R., Sharma, Y., Silverberg, M. S., Spears, D., Steinhart, A. H., Stempak, J. M., Swoger, J. M., Tsagarelis, C., Zhang, C., Zhao, H., Aerts, J., Ahmad, T., Arbury, H., Attwood, A., Auton, A., Ball, S. G., Balmforth, A. J., Barnes, C., Barrett, J. C., Barroso, I., Barton, A., Bennett, A. J., Bhaskar, S., Blaszczyk, K., Bowes, J., Brand, O. J., Braund, P. S., Bredin, F., Breen, G., Brown, M. J., Bruce, I. N., Bull, J., Burren, O. S., Burton, J., Byrnes, J., Caesar, S., Cardin, N., Clee, C. M., Coffey, A. J., MC Connell, J., Conrad, D. F., Cooper, J. D., Dominiczak, A. F., Downes, K., Drummond, H. E., Dudakia, D., Dunham, A., Ebbs, B., Eccles, D., Edkins, S., Edwards, C., Elliot, A., Emery, P., Evans, D. M., Evans, G., Eyre, S., Farmer, A., Ferrier, I. N., Flynn, E., Forbes, A., Forty, L., Franklyn, J. A., Frayling, T. M., Freathy, R. M., Giannoulatou, E., Gibbs, P., Gilbert, P., Gordon-Smith, K., Gray, E., Green, E., Groves, C. J., Grozeva, D., Gwilliam, R., Hall, A., Hammond, N., Hardy, M., Harrison, P., Hassanali, N., Hebaishi, H., Hines, S., Hinks, A., Hitman, G. A., Hocking, L., Holmes, C., Howard, E., Howard, P., Howson, J. M. M., Hughes, D., Hunt, S., Isaacs, J. D., Jain, M., Jewell, D. P., Johnson, T., Jolley, J. D., Jones, I. R., Jones, L. A., Kirov, G., Langford, C. F., Lango-Allen, H., Lathrop, G. M., Lee, J., Lee, K. L., Lees, C., Lewis, K., Lindgren, C. M., Maisuria-Armer, M., Maller, J., Mansfield, J., Marchini, J. L., Martin, P., Massey, D. C., Mcardle, W. L., Mcguffin, P., Mclay, K. E., Mcvean, G., Mentzer, A., Mimmack, M. L., Morgan, A. E., Morris, A. P., Mowat, C., Munroe, P. B., Myers, S., Newman, W., Nimmo, E. R., O'Donovan, M. C., Onipinla, A., Ovington, N. R., Owen, M. J., Palin, K., Palotie, A., Parnell, K., Pearson, R., Pernet, D., Perry, J. R., Phillips, A., Plagnol, V., Prescott, N. J., Prokopenko, I., Quail, M. A., Rafelt, S., Rayner, N. W., Reid, D. M., Renwick, A., Ring, S. M., Robertson, N., Robson, S., Russell, E., Clair, D. S., Sambrook, J. G., Sanderson, J. D., Sawcer, S. J., Schuilenburg, H., Scott, C. E., Seal, S., Shaw-Hawkins, S., Shields, B. M., Simmonds, M. J., Smyth, D. J., Somaskantharajah, E., Spanova, K., Steer, S., Stephens, J., Stevens, H. E., Stirrups, K., Stone, M. A., Strachan, D. P., Su, Z., Symmons, D. P. M., Thompson, J. R., Thomson, W., Tobin, M. D., Travers, M. E., Turnbull, C., Vukcevic, D., Wain, L. V., Walker, M., Walker, N. M., Wallace, C., Warren-Perry, M., Watkins, N. A., Webster, J., Weedon, M. N., Wilson, A. G., Woodburn, M., Wordsworth, B. P., Yau, C., Young, A. H., Zeggini, E., Brown, M. A., Burton, P. R., Caulfield, M. J., Compston, A., Farrall, M., Gough, S. C. L., Hall, A. S., Hattersley, A. T., Hill, A. V. S., Mathew, C. G., Pembrey, M., Satsangi, J., Stratton, M. R., Worthington, J., Hurles, M. E., Duncanson, A., Ouwehand, W. H., Parkes, M., Rahman, N., Todd, J. A., Samani, N. J., Kwiatkowski, D. P., Mccarthy, M. I., Craddock, N., Deloukas, P., Donnelly, P., Blackwell, J. M., Bramon, E., Casas, J. P., Corvin, A., Jankowski, J., Markus, H. S., Palmer, C. N., Plomin, R., Rautanen, A., Trembath, R. C., Viswanathan, A. C., Wood, N. W., Spencer, C. C. A., Band, G., Bellenguez, C., Freeman, C., Hellenthal, G., Pirinen, M., Strange, A., Blackburn, H., Bumpstead, S. J., Dronov, S., Gillman, M., Jayakumar, A., Mccann, O. T., Liddle, J., Potter, S. C., Ravindrarajah, R., Ricketts, M., Waller, M., Weston, P., Widaa, S., Whittaker, P., Romagnoni, A., Jegou, S., Van Steen, K., Wainrib, G., Hugot, J. -P., Peyrin-Biroulet, L., Chamaillard, M., Colombel, J. -F., Cottone, M., D'Amato, M., D'Inca, R., Halfvarson, J., Henderson, P., Karban, A., Kennedy, N. A., Khan, M. A., Lemann, M., Levine, A., Massey, D., Milla, M., Ng, S. M. E., Oikonomou, I., Peeters, H., Proctor, D. D., Rahier, J. -F., Rutgeerts, P., Seibold, F., Stronati, L., Taylor, K. M., Torkvist, L., Ublick, K., Van Limbergen, J., Van Gossum, A., Vatn, M. H., Zhang, H., Zhang, W., Andrews, J. M., Bampton, P. A., Barclay, M., Florin, T. H., Gearry, R., Krishnaprasad, K., Lawrance, I. C., Mahy, G., Montgomery, G. W., Radford-Smith, G., Roberts, R. L., Simms, L. A., Hanigan, K., Croft, A., Amininijad, L., Cleynen, I., Dewit, O., Franchimont, D., Georges, M., Laukens, D., Theatre, E., Vermeire, S., Aumais, G., Baidoo, L., Barrie, A. M., Beck, K., Bernard, E. -J., Binion, D. G., Bitton, A., Brant, S. R., Cho, J. H., Cohen, A., Croitoru, K., Daly, M. J., Datta, L. W., Deslandres, C., Duerr, R. H., Dutridge, D., Ferguson, J., Fultz, J., Goyette, P., Greenberg, G. R., Haritunians, T., Jobin, G., Katz, S., Lahaie, R. G., Mcgovern, D. P., Nelson, L., Ng, S. M., Ning, K., Pare, P., Regueiro, M. D., Rioux, J. D., Ruggiero, E., Schumm, L. P., Schwartz, M., Scott, R., Sharma, Y., Silverberg, M. S., Spears, D., Steinhart, A. H., Stempak, J. M., Swoger, J. M., Tsagarelis, C., Zhang, C., Zhao, H., Aerts, J., Ahmad, T., Arbury, H., Attwood, A., Auton, A., Ball, S. G., Balmforth, A. J., Barnes, C., Barrett, J. C., Barroso, I., Barton, A., Bennett, A. J., Bhaskar, S., Blaszczyk, K., Bowes, J., Brand, O. J., Braund, P. S., Bredin, F., Breen, G., Brown, M. J., Bruce, I. N., Bull, J., Burren, O. S., Burton, J., Byrnes, J., Caesar, S., Cardin, N., Clee, C. M., Coffey, A. J., MC