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2. Oral and non-oral lichen planus show genetic heterogeneity and differential risk for autoimmune disease and oral cancer

Author

Reeve, Mary Pat, Vehviläinen, Mari, Luo, Shuang, Ritari, Jarmo, Karjalainen, Juha, Gracia-Tabuenca, Javier, Mehtonen, Juha, Padmanabhuni, Shanmukha Sampath, Kolosov, Nikita, Artomov, Mykyta, Siirtola, Harri, Ollila, Hanna M., Graham, Daniel, Partanen, Jukka, Xavier, Ramnik J., Daly, Mark J., Ripatti, Samuli, Salo, Tuula, and Siponen, Maria

Published
2024
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3. Thrombosis risk in single- and double-heterozygous carriers of factor V Leiden and prothrombin G20210A in FinnGen and the UK Biobank

Author

Palotie, Aarno, Daly, Mark, Riley-Gills, Bridget, Jacob, Howard, Viollet, Coralie, Petrovski, Slavé, Chen, Chia-Yen, John, Sally, Okafo, George, Plenge, Robert, Maranville, Joseph, McCarthy, Mark, Pendergrass, Rion, Ehm, Margaret G., Auro, Kirsi, Longerich, Simonne, Mälarstig, Anders, Vlahiotis, Anna, Klinger, Katherine, Chatelain, Clement, Gossel, Matthias, Estrada, Karol, Graham, Robert, Waterworth, Dawn, O´Donnell, Chris, Renaud, Nicole, Mäkelä, Tomi P., Kaprio, Jaakko, Ruddock, Minna, Virolainen, Petri, Hakanen, Antti, Kilpi, Terhi, Perola, Markus, Partanen, Jukka, Raivio, Taneli, Tikkanen, Jani, Serpi, Raisa, Kristiansson, Kati, Kosma, Veli-Matti, Laukkanen, Jari, Hautalahti, Marco, Tuovila, Outi, Waring, Jeffrey, Riley-Gillis, Bridget, Rahimov, Fedik, Tachmazidou, Ioanna, Ding, Zhihao, Jung, Marc, Tuoken, Hanati, Biswas, Shameek, Pulford, David, Raghavan, Neha, Huertas-Vazquez, Adriana, Sul, Jae-Hoon, Hu, Xinli, Hedman, Åsa, Obeidat, Ma´en, Chung, Jonathan, Zierer, Jonas, Niemi, Mari, Ripatti, Samuli, Schleutker, Johanna, Arvas, Mikko, Carpén, Olli, Hinttala, Reetta, Kettunen, Johannes, Mannermaa, Arto, Aalto-Setälä, Katriina, Kähönen, Mika, Mäkelä, Johanna, Kälviäinen, Reetta, Julkunen, Valtteri, Soininen, Hilkka, Remes, Anne, Hiltunen, Mikko, Peltola, Jukka, Raivio, Minna, Tienari, Pentti, Rinne, Juha, Kallionpää, Roosa, Partanen, Juulia, Ziemann, Adam, Smaoui, Nizar, Lehtonen, Anne, Eaton, Susan, Runz, Heiko, Lahdenperä, Sanni, Bowers, Natalie, Teng, Edmond, Xu, Fanli, Addis, Laura, Eicher, John, Li, Qingqin S., He, Karen, Khramtsova, Ekaterina, Färkkilä, Martti, Koskela, Jukka, Pikkarainen, Sampsa, Jussila, Airi, Kaukinen, Katri, Blomster, Timo, Kiviniemi, Mikko, Voutilainen, Markku, Lu, Tim, McCarthy, Linda, Hart, Amy, Guan, Meijian, Miller, Jason, Kalpala, Kirsi, Miller, Melissa, Eklund, Kari, Palomäki, Antti, Isomäki, Pia, Pirilä, Laura, Kaipiainen-Seppänen, Oili, Huhtakangas, Johanna, Mars, Nina, Lertratanakul, Apinya, Hochfeld, Marla, Gordillo, Jorge Esparza, Farias, Fabiana, Bing, Nan, Laitinen, Tarja, Pelkonen, Margit, Kauppi, Paula, Kankaanranta, Hannu, Harju, Terttu, Lahesmaa, Riitta, Chen, Hubert, Betts, Joanna, Mishra, Rajashree, Mouded, Majd, Ngo, Debby, Niiranen, Teemu, Vaura, Felix, Salomaa, Veikko, Metsärinne, Kaj, Aittokallio, Jenni, Hernesniemi, Jussi, Gordin, Daniel, Sinisalo, Juha, Taskinen, Marja-Riitta, Tuomi, Tiinamaija, Hiltunen, Timo, Elliott, Amanda, Reeve, Mary Pat, Ruotsalainen, Sanni, Paul, Dirk, Chu, Audrey, Reilly, Dermot, Mendelson, Mike, Parkkinen, Jaakko, Meretoja, Tuomo, Joensuu, Heikki, Mattson, Johanna, Salminen, Eveliina, Auranen, Annika, Karihtala, Peeter, Auvinen, Päivi, Elenius, Klaus, Pitkänen, Esa, Popovic, Relja, Fabre, Margarete, Schutzman, Jennifer, Kulkarni, Diptee, Porello, Alessandro, Loboda, Andrey, Lehtonen, Heli, McDonough, Stefan, Vuoti, Sauli, Kaarniranta, Kai, Turunen, Joni A., Ollila, Terhi, Uusitalo, Hannu, Karjalainen, Juha, Liu, Mengzhen, Loomis, Stephanie, Strauss, Erich, Chen, Hao, Tasanen, Kaisa, Huilaja, Laura, Hannula-Jouppi, Katariina, Salmi, Teea, Peltonen, Sirkku, Koulu, Leena, Choy, David, Wu, Ying, Pussinen, Pirkko, Salminen, Aino, Salo, Tuula, Rice, David, Nieminen, Pekka, Palotie, Ulla, Siponen, Maria, Suominen, Liisa, Mäntylä, Päivi, Gursoy, Ulvi, Anttonen, Vuokko, Sipilä, Kirsi, Laivuori, Hannele, Kurra, Venla, Kotaniemi-Talonen, Laura, Heikinheimo, Oskari, Kalliala, Ilkka, Aaltonen, Lauri, Jokimaa, Varpu, Vääräsmäki, Marja, Uimari, Outi, Morin-Papunen, Laure, Niinimäki, Maarit, Piltonen, Terhi, Kivinen, Katja, Widen, Elisabeth, Tukiainen, Taru, Välimäki, Niko, Laakkonen, Eija, Tyrmi, Jaakko, Silven, Heidi, Sliz, Eeva, Arffman, Riikka, Savukoski, Susanna, Laisk, Triin, Pujol, Natalia, Kumar, Janet, Hovatta, Iiris, Isometsä, Erkki, Ollila, Hanna, Suvisaari, Jaana, Mäkitie, Antti, Bizaki-Vallaskangas, Argyro, Toppila-Salmi, Sanna, Willberg, Tytti, Saarentaus, Elmo, Aarnisalo, Antti, Rahikkala, Elisa, Aittomäki, Kristiina, Åberg, Fredrik, Kurki, Mitja, Havulinna, Aki, Mehtonen, Juha, Palta, Priit, Hassan, Shabbeer, Della Briotta Parolo, Pietro, Zhou, Wei, Maasha, Mutaamba, Lemmelä, Susanna, Rivas, Manuel, Liu, Aoxing, Lehisto, Arto, Ganna, Andrea, Llorens, Vincent, Heyne, Henrike, Rämö, Joel, Rodosthenous, Rodos, Strausz, Satu, Palotie, Tuula, Palin, Kimmo, Garcia-Tabuenca, Javier, Siirtola, Harri, Kiiskinen, Tuomo, Lee, Jiwoo, Tsuo, Kristin, Hyvärinen, Kati, Ritari, Jarmo, Pylkäs, Katri, Karjalainen, Minna, Mantere, Tuomo, Kangasniemi, Eeva, Heikkinen, Sami, Pitkänen, Nina, Lessard, Samuel, Chatelain, Clément, Kallio, Lila, Wahlfors, Tiina, Punkka, Eero, Siltanen, Sanna, Kuopio, Teijo, Jalanko, Anu, Shen, Huei-Yi, Kajanne, Risto, Aavikko, Mervi, Cooper, Helen, Öller, Denise, Leinonen, Rasko, Palin, Henna, Linna, Malla-Maria, Kanai, Masahiro, Zheng, Zhili, Lahtela, L. Elisa, Kaunisto, Mari, Kilpeläinen, Elina, Sipilä, Timo P., Dada, Oluwaseun Alexander, Ghazal, Awaisa, Kytölä, Anastasia, Weldatsadik, Rigbe, Donner, Kati, Loukola, Anu, Laiho, Päivi, Sistonen, Tuuli, Kaiharju, Essi, Laukkanen, Markku, Järvensivu, Elina, Lähteenmäki, Sini, Männikkö, Lotta, Wong, Regis, Toivola, Auli, Brunfeldt, Minna, Mattsson, Hannele, Koskelainen, Sami, Hiekkalinna, Tero, Paajanen, Teemu, Luo, Shuang, Padmanabhuni, Shanmukha Sampath, Niemi, Marianna, Gracia-Tabuenca, Javier, Helminen, Mika, Luukkaala, Tiina, Vähätalo, Iida, Tammerluoto, Jyrki, Smith, Sarah, Southerington, Tom, Lehto, Petri, Ryu, Justine, Rämö, Joel T., Jurgens, Sean J., Sanna-Cherchi, Simone, Bauer, Kenneth A., Haj, Amelia, Choi, Seung Hoan, Ellinor, Patrick T., and Bendapudi, Pavan K.

Published
2024
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5. High-Resolution Genotyping of Formalin-Fixed Tissue Accurately Estimates Polygenic Risk Scores in Human Diseases