Connell, J., Conrad, D. F., Cooper, J. D., Dominiczak, A. F., Downes, K., Drummond, H. E., Dudakia, D., Dunham, A., Ebbs, B., Eccles, D., Edkins, S., Edwards, C., Elliot, A., Emery, P., Evans, D. M., Evans, G., Eyre, S., Farmer, A., Ferrier, I. N., Flynn, E., Forbes, A., Forty, L., Franklyn, J. A., Frayling, T. M., Freathy, R. M., Giannoulatou, E., Gibbs, P., Gilbert, P., Gordon-Smith, K., Gray, E., Green, E., Groves, C. J., Grozeva, D., Gwilliam, R., Hall, A., Hammond, N., Hardy, M., Harrison, P., Hassanali, N., Hebaishi, H., Hines, S., Hinks, A., Hitman, G. A., Hocking, L., Holmes, C., Howard, E., Howard, P., Howson, J. M. M., Hughes, D., Hunt, S., Isaacs, J. D., Jain, M., Jewell, D. P., Johnson, T., Jolley, J. D., Jones, I. R., Jones, L. A., Kirov, G., Langford, C. F., Lango-Allen, H., Lathrop, G. M., Lee, J., Lee, K. L., Lees, C., Lewis, K., Lindgren, C. M., Maisuria-Armer, M., Maller, J., Mansfield, J., Marchini, J. L., Martin, P., Massey, D. C., Mcardle, W. L., Mcguffin, P., Mclay, K. E., Mcvean, G., Mentzer, A., Mimmack, M. L., Morgan, A. E., Morris, A. P., Mowat, C., Munroe, P. B., Myers, S., Newman, W., Nimmo, E. R., O'Donovan, M. C., Onipinla, A., Ovington, N. R., Owen, M. J., Palin, K., Palotie, A., Parnell, K., Pearson, R., Pernet, D., Perry, J. R., Phillips, A., Plagnol, V., Prescott, N. J., Prokopenko, I., Quail, M. A., Rafelt, S., Rayner, N. W., Reid, D. M., Renwick, A., Ring, S. M., Robertson, N., Robson, S., Russell, E., Clair, D. S., Sambrook, J. G., Sanderson, J. D., Sawcer, S. J., Schuilenburg, H., Scott, C. E., Seal, S., Shaw-Hawkins, S., Shields, B. M., Simmonds, M. J., Smyth, D. J., Somaskantharajah, E., Spanova, K., Steer, S., Stephens, J., Stevens, H. E., Stirrups, K., Stone, M. A., Strachan, D. P., Su, Z., Symmons, D. P. M., Thompson, J. R., Thomson, W., Tobin, M. D., Travers, M. E., Turnbull, C., Vukcevic, D., Wain, L. V., Walker, M., Walker, N. M., Wallace, C., Warren-Perry, M., Watkins, N. A., Webster, J., Weedon, M. N., Wilson, A. G., Woodburn, M., Wordsworth, B. P., Yau, C., Young, A. H., Zeggini, E., Brown, M. A., Burton, P. R., Caulfield, M. J., Compston, A., Farrall, M., Gough, S. C. L., Hall, A. S., Hattersley, A. T., Hill, A. V. S., Mathew, C. G., Pembrey, M., Satsangi, J., Stratton, M. R., Worthington, J., Hurles, M. E., Duncanson, A., Ouwehand, W. H., Parkes, M., Rahman, N., Todd, J. A., Samani, N. J., Kwiatkowski, D. P., Mccarthy, M. I., Craddock, N., Deloukas, P., Donnelly, P., Blackwell, J. M., Bramon, E., Casas, J. P., Corvin, A., Jankowski, J., Markus, H. S., Palmer, C. N., Plomin, R., Rautanen, A., Trembath, R. C., Viswanathan, A. C., Wood, N. W., Spencer, C. C. A., Band, G., Bellenguez, C., Freeman, C., Hellenthal, G., Pirinen, M., Strange, A., Blackburn, H., Bumpstead, S. J., Dronov, S., Gillman, M., Jayakumar, A., Mccann, O. T., Liddle, J., Potter, S. C., Ravindrarajah, R., Ricketts, M., Waller, M., Weston, P., Widaa, S., Whittaker, P., Daly, Mark J. [0000-0002-0949-8752], Apollo - University of Cambridge Repository, Hugot, Jean-Pierre [0000-0002-8446-6056], UCL - SSS/IREC/GAEN - Pôle d'Hépato-gastro-entérologie, UCL - (MGD) Service de gastro-entérologie, Romagnoni, A, Jegou, S, VAN STEEN, Kristel, Wainrib, G, Hugot, JP, Peyrin-Biroulet, L, Chamaillard, M, Colombel, JF, Cottone, M, D'Amato, M, D'Inca, R, Halfvarson, J, Henderson, P, Karban, A, Kennedy, NA, Khan, MA, Lemann, M, Levine, A, Massey, D, Milla, M, Ng, SME, Oikonomou, I, Peeters, H, Proctor, DD, Rahier, JF, Rutgeerts, P, Seibold, F, Stronati, L, Taylor, KM, Torkvist, L, Ublick, K, Van Limbergen, J, Van Gossum, A, Vatn, MH, Zhang, H, Zhang, W, Andrews, JM, Bampton, PA, Barclay, M, Florin, TH, Gearry, R, Krishnaprasad, K, Lawrance, IC, Mahy, G, Montgomery, GW, Radford-Smith, G, Roberts, RL, Simms, LA, Hanigan, K, Croft, A, Amininijad, L, Cleynen, I, Dewit, O, Franchimont, D, Georges, M, Laukens, D, Theatre, E, Vermeire, S, Aumais, G, Baidoo, L, Barrie, AM, Beck, K, Bernard, EJ, Binion, DG, Bitton, A, Brant, SR, Cho, JH, Cohen, A, Croitoru, K, Daly, MJ, Datta, LW, Deslandres, C, Duerr, RH, Dutridge, D, Ferguson, J, Fultz, J, Goyette, P, Greenberg, GR, Haritunians, T, Jobin, G, Katz, S, Lahaie, RG, McGovern, DP, Nelson, L, Ng, SM, Ning, K, Pare, P, Regueiro, MD, Rioux, JD, Ruggiero, E, Schumm, LP, Schwartz, M, Scott, R, Sharma, Y, Silverberg, MS, Spears, D, Steinhart, AH, Stempak, JM, Swoger, JM, Tsagarelis, C, Zhang, C, Zhao, HY, AERTS, Jan, Ahmad, T, Arbury, H, Attwood, A, Auton, A, Ball, SG, Balmforth, AJ, Barnes, C, Barrett, JC, Barroso, I, Barton, A, Bennett, AJ, Bhaskar, S, Blaszczyk, K, Bowes, J, Brand, OJ, Braund, PS, Bredin, F, Breen, G, Brown, MJ, Bruce, IN, Bull, J, Burren, OS, Burton, J, Byrnes, J, Caesar, S, Cardin, N, Clee, CM, Coffey, AJ, Mc Connell, J, Conrad, DF, Cooper, JD, Dominiczak, AF, Downes, K, Drummond, HE, Dudakia, D, Dunham, A, Ebbs, B, Eccles, D, Edkins, S, Edwards, C, Elliot, A, Emery, P, Evans, DM, Evans, G, Eyre, S, Farmer, A, Ferrier, IN, Flynn, E, Forbes, A, Forty, L, Franklyn, JA, Frayling, TM, Freathy, RM, Giannoulatou, E, Gibbs, P, Gilbert, P, Gordon-Smith, K, Gray, E, Green, E, Groves, CJ, Grozeva, D, Gwilliam, R, Hall, A, Hammond, N, Hardy, M, Harrison, P, Hassanali, N, Hebaishi, H, Hines, S, Hinks, A, Hitman, GA, Hocking, L, Holmes, C, Howard, E, Howard, P, Howson, JMM, Hughes, D, Hunt, S, Isaacs, JD, Jain, M, Jewell, DP, Johnson, T, Jolley, JD, Jones, IR, Jones, LA, Kirov, G, Langford, CF, Lango-Allen, H, Lathrop, GM, Lee, J, Lee, KL, Lees, C, Lewis, K, Lindgren, CM, Maisuria-Armer, M, Maller, J, Mansfield, J, Marchini, JL, Martin, P, Massey, DCO, McArdle, WL, McGuffin, P, McLay, KE, McVean, G, Mentzer, A, Mimmack, ML, Morgan, AE, Morris, AP, Mowat, C, Munroe, PB, Myers, S, Newman, W, Nimmo, ER, O'Donovan, MC, Onipinla, A, Ovington, NR, Owen, MJ, Palin, K, Palotie, A, Parnell, K, Pearson, R, Pernet, D, Perry, JRB, Phillips, A, Plagnol, V, Prescott, NJ, Prokopenko, I, Quail, MA, Rafelt, S, Rayner, NW, Reid, DM, Renwick, A, Ring, SM, Robertson, N, Robson, S, Russell, E, St Clair, D, Sambrook, JG, Sanderson, JD, Sawcer, SJ, Schuilenburg, H, Scott, CE, Seal, S, Shaw-Hawkins, S, Shields, BM, Simmonds, MJ, Smyth, DJ, Somaskantharajah, E, Spanova, K, Steer, S, Stephens, J, Stevens, HE, Stirrups, K, Stone, MA, Strachan, DP, Su, Z, Symmons, DPM, Thompson, JR, Thomson, W, Tobin, MD, Travers, ME, Turnbull, C, Vukcevic, D, Wain, LV, Walker, M, Walker, NM, Wallace, C, Warren-Perry, M, Watkins, NA, Webster, J, Weedon, MN, Wilson, AG, Woodburn, M, Wordsworth, BP, Yau, C, Young, AH, Zeggini, E, Brown, MA, Burton, PR, Caulfield, MJ, Compston, A, Farrall, M, Gough, SCL, Hall, AS, Hattersley, AT, Hill, AVS, Mathew, CG, Pembrey, M, Satsangi, J, Stratton, MR, Worthington, J, Hurles, ME, Duncanson, A, Ouwehand, WH, Parkes, M, Rahman, N, Todd, JA, Samani, NJ, Kwiatkowski, DP, McCarthy, MI, Craddock, N, Deloukas, P, Donnelly, P, Blackwell, JM, Bramon, E, Casas, JP, Corvin, A, Jankowski, J, Markus, HS, Palmer, CNA, Plomin, R, Rautanen, A, Trembath, RC, Viswanathan, AC, Wood, NW, Spencer, CCA, Band, G, Bellenguez, C, Freeman, C, Hellenthal, G, Pirinen, M, Strange, A, Blackburn, H, Bumpstead, SJ, Dronov, S, Gillman, M, Jayakumar, A, McCann, OT, Liddle, J, Potter, SC, Ravindrarajah, R, Ricketts, M, Waller, M, Weston, P, Widaa, S, Whittaker, P, and Kwiatkowski, D