Author

Palotie, Aarno, Daly, Mark, Riley-Gills, Bridget, Jacob, Howard, Paul, Dirk, Petrovski, Slavé, Runz, Heiko, John, Sally, Okafo, George, Lawless, Nathan, Salminen-Mankonen, Heli, Plenge, Robert, Maranville, Joseph, McCarthy, Mark, Ehm, Margaret G., Auro, Kirsi, Longerich, Simonne, Mälarstig, Anders, Klinger, Katherine, Chatelain, Clement, Gossel, Matthias, Estrada, Karol, Graham, Robert, Yang, Robert, ODonnell, Chris, Mäkelä, Tomi P., Kaprio, Jaakko, Virolainen, Petri, Hakanen, Antti, Kilpi, Terhi, Perola, Markus, Partanen, Jukka, Pitkäranta, Anne, Raivio, Taneli, Tikkanen, Jani, Serpi, Raisa, Laitinen, Tarja, Kosma, Veli-Matti, Laukkanen, Jari, Hautalahti, Marco, Tuovila, Outi, Pakkanen, Raimo, Waring, Jeffrey, Riley-Gillis, Bridget, Rahimov, Fedik, Tachmazidou, Ioanna, Chen, Chia-Yen, Ding, Zhihao, Jung, Marc, Biswas, Shameek, Pendergrass, Rion, Pulford, David, Raghavan, Neha, Huertas-Vazquez, Adriana, Sul, Jae-Hoon, Hu, Xinli, Hedman, Åsa, Rivas, Manuel, Waterworth, Dawn, Renaud, Nicole, Obeidat, Maen, Ripatti, Samuli, Schleutker, Johanna, Arvas, Mikko, Carpén, Olli, Hinttala, Reetta, Kettunen, Johannes, Mannermaa, Arto, Aalto-Setälä, Katriina, Kähönen, Mika, Mäkelä, Johanna, Kälviäinen, Reetta, Julkunen, Valtteri, Soininen, Hilkka, Remes, Anne, Hiltunen, Mikko, Peltola, Jukka, Raivio, Minna, Tienari, Pentti, Rinne, Juha, Kallionpää, Roosa, Partanen, Juulia, Abbasi, Ali, Ziemann, Adam, Smaoui, Nizar, Lehtonen, Anne, Eaton, Susan, Lahdenperä, Sanni, Bowers, Natalie, Teng, Edmond, Xu, Fanli, Addis, Laura, Eicher, John, Li, Qingqin S., He, Karen, Khramtsova, Ekaterina, Färkkilä, Martti, Koskela, Jukka, Pikkarainen, Sampsa, Jussila, Airi, Kaukinen, Katri, Blomster, Timo, Kiviniemi, Mikko, Voutilainen, Markku, Lu, Tim, McCarthy, Linda, Hart, Amy, Guan, Meijian, Miller, Jason, Kalpala, Kirsi, Miller, Melissa, Eklund, Kari, Palomäki, Antti, Isomäki, Pia, Pirilä, Laura, Kaipiainen-Seppänen, Oili, Huhtakangas, Johanna, Mars, Nina, Lertratanakul, Apinya, Viollet, Coralie, Hochfeld, Marla, Gordillo, Jorge Esparza, Farias, Fabiana, Bing, Nan, Pelkonen, Margit, Kauppi, Paula, Kankaanranta, Hannu, Harju, Terttu, Lahesmaa, Riitta, Chen, Hubert, Betts, Joanna, Mishra, Rajashree, Mouded, Majd, Ngo, Debby, Niiranen, Teemu, Vaura, Felix, Salomaa, Veikko, Metsärinne, Kaj, Aittokallio, Jenni, Hernesniemi, Jussi, Gordin, Daniel, Sinisalo, Juha, Taskinen, Marja-Riitta, Tuomi, Tiinamaija, Hiltunen, Timo, Elliott, Amanda, Reeve, Mary Pat, Ruotsalainen, Sanni, Chu, Audrey, Reilly, Dermot, Mendelson, Mike, Parkkinen, Jaakko, Meretoja, Tuomo, Joensuu, Heikki, Mattson, Johanna, Salminen, Eveliina, Auranen, Annika, Karihtala, Peeter, Auvinen, Päivi, Elenius, Klaus, Pitkänen, Esa, Popovic, Relja, Fabre, Margarete, Schutzman, Jennifer, Kulkarni, Diptee, Porello, Alessandro, Loboda, Andrey, Lehtonen, Heli, McDonough, Stefan, Vuoti, Sauli, Kaarniranta, Kai, Turunen, Joni A., Ollila, Terhi, Uusitalo, Hannu, Karjalainen, Juha, Liu, Mengzhen, Loomis, Stephanie, Strauss, Erich, Chen, Hao, Tasanen, Kaisa, Huilaja, Laura, Hannula-Jouppi, Katariina, Salmi, Teea, Peltonen, Sirkku, Koulu, Leena, Choy, David, Wu, Ying, Pussinen, Pirkko, Salminen, Aino, Salo, Tuula, Rice, David, Nieminen, Pekka, Palotie, Ulla, Siponen, Maria, Suominen, Liisa, Mäntylä, Päivi, Gursoy, Ulvi, Anttonen, Vuokko, Sipilä, Kirsi, Laivuori, Hannele, Kurra, Venla, Kotaniemi-Talonen, Laura, Heikinheimo, Oskari, Kalliala, Ilkka, Aaltonen, Lauri, Jokimaa, Varpu, Vääräsmäki, Marja, Uimari, Outi, Morin-Papunen, Laure, Niinimäki, Maarit, Piltonen, Terhi, Kivinen, Katja, Widen, Elisabeth, Tukiainen, Taru, Välimäki, Niko, Laakkonen, Eija, Tyrmi, Jaakko, Silven, Heidi, Sliz, Eeva, Arffman, Riikka, Savukoski, Susanna, Laisk, Triin, Pujol, Natalia, Kumar, Janet, Hovatta, Iiris, Isometsä, Erkki, Ollila, Hanna, Suvisaari, Jaana, Als, Thomas Damm, Mäkitie, Antti, Bizaki-Vallaskangas, Argyro, Toppila-Salmi, Sanna, Willberg, Tytti, Saarentaus, Elmo, Aarnisalo, Antti, Rahikkala, Elisa, Aittomäki, Kristiina, Åberg, Fredrik, Kurki, Mitja, Havulinna, Aki, Mehtonen, Juha, Palta, Priit, Hassan, Shabbeer, Della Briotta Parolo, Pietro, Zhou, Wei, Maasha, Mutaamba, Lemmelä, Susanna, Liu, Aoxing, Lehisto, Arto, Ganna, Andrea, Llorens, Vincent, Heyne, Henrike, Rämö, Joel, Rodosthenous, Rodos, Strausz, Satu, Palotie, Tuula, Palin, Kimmo, Garcia-Tabuenca, Javier, Siirtola, Harri, Kiiskinen, Tuomo, Lee, Jiwoo, Tsuo, Kristin, Kristiansson, Kati, Hyvärinen, Kati, Ritari, Jarmo, Pylkäs, Katri, Karjalainen, Minna, Mantere, Tuomo, Kangasniemi, Eeva, Heikkinen, Sami, Pitkänen, Nina, Lessard, Samuel, Chatelain, Clément, Kallio, Lila, Wahlfors, Tiina, Punkka, Eero, Siltanen, Sanna, Kuopio, Teijo, Jalanko, Anu, Shen, Huei-Yi, Kajanne, Risto, Aavikko, Mervi, Cooper, Helen, Öller, Denise, Leinonen, Rasko, Palin, Henna, Linna, Malla-Maria, Kanai, Masahiro, Zheng, Zhili, Lahtela, L. Elisa, Kaunisto, Mari, Kilpeläinen, Elina, Sipilä, Timo P., Dada, Oluwaseun Alexander, Ghazal, Awaisa, Kytölä, Anastasia, Weldatsadik, Rigbe, Donner, Kati, Loukola, Anu, Laiho, Päivi, Sistonen, Tuuli, Kaiharju, Essi, Laukkanen, Markku, Järvensivu, Elina, Lähteenmäki, Sini, Männikkö, Lotta, Wong, Regis, Toivola, Auli, Brunfeldt, Minna, Mattsson, Hannele, Koskelainen, Sami, Hiekkalinna, Tero, Paajanen, Teemu, Pärn, Kalle, Kals, Mart, Luo, Shuang, Padmanabhuni, Shanmukha Sampath, Niemi, Marianna, Gracia-Tabuenca, Javier, Helminen, Mika, Luukkaala, Tiina, Vähätalo, Iida, Tammerluoto, Jyrki, Smith, Sarah, Southerington, Tom, Lehto, Petri, Youssef, Omar, Zidi-Mouaffak, Yossra H.S., and Tamlander, Max

Published
2024
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7. The public health impact of poor sleep on severe COVID-19, influenza and upper respiratory infections

Author

Palotie, Aarno, Daly, Mark, Riley-Gills, Bridget, Jacob, Howard, Paul, Dirk, Petrovski, Slavé, Runz, Heiko, John, Sally, Okafo, George, Lawless, Nathan, Salminen-Mankonen, Heli, Plenge, Robert, Maranville, Joseph, McCarthy, Mark, Ehm, Margaret G., Auro, Kirsi, Longerich, Simonne, Mälarstig, Anders, Klinger, Katherine, Chatelain, Clement, Gossel, Matthias, Estrada, Karol, Graham, Robert, Yang, Robert, O´Donnell, Chris, Mäkelä, Tomi P., Kaprio, Jaakko, Virolainen, Petri, Hakanen, Antti, Kilpi, Terhi, Perola, Markus, Partanen, Jukka, Pitkäranta, Anne, Raivio, Taneli, Tikkanen, Jani, Serpi, Raisa, Laitinen, Tarja, Kosma, Veli-Matti, Laukkanen, Jari, Hautalahti, Marco, Tuovila, Outi, Pakkanen, Raimo, Waring, Jeffrey, Riley-Gillis, Bridget, Rahimov, Fedik, Tachmazidou, Ioanna, Chen, Chia-Yen, Ding, Zhihao, Jung, Marc, Biswas, Shameek, Pendergrass, Rion, Pulford, David, Raghavan, Neha, Huertas-Vazquez, Adriana, Sul, Jae-Hoon, Hu, Xinli, Hedman, Åsa, Rivas, Manuel, Waterworth, Dawn, Renaud, Nicole, Obeidat, Ma´en, Ripatti, Samuli, Schleutker, Johanna, Arvas, Mikko, Carpén, Olli, Hinttala, Reetta, Kettunen, Johannes, Mannermaa, Arto, Aalto-Setälä, Katriina, Kähönen, Mika, Mäkelä, Johanna, Kälviäinen, Reetta, Julkunen, Valtteri, Soininen, Hilkka, Remes, Anne, Hiltunen, Mikko, Peltola, Jukka, Raivio, Minna, Tienari, Pentti, Rinne, Juha, Kallionpää, Roosa, Partanen, Juulia, Abbasi, Ali, Ziemann, Adam, Smaoui, Nizar, Lehtonen, Anne, Eaton, Susan, Lahdenperä, Sanni, Bowers, Natalie, Teng, Edmond, Xu, Fanli, Addis, Laura, Eicher, John, Li, Qingqin S., He, Karen, Khramtsova, Ekaterina, Färkkilä, Martti, Koskela, Jukka, Pikkarainen, Sampsa, Jussila, Airi, Kaukinen, Katri, Blomster, Timo, Kiviniemi, Mikko, Voutilainen, Markku, Lu, Tim, McCarthy, Linda, Hart, Amy, Guan, Meijian, Miller, Jason, Kalpala, Kirsi, Miller, Melissa, Eklund, Kari, Palomäki, Antti, Isomäki, Pia, Pirilä, Laura, Kaipiainen-Seppänen, Oili, Huhtakangas, Johanna, Mars, Nina, Lertratanakul, Apinya, Viollet, Coralie, Hochfeld, Marla, Gordillo, Jorge Esparza, Farias, Fabiana, Bing, Nan, Pelkonen, Margit, Kauppi, Paula, Kankaanranta, Hannu, Harju, Terttu, Lahesmaa, Riitta, Chen, Hubert, Betts, Joanna, Mishra, Rajashree, Mouded, Majd, Ngo, Debby, Niiranen, Teemu, Vaura, Felix, Salomaa, Veikko, Metsärinne, Kaj, Aittokallio, Jenni, Hernesniemi, Jussi, Gordin, Daniel, Sinisalo, Juha, Taskinen, Marja-Riitta, Tuomi, Tiinamaija, Hiltunen, Timo, Elliott, Amanda, Reeve, Mary Pat, Ruotsalainen, Sanni, Chu, Audrey, Reilly, Dermot, Mendelson, Mike, Parkkinen, Jaakko, Meretoja, Tuomo, Joensuu, Heikki, Mattson, Johanna, Salminen, Eveliina, Auranen, Annika, Karihtala, Peeter, Auvinen, Päivi, Elenius, Klaus, Pitkänen, Esa, Popovic, Relja, Fabre, Margarete, Schutzman, Jennifer, Kulkarni, Diptee, Porello, Alessandro, Loboda, Andrey, Lehtonen, Heli, McDonough, Stefan, Vuoti, Sauli, Kaarniranta, Kai, Turunen, Joni A., Ollila, Terhi, Uusitalo, Hannu, Karjalainen, Juha, Liu, Mengzhen, Loomis, Stephanie, Strauss, Erich, Chen, Hao, Tasanen, Kaisa, Huilaja, Laura, Hannula-Jouppi, Katariina, Salmi, Teea, Peltonen, Sirkku, Koulu, Leena, Choy, David, Wu, Ying, Pussinen, Pirkko, Salminen, Aino, Salo, Tuula, Rice, David, Nieminen, Pekka, Palotie, Ulla, Siponen, Maria, Suominen, Liisa, Mäntylä, Päivi, Gursoy, Ulvi, Anttonen, Vuokko, Sipilä, Kirsi, Laivuori, Hannele, Kurra, Venla, Kotaniemi-Talonen, Laura, Heikinheimo, Oskari, Kalliala, Ilkka, Aaltonen, Lauri, Jokimaa, Varpu, Vääräsmäki, Marja, Uimari, Outi, Morin-Papunen, Laure, Niinimäki, Maarit, Piltonen, Terhi, Kivinen, Katja, Widen, Elisabeth, Tukiainen, Taru, Välimäki, Niko, Laakkonen, Eija, Tyrmi, Jaakko, Silven, Heidi, Sliz, Eeva, Arffman, Riikka, Savukoski, Susanna, Laisk, Triin, Pujol, Natalia, Kumar, Janet, Hovatta, Iiris, Isometsä, Erkki, Ollila, Hanna, Suvisaari, Jaana, Als, Thomas Damm, Mäkitie, Antti, Bizaki-Vallaskangas, Argyro, Toppila-Salmi, Sanna, Willberg, Tytti, Saarentaus, Elmo, Aarnisalo, Antti, Rahikkala, Elisa, Aittomäki, Kristiina, Åberg, Fredrik, Kurki, Mitja, Havulinna, Aki, Mehtonen, Juha, Palta, Priit, Hassan, Shabbeer, Della Briotta Parolo, Pietro, Zhou, Wei, Maasha, Mutaamba, Lemmelä, Susanna, Liu, Aoxing, Lehisto, Arto, Ganna, Andrea, Llorens, Vincent, Heyne, Henrike, Rämö, Joel, Rodosthenous, Rodos, Strausz, Satu, Palotie, Tuula, Palin, Kimmo, Garcia-Tabuenca, Javier, Siirtola, Harri, Kiiskinen, Tuomo, Lee, Jiwoo, Tsuo, Kristin, Kristiansson, Kati, Hyvärinen, Kati, Ritari, Jarmo, Pylkäs, Katri, Karjalainen, Minna, Mantere, Tuomo, Kangasniemi, Eeva, Heikkinen, Sami, Pitkänen, Nina, Lessard, Samuel, Chatelain, Clément, Kallio, Lila, Wahlfors, Tiina, Punkka, Eero, Siltanen, Sanna, Kuopio, Teijo, Jalanko, Anu, Shen, Huei-Yi, Kajanne, Risto, Aavikko, Mervi, Leinonen, Rasko, Palin, Henna, Linna, Malla-Maria, Kanai, Masahiro, Zheng, Zhili, Lahtela, L. Elisa, Kaunisto, Mari, Kilpeläinen, Elina, Sipilä, Timo P., Dada, Oluwaseun Alexander, Ghazal, Awaisa, Kytölä, Anastasia, Weldatsadik, Rigbe, Donner, Kati, Loukola, Anu, Laiho, Päivi, Sistonen, Tuuli, Kaiharju, Essi, Laukkanen, Markku, Järvensivu, Elina, Lähteenmäki, Sini, Männikkö, Lotta, Wong, Regis, Toivola, Auli, Brunfeldt, Minna, Mattsson, Hannele, Koskelainen, Sami, Hiekkalinna, Tero, Paajanen, Teemu, Pärn, Kalle, Kals, Mart, Luo, Shuang, Padmanabhuni, Shanmukha Sampath, Niemi, Marianna, Gracia-Tabuenca, Javier, Helminen, Mika, Luukkaala, Tiina, Vähätalo, Iida, Tammerluoto, Jyrki, Smith, Sarah, Southerington, Tom, Lehto, Petri, Jones, Samuel E., Maisha, Fahrisa I., Strausz, Satu J., Lammi, Vilma, Cade, Brian E., Tervi, Anniina, Helaakoski, Viola, Broberg, Martin E., Lane, Jacqueline M., Redline, Susan, Saxena, Richa, and Ollila, Hanna M.

Published
2023
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8. Risk of Midlife Stroke After Adverse Pregnancy Outcomes: The FinnGen Study

Author

Miller, Eliza C., Kauko, Anni, Tom, Sarah E., Laivuori, Hannele, Niiranen, Teemu, Bello, Natalie A., Palotie, Aarno, Daly, Mark, Riley-Gills, Bridget, Jacob, Howard, Paul, Dirk, Matakidou, Athena, Platt, Adam, Runz, Heiko, John, Sally, Okafo, George, Lawless, Nathan, Salminen-Mankonen, Heli, Plenge, Robert, Maranville, Joseph, McCarthy, Mark, Hunkapiller, Julie, Ehm, Margaret G., Auro, Kirsi, Longerich, Simonne, Fox, Caroline, Mälarstig, Anders, Klinger, Katherine, Raipal, Deepak, Green, Eric, Graham, Robert, Yang, Robert, Donnell, Chris O´, Mäkelä, Tomi P., Kaprio, Jaakko, Virolainen, Petri, Hakanen, Antti, Kilpi, Terhi, Perola, Markus, Partanen, Jukka, Pitkäranta, Anne, Raivio, Taneli, Serpi, Raisa, Laitinen, Tarja, Kosma, Veli-Matti, Laukkanen, Jari, Hautalahti, Marco, Tuovila, Outi, Pakkanen, Raimo, Waring, Jeffrey, Riley-Gillis, Bridget, Rahimov, Fedik, Tachmazidou, Ioanna, Chen, Chia-Yen, Runz, Heiko, Ding, Zhihao, Jung, Marc, Biswas, Shameek, Pendergrass, Rion, Hunkapiller, Julie, Ehm, Margaret G., Pulford, David, Raghavan, Neha, Huertas-Vazquez, Adriana, Sul, Jae-Hoon, Mälarstig, Anders, Hu, Xinli, Klinger, Katherine, Graham, Robert, Green, Eric, Mozaffari, Sahar, Waterworth, Dawn, Renaud, Nicole, Obeidat, Ma´en, Ripatti, Samuli, Schleutker, Johanna, Perola, Markus, Arvas, Mikko, Carpén, Olli, Hinttala, Reetta, Kettunen, Johannes, Mannermaa, Arto, Aalto-Setälä, Katriina, Kähönen, Mika, Laukkanen, Jari, Mäkelä, Johanna, Kälviäinen, Reetta, Julkunen, Valtteri, Soininen, Hilkka, Remes, Anne, Hiltunen, Mikko, Peltola, Jukka, Raivio, Minna, Tienari, Pentti, Rinne, Juha, Kallionpää, Roosa, Partanen, Juulia, Abbasi, Ali, Ziemann, Adam, Smaoui, Nizar, Lehtonen, Anne, Eaton, Susan, Runz, Heiko, Lahdenperä, Sanni, Biswas, Shameek, Hunkapiller, Julie, Bowers, Natalie, Teng, Edmond, Pendergrass, Rion, Xu, Fanli, Pulford, David, Auro, Kirsi, Addis, Laura, Eicher, John, Li, Qingqin S, He, Karen, Khramtsova, Ekaterina, Raghavan, Neha, Färkkilä, Martti, Koskela, Jukka, Pikkarainen, Sampsa, Jussila, Airi, Kaukinen, Katri, Blomster, Timo, Kiviniemi, Mikko, Voutilainen, Markku, Daly, Mark, Abbasi, Ali, Waring, Jeffrey, Smaoui, Nizar, Rahimov, Fedik, Lehtonen, Anne, Lu, Tim, Bowers, Natalie, Pendergrass, Rion, McCarthy, Linda, Hart, Amy, Guan, Meijian, Miller, Jason, Kalpala, Kirsi, Miller, Melissa, Hu, Xinli, Eklund, Kari, Palomäki, Antti, Isomäki, Pia, Pirilä, Laura, Kaipiainen-Seppänen, Oili, Huhtakangas, Johanna, Mars, Nina, Abbasi, Ali, Waring, Jeffrey, Rahimov, Fedik, Lertratanakul, Apinya, Smaoui, Nizar, Lehtonen, Anne, Hochfeld, Marla, Bowers, Natalie, Pendergrass, Rion, Esparza Gordillo, Jorge, Auro, Kirsi, Waterworth, Dawn, Farias, Fabiana, Kalpala, Kirsi, Bing, Nan, Hu, Xinli, Laitinen, Tarja, Pelkonen, Margit, Kauppi, Paula, Kankaanranta, Hannu, Harju, Terttu, Lahesmaa, Riitta, Smaoui, Nizar, Lassi, Glenda, Eaton, Susan, Chen, Hubert, Pendergrass, Rion, Bowers, Natalie, Betts, Joanna, Auro, Kirsi, Mishra, Rajashree, Mouded, Majd, Ngo, Debby, Vaura, Felix, Salomaa, Veikko, Metsärinne, Kaj, Aittokallio, Jenni, Kähönen, Mika, Hernesniemi, Jussi, Gordin, Daniel, Sinisalo, Juha, Taskinen, Marja-Riitta, Tuomi, Tiinamaija, Hiltunen, Timo, Laukkanen, Jari, Elliott, Amanda, Pat Reeve, Mary, Ruotsalainen, Sanni, Challis, Benjamin, Paul, Dirk, Hunkapiller, Julie, Bowers, Natalie, Pendergrass, Rion, Chu, Audrey, Auro, Kirsi, Reilly, Dermot, Mendelson, Mike, Parkkinen, Jaakko, Miller, Melissa, Meretoja, Tuomo, Joensuu, Heikki, Carpén, Olli, Mattson, Johanna, Salminen, Eveliina, Auranen, Annika, Karihtala, Peeter, Elenius, Päivi Auvinen Klaus, Schleutker, Johanna, Pitkänen, Esa, Mars, Nina, Daly, Mark, Popovic, Relja, Waring, Jeffrey, Riley-Gillis, Bridget, Lehtonen, Anne, Schutzman, Jennifer, Hunkapiller, Julie, Bowers, Natalie, Pendergrass, Rion, Kulkarni, Diptee, Auro, Kirsi, Porello, Alessandro, Loboda, Andrey, Lehtonen, Heli, McDonough, Stefan, Vuoti, Sauli, Kaarniranta, Kai, Turunen, Joni A, Ollila, Terhi, Uusitalo, Hannu, Karjalainen, Juha, Pitkänen, Esa, Liu, Mengzhen, Runz, Heiko, Loomis, Stephanie, Strauss, Erich, Bowers, Natalie, Chen, Hao, Pendergrass, Rion, Tasanen, Kaisa, Huilaja, Laura, Hannula-Jouppi, Katariina, Salmi, Teea, Peltonen, Sirkku, Koulu, Leena, Smaoui, Nizar, Rahimov, Fedik, Lehtonen, Anne, Choy, David, Pendergrass, Rion, Waterworth, Dawn, Kalpala, Kirsi, Wu, Ying, Pussinen, Pirkko, Salminen, Aino, Salo, Tuula, Rice, David, Nieminen, Pekka, Palotie, Ulla, Siponen, Maria, Suominen, Liisa, Mäntylä, Päivi, Gursoy, Ulvi, Anttonen, Vuokko, Sipilä, Kirsi, Pendergrass, Rion, Kurra, Venla, Kotaniemi-Talonen, Laura, Heikinheimo, Oskari, Kalliala, Ilkka, Aaltonen, Lauri, Jokimaa, Varpu, Kettunen, Johannes, Vääräsmäki, Marja, Uimari, Outi, Morin-Papunen, Laure, Niinimäki, Maarit, Piltonen, Terhi, Kivinen, Katja, Widen, Elisabeth, Tukiainen, Taru, Pat Reeve, Mary, Daly, Mark, Välimäki, Niko, Laakkonen, Eija, Tyrmi, Jaakko, Silven, Heidi, Sliz, Eeva, Arffman, Riikka, Savukoski, Susanna, Laisk, Triin, Pujol, Natalia, Liu, Mengzhen, Riley-Gillis, Bridget, Pendergrass, Rion, Kumar, Janet, Auro, Kirsi, Hovatta, Iiris, Chen, Chia-Yen, Isometsä, Erkki, Ollila, Hanna, Suvisaari, Jaana, Damm Als, Thomas, Mäkitie, Antti, Bizaki-Vallaskangas, Argyro, Toppila-Salmi, Sanna, Willberg, Tytti, Saarentaus, Elmo, Aarnisalo, Antti, Salminen, Eveliina, Rahikkala, Elisa, Kettunen, Johannes, Aittomäki, Kristiina, Åberg, Fredrik, Kurki, Mitja, Ripatti, Samuli, Daly, Mark, Karjalainen, Juha, Havulinna, Aki, Mehtonen, Juha, Palta, Priit, Hassan, Shabbeer, Della, Pietro, Parolo, Briotta, Zhou, Wei, Maasha, Mutaamba, Hassan, Shabbeer, Lemmelä, Susanna, Rivas, Manuel, Niemi, Mari E., Palotie, Aarno, Liu, Aoxing, Lehisto, Arto, Ganna, Andrea, Llorens, Vincent, Tukiainen, Taru, Pat Reeve, Mary, Heyne, Henrike, Mars, Nina, Rämö, Joel, Saarentaus, Elmo, Ollila, Hanna, Rodosthenous, Rodos, Strausz, Satu, Palotie, Tuula, Palin, Kimmo, Garcia-Tabuenca, Javier, Siirtola, Harri, Kiiskinen, Tuomo, Lee, Jiwoo, Tsuo, Kristin, Elliott, Amanda, Kristiansson, Kati, Arvas, Mikko, Hyvärinen, Kati, Ritari, Jarmo, Carpén, Olli, Kettunen, Johannes, Pylkäs, Katri, Sliz, Eeva, Karjalainen, Minna, Mantere, Tuomo, Kangasniemi, Eeva, Heikkinen, Sami, Mannermaa, Arto, Laakkonen, Eija, Pitkänen, Nina, Lessard, Samuel, Chatelain, Clément, Terho, Perttu, Soini, Sirpa, Partanen, Jukka, Punkka, Eero, Serpi, Raisa, Siltanen, Sanna, Kosma, Veli-Matti, Kuopio, Teijo, Jalanko, Anu, Shen, Huei-Yi, Kajanne, Risto, Aavikko, Mervi, Palin, Henna, Linna, Malla-Maria, Kurki, Mitja, Karjalainen, Juha, Della, Pietro, Parolo, Briotta, Lehisto, Arto, Mehtonen, Juha, Zhou, Wei, Kanai, Masahiro, Maasha, Mutaamba, Havulinna, Aki, Lemmelä, Susanna, Kiiskinen, Tuomo, Elisa Lahtela, L., Kaunisto, Mari, Kilpeläinen, Elina, Sipilä, Timo P., Alexander Dada, Oluwaseun, Ghazal, Awaisa, Kytölä, Anastasia, Weldatsadik, Rigbe, Ruotsalainen, Sanni, Donner, Kati, Sipilä, Timo P., Loukola, Anu, Laiho, Päivi, Sistonen, Tuuli, Kaiharju, Essi, Laukkanen, Markku, Järvensivu, Elina, Lähteenmäki, Sini, Männikkö, Lotta, Wong, Regis, Toivola, Auli, Brunfeldt, Minna, Mattsson, Hannele, Kristiansson, Kati, Lemmelä, Susanna, Koskelainen, Sami, Hiekkalinna, Tero, Paajanen, Teemu, Palta, Priit, Pärn, Kalle, Kals, Mart, Luo, Shuang, Laitinen, Tarja, Pat Reeve, Mary, Sampath Padmanabhuni, Shanmukha, Niemi, Marianna, Siirtola, Harri, Gracia-Tabuenca, Javier, Helminen, Mika, Luukkaala, Tiina, Vähätalo, Iida, Pitkänen, Jyrki, Hautalahti, Marco, Mäkelä, Johanna, Smith, Sarah, and Southerington, Tom