- Subjects
Male ,692/4020/1503/257/1402 ,Genotype ,Genotyping Techniques ,LOCI ,45/43 ,lcsh:Medicine ,Polymorphism, Single Nucleotide ,Crohn's disease, genetics, genome wide association ,Article ,Deep Learning ,Crohn Disease ,INDEL Mutation ,Genetics research ,Humans ,genetics ,Genetic Predisposition to Disease ,129 ,lcsh:Science ,Alleles ,Science & Technology ,genome wide association ,RISK PREDICTION ,45 ,Models, Genetic ,lcsh:R ,Decision Trees ,692/308/2056 ,ASSOCIATION ,Multidisciplinary Sciences ,Crohn's disease ,Logistic Models ,Nonlinear Dynamics ,ROC Curve ,Area Under Curve ,Science & Technology - Other Topics ,lcsh:Q ,Female ,Neural Networks, Computer ,INFLAMMATORY-BOWEL-DISEASE ,Genome-Wide Association Study - Abstract
Crohn Disease (CD) is a complex genetic disorder for which more than 140 genes have been identified using genome wide association studies (GWAS). However, the genetic architecture of the trait remains largely unknown. The recent development of machine learning (ML) approaches incited us to apply them to classify healthy and diseased people according to their genomic information. The Immunochip dataset containing 18,227 CD patients and 34,050 healthy controls enrolled and genotyped by the international Inflammatory Bowel Disease genetic consortium (IIBDGC) has been re-analyzed using a set of ML methods: penalized logistic regression (LR), gradient boosted trees (GBT) and artificial neural networks (NN). The main score used to compare the methods was the Area Under the ROC Curve (AUC) statistics. The impact of quality control (QC), imputing and coding methods on LR results showed that QC methods and imputation of missing genotypes may artificially increase the scores. At the opposite, neither the patient/control ratio nor marker preselection or coding strategies significantly affected the results. LR methods, including Lasso, Ridge and ElasticNet provided similar results with a maximum AUC of 0.80. GBT methods like XGBoost, LightGBM and CatBoost, together with dense NN with one or more hidden layers, provided similar AUC values, suggesting limited epistatic effects in the genetic architecture of the trait. ML methods detected near all the genetic variants previously identified by GWAS among the best predictors plus additional predictors with lower effects. The robustness and complementarity of the different methods are also studied. Compared to LR, non-linear models such as GBT or NN may provide robust complementary approaches to identify and classify genetic markers. Tis work was supported by Fondation pour la Recherche Médical (ref DEI20151234405) and Investissements d’Avenir programme ANR-11-IDEX-0005-02, Sorbonne Paris Cite, Laboratoire d’excellence INFLAMEX. Te authors thank the students that participated to the wisdom of the crowd exercise.
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- 2019
24. MAST3: a novel IBD risk factor that modulates TLR4 signaling
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Labbé, C, Goyette, P, Lefebvre, C, Stevens, C, Green, T, Tello-Ruiz, M K, Cao, Z, Landry, A L, Stempak, J, Annese, V, Latiano, A, Brant, S R, Duerr, R H, Taylor, K D, Cho, J H, Steinhart, A H, Daly, M J, Silverberg, M S, Xavier, R J, and Rioux, J D
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- 2008
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25. Whole-genome association study of bipolar disorder
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Sklar, P, Smoller, J W, Fan, J, Ferreira, M A R, Perlis, R H, Chambert, K, Nimgaonkar, V L, McQueen, M B, Faraone, S V, Kirby, A, de Bakker, P I W, Ogdie, M N, Thase, M E, Sachs, G S, Todd-Brown, K, Gabriel, S B, Sougnez, C, Gates, C, Blumenstiel, B, Defelice, M, Ardlie, K G, Franklin, J, Muir, W J, McGhee, K A, MacIntyre, D J, McLean, A, VanBeck, M, McQuillin, A, Bass, N J, Robinson, M, Lawrence, J, Anjorin, A, Curtis, D, Scolnick, E M, Daly, M J, Blackwood, D H, Gurling, H M, and Purcell, S M
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- 2008
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26. The role of the Toll receptor pathway in susceptibility to inflammatory bowel diseases
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De Jager, P L, Franchimont, D, Waliszewska, A, Bitton, A, Cohen, A, Langelier, D, Belaiche, J, Vermeire, S, Farwell, L, Goris, A, Libioulle, C, Jani, N, Dassopoulos, T, Bromfield, G P, Dubois, B, Cho, J H, Brant, S R, Duerr, R H, Yang, H, Rotter, J I, Silverberg, M S, Steinhart, A H, Daly, M J, Podolsky, D K, Louis, E, Hafler, D A, and Rioux, J D
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- 2007
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27. Association testing of common variants in the insulin receptor substrate-1 gene (IRS1) with type 2 diabetes
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Florez, J. C., Sjögren, M., Agapakis, C. M., Burtt, N. P., Almgren, P., Lindblad, U., Berglund, G., Tuomi, T., Gaudet, D., Daly, M. J., Ardlie, K. G., Hirschhorn, J. N., Altshuler, D., and Groop, L.