Published
2023
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11. Accurate multi-population imputation of MICA, MICB, HLA-E, HLA-F and HLA-G alleles from genome SNP data.

Author

Tammi, Silja, Koskela, Satu, Biobank, Blood Service, Hyvärinen, Kati, Partanen, Jukka, and Ritari, Jarmo

Subjects
GENETIC variation, CHROMOSOMES, HISTOCOMPATIBILITY class I antigens, GENOMES, INDIVIDUALIZED medicine
Abstract

In addition to the classical HLA genes, the major histocompatibility complex (MHC) harbors a high number of other polymorphic genes with less established roles in disease associations and transplantation matching. To facilitate studies of the non-classical and non-HLA genes in large patient and biobank cohorts, we trained imputation models for MICA, MICB, HLA-E, HLA-F and HLA-G alleles on genome SNP array data. We show, using both population-specific and multi-population 1000 Genomes references, that the alleles of these genes can be accurately imputed for screening and research purposes. The best imputation model for MICA, MICB, HLA-E, -F and -G achieved a mean accuracy of 99.3% (min, max: 98.6, 99.9). Furthermore, validation of the 1000 Genomes exome short-read sequencing-based allele calling against a clinical-grade reference data showed an average accuracy of 99.8%, testifying for the quality of the 1000 Genomes data as an imputation reference. We also fitted the models for Infinium Global Screening Array (GSA, Illumina, Inc.) and Axiom Precision Medicine Research Array (PMRA, Thermo Fisher Scientific Inc.) SNP content, with mean accuracies of 99.1% (97.2, 100) and 98.9% (97.4, 100), respectively. Author summary: The major histocompatibility complex (MHC) region on chromosome 6 significantly influences disease risk, particularly in autoimmune conditions. To improve fine-mapping of potentially causal genetic variants within this region, we developed accurate imputation methods for inferring functional allelic variation from MHC SNP data. While existing tools primarily focus on classical HLA genes, our study extends to non-classical HLA genes (HLA-E, HLA-F, and HLA-G) and MHC Class I Chain-Related MIC genes (MICA and MICB) which have specific functions in innate and adaptive immunity. Leveraging population-specific Finnish and multi-population 1000 Genomes references, our imputation models demonstrate high accuracy. Moreover, we tailored models for two widely used genome SNP arrays: the Infinium Global Screening Array (Illumina, Inc.) and the Axiom Precision Medicine Research Array (Thermo Fisher Scientific Inc.). These freely available, multi-population models empower researchers to explore genetic MHC associations in more detail and contribute to our understanding of immune-related disease mechanisms. [ABSTRACT FROM AUTHOR]

Published
2024
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12. Comprehensive Inherited Risk Estimation for Risk-Based Breast Cancer Screening in Women

Author

Mars, Nina, primary, Kerminen, Sini, additional, Tamlander, Max, additional, Pirinen, Matti, additional, Jakkula, Eveliina, additional, Aaltonen, Kirsimari, additional, Meretoja, Tuomo, additional, Heinävaara, Sirpa, additional, Widén, Elisabeth, additional, Ripatti, Samuli, additional, Palotie, Aarno, additional, Daly, Mark, additional, Riley-Gills, Bridget, additional, Jacob, Howard, additional, Paul, Dirk, additional, Matakidou, Athena, additional, Platt, Adam, additional, Runz, Heiko, additional, John, Sally, additional, Okafo, George, additional, Lawless, Nathan, additional, Plenge, Robert, additional, Maranville, Joseph, additional, McCarthy, Mark, additional, Hunkapiller, Julie, additional, Ehm, Margaret G., additional, Auro, Kirsi, additional, Longerich, Simonne, additional, Fox, Caroline, additional, Mälarstig, Anders, additional, Klinger, Katherine, additional, Raipal, Deepak, additional, Green, Eric, additional, Graham, Robert, additional, Yang, Robert, additional, O'Donnell, Chris, additional, Mäkelä, Tomi P., additional, Kaprio, Jaakko, additional, Virolainen, Petri, additional, Hakanen, Antti, additional, Kilpi, Terhi, additional, Perola, Markus, additional, Partanen, Jukka, additional, Pitkäranta, Anne, additional, Junttila, Juhani, additional, Serpi, Raisa, additional, Laitinen, Tarja, additional, Kosma, Veli-Matti, additional, Laukkanen, Jari, additional, Hautalahti, Marco, additional, Tuovila, Outi, additional, Pakkanen, Raimo, additional, Waring, Jeffrey, additional, Riley-Gillis, Bridget, additional, Rahimov, Fedik, additional, Tachmazidou, Ioanna, additional, Chen, Chia-Yen, additional, Ding, Zhihao, additional, Jung, Marc, additional, Biswas, Shameek, additional, Pendergrass, Rion, additional, Pulford, David, additional, Raghavan, Neha, additional, Huertas-Vazquez, Adriana, additional, Sul, Jae-Hoon, additional, Hu, Xinli, additional, Mozaffari, Sahar, additional, Waterworth, Dawn, additional, Renaud, Nicole, additional, Obeidat, Ma'en, additional, Schleutker, Johanna, additional, Arvas, Mikko, additional, Carpén, Olli, additional, Hinttala, Reetta, additional, Kettunen, Johannes, additional, Mannermaa, Arto, additional, Aalto-Setälä, Katriina, additional, Kähönen, Mika, additional, Mäkelä, Johanna, additional, Kälviäinen, Reetta, additional, Julkunen, Valtteri, additional, Soininen, Hilkka, additional, Remes, Anne, additional, Hiltunen, Mikko, additional, Peltola, Jukka, additional, Raivio, Minna, additional, Tienari, Pentti, additional, Rinne, Juha, additional, Kallionpää, Roosa, additional, Partanen, Juulia, additional, Abbasi, Ali, additional, Ziemann, Adam, additional, Smaoui, Nizar, additional, Lehtonen, Anne, additional, Eaton, Susan, additional, Lahdenperä, Sanni, additional, Bowers, Natalie, additional, Teng, Edmond, additional, Xu, Fanli, additional, Addis, Laura, additional, Eicher, John, additional, Li, Qingqin S, additional, He, Karen, additional, Khramtsova, Ekaterina, additional, Färkkilä, Martti, additional, Koskela, Jukka, additional, Pikkarainen, Sampsa, additional, Jussila, Airi, additional, Kaukinen, Katri, additional, Blomster, Timo, additional, Kiviniemi, Mikko, additional, Voutilainen, Markku, additional, Lu, Tim, additional, McCarthy, Linda, additional, Hart, Amy, additional, Guan, Meijian, additional, Miller, Jason, additional, Kalpala, Kirsi, additional, Miller, Melissa, additional, Eklund, Kari, additional, Palomäki, Antti, additional, Isomäki, Pia, additional, Pirilä, Laura, additional, Kaipiainen-Seppänen, Oili, additional, Huhtakangas, Johanna, additional, Mars, Nina, additional, Lertratanakul, Apinya, additional, Close, David, additional, Hochfeld, Marla, additional, Gordillo, Jorge Esparza, additional, Farias, Fabiana, additional, Bing, Nan, additional, Pelkonen, Margit, additional, Kauppi, Paula, additional, Kankaanranta, Hannu, additional, Harju, Terttu, additional, Lahesmaa, Riitta, additional, Mackay, Alex, additional, Lassi, Glenda, additional, Chen, Hubert, additional, Betts, Joanna, additional, Mishra, Rajashree, additional, Mouded, Majd, additional, Ngo, Debby, additional, Niiranen, Teemu, additional, Vaura, Felix, additional, Salomaa, Veikko, additional, Metsärinne, Kaj, additional, Aittokallio, Jenni, additional, Hernesniemi, Jussi, additional, Gordin, Daniel, additional, Sinisalo, Juha, additional, Taskinen, Marja-Riitta, additional, Tuomi, Tiinamaija, additional, Hiltunen, Timo, additional, Elliott, Amanda, additional, Reeve, Mary Pat, additional, Ruotsalainen, Sanni, additional, Challis, Benjamin, additional, Chu, Audrey, additional, Reilly, Dermot, additional, Mendelson, Mike, additional, Parkkinen, Jaakko, additional, Joensuu, Heikki, additional, Mattson, Johanna, additional, Salminen, Eveliina, additional, Auranen, Annika, additional, Karihtala, Peeter, additional, Auvinen, Päivi, additional, Elenius, Klaus, additional, Pitkänen, Esa, additional, Popovic, Relja, additional, Schutzman, Jennifer, additional, Kulkarni, Diptee, additional, Porello, Alessandro, additional, Loboda, Andrey, additional, Lehtonen, Heli, additional, McDonough, Stefan, additional, Vuoti, Sauli, additional, Kaarniranta, Kai, additional, Turunen, Joni A, additional, Ollila, Terhi, additional, Uusitalo, Hannu, additional, Karjalainen, Juha, additional, Liu, Mengzhen, additional, Loomis, Stephanie, additional, Strauss, Erich, additional, Chen, Hao, additional, Tasanen, Kaisa, additional, Huilaja, Laura, additional, Hannula-Jouppi, Katariina, additional, Salmi, Teea, additional, Peltonen, Sirkku, additional, Koulu, Leena, additional, Choy, David, additional, Wu, Ying, additional, Pussinen, Pirkko, additional, Salminen, Aino, additional, Salo, Tuula, additional, Rice, David, additional, Nieminen, Pekka, additional, Palotie, Ulla, additional, Siponen, Maria, additional, Suominen, Liisa, additional, Mäntylä, Päivi, additional, Gursoy, Ulvi, additional, Anttonen, Vuokko, additional, Sipilä, Kirsi, additional, Laivuori, Hannele, additional, Kurra, Venla, additional, Kotaniemi-Talonen, Laura, additional, Heikinheimo, Oskari, additional, Kalliala, Ilkka, additional, Aaltonen, Lauri, additional, Jokimaa, Varpu, additional, Vääräsmäki, Marja, additional, Uimari, Outi, additional, Morin-Papunen, Laure, additional, Niinimäki, Maarit, additional, Piltonen, Terhi, additional, Kivinen, Katja, additional, Widen, Elisabeth, additional, Tukiainen, Taru, additional, Välimäki, Niko, additional, Laakkonen, Eija, additional, Tyrmi, Jaakko, additional, Silven, Heidi, additional, Sliz, Eeva, additional, Arffman, Riikka, additional, Savukoski, Susanna, additional, Laisk, Triin, additional, Pujol, Natalia, additional, Kumar, Janet, additional, Hovatta, Iiris, additional, Isometsä, Erkki, additional, Veerapen, Kumar, additional, Ollila, Hanna, additional, Suvisaari, Jaana, additional, Als, Thomas Damm, additional, Mäkitie, Antti, additional, Bizaki-Vallaskangas, Argyro, additional, Toppila-Salmi, Sanna, additional, Willberg, Tytti, additional, Saarentaus, Elmo, additional, Aarnisalo, Antti, additional, Rahikkala, Elisa, additional, Aittomäki, Kristiina, additional, Åberg, Fredrik, additional, Kurki, Mitja, additional, Havulinna, Aki, additional, Mehtonen, Juha, additional, Palta, Priit, additional, Hassan, Shabbeer, additional, Della Briotta Parolo, Pietro, additional, Zhou, Wei, additional, Maasha, Mutaamba, additional, Lemmelä, Susanna, additional, Rivas, Manuel, additional, Niemi, Mari E., additional, Liu, Aoxing, additional, Lehisto, Arto, additional, Ganna, Andrea, additional, Llorens, Vincent, additional, Heyne, Henrike, additional, Rämö, Joel, additional, Rodosthenous, Rodos, additional, Strausz, Satu, additional, Palotie, Tuula, additional, Palin, Kimmo, additional, Garcia-Tabuenca, Javier, additional, Siirtola, Harri, additional, Kiiskinen, Tuomo, additional, Lee, Jiwoo, additional, Tsuo, Kristin, additional, Kristiansson, Kati, additional, Hyvärinen, Kati, additional, Ritari, Jarmo, additional, Pylkäs, Katri, additional, Karjalainen, Minna, additional, Mantere, Tuomo, additional, Kangasniemi, Eeva, additional, Heikkinen, Sami, additional, Pitkänen, Nina, additional, Lessard, Samuel, additional, Chatelain, Clément, additional, Terho, Perttu, additional, Soini, Sirpa, additional, Punkka, Eero, additional, Siltanen, Sanna, additional, Kuopio, Teijo, additional, Jalanko, Anu, additional, Shen, Huei-Yi, additional, Kajanne, Risto, additional, Aavikko, Mervi, additional, Kanai, Masahiro, additional, Lahtela, L. Elisa, additional, Kaunisto, Mari, additional, Kilpeläinen, Elina, additional, Sipilä, Timo P., additional, Dada, Oluwaseun Alexander, additional, Ghazal, Awaisa, additional, Kytölä, Anastasia, additional, Weldatsadik, Rigbe, additional, Donner, Kati, additional, Loukola, Anu, additional, Laiho, Päivi, additional, Sistonen, Tuuli, additional, Kaiharju, Essi, additional, Laukkanen, Markku, additional, Järvensivu, Elina, additional, Lähteenmäki, Sini, additional, Männikkö, Lotta, additional, Wong, Regis, additional, Toivola, Auli, additional, Brunfeldt, Minna, additional, Mattsson, Hannele, additional, Koskelainen, Sami, additional, Hiekkalinna, Tero, additional, Paajanen, Teemu, additional, Pärn, Kalle, additional, Kals, Mart, additional, Luo, Shuang, additional, Sinha, Vishal, additional, Niemi, Marianna, additional, Gracia-Tabuenca, Javier, additional, Helminen, Mika, additional, Luukkaala, Tiina, additional, Vähätalo, Iida, additional, Pitkänen, Jyrki, additional, Smith, Sarah, additional, and Southerington, Tom, additional

Published
2024
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13. Effect of NK cell receptor genetic variation on allogeneic stem cell transplantation outcome and in vitro NK cell cytotoxicity

Author

Nihtilä, Julia, primary, Penna, Leena, additional, Salmenniemi, Urpu, additional, Itälä-Remes, Maija, additional, Crossland, Rachel E, additional, Gallardo, David, additional, Bogunia-Kubik, Katarzyna, additional, Lacina, Piotr, additional, Bieniaszewska, Maria, additional, Giebel, Sebastian, additional, Karjalainen, Katariina, additional, Jahan, Farhana, additional, Kerkelä, Erja, additional, Hyvärinen, Kati, additional, Koskela, Satu, additional, Ritari, Jarmo, additional, and Partanen, Jukka, additional

Published
2024
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15. HLA-DQ and HLA-DRB1 alleles associated with Henoch-Schönlein purpura nephritis in Finnish pediatric population: a genome-wide association study

Author

Koskela, Mikael, Nihtilä, Julia, Ylinen, Elisa, Kolho, Kaija-Leena, Nuutinen, Matti, Ritari, Jarmo, and Jahnukainen, Timo

Subjects
HLA histocompatibility antigens -- Genetic aspects -- Health aspects, Nephritis -- Genetic aspects -- Risk factors, Genetic polymorphisms -- Research, Schonlein-Henoch purpura -- Genetic aspects -- Risk factors, Pediatric research, Allelomorphism -- Research, Histocompatibility antigens -- Genetic aspects -- Health aspects, Health
Abstract

Background The pathophysiology of Henoch-Schönlein purpura (HSP) is still unclear, but several findings suggest that genetic factors may influence disease susceptibility. We aimed to perform a genome-wide association study (GWAS) in pediatric HSP patients with an emphasis on severe HSP nephritis. Methods The study included 46 HSP patients, 42 of whom had undergone kidney biopsy. Forty-nine pediatric patients with an inflammatory bowel disease (IBD) served as an autoimmune disease control group while Finnish bone marrow and blood donors represented the general reference population (n = 18,757). GWAS was performed for HSP and IBD samples in a case-control manner against the reference population. The analysis also included imputation of human leukocyte antigen (HLA) alleles. Results GWAS analysis in HSP revealed several polymorphisms from the HLA region that surpassed the genome-wide significance level. Three HLA class II alleles were also significantly more frequent in HSP than in the reference population: DQA1*01:01, DQB1*05:01, and DRB1*01:01. Haplotype DQA1*01:01/DQB1*05:01/DRB1*01:01 occurred in 43.5% of HSP patients, whereas its frequency was 8.2% in IBD patients and 15.0% in the reference population. HSP patients with this haplotype showed similar baseline clinical findings and outcome as HSP patients negative for the haplotype. In IBD patients, no polymorphism or HLA allele appeared significant at the genome-wide level. Conclusions Our results suggest that haplotype DQA1*01:01/DQB1*05:01/DRB1*01:01 is associated with susceptibility to HSP, but not with the severity of the kidney involvement. These HLA associations did not occur in IBD patients, suggesting that they are specific to HSP and not related to susceptibility to autoimmune diseases in general. Graphical abstract, Author(s): Mikael Koskela [sup.1] [sup.2] , Julia Nihtilä [sup.3] [sup.4] , Elisa Ylinen [sup.2] , Kaija-Leena Kolho [sup.1] [sup.5] , Matti Nuutinen [sup.6] [sup.7] , Jarmo Ritari [sup.4] , Timo [...]

Published
2021
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16. A machine-learning method for biobank-scale genetic prediction of blood group antigens

Author

Hyvärinen, Kati, Haimila, Katri, Moslemi, Camous, Biobank, Blood Service, Olsson, Martin L., Ostrowski, Sisse R., Pedersen, Ole B., Erikstrup, Christian, Partanen, Jukka, Ritari, Jarmo, Hyvärinen, Kati, Haimila, Katri, Moslemi, Camous, Biobank, Blood Service, Olsson, Martin L., Ostrowski, Sisse R., Pedersen, Ole B., Erikstrup, Christian, Partanen, Jukka, and Ritari, Jarmo

Abstract

A key element for successful blood transfusion is compatibility of the patient and donor red blood cell (RBC) antigens. Precise antigen matching reduces the risk for immunization and other adverse transfusion outcomes. RBC antigens are encoded by specific genes, which allows developing computational methods for determining antigens from genomic data. We describe here a classification method for determining RBC antigens from genotyping array data. Random forest models for 39 RBC antigens in 14 blood group systems and for human platelet antigen (HPA)-1 were trained and tested using genotype and RBC antigen and HPA-1 typing data available for 1,192 blood donors in the Finnish Blood Service Biobank. The algorithm and models were further evaluated using a validation cohort of 111,667 Danish blood donors. In the Finnish test data set, the median (interquartile range [IQR]) balanced accuracy for 39 models was 99.9 (98.9–100)%. We were able to replicate 34 out of 39 Finnish models in the Danish cohort and the median (IQR) balanced accuracy for classifications was 97.1 (90.1–99.4)%. When applying models trained with the Danish cohort, the median (IQR) balanced accuracy for the 40 Danish models in the Danish test data set was 99.3 (95.1–99.8)%. The RBC antigen and HPA-1 prediction models demonstrated high overall accuracies suitable for probabilistic determination of blood groups and HPA-1 at biobank-scale. Furthermore, population-specific training cohort increased the accuracies of the models. This stand-alone and freely available method is applicable for research and screening for antigen-negative blood donors., A key element for successful blood transfusion is compatibility of the patient and donor red blood cell (RBC) antigens. Precise antigen matching reduces the risk for immunization and other adverse transfusion outcomes. RBC antigens are encoded by specific genes, which allows developing computational methods for determining antigens from genomic data. We describe here a classification method for determining RBC antigens from genotyping array data. Random forest models for 39 RBC antigens in 14 blood group systems and for human platelet antigen (HPA)-1 were trained and tested using genotype and RBC antigen and HPA-1 typing data available for 1,192 blood donors in the Finnish Blood Service Biobank. The algorithm and models were further evaluated using a validation cohort of 111,667 Danish blood donors. In the Finnish test data set, the median (interquartile range [IQR]) balanced accuracy for 39 models was 99.9 (98.9-100)%. We were able to replicate 34 out of 39 Finnish models in the Danish cohort and the median (IQR) balanced accuracy for classifications was 97.1 (90.1-99.4)%. When applying models trained with the Danish cohort, the median (IQR) balanced accuracy for the 40 Danish models in the Danish test data set was 99.3 (95.1-99.8)%. The RBC antigen and HPA-1 prediction models demonstrated high overall accuracies suitable for probabilistic determination of blood groups and HPA-1 at biobank- scale. Furthermore, population-specific training cohort increased the accuracies of the models. This stand-alone and freely available method is applicable for research and screening for antigen-negative blood donors.