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- 2007
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28. Gene family information facilitates variant interpretation and identification of disease-associated genes in neurodevelopmental disorders
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Lal, D., May, P., Perez-Palma, E., Samocha, K. E., Kosmicki, J. A., Robinson, E. B., Moller, R. S., Krause, R., Nurnberg, P., Weckhuysen, S., De Jonghe, P., Guerrini, R., Niestroj, L. M., Du, J., Marini, C., Balling, R., Barisic, N., Baulac, S., Caglayan, H., Craiu, D. C., Depienne, C., Helbig, I., Hjalgrim, H., Hoffman-Zacharska, D., Jahn, J., Klein, K. M., Koeleman, B. P. C., Komarek, V., Leguern, E., Lehesjoki, A. -E., Lemke, J. R., Lerche, H., Linnankivi, T., Muhle, H., Pal, D. K., Palotie, A., Rosenow, F., Schubert-Bast, S., Selmer, K., Serratosa, J. M., Stephani, U., Sterbova, K., Striano, P., Suls, A., Talvik, T., Von Spiczak, S., Weber, Y. G., Zara, F., Ware, J. S., Kurki, M., Gormley, P., Tang, S., Wu, S., Biskup, S., Poduri, A., Neubauer, B. A., Helbig, K. L., Majithia, A. R., Daly, M. J., EuroEPINOMICS-RES Consortium, Centre of Excellence in Complex Disease Genetics, Aarno Palotie / Principal Investigator, Institute for Molecular Medicine Finland, Genomics of Neurological and Neuropsychiatric Disorders, University of Helsinki, Department of Medical and Clinical Genetics, Medicum, HUS Helsinki and Uusimaa Hospital District, and Wellcome Trust
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Candidate gene ,lcsh:QH426-470 ,Developmental Disabilities ,Mutation, Missense ,Sequence Homology ,lcsh:Medicine ,ORTHOLOGS ,Computational biology ,Conservation ,Gene family ,Missense variants ,Neurodevelopmental disorders ,Paralogs ,Biology ,03 medical and health sciences ,MULTIPLE SEQUENCE ALIGNMENT ,PHYLOGENETIC TREES ,Genetics ,Missense mutation ,Ensembl ,Molecular Biology ,Gene ,Genetics (clinical) ,Phylogeny ,030304 developmental biology ,0303 health sciences ,0604 Genetics ,Phylogenetic tree ,Research ,030305 genetics & heredity ,lcsh:R ,1184 Genetics, developmental biology, physiology ,1103 Clinical Sciences ,EuroEPINOMICS-RES Consortium ,Human genetics ,lcsh:Genetics ,Genetic Loci ,DE-NOVO MUTATIONS ,Multigene Family ,Molecular Medicine ,Human medicine ,Orthologous Gene ,Genome-Wide Association Study - Abstract
Background Classifying pathogenicity of missense variants represents a major challenge in clinical practice during the diagnoses of rare and genetic heterogeneous neurodevelopmental disorders (NDDs). While orthologous gene conservation is commonly employed in variant annotation, approximately 80% of known disease-associated genes belong to gene families. The use of gene family information for disease gene discovery and variant interpretation has not yet been investigated on a genome-wide scale. We empirically evaluate whether paralog-conserved or non-conserved sites in human gene families are important in NDDs. Methods Gene family information was collected from Ensembl. Paralog-conserved sites were defined based on paralog sequence alignments; 10,068 NDD patients and 2078 controls were statistically evaluated for de novo variant burden in gene families. Results We demonstrate that disease-associated missense variants are enriched at paralog-conserved sites across all disease groups and inheritance models tested. We developed a gene family de novo enrichment framework that identified 43 exome-wide enriched gene families including 98 de novo variant carrying genes in NDD patients of which 28 represent novel candidate genes for NDD which are brain expressed and under evolutionary constraint. Conclusion This study represents the first method to incorporate gene family information into a statistical framework to interpret variant data for NDDs and to discover new NDD-associated genes.
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- 2020
29. Genetic architecture of tuberculosis resistance in a mouse model of infection
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Yan, B-S, Kirby, A, Shebzukhov, Y V, Daly, M J, and Kramnik, I
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- 2006
- Full Text
- View/download PDF
30. De novo variants in neurodevelopmental disorders with epilepsy
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Heyne, H. O., Singh, T., Stamberger, H., Abou Jamra, R., Caglayan, H., Craiu, D., De Jonghe, P., Guerrini, R., Helbig, K. L., Koeleman, B. P. C., Kosmicki, J. A., Linnankivi, T., May, P., Muhle, H., Moller, R. S., Neubauer, B. A., Palotie, A., Pendziwiat, M., Striano, P., Tang, S., Wu, S., Afawi, Z., De Kovel, C., Dimova, P., Djemie, T., Endziniene, M., Hoffman-Zacharska, D., Jahn, J., Korff, C., Lehesjoki, A. -E., Marini, C., Muller, S. H., Pal, D., Schwarz, N., Selmer, K., Serratosa, J., Stephani, U., Sterbova, K., Suls, A., Syrbe, S., Talvik, I., Von Spiczak, S., Zara, F., Poduri, A., Weber, Y. G., Weckhuysen, S., Sisodiya, S. M., Daly, M. J., Helbig, I., Lal, D., Lemke, J. R., Children's Hospital, Lastenneurologian yksikkö, Clinicum, University of Helsinki, Centre of Excellence in Complex Disease Genetics, Aarno Palotie / Principal Investigator, Institute for Molecular Medicine Finland, Research Programme for Molecular Neurology, Neuroscience Center, HUS Children and Adolescents, Genomics of Neurological and Neuropsychiatric Disorders, Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], University of Luxembourg: High Performance Computing - ULHPC [research center], Korff, Christian, and EuroEPINOMICS RES Consortium
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Exome/genetics ,Male ,0301 basic medicine ,ILAE COMMISSION ,Joint analysis ,Neurodevelopmental Disorders/genetics ,Bioinformatics ,Epilepsy/genetics ,Epilepsy ,0302 clinical medicine ,Intellectual disability ,SEQUENCE VARIANTS ,Missense mutation ,Epilepsy is a frequent feature ,Exome ,TERMINOLOGY ,Disease gene ,0303 health sciences ,ddc:618 ,medicine.diagnostic_test ,Genetic Predisposition to Disease/genetics ,Neurodevelopmental disorders ,1184 Genetics, developmental biology, physiology ,HUMAN-DISEASE ,PREVALENCE ,3. Good health ,Genetic Variation/genetics ,De novo variants ,Female ,Genetics & genetic processes [F10] [Life sciences] ,Génétique & processus génétiques [F10] [Sciences du vivant] ,Genetic Testing/methods ,Disease Association ,Biology ,CLASSIFICATION ,03 medical and health sciences ,Intellectual Disability ,Genetics ,medicine ,Humans ,Genetic Predisposition to Disease ,Genetic Testing ,Limited evidence ,030304 developmental biology ,Genetic testing ,business.industry ,MUTATIONS ,AUTISM SPECTRUM DISORDER ,Genetic Variation ,medicine.disease ,Intellectual Disability/genetics ,030104 developmental biology ,Neurodevelopmental Disorders ,epilepsy ,KCNQ2 ENCEPHALOPATHY ,Human medicine ,3111 Biomedicine ,business ,Genetic diagnosis ,030217 neurology & neurosurgery - Abstract
Epilepsy is a frequent feature of neurodevelopmental disorders (NDD) but little is known about genetic differences between NDD with and without epilepsy. We analyzed de novo variants (DNV) in 6753 parent-offspring trios ascertained for different NDD. In the subset of 1942 individuals with NDD with epilepsy, we identified 33 genes with a significant excess of DNV, of which SNAP25 and GABRB2 had previously only limited evidence for disease association. Joint analysis of all individuals with NDD also implicated CACNA1E as a novel disease gene. Comparing NDD with and without epilepsy, we found missense DNV, DNV in specific genes, age of recruitment and severity of intellectual disability to be associated with epilepsy. We further demonstrate to what extent our results impact current genetic testing as well as treatment, emphasizing the benefit of accurate genetic diagnosis in NDD with epilepsy.