Published
2024

19. CHEK2 GERMLINE VARIANTS AND ALLOGENEIC HEMATOPOIETIC STEM CELL TRANSPLANT OUTCOMES

Author

Lahtinen, Atte K, primary, Koski, Jessica, additional, Ritari, Jarmo, additional, Hyvärinen, Kati, additional, Koskela, Satu, additional, Partanen, Jukka, additional, Vettenranta, Kim, additional, Koskenvuo, Minna, additional, Niittyvuopio, Riitta, additional, Salmenniemi, Urpu, additional, Itälä-Remes, Maija, additional, Jahnukainen, Kirsi, additional, Kilpivaara, Outi, additional, Wartiovaara- Kautto, Ulla, additional, and Karu, Maarja, additional

Published
2023
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24. Thrombosis risk in single- and double-heterozygous carriers of factor V Leiden and prothrombin G20210A in FinnGen and the UK Biobank

Author

Ryu, Justine, Rämö, Joel T., Jurgens, Sean J., Palotie, Aarno, Daly, Mark, Riley-Gills, Bridget, Jacob, Howard, Viollet, Coralie, Petrovski, Slavé, Chen, Chia-Yen, John, Sally, Okafo, George, Plenge, Robert, Maranville, Joseph, McCarthy, Mark, Pendergrass, Rion, Ehm, Margaret G., Auro, Kirsi, Longerich, Simonne, Mälarstig, Anders, Vlahiotis, Anna, Klinger, Katherine, Chatelain, Clement, Gossel, Matthias, Estrada, Karol, Graham, Robert, Waterworth, Dawn, O´Donnell, Chris, Renaud, Nicole, Mäkelä, Tomi P., Kaprio, Jaakko, Ruddock, Minna, Virolainen, Petri, Hakanen, Antti, Kilpi, Terhi, Perola, Markus, Partanen, Jukka, Raivio, Taneli, Tikkanen, Jani, Serpi, Raisa, Kristiansson, Kati, Kosma, Veli-Matti, Laukkanen, Jari, Hautalahti, Marco, Tuovila, Outi, Waring, Jeffrey, Riley-Gillis, Bridget, Rahimov, Fedik, Tachmazidou, Ioanna, Chen, Chia-Yen, Ding, Zhihao, Jung, Marc, Tuoken, Hanati, Biswas, Shameek, Pendergrass, Rion, Ehm, Margaret G., Pulford, David, Raghavan, Neha, Huertas-Vazquez, Adriana, Sul, Jae-Hoon, Mälarstig, Anders, Hu, Xinli, Hedman, Åsa, Klinger, Katherine, Graham, Robert, Waterworth, Dawn, Renaud, Nicole, Obeidat, Ma´en, Chung, Jonathan, Zierer, Jonas, Niemi, Mari, Ripatti, Samuli, Schleutker, Johanna, Perola, Markus, Arvas, Mikko, Carpén, Olli, Hinttala, Reetta, Kettunen, Johannes, Mannermaa, Arto, Aalto-Setälä, Katriina, Kähönen, Mika, Laukkanen, Jari, Mäkelä, Johanna, Kälviäinen, Reetta, Julkunen, Valtteri, Soininen, Hilkka, Remes, Anne, Hiltunen, Mikko, Peltola, Jukka, Raivio, Minna, Tienari, Pentti, Rinne, Juha, Kallionpää, Roosa, Partanen, Juulia, Ziemann, Adam, Smaoui, Nizar, Lehtonen, Anne, Eaton, Susan, Runz, Heiko, Lahdenperä, Sanni, Biswas, Shameek, Bowers, Natalie, Teng, Edmond, Pendergrass, Rion, Xu, Fanli, Pulford, David, Auro, Kirsi, Addis, Laura, Eicher, John, Li, Qingqin S., He, Karen, Khramtsova, Ekaterina, Raghavan, Neha, Färkkilä, Martti, Koskela, Jukka, Pikkarainen, Sampsa, Jussila, Airi, Kaukinen, Katri, Blomster, Timo, Kiviniemi, Mikko, Voutilainen, Markku, Daly, Mark, Waring, Jeffrey, Smaoui, Nizar, Rahimov, Fedik, Lehtonen, Anne, Lu, Tim, Bowers, Natalie, Pendergrass, Rion, McCarthy, Linda, Hart, Amy, Guan, Meijian, Miller, Jason, Kalpala, Kirsi, Miller, Melissa, Hu, Xinli, Eklund, Kari, Palomäki, Antti, Isomäki, Pia, Pirilä, Laura, Kaipiainen-Seppänen, Oili, Huhtakangas, Johanna, Mars, Nina, Waring, Jeffrey, Rahimov, Fedik, Lertratanakul, Apinya, Smaoui, Nizar, Lehtonen, Anne, Viollet, Coralie, Hochfeld, Marla, Bowers, Natalie, Pendergrass, Rion, Gordillo, Jorge Esparza, Auro, Kirsi, Waterworth, Dawn, Farias, Fabiana, Kalpala, Kirsi, Bing, Nan, Hu, Xinli, Laitinen, Tarja, Pelkonen, Margit, Kauppi, Paula, Kankaanranta, Hannu, Harju, Terttu, Lahesmaa, Riitta, Smaoui, Nizar, Viollet, Coralie, Eaton, Susan, Chen, Hubert, Pendergrass, Rion, Bowers, Natalie, Betts, Joanna, Auro, Kirsi, Mishra, Rajashree, Mouded, Majd, Ngo, Debby, Niiranen, Teemu, Vaura, Felix, Salomaa, Veikko, Metsärinne, Kaj, Aittokallio, Jenni, Kähönen, Mika, Hernesniemi, Jussi, Gordin, Daniel, Sinisalo, Juha, Taskinen, Marja-Riitta, Tuomi, Tiinamaija, Hiltunen, Timo, Laukkanen, Jari, Elliott, Amanda, Reeve, Mary Pat, Ruotsalainen, Sanni, Paul, Dirk, Bowers, Natalie, Pendergrass, Rion, Chu, Audrey, Auro, Kirsi, Reilly, Dermot, Mendelson, Mike, Parkkinen, Jaakko, Miller, Melissa, Meretoja, Tuomo, Joensuu, Heikki, Carpén, Olli, Mattson, Johanna, Salminen, Eveliina, Auranen, Annika, Karihtala, Peeter, Auvinen, Päivi, Elenius, Klaus, Schleutker, Johanna, Pitkänen, Esa, Mars, Nina, Daly, Mark, Popovic, Relja, Waring, Jeffrey, Riley-Gillis, Bridget, Lehtonen, Anne, Fabre, Margarete, Schutzman, Jennifer, Bowers, Natalie, Pendergrass, Rion, Kulkarni, Diptee, Auro, Kirsi, Porello, Alessandro, Loboda, Andrey, Lehtonen, Heli, McDonough, Stefan, Vuoti, Sauli, Kaarniranta, Kai, Turunen, Joni A., Ollila, Terhi, Uusitalo, Hannu, Karjalainen, Juha, Pitkänen, Esa, Liu, Mengzhen, Runz, Heiko, Loomis, Stephanie, Strauss, Erich, Bowers, Natalie, Chen, Hao, Pendergrass, Rion, Tasanen, Kaisa, Huilaja, Laura, Hannula-Jouppi, Katariina, Salmi, Teea, Peltonen, Sirkku, Koulu, Leena, Smaoui, Nizar, Rahimov, Fedik, Lehtonen, Anne, Choy, David, Pendergrass, Rion, Waterworth, Dawn, Kalpala, Kirsi, Wu, Ying, Pussinen, Pirkko, Salminen, Aino, Salo, Tuula, Rice, David, Nieminen, Pekka, Palotie, Ulla, Siponen, Maria, Suominen, Liisa, Mäntylä, Päivi, Gursoy, Ulvi, Anttonen, Vuokko, Sipilä, Kirsi, Pendergrass, Rion, Laivuori, Hannele, Kurra, Venla, Kotaniemi-Talonen, Laura, Heikinheimo, Oskari, Kalliala, Ilkka, Aaltonen, Lauri, Jokimaa, Varpu, Kettunen, Johannes, Vääräsmäki, Marja, Uimari, Outi, Morin-Papunen, Laure, Niinimäki, Maarit, Piltonen, Terhi, Kivinen, Katja, Widen, Elisabeth, Tukiainen, Taru, Reeve, Mary Pat, Daly, Mark, Välimäki, Niko, Laakkonen, Eija, Tyrmi, Jaakko, Silven, Heidi, Sliz, Eeva, Arffman, Riikka, Savukoski, Susanna, Laisk, Triin, Pujol, Natalia, Liu, Mengzhen, Riley-Gillis, Bridget, Pendergrass, Rion, Kumar, Janet, Auro, Kirsi, Hovatta, Iiris, Chen, Chia-Yen, Isometsä, Erkki, Ollila, Hanna, Suvisaari, Jaana, Mäkitie, Antti, Bizaki-Vallaskangas, Argyro, Toppila-Salmi, Sanna, Willberg, Tytti, Saarentaus, Elmo, Aarnisalo, Antti, Salminen, Eveliina, Rahikkala, Elisa, Kettunen, Johannes, Aittomäki, Kristiina, Åberg, Fredrik, Kurki, Mitja, Ripatti, Samuli, Daly, Mark, Karjalainen, Juha, Havulinna, Aki, Mehtonen, Juha, Palta, Priit, Hassan, Shabbeer, Della Briotta Parolo, Pietro, Zhou, Wei, Maasha, Mutaamba, Hassan, Shabbeer, Lemmelä, Susanna, Rivas, Manuel, Palotie, Aarno, Liu, Aoxing, Lehisto, Arto, Ganna, Andrea, Llorens, Vincent, Laivuori, Hannele, Tukiainen, Taru, Reeve, Mary Pat, Heyne, Henrike, Mars, Nina, Rämö, Joel, Saarentaus, Elmo, Ollila, Hanna, Rodosthenous, Rodos, Strausz, Satu, Palotie, Tuula, Palin, Kimmo, Garcia-Tabuenca, Javier, Siirtola, Harri, Kiiskinen, Tuomo, Lee, Jiwoo, Tsuo, Kristin, Elliott, Amanda, Kristiansson, Kati, Arvas, Mikko, Hyvärinen, Kati, Ritari, Jarmo, Carpén, Olli, Kettunen, Johannes, Pylkäs, Katri, Sliz, Eeva, Karjalainen, Minna, Mantere, Tuomo, Kangasniemi, Eeva, Heikkinen, Sami, Mannermaa, Arto, Laakkonen, Eija, Pitkänen, Nina, Lessard, Samuel, Chatelain, Clément, Kallio, Lila, Wahlfors, Tiina, Partanen, Jukka, Punkka, Eero, Serpi, Raisa, Siltanen, Sanna, Kosma, Veli-Matti, Kuopio, Teijo, Jalanko, Anu, Shen, Huei-Yi, Kajanne, Risto, Aavikko, Mervi, Cooper, Helen, Öller, Denise, Leinonen, Rasko, Palin, Henna, Linna, Malla-Maria, Kurki, Mitja, Karjalainen, Juha, Della Briotta Parolo, Pietro, Lehisto, Arto, Mehtonen, Juha, Zhou, Wei, Kanai, Masahiro, Maasha, Mutaamba, Zheng, Zhili, Laivuori, Hannele, Havulinna, Aki, Lemmelä, Susanna, Kiiskinen, Tuomo, Lahtela, L. Elisa, Kaunisto, Mari, Kilpeläinen, Elina, Sipilä, Timo P., Dada, Oluwaseun Alexander, Ghazal, Awaisa, Kytölä, Anastasia, Weldatsadik, Rigbe, Ruotsalainen, Sanni, Donner, Kati, Sipilä, Timo P., Loukola, Anu, Laiho, Päivi, Sistonen, Tuuli, Kaiharju, Essi, Laukkanen, Markku, Järvensivu, Elina, Lähteenmäki, Sini, Männikkö, Lotta, Wong, Regis, Toivola, Auli, Brunfeldt, Minna, Mattsson, Hannele, Kristiansson, Kati, Lemmelä, Susanna, Koskelainen, Sami, Hiekkalinna, Tero, Paajanen, Teemu, Palta, Priit, Luo, Shuang, Laitinen, Tarja, Reeve, Mary Pat, Padmanabhuni, Shanmukha Sampath, Niemi, Marianna, Siirtola, Harri, Gracia-Tabuenca, Javier, Helminen, Mika, Luukkaala, Tiina, Vähätalo, Iida, Tammerluoto, Jyrki, Hautalahti, Marco, Mäkelä, Johanna, Smith, Sarah, Southerington, Tom, Lehto, Petri, Niiranen, Teemu, Sanna-Cherchi, Simone, Bauer, Kenneth A., Haj, Amelia, Choi, Seung Hoan, Palotie, Aarno, Daly, Mark, Ellinor, Patrick T., and Bendapudi, Pavan K.

Abstract

•Population-scale genomics (N = 937 939) allowed assembly of a large FVL/PTGM double-heterozygous cohort while mitigating ascertainment bias.•FVL/PTGM DH appeared to be more common than FVL homozygosity and conferred a similar risk of venous thrombosis.

Published
2024
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25. The public health impact of poor sleep on severe COVID-19, influenza and upper respiratory infections

Author

Jones, Samuel E., primary, Maisha, Fahrisa I., additional, Strausz, Satu J., additional, Lammi, Vilma, additional, Cade, Brian E., additional, Tervi, Anniina, additional, Helaakoski, Viola, additional, Broberg, Martin E., additional, Lane, Jacqueline M., additional, Redline, Susan, additional, Saxena, Richa, additional, Ollila, Hanna M., additional, Palotie, Aarno, additional, Daly, Mark, additional, Riley-Gills, Bridget, additional, Jacob, Howard, additional, Paul, Dirk, additional, Petrovski, Slavé, additional, Runz, Heiko, additional, John, Sally, additional, Okafo, George, additional, Lawless, Nathan, additional, Salminen-Mankonen, Heli, additional, Plenge, Robert, additional, Maranville, Joseph, additional, McCarthy, Mark, additional, Ehm, Margaret G., additional, Auro, Kirsi, additional, Longerich, Simonne, additional, Mälarstig, Anders, additional, Klinger, Katherine, additional, Chatelain, Clement, additional, Gossel, Matthias, additional, Estrada, Karol, additional, Graham, Robert, additional, Yang, Robert, additional, O´Donnell, Chris, additional, Mäkelä, Tomi P., additional, Kaprio, Jaakko, additional, Virolainen, Petri, additional, Hakanen, Antti, additional, Kilpi, Terhi, additional, Perola, Markus, additional, Partanen, Jukka, additional, Pitkäranta, Anne, additional, Raivio, Taneli, additional, Tikkanen, Jani, additional, Serpi, Raisa, additional, Laitinen, Tarja, additional, Kosma, Veli-Matti, additional, Laukkanen, Jari, additional, Hautalahti, Marco, additional, Tuovila, Outi, additional, Pakkanen, Raimo, additional, Waring, Jeffrey, additional, Riley-Gillis, Bridget, additional, Rahimov, Fedik, additional, Tachmazidou, Ioanna, additional, Chen, Chia-Yen, additional, Ding, Zhihao, additional, Jung, Marc, additional, Biswas, Shameek, additional, Pendergrass, Rion, additional, Pulford, David, additional, Raghavan, Neha, additional, Huertas-Vazquez, Adriana, additional, Sul, Jae-Hoon, additional, Hu, Xinli, additional, Hedman, Åsa, additional, Rivas, Manuel, additional, Waterworth, Dawn, additional, Renaud, Nicole, additional, Obeidat, Ma´en, additional, Ripatti, Samuli, additional, Schleutker, Johanna, additional, Arvas, Mikko, additional, Carpén, Olli, additional, Hinttala, Reetta, additional, Kettunen, Johannes, additional, Mannermaa, Arto, additional, Aalto-Setälä, Katriina, additional, Kähönen, Mika, additional, Mäkelä, Johanna, additional, Kälviäinen, Reetta, additional, Julkunen, Valtteri, additional, Soininen, Hilkka, additional, Remes, Anne, additional, Hiltunen, Mikko, additional, Peltola, Jukka, additional, Raivio, Minna, additional, Tienari, Pentti, additional, Rinne, Juha, additional, Kallionpää, Roosa, additional, Partanen, Juulia, additional, Abbasi, Ali, additional, Ziemann, Adam, additional, Smaoui, Nizar, additional, Lehtonen, Anne, additional, Eaton, Susan, additional, Lahdenperä, Sanni, additional, Bowers, Natalie, additional, Teng, Edmond, additional, Xu, Fanli, additional, Addis, Laura, additional, Eicher, John, additional, Li, Qingqin S., additional, He, Karen, additional, Khramtsova, Ekaterina, additional, Färkkilä, Martti, additional, Koskela, Jukka, additional, Pikkarainen, Sampsa, additional, Jussila, Airi, additional, Kaukinen, Katri, additional, Blomster, Timo, additional, Kiviniemi, Mikko, additional, Voutilainen, Markku, additional, Lu, Tim, additional, McCarthy, Linda, additional, Hart, Amy, additional, Guan, Meijian, additional, Miller, Jason, additional, Kalpala, Kirsi, additional, Miller, Melissa, additional, Eklund, Kari, additional, Palomäki, Antti, additional, Isomäki, Pia, additional, Pirilä, Laura, additional, Kaipiainen-Seppänen, Oili, additional, Huhtakangas, Johanna, additional, Mars, Nina, additional, Lertratanakul, Apinya, additional, Viollet, Coralie, additional, Hochfeld, Marla, additional, Gordillo, Jorge Esparza, additional, Farias, Fabiana, additional, Bing, Nan, additional, Pelkonen, Margit, additional, Kauppi, Paula, additional, Kankaanranta, Hannu, additional, Harju, Terttu, additional, Lahesmaa, Riitta, additional, Chen, Hubert, additional, Betts, Joanna, additional, Mishra, Rajashree, additional, Mouded, Majd, additional, Ngo, Debby, additional, Niiranen, Teemu, additional, Vaura, Felix, additional, Salomaa, Veikko, additional, Metsärinne, Kaj, additional, Aittokallio, Jenni, additional, Hernesniemi, Jussi, additional, Gordin, Daniel, additional, Sinisalo, Juha, additional, Taskinen, Marja-Riitta, additional, Tuomi, Tiinamaija, additional, Hiltunen, Timo, additional, Elliott, Amanda, additional, Reeve, Mary Pat, additional, Ruotsalainen, Sanni, additional, Chu, Audrey, additional, Reilly, Dermot, additional, Mendelson, Mike, additional, Parkkinen, Jaakko, additional, Meretoja, Tuomo, additional, Joensuu, Heikki, additional, Mattson, Johanna, additional, Salminen, Eveliina, additional, Auranen, Annika, additional, Karihtala, Peeter, additional, Auvinen, Päivi, additional, Elenius, Klaus, additional, Pitkänen, Esa, additional, Popovic, Relja, additional, Fabre, Margarete, additional, Schutzman, Jennifer, additional, Kulkarni, Diptee, additional, Porello, Alessandro, additional, Loboda, Andrey, additional, Lehtonen, Heli, additional, McDonough, Stefan, additional, Vuoti, Sauli, additional, Kaarniranta, Kai, additional, Turunen, Joni A., additional, Ollila, Terhi, additional, Uusitalo, Hannu, additional, Karjalainen, Juha, additional, Liu, Mengzhen, additional, Loomis, Stephanie, additional, Strauss, Erich, additional, Chen, Hao, additional, Tasanen, Kaisa, additional, Huilaja, Laura, additional, Hannula-Jouppi, Katariina, additional, Salmi, Teea, additional, Peltonen, Sirkku, additional, Koulu, Leena, additional, Choy, David, additional, Wu, Ying, additional, Pussinen, Pirkko, additional, Salminen, Aino, additional, Salo, Tuula, additional, Rice, David, additional, Nieminen, Pekka, additional, Palotie, Ulla, additional, Siponen, Maria, additional, Suominen, Liisa, additional, Mäntylä, Päivi, additional, Gursoy, Ulvi, additional, Anttonen, Vuokko, additional, Sipilä, Kirsi, additional, Laivuori, Hannele, additional, Kurra, Venla, additional, Kotaniemi-Talonen, Laura, additional, Heikinheimo, Oskari, additional, Kalliala, Ilkka, additional, Aaltonen, Lauri, additional, Jokimaa, Varpu, additional, Vääräsmäki, Marja, additional, Uimari, Outi, additional, Morin-Papunen, Laure, additional, Niinimäki, Maarit, additional, Piltonen, Terhi, additional, Kivinen, Katja, additional, Widen, Elisabeth, additional, Tukiainen, Taru, additional, Välimäki, Niko, additional, Laakkonen, Eija, additional, Tyrmi, Jaakko, additional, Silven, Heidi, additional, Sliz, Eeva, additional, Arffman, Riikka, additional, Savukoski, Susanna, additional, Laisk, Triin, additional, Pujol, Natalia, additional, Kumar, Janet, additional, Hovatta, Iiris, additional, Isometsä, Erkki, additional, Ollila, Hanna, additional, Suvisaari, Jaana, additional, Als, Thomas Damm, additional, Mäkitie, Antti, additional, Bizaki-Vallaskangas, Argyro, additional, Toppila-Salmi, Sanna, additional, Willberg, Tytti, additional, Saarentaus, Elmo, additional, Aarnisalo, Antti, additional, Rahikkala, Elisa, additional, Aittomäki, Kristiina, additional, Åberg, Fredrik, additional, Kurki, Mitja, additional, Havulinna, Aki, additional, Mehtonen, Juha, additional, Palta, Priit, additional, Hassan, Shabbeer, additional, Della Briotta Parolo, Pietro, additional, Zhou, Wei, additional, Maasha, Mutaamba, additional, Lemmelä, Susanna, additional, Liu, Aoxing, additional, Lehisto, Arto, additional, Ganna, Andrea, additional, Llorens, Vincent, additional, Heyne, Henrike, additional, Rämö, Joel, additional, Rodosthenous, Rodos, additional, Strausz, Satu, additional, Palotie, Tuula, additional, Palin, Kimmo, additional, Garcia-Tabuenca, Javier, additional, Siirtola, Harri, additional, Kiiskinen, Tuomo, additional, Lee, Jiwoo, additional, Tsuo, Kristin, additional, Kristiansson, Kati, additional, Hyvärinen, Kati, additional, Ritari, Jarmo, additional, Pylkäs, Katri, additional, Karjalainen, Minna, additional, Mantere, Tuomo, additional, Kangasniemi, Eeva, additional, Heikkinen, Sami, additional, Pitkänen, Nina, additional, Lessard, Samuel, additional, Chatelain, Clément, additional, Kallio, Lila, additional, Wahlfors, Tiina, additional, Punkka, Eero, additional, Siltanen, Sanna, additional, Kuopio, Teijo, additional, Jalanko, Anu, additional, Shen, Huei-Yi, additional, Kajanne, Risto, additional, Aavikko, Mervi, additional, Leinonen, Rasko, additional, Palin, Henna, additional, Linna, Malla-Maria, additional, Kanai, Masahiro, additional, Zheng, Zhili, additional, Lahtela, L. Elisa, additional, Kaunisto, Mari, additional, Kilpeläinen, Elina, additional, Sipilä, Timo P., additional, Dada, Oluwaseun Alexander, additional, Ghazal, Awaisa, additional, Kytölä, Anastasia, additional, Weldatsadik, Rigbe, additional, Donner, Kati, additional, Loukola, Anu, additional, Laiho, Päivi, additional, Sistonen, Tuuli, additional, Kaiharju, Essi, additional, Laukkanen, Markku, additional, Järvensivu, Elina, additional, Lähteenmäki, Sini, additional, Männikkö, Lotta, additional, Wong, Regis, additional, Toivola, Auli, additional, Brunfeldt, Minna, additional, Mattsson, Hannele, additional, Koskelainen, Sami, additional, Hiekkalinna, Tero, additional, Paajanen, Teemu, additional, Pärn, Kalle, additional, Kals, Mart, additional, Luo, Shuang, additional, Padmanabhuni, Shanmukha Sampath, additional, Niemi, Marianna, additional, Gracia-Tabuenca, Javier, additional, Helminen, Mika, additional, Luukkaala, Tiina, additional, Vähätalo, Iida, additional, Tammerluoto, Jyrki, additional, Smith, Sarah, additional, Southerington, Tom, additional, and Lehto, Petri, additional

Published
2023
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27. MICA and MICB allele assortment in Finland

Author

Koskela, Satu, primary, Tammi, Silja, additional, Clancy, Jonna, additional, Lucas, Jonathan A. M., additional, Turner, Thomas R., additional, Hyvärinen, Kati, additional, Ritari, Jarmo, additional, and Partanen, Jukka, additional

Published
2023
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28. Blood donor biobank as a resource in personalised biomedical genetic research

Author

Clancy, Jonna, Ritari, Jarmo, Vaittinen, Eevaleena, Arvas, Mikko, Tammi, Silja, Koskela, Satu, and Partanen, Jukka

Abstract

Health questionnaires and donation criteria result in accumulation of highly selected individuals in a blood donor population. To understand better the usefulness of a blood donor-based biobank in personalised disease-associated genetic studies, and for possible personalised blood donation policies, we evaluated the occurrence and distributions of common and rare disease-associated genetic variants in Finnish Blood Service Biobank. We analysed among 31,880 blood donors the occurrence and geographical distribution of (i) 53 rare Finnish-enriched disease-associated variants, (ii) mutations assumed to influence blood donation: four Bernard-Soulier syndrome and two hemochromatosis mutations, (iii) type I diabetes risk genotype HLA-DQ2/DQ8. In addition, we analysed the level of consanguinity in Blood Service Biobank. 80.3% of blood donors carried at least one (range 0–9 per donor) of the rare variants, many in homozygous form, as well. Donors carrying multiple rare variants were enriched in Eastern Finland. Haemochromatosis mutation HFE C282Y homozygosity was 43.8% higher than expected, whereas mutations leading to Bernard-Soulier thrombocytopenia were rare. The frequency of HLA-DQ2/DQ8 genotype was slightly lower than expected. First-degree consanguinity was higher in Blood Service Biobank than in the general population. We demonstrate that despite donor selection, the Blood Service Biobank is a valuable resource for personalised medical research and for genotype-selected samples from unaffected individuals. The geographical genetic substructure of Finland enables efficient recruitment of donors carrying rare variants. Furthermore, we show that blood donor biobank material can be utilised for personalised blood donation policies.