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- 2018
31. Genetic investigation of chromosome 5q GABAA receptor subunit genes in schizophrenia
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Petryshen, T L, Middleton, F A, Tahl, A R, Rockwell, G N, Purcell, S, Aldinger, K A, Kirby, A, Morley, C P, McGann, L, Gentile, K L, Waggoner, S G, Medeiros, H M, Carvalho, C, Macedo, A, Albus, M, Maier, W, Trixler, M, Eichhammer, P, Schwab, S G, Wildenauer, D B, Azevedo, M H, Pato, M T, Pato, C N, Daly, M J, and Sklar, P
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- 2005
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32. Support for involvement of neuregulin 1 in schizophrenia pathophysiology
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Petryshen, T L, Middleton, F A, Kirby, A, Aldinger, K A, Purcell, S, Tahl, A R, Morley, C P, McGann, L, Gentile, K L, Rockwell, G N, Medeiros, H M, Carvalho, C, Macedo, A, Dourado, A, Valente, J, Ferreira, C P, Patterson, N J, Azevedo, M H, Daly, M J, Pato, C N, Pato, M T, and Sklar, P
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- 2005
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33. Genome-wide scan in Portuguese Island families identifies 5q31–5q35 as a susceptibility locus for schizophrenia and psychosis
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Sklar, P, Pato, M T, Kirby, A, Petryshen, T L, Medeiros, H, Carvalho, C, Macedo, A, Dourado, A, Coelho, I, Valente, J, Soares, M J, Ferreira, C P, Lei, M, Verner, A, Hudson, T J, Morley, C P, Kennedy, J L, Azevedo, M H, Lander, E, Daly, M J, and Pato, C N
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- 2004
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34. Comparative assessment of student pharmacists’ performance in computer- and paper-based dispensing exercises
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Daly, M. J., Purnell, E., and Rutter, P.
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- 2013
35. Effects of Mn levels on resistance of Bacillus megaterium spores to heat, radiation and hydrogen peroxide
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Ghosh, S., Ramirez-Peralta, A., Gaidamakova, E., Zhang, P., Li, Y. Q., Daly, M. J., and Setlow, P.
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- 2011
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36. Synthetic and pharmacological studies on some compounds related to aminoglutethimide
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Daly, M. J.
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572 ,Biochemistry - Published
- 1985
37. FURTHER INVESTIGATION OF ASSOCIATION BETWEEN BIPOLAR DISORDER AND BDNF: CHARACTERIZATION OF POPULATION GENETIC STRUCTURE AND HAPLOTYPE ASSOCIATION STUDIES IN FOUR PATIENT SAMPLES
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Petryshen, T. L., Sabeti, P. C., Aldinger, K. A., Tahl, A. R., Frye, B., Waggoner, S. G., Lim, Y., Daly, M. J., McInnis, M. G., DePaulo, R. J., Smoller, J. W., Pulver, A. E., and Sklar, P.
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- 2009
38. A GENE-BASED APPROACH TO EPISTASIS IN LARGE-SCALE ASSOCIATION STUDIES
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Purcell, S. M., Smoller, J. W., Daly, M. J., Sham, P. C., and Sklar, P.
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- 2009
39. IDENTIFICATION OF GENES INVOLVED IN PREPULSE INHIBITION OF STARTLE, AN ENDOPHENOTYPE OF SCHIZOPHRENIA, IN MOUSE CHROMOSOME SUBSTITUTION STRAINS
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Petryshen, T. L., Kirby, A., Rockwell, G. N., Waggoner, S. G., OʼLeary, S. B., Aldinger, K. A., Daly, M. J., and Sklar, P.
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- 2009
40. Genetic variants in the region harbouring IL2/IL21 associated with ulcerative colitis
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Festen, E A M, Goyette, P, Scott, R, Annese, V, Zhernakova, A, Lian, J, Lefèbvre, C, Brant, S R, Cho, J H, Silverberg, M S, Taylor, K D, de Jong, D J, Stokkers, P C, Mcgovern, D, Palmieri, O, Achkar, J-P, Xavier, R J, Daly, M J, Duerr, R H, Wijmenga, C, Weersma, R K, and Rioux, J D
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- 2009
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41. Microdeletion/duplication at 15q13.2q13.3 among individuals with features of autism and other neuropsychiatric disorders
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Miller, D T, Shen, Y, Weiss, L A, Korn, J, Anselm, I, Bridgemohan, C, Cox, G F, Dickinson, H, Gentile, J, Harris, D J, Hegde, V, Hundley, R, Khwaja, O, Kothare, S, Luedke, C, Nasir, R, Poduri, A, Prasad, K, Raffalli, P, Reinhard, A, Smith, S E, Sobeih, M M, Soul, J S, Stoler, J, Takeoka, M, Tan, W-H, Thakuria, J, Wolff, R, Yusupov, R, Gusella, J F, Daly, M J, and Wu, B-L
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- 2009
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42. Polygenic burden in focal and generalized epilepsies
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Leu C., Stevelink R., Smith A. W., Goleva S. B., Kanai M., Ferguson L., Campbell C., Kamatani Y., Okada Y., Sisodiya S. M., Cavalleri G. L., Koeleman B. P. C., Lerche H., Jehi L., Davis L. K., Najm I. M., Palotie A., Daly M. J., Busch R. M., Lal D., Feng Y. -C. A., Howrigan D. P., Abbott L. E., Tashman K., Cerrato F., Churchhouse C., Gupta N., Neale B. M., Berkovic S. F., Goldstein D. B., Lowenstein D. H., Cossette P., Cotsapas C., De Jonghe P., Dixon-Salazar T., Guerrini R., Hakonarson H., Heinzen E. L., Helbig I., Kwan P., Marson A. G., Petrovski S., Kamalakaran S., Stewart R., Weckhuysen S., Depondt C., Dlugos D. J., Scheffer I. E., Striano P., Freyer C., Krause R., May P., McKenna K., Regan B. M., Bellows S. T., Bennett C. A., Johns E. M. C., Macdonald A., Shilling H., Burgess R., Weckhuysen D., Bahlo M., O'Brien T. J., Todaro M., Stamberger H., Andrade D. M., Sadoway T. R., Mo K., Krestel H., Gallati S., Papacostas S. S., Kousiappa I., Tanteles G. A., Sterbova K., Vlckova M., Sedlackova L., Lassuthova P., Klein K. M., Rosenow F., Reif P. S., Knake S., Kunz W. S., Zsurka G., Elger C. E., Bauer J., Rademacher M., Pendziwiat M., Muhle H., Rademacher A., Van Baalen A., Von Spiczak S., Stephani U., Afawi Z., Korczyn A. D., Kanaan M., Canavati C., Kurlemann G., Muller-Schluter K., Kluger G., Hausler M., Blatt I., Lemke J. R., Krey I., Weber Y. G., Wolking S., Becker F., Hengsbach C., Rau S., Maisch A. F., Steinhoff B. J., Schulze-Bonhage A., Schubert-Bast S., Schreiber H., Borggrafe I., Schankin C. J., Mayer T., Korinthenberg R., Brockmann K., Dennig D., Madeleyn R., Kalviainen R., Auvinen P., Saarela A., Linnankivi T., Lehesjoki A. -E., Rees M. I., Chung S. -K., Pickrell W. O., Powell R., Schneider N., Balestrini S., Zagaglia S., Braatz V., Johnson M. R., Auce P., Sills G. J., Baum L. W., Sham P. C., Cherny S. S., Lui C. H. T., Barisic N., Delanty N., Doherty C. P., Shukralla A., McCormack M., El-Naggar H., Canafoglia L., Franceschetti S., Castellotti B., Granata T., Zara F., Iacomino M., Madia F., Vari M. S., Mancardi M. M., Salpietro V., Bisulli F., Tinuper P., Licchetta L., Pippucci T., Stipa C., Muccioli L., Minardi R., Gambardella A., Labate A., Annesi G., Manna L., Gagliardi M., Parrini E., Mei D., Vetro A., Bianchini C., Montomoli M., Doccini V., Marini C., Suzuki T., Inoue Y., Yamakawa K., Birute T., Ruta M., Algirdas U., Ruta P., Jurgita G., Ruta S., Sadleir L. G., King C., Mountier E., Caglayan S. H., Arslan M., Yapici Z., Yis U., Topaloglu P., Kara B., Turkdogan D., Gundogdu-Eken A., Bebek N., Ugur-Iseri S., Baykan B., Salman B., Haryanyan G., Yucesan E., Kesim Y., Ozkara C., Sheidley B. R., Shain C., Poduri A., Buono R. J., Ferraro T. N., Sperling M. R., Lo W., Privitera M., French J. A., Schachter S., Kuzniecky R. I., Devinsky O., Hegde M., Khankhanian P., Helbig K. L., Ellis C. A., Spalletta G., Piras F., Gili T., Ciullo V., Leu C., Stevelink R., Smith A.W., Goleva S.B., Kanai M., Ferguson L., Campbell C., Kamatani Y., Okada Y., Sisodiya S.M., Cavalleri G.L., Koeleman B.P.C., Lerche H., Jehi L., Davis L.K., Najm I.M., Palotie A., Daly M.J., Busch R.M., Lal D., Feng Y.-C.A., Howrigan D.P., Abbott L.E., Tashman K., Cerrato F., Churchhouse C., Gupta N., Neale B.M., Berkovic S.F., Goldstein D.B., Lowenstein D.H., Cossette P., Cotsapas C., De Jonghe P., Dixon-Salazar T., Guerrini R., Hakonarson H., Heinzen E.L., Helbig I., Kwan P., Marson A.G., Petrovski S., Kamalakaran S., Stewart R., Weckhuysen S., Depondt C., Dlugos D.J., Scheffer I.E., Striano P., Freyer C., Krause R., May P., McKenna K., Regan B.M., Bellows S.T., Bennett C.A., Johns E.M.C., Macdonald A., Shilling H., Burgess R., Weckhuysen D., Bahlo M., O'Brien T.J., Todaro M., Stamberger H., Andrade D.M., Sadoway T.R., Mo K., Krestel H., Gallati S., Papacostas S.S., Kousiappa I., Tanteles G.A., Sterbova K., Vlckova M., Sedlackova L., Lassuthova P., Klein K.M., Rosenow F., Reif P.S., Knake S., Kunz W.S., Zsurka G., Elger C.E., Bauer J., Rademacher M., Pendziwiat M., Muhle H., Rademacher A., Van Baalen A., Von Spiczak S., Stephani U., Afawi Z., Korczyn A.D., Kanaan M., Canavati C., Kurlemann G., Muller-Schluter K., Kluger G., Hausler M., Blatt I., Lemke J.R., Krey I., Weber Y.G., Wolking S., Becker F., Hengsbach C., Rau S., Maisch A.F., Steinhoff B.J., Schulze-Bonhage A., Schubert-Bast S., Schreiber H., Borggrafe I., Schankin C.J., Mayer T., Korinthenberg R., Brockmann K., Dennig D., Madeleyn R., Kalviainen R., Auvinen P., Saarela A., Linnankivi T., Lehesjoki A.-E., Rees M.I., Chung S.-K., Pickrell W.O., Powell R., Schneider N., Balestrini S., Zagaglia S., Braatz V., Johnson M.R., Auce P., Sills G.J., Baum L.W., Sham P.C., Cherny S.S., Lui C.H.T., Barisic N., Delanty N., Doherty C.P., Shukralla A., McCormack M., El-Naggar H., Canafoglia L., Franceschetti S., Castellotti B., Granata T., Zara F., Iacomino M., Madia F., Vari M.S., Mancardi M.M., Salpietro V., Bisulli F., Tinuper P., Licchetta L., Pippucci T., Stipa C., Muccioli L., Minardi R., Gambardella A., Labate A., Annesi G., Manna L., Gagliardi M., Parrini E., Mei D., Vetro A., Bianchini C., Montomoli M., Doccini V., Marini C., Suzuki T., Inoue Y., Yamakawa K., Birute T., Ruta M., Algirdas U., Ruta P., Jurgita G., Ruta S., Sadleir L.G., King C., Mountier E., Caglayan S.H., Arslan M., Yapici Z., Yis U., Topaloglu P., Kara B., Turkdogan D., Gundogdu-Eken A., Bebek N., Ugur-Iseri S., Baykan B., Salman B., Haryanyan G., Yucesan E., Kesim Y., Ozkara C., Sheidley B.R., Shain C., Poduri A., Buono R.J., Ferraro T.N., Sperling M.R., Lo W., Privitera M., French J.A., Schachter S., Kuzniecky R.I., Devinsky O., Hegde M., Khankhanian P., Helbig K.L., Ellis C.A., Spalletta G., Piras F., Gili T., Ciullo V., Commission of the European Communities, Medical Research Council (MRC), Tumienė, Birutė, Mameniškienė, Rūta, Utkus, Algirdas, Praninskienė, Rūta, Grikinienė, Jurgita, Samaitienė-Aleknienė, Rūta, Centre of Excellence in Complex Disease Genetics, Aarno Palotie / Principal Investigator, Institute for Molecular Medicine Finland, Genomics of Neurological and Neuropsychiatric Disorders, University of Helsinki, Helsinki Institute of Life Science HiLIFE, and Department of Medical and Clinical Genetics
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0301 basic medicine ,Male ,Multifactorial Inheritance ,Epi25 Consortium ,Databases, Factual ,FEATURES ,Genome-wide association study ,Epilepsies ,3124 Neurology and psychiatry ,Cohort Studies ,Epilepsy ,0302 clinical medicine ,Cost of Illness ,1ST SEIZURE ,HISTORY ,genetics ,POPULATION ,11 Medical and Health Sciences ,education.field_of_study ,medicine.diagnostic_test ,SCORES ,Single Nucleotide ,Biobank ,3. Good health ,17 Psychology and Cognitive Sciences ,Genetic generalized epilepsy ,Epilepsy, Generalized ,Female ,Partial ,Cohort study ,Human ,medicine.medical_specialty ,Population ,European Continental Ancestry Group ,Clinical Neurology ,BIOBANK ,Polymorphism, Single Nucleotide ,epilepsy ,genetic generalized epilepsy ,common variant risk ,Databases ,03 medical and health sciences ,Genetic ,Internal medicine ,medicine ,Journal Article ,Genetics ,Humans ,Genetic Predisposition to Disease ,Polymorphism ,GENOME-WIDE ASSOCIATION ,Generalized epilepsy ,education ,SEIZURE RECURRENCE ,Factual ,METAANALYSIS ,Genetic testing ,Neurology & Neurosurgery ,RISK PREDICTION ,Generalized ,business.industry ,3112 Neurosciences ,Common variant risk ,Genetic Variation ,Original Articles ,medicine.disease ,Comorbidity ,Cost of Illne ,Epilepsies, Partial ,Genome-Wide Association Study ,030104 developmental biology ,Neurology (clinical) ,Cohort Studie ,business ,030217 neurology & neurosurgery - Abstract
See Hansen and Møller (doi:10.1093/brain/awz318) for a scientific commentary on this article. Using polygenic risk scores from a genome-wide association study in generalized and focal epilepsy, Leu et al. reveal a significantly higher genetic burden for epilepsy in multiple cohorts of people with epilepsy compared to population controls. Quantification of common variant burden may be valuable for epilepsy prognosis and treatment., Rare genetic variants can cause epilepsy, and genetic testing has been widely adopted for severe, paediatric-onset epilepsies. The phenotypic consequences of common genetic risk burden for epilepsies and their potential future clinical applications have not yet been determined. Using polygenic risk scores (PRS) from a European-ancestry genome-wide association study in generalized and focal epilepsy, we quantified common genetic burden in patients with generalized epilepsy (GE-PRS) or focal epilepsy (FE-PRS) from two independent non-Finnish European cohorts (Epi25 Consortium, n = 5705; Cleveland Clinic Epilepsy Center, n = 620; both compared to 20 435 controls). One Finnish-ancestry population isolate (Finnish-ancestry Epi25, n = 449; compared to 1559 controls), two European-ancestry biobanks (UK Biobank, n = 383 656; Vanderbilt biorepository, n = 49 494), and one Japanese-ancestry biobank (BioBank Japan, n = 168 680) were used for additional replications. Across 8386 patients with epilepsy and 622 212 population controls, we found and replicated significantly higher GE-PRS in patients with generalized epilepsy of European-ancestry compared to patients with focal epilepsy (Epi25: P = 1.64×10−15; Cleveland: P = 2.85×10−4; Finnish-ancestry Epi25: P = 1.80×10−4) or population controls (Epi25: P = 2.35×10−70; Cleveland: P = 1.43×10−7; Finnish-ancestry Epi25: P = 3.11×10−4; UK Biobank and Vanderbilt biorepository meta-analysis: P = 7.99×10−4). FE-PRS were significantly higher in patients with focal epilepsy compared to controls in the non-Finnish, non-biobank cohorts (Epi25: P = 5.74×10−19; Cleveland: P = 1.69×10−6). European ancestry-derived PRS did not predict generalized epilepsy or focal epilepsy in Japanese-ancestry individuals. Finally, we observed a significant 4.6-fold and a 4.5-fold enrichment of patients with generalized epilepsy compared to controls in the top 0.5% highest GE-PRS of the two non-Finnish European cohorts (Epi25: P = 2.60×10−15; Cleveland: P = 1.39×10−2). We conclude that common variant risk associated with epilepsy is significantly enriched in multiple cohorts of patients with epilepsy compared to controls—in particular for generalized epilepsy. As sample sizes and PRS accuracy continue to increase with further common variant discovery, PRS could complement established clinical biomarkers and augment genetic testing for patient classification, comorbidity research, and potentially targeted treatment.
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- 2019
43. Genetic architecture of human plasma lipidome and its link to cardiovascular disease
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Tabassum, R. (Rubina), Ramo, J. T. (Joel T.), Ripatti, P. (Pietari), Koskela, J. T. (Jukka T.), Kurki, M. (Mitja), Karjalainen, J. (Juha), Palta, P. (Priit), Hassan, S. (Shabbeer), Nunez-Fontarnau, J. (Javier), Kiiskinen, T. T. (Tuomo T. J.), Soderlund, S. (Sanni), Matikainen, N. (Niina), Gerl, M. J. (Mathias J.), Surma, M. A. (Michal A.), Klose, C. (Christian), Stitziel, N. O. (Nathan O.), Laivuori, H. (Hannele), Havulinna, A. S. (Aki S.), Service, S. K. (Susan K.), Salomaa, V. (Veikko), Pirinen, M. (Matti), Jauhiainen, M. (Matti), Daly, M. J. (Mark J.), Freimer, N. B. (Nelson B.), Palotie, A. (Aarno), Taskinen, M.-R. (Marja-Riitta), Simons, K. (Kai), Ripatti, S. (Samuli), Jalanko, A. (Anu), Kaprio, J. (Jaakko), Donner, K. (Kati), Kaunisto, M. (Mari), Mars, N. (Nina), Dada, A. (Alexander), Shcherban, A. (Anastasia), Ganna, A. (Andrea), Lehisto, A. (Arto), Kilpelainen, E. (Elina), Brein, G. (Georg), Awaisa, G. (Ghazal), Harju, J. (Jarmo), Parr, K. (Kalle), Parolo, P. D. (Pietro Della Briotta), Kajanne, R. (Risto), Lemmela, S. (Susanna), Sipila, T. P. (Timo P.), Sipila, T. (Tuomas), Lyhs, U. (Ulrike), Llorens, V. (Vincent), Niiranen, T. (Teemu), Kristiansson, K. (Kati), Mannikko, L. (Lotta), Jimenez, M. G. (Manuel Gonzalez), Perola, M. (Markus), Wong, R. (Regis), Kilpi, T. (Terhi), Hiekkalinna, T. (Tero), Jarvensivu, E. (Elina), Kaiharju, E. (Essi), Mattsson, H. (Hannele), Laukkanen, M. (Markku), Laiho, P. (Paivi), Lahteenmaki, S. (Sini), Sistonen, T. (Tuuli), Soini, S. (Sirpa), Ziemann, A. (Adam), Lehtonen, A. (Anne), Lertratanakul, A. (Apinya), Georgantas, B. (Bob), Riley-Gillis, B. (Bridget), Quarless, D. (Danjuma), Rahimov, F. (Fedik), Heap, G. (Graham), Jacob, H. (Howard), Waring, J. (Jeffrey), Davis, J. W. (Justin Wade), Smaoui, N. (Nizar), Popovic, R. (Relja), Esmaeeli, S. (Sahar), Waring, J. (Jeff), Matakidou, A. (Athena), Challis, B. (Ben), Close, D. (David), Petrovski, S. (Slave), Karlsson, A. (Antti), Schleutker, J. (Johanna), Pulkki, K. (Kari), Virolainen, P. (Petri), Kallio, L. (Lila), Mannermaa, A. (Arto), Heikkinen, S. (Sami), Kosma, V.-M. (Veli-Matti), Chen, C.-Y. (Chia-Yen), Runz, H. (Heiko), Liu, J. (Jimmy), Bronson, P. (Paola), John, S. (Sally), Landenpera, S. (Sanni), Eaton, S. (Susan), Zhou, W. (Wei), Hendolin, M. (Minna), Tuovila, O. (Outi), Pakkanen, R. (Raimo), Maranville, J. (Joseph), Usiskin, K. (Keith), Hochfeld, M. (Marla), Plenge, R. (Robert), Yang, R. (Robert), Biswas, S. (Shameek), Greenberg, S. (Steven), Laakkonen, E. (Eija), Kononen, J. (Juha), Paloneva, J. (Juha), Kujala, U. (Urho), Kuopio, T. (Teijo), Laukkanen, J. (Jari), Kangasniemi, E. (Eeva), Savinainen, K. (Kimmo), Laaksonen, R. (Reijo), Arvas, M. (Mikko), Ritari, J. (Jarmo), Partanen, J. (Jukka), Hyvarinen, K. (Kati), Wahlfors, T. (Tiina), Peterson, A. (Andrew), Oh, D. (Danny), Chang, D. (Diana), Teng, E. (Edmond), Strauss, E. (Erich), Kerchner, G. (Geoff), Chen, H. (Hao), Chen, H. (Hubert), Schutzman, J. (Jennifer), Michon, J. (John), Hunkapiller, J. (Julie), McCarthy, M. (Mark), Bowers, N. (Natalie), Lu, T. (Tim), Bhangale, T. (Tushar), Pulford, D. (David), Waterworth, D. (Dawn), Kulkarni, D. (Diptee), Xu, F. (Fanli), Betts, J. (Jo), Gordillo, J. E. (Jorge Esparza), Hoffman, J. (Joshua), Auro, K. (Kirsi), McCarthy, L. (Linda), Ghosh, S. (Soumitra), Ehm, M. (Meg), Pitkanen, K. (Kimmo), Makela, T. (Tomi), Loukola, A. (Anu), Joensuu, H. (Heikki), Sinisalo, J. (Juha), Eklund, K. (Kari), Aaltonen, L. (Lauri), Farkkila, M. (Martti), Carpen, O. (Olli), Kauppi, P. (Paula), Tienari, P. (Pentti), Ollila, T. (Terhi), Tuomi, T. (Tiinamaija), Meretoja, T. (Tuomo), Pitkaranta, A. (Anne), Turunen, J. (Joni), Hannula-Jouppi, K. (Katariina), Pikkarainen, S. (Sampsa), Seitsonen, S. (Sanna), Koskinen, M. (Miika), Palomaki, A. (Antti), Rinne, J. (Juha), Metsarinne, K. (Kaj), Elenius, K. (Klaus), Pirila, L. (Laura), Koulu, L. (Leena), Voutilainen, M. (Markku), Juonala, M. (Markus), Peltonen, S. (Sirkku), Aaltonen, V. (Vesa), Loboda, A. (Andrey), Podgornaia, A. (Anna), Chhibber, A. (Aparna), Chu, A. (Audrey), Fox, C. (Caroline), Diogo, D. (Dorothee), Holzinger, E. (Emily), Eicher, J. (John), Gormley, P. (Padhraig), Mehta, V. (Vinay), Wang, X. (Xulong), Kettunen, J. (Johannes), Pylkas, K. (Katri), Kalaoja, M. (Marita), Karjalainen, M. (Minna), Hinttala, R. (Reetta), Kaarteenaho, R. (Riitta), Vainio, S. (Seppo), Mantere, T. (Tuomo), Remes, A. (Anne), Huhtakangas, J. (Johanna), Junttila, J. (Juhani), Tasanen, K. (Kaisa), Huilaja, L. (Laura), Luodonpaa, M. (Marja), Hautala, N. (Nina), Karihtala, P. (Peeter), Kauppila, S. (Saila), Harju, T. (Terttu), Blomster, T. (Timo), Soininen, H. (Hilkka), Harvima, I. (Ilkka), Pihlajamaki, J. (Jussi), Kaarniranta, K. (Kai), Pelkonen, M. (Margit), Laakso, M. (Markku), Hiltunen, M. (Mikko), Kiviniemi, M. (Mikko), Kaipiainen-Seppanen, O. (Oili), Auvinen, P. (Paivi), Kalviainen, R. (Reetta), Julkunen, V. (Valtteri), Malarstig, A. (Anders), Hedman, A. (Asa), Marshal, C. (Catherine), Whelan, C. (Christopher), Lehtonen, H. (Heli), Parkkinen, J. (Jaakko), Linden, K. (Kari), Kalpala, K. (Kirsi), Miller, M. (Melissa), Bing, N. (Nan), McDonough, S. (Stefan), Chen, X. (Xing), Hu, X. (Xinli), Wu, Y. (Ying), Auranen, A. (Annika), Jussila, A. (Airi), Uusitalo-Jarvinen, H. (Hannele), Kankaanranta, H. (Hannu), Uusitalo, H. (Hannu), Peltola, J. (Jukka), Kahonen, M. (Mika), Isomaki, P. (Pia), Laitinen, T. (Tarja), Salmi, T. (Teea), Muslin, A. (Anthony), Wang, C. (Clarence), Chatelain, C. (Clement), Xu, E. (Ethan), Auge, F. (Franck), Call, K. (Kathy), Klinger, K. (Kathy), Crohns, M. (Marika), Gossel, M. (Matthias), Palin, K. (Kimmo), Rivas, M. (Manuel), Siirtola, H. (Harri), and Tabuenca, J. G. (Javier Gracia)
- Subjects
lipids (amino acids, peptides, and proteins) - Abstract
Understanding genetic architecture of plasma lipidome could provide better insights into lipid metabolism and its link to cardiovascular diseases (CVDs). Here, we perform genome-wide association analyses of 141 lipid species (n = 2,181 individuals), followed by phenome-wide scans with 25 CVD related phenotypes (n = 511,700 individuals). We identify 35 lipid-species-associated loci (P
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- 2019
44. IBD5 is associated with an extensive complicated Crohn’s disease feature: implications from genotype–phenotype analysis
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Brescianini, S, Trinh, T, Stoll, M, Schreiber, S, Rioux, J D, and Daly, M J
- Published
- 2007
45. Subpopulation difference scanning: a strategy for exclusion mapping of susceptibility genes
- Author
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Salmela, E, Taskinen, O, Seppänen, J K, Sistonen, P, Daly, M J, Lahermo, P, Savontaus, M-L, and Kere, J
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- 2006
46. Irish society for rheumatology: Proceedings of annual general meeting held in Beaumont Hospital on Friday 22nd October, 1993
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Mulherin, Diarmuid, FitzGerald, Oliver, Bresnihan, Barry, Bruce, I. N., McNally, J. A., Bell, A. L., Yanni, G., Cauli, A., Challacombe, S., Panayi, G. S., Foley-Nolan, D., Akil, M., Anthony, M., Cundall, D., Bourne, J., Arthur, R., Chamberlain, M. A., Byrne, P., Mahon, N., Robinson, H., Sant, S. M., Donnelly, S., Barnes, L., Watson, R., Casey, E. B., Donnelly, S., Casey, E. B., Bruce, I. N., Edgar, D. E., McMillan, S. A., Conlan, S. K., McNeill, T. A., Bell, A. L., Robinson, H., Byrne, P., Mahon, N., Sant, S. M., Abuzakouk, M., Feighery, C., Jones, E., O’Briain, S., Goggins, M., Weir, D. G., Casey, E., O’Farrelly, C., Kelleher, D., Murphy, A., Casey, E. B., Veale, D. J., Kirk, G., McLaren, M., Belch, J. J. F., Byrne, P., Mahon, N., Robinson, H., Sant, S. M., Foley-Nolan, D., Daly, M. J., Mahon, N., Robinson, H., Byrne, P., Sant, S. M., Donnelly, S., Murphy, J., Lynch, M., Casey, E. B., McKernan, S., Donnelly, S., Casey, E. B., Sothinathan, R., Donnelly, S., Casey, E. B., Blake, C., Garrett, M., Robinson, H., Byrne, P., Mahon, N., Sant, S. M., Gourley, I. S., Bell, A. L., Bresnihan, B., FitzGerald, O., Cunnane, G., Abuzakouk, M., Feighery, C., Bergin, C., Cherukuri, A., Weir, D. G., Casey, E., O’Farrelly, C., Mulherin, D., Kirk, G., Veale, D. J., Belch, J. J. F., Bresnihan, B., FitzGerald, O., Kelleher, D., Hall, N., Murphy, A., Casey, E. B., Mulcahy, B., Molloy, M., Phelan, M., O’Gara, F., McConnell, F., Shanahan, F., FitzGerald, O., Heffernan, M., Mulcahy, B., Neary, P., and Molloy, M.
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- 1994
- Full Text
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47. Linkage disequilibrium and haplotype structure of five GABAA receptor subunit genes investigated for association with schizophrenia
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Petryshen, T L, Middleton, F A, Tahl, A R, Rockwell, G N, Purcell, S, Aldinger, K A, Kirby, A, Morley, C P, McGann, L, Gentile, K L, Waggoner, S G, Medeiros, H M, Carvalho, C, Macedo, A, Albus, M, Maier, W, Trixler, M, Eichhammer, P, Schwab, S G, Wildenauer, D B, Azevedo, M H, Pato, M T, Pato, C N, Daly, M J, and Sklar, P
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- 2005
48. Abstracts of oral presentations
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Wolschrijn, Hilka, Bruring, Dot P., Sirpa, Peura, Coombes, J. A., Horne, R., Blom, AhG, Bakker, A., Jonkers, R., Strømnes, Bjørg, Adams, P. R., Luscombe, D. K., Woods, F. J., van Mil, J. W. Foppe, Simiaer, K. L., Yorke, D. A., Rowe, P., Timmer, J. W., Snelling, Melanie, Smith, Cheryl, Luscomhe, David, Herholdt, Annette, Bador, P., Picard, A., Belbenoit, P., Locher, F., Grosset-Grange, I., Cortés, E., Cuesta, T., Ferré, P., Daly, M. J., Baxter, H., Swallow, R., Taggiasco, N., Samit, B., Beuzon, S., Doreau, C., Blake, J., Godman, B., Frias, Sara, Scroccaro, G., Olivato, R., Messori, A., Casara, M., Martini, N., Hardman, Colin, Husson, M. C., and Shashkova, Galina V.
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- 1993
- Full Text
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49. FURTHER INVESTIGATION OF ASSOCIATION BETWEEN BIPOLAR DISORDER AND BDNF: CHARACTERIZATION OF POPULATION GENETIC STRUCTURE AND HAPLOTYPE ASSOCIATION STUDIES IN FOUR PATIENT SAMPLES
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Petryshen, T. L., Sabeti, P. C., Aldinger, K. A., Tahl, A. R., Frye, B., Waggoner, S. G., Lim, Y., Daly, M. J., McInnis, M. G., DePaulo, R. J., Smoller, J. W., Pulver, A. E., and Sklar, P.
- Published
- 2005
50. A GENE-BASED APPROACH TO EPISTASIS IN LARGE-SCALE ASSOCIATION STUDIES
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Purcell, S. M., Smoller, J. W., Daly, M. J., Sham, P. C., and Sklar, P.
- Published
- 2005
Catalog
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