Published
2024
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29. Clinically relevant germline variants in allogeneic hematopoietic stem cell transplant recipients

Author

Lahtinen, Atte K., primary, Koski, Jessica, additional, Ritari, Jarmo, additional, Hyvärinen, Kati, additional, Koskela, Satu, additional, Partanen, Jukka, additional, Vettenranta, Kim, additional, Koskenvuo, Minna, additional, Niittyvuopio, Riitta, additional, Salmenniemi, Urpu, additional, Itälä-Remes, Maija, additional, Jahnukainen, Kirsi, additional, Kilpivaara, Outi, additional, and Wartiovaara-Kautto, Ulla, additional

Published
2022
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32. Additional file 1 of Blood donor biobank and HLA imputation as a resource for HLA homozygous cells for therapeutic and research use

Author

Clancy, Jonna, Hyvärinen, Kati, Ritari, Jarmo, Wahlfors, Tiina, Partanen, Jukka, and Koskela, Satu

Abstract

Additional file 1: Figure 1Posterior probabilities of the imputed HLA alleles in a given HLA haplotype. Number of individuals homozygous for each haplotype (1-41) is stated in Table 1. Median, highest and lowest values of posterior probabilities are shown in haplotypes 1-21, and the actual posterior probability value in haplotypes (22-41) where one individual was identified.

Published
2022
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34. Comparative Genomic Analysis of Lactobacillus rhamnosus GG Reveals Pili Containing a Humanmucus Binding Protein

Author

Kankainen, Matti, Paulin, Lars, Tynkkynen, Soile, von Ossowski, Ingemar, Reunanen, Justus, Partanen, Pasi, Satokari, Reetta, Vesterlund, Satu, Hendrickx, Antoni P. A., Lebeer, Sarah, De Keersmaecker, Sigrid C. J., Vanderleyden, Jos, Hämäläinen, Tuula, Laukkanen, Suvi, Salovuori, Noora, Ritari, Jarmo, Alatalo, Edward, Korpela, Riitta, Mattila-Sandholm, Tiina, Lassig, Anna, Hatakka, Katja, Kinnunen, Katri T., Karjalainen, Heli, Saxelin, Maija, Laakso, Kati, Surakka, Anu, Palva, Airi, Salusjärvi, Tuomas, Auvinen, Petri, de Vos, Willem M., and Klaenhammer, Todd R.

Published
2009
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39. Additional file 4 of Genomic convergence between Akkermansia muciniphila in different mammalian hosts

Author

Geerlings, Sharon Y., Ouwerkerk, Janneke P., Koehorst, Jasper J., Ritari, Jarmo, Aalvink, Steven, Stecher, B��rbel, Schaap, Peter J., Paulin, Lars, de Vos, Willem M., and Belzer, Clara

Subjects
genetic structures
Abstract

Additional file 4: Figure S2. Pan-genome of the type strain and all new A. muciniphila isolates visualized using Phandango.

Published
2021
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41. Selection and characterization of a SpaCBA pilus-secreting food-grade derivative of Lacticaseibacillus rhamnosus GG

Author

Tytgat, Hanne L.P., Rasinkangas, Pia, Ritari, Jarmo, Reunanen, Justus, Aalvink, Steven, Lin, Chia Wei, Palva, Airi, Douillard, François P., de Vos, Willem M., Tytgat, Hanne L.P., Rasinkangas, Pia, Ritari, Jarmo, Reunanen, Justus, Aalvink, Steven, Lin, Chia Wei, Palva, Airi, Douillard, François P., and de Vos, Willem M.

Abstract

Many studies have established the functional properties of Lacticaseibacillus rhamnosus GG, previously known as Lactobacillus rhamnosus GG, marketed worldwide as a probiotic. The extraordinary capacity of L. rhamnosus GG to bind to human mucus and influence the immune system especially stand out. Earlier, we have shown the key role of its SpaCBA sortase-dependent pili encoded by the spaCBA-srtC1 gene cluster herein. These heterotrimeric pili consist of a shaft pilin SpaA, a basal pilin SpaB, and tip pilin SpaC that contains a mucus-binding domain. Here, we set out to characterize a food-grade non-GMO mutant of L. rhamnosus GG, strain PA11, which secretes its pilins, rather than coupling them to the cell surface, due to a defect in the housekeeping sortase A. The sortase-negative strain PA11 was extensively characterized using functional genomics and biochemical approaches and found to secrete the SpaCBA pili into the supernatant. Given the functional importance and uniqueness of the mucus-binding pili of L. rhamnosus GG, strain PA11 offers novel opportunities towards the characterization and further therapeutic application of SpaCBA pili and their low-cost, large-scale production. Key points: •Creation of pilus-secreting mutant (PA11) of the key probiotic LGG. •Strain PA11 is defective in a functional housekeeping sortase SrtA. •Strain PA11 opens novel biotherapeutic application avenues. Graphical abstract[Figure not available: see fulltext.]

Published
2021

42. Selection and characterization of a SpaCBA pilus-secreting food-grade derivative of Lacticaseibacillus rhamnosus GG

Author

Tytgat, Hanne L P; https://orcid.org/0000-0001-6270-2110, Rasinkangas, Pia, Ritari, Jarmo; https://orcid.org/0000-0002-3458-9314, Reunanen, Justus, Aalvink, Steven; https://orcid.org/0000-0001-7554-1723, Lin, Chia-Wei; https://orcid.org/0000-0003-4777-2916, Palva, Airi, Douillard, François P, de Vos, Willem M; https://orcid.org/0000-0002-0273-3166, Tytgat, Hanne L P; https://orcid.org/0000-0001-6270-2110, Rasinkangas, Pia, Ritari, Jarmo; https://orcid.org/0000-0002-3458-9314, Reunanen, Justus, Aalvink, Steven; https://orcid.org/0000-0001-7554-1723, Lin, Chia-Wei; https://orcid.org/0000-0003-4777-2916, Palva, Airi, Douillard, François P, and de Vos, Willem M; https://orcid.org/0000-0002-0273-3166

Abstract

Many studies have established the functional properties of Lacticaseibacillus rhamnosus GG, previously known as Lactobacillus rhamnosus GG, marketed worldwide as a probiotic. The extraordinary capacity of L. rhamnosus GG to bind to human mucus and influence the immune system especially stand out. Earlier, we have shown the key role of its SpaCBA sortase-dependent pili encoded by the spaCBA-srtC1 gene cluster herein. These heterotrimeric pili consist of a shaft pilin SpaA, a basal pilin SpaB, and tip pilin SpaC that contains a mucus-binding domain. Here, we set out to characterize a food-grade non-GMO mutant of L. rhamnosus GG, strain PA11, which secretes its pilins, rather than coupling them to the cell surface, due to a defect in the housekeeping sortase A. The sortase-negative strain PA11 was extensively characterized using functional genomics and biochemical approaches and found to secrete the SpaCBA pili into the supernatant. Given the functional importance and uniqueness of the mucus-binding pili of L. rhamnosus GG, strain PA11 offers novel opportunities towards the characterization and further therapeutic application of SpaCBA pili and their low-cost, large-scale production. KEY POINTS: •Creation of pilus-secreting mutant (PA11) of the key probiotic LGG. •Strain PA11 is defective in a functional housekeeping sortase SrtA. •Strain PA11 opens novel biotherapeutic application avenues. Graphical abstract. Keywords: L. rhamnosus GG; Non-GMO derivative; Pili; Pilus biogenesis.

Published
2021

45. Characterization of Highly Mucus-Adherent Non-GMO Derivatives of Lacticaseibacillus rhamnosus GG

Author

Rasinkangas, Pia, Tytgat, Hanne L.P., Ritari, Jarmo, Reunanen, Justus, Salminen, Seppo, Palva, Airi, Douillard, François P., de Vos, Willem M., Rasinkangas, Pia, Tytgat, Hanne L.P., Ritari, Jarmo, Reunanen, Justus, Salminen, Seppo, Palva, Airi, Douillard, François P., and de Vos, Willem M.

Abstract

Lacticaseibacillus rhamnosus GG is one of the best studied lactic acid bacteria in the context of probiotic effects. L. rhamnosus GG has been shown to prevent diarrhea in children and adults and has been implicated to have mitigating or preventive effects in several disorders connected to microbiota dysbiosis. The probiotic effects are largely attributed to its adhesive heterotrimeric sortase-dependent pili, encoded by the spaCBA-srtC1 gene cluster. Indeed, the strain-specific SpaCBA pili have been shown to contribute to adherence, biofilm formation and host signaling. In this work we set out to generate non-GMO derivatives of L. rhamnosus GG that adhere stronger to mucus compared to the wild-type strain using chemical mutagenesis. We selected 13 derivatives that showed an increased mucus-adherent phenotype. Deep shotgun resequencing of the strains enabled division of the strains into three classes, two of which revealed SNPs (single nucleotide polymorphisms) in the spaA and spaC genes encoding the shaft and tip adhesive pilins, respectively. Strikingly, the other class derivatives demonstrated less clear genotype – phenotype relationships, illustrating that pili biogenesis and structure is also affected by other processes. Further characterization of the different classes of derivatives was performed by PacBio SMRT sequencing and RNAseq analysis, which resulted in the identification of molecular candidates driving pilin biosynthesis and functionality. In conclusion, we report on the generation and characterization of three classes of strongly adherent L. rhamnosus GG derivatives that show an increase in adhesion to mucus. These are of special interest as they provide a window on processes and genes driving piliation and its control in L. rhamnosus GG and offer a variety of non-GMO derivatives of this key probiotic strain that are applicable in food products.

Published
2020

48. Meta-Analysis of Genome-Wide Association and Gene Expression Studies Implicates Donor T Cell Function and Cytokine Pathways in Acute GvHD

Author

Hyvärinen, Kati, primary, Koskela, Satu, additional, Niittyvuopio, Riitta, additional, Nihtinen, Anne, additional, Volin, Liisa, additional, Salmenniemi, Urpu, additional, Putkonen, Mervi, additional, Buño, Ismael, additional, Gallardo, David, additional, Itälä-Remes, Maija, additional, Partanen, Jukka, additional, and Ritari, Jarmo, additional

Published
2020
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49. Molecular analysis of meso- and thermophilic microbiota associated with anaerobic biowaste degradation

Author

Ritari Jarmo, Koskinen Kaisa, Hultman Jenni, Kurola Jukka M, Kymäläinen Maritta, Romantschuk Martin, Paulin Lars, and Auvinen Petri

Subjects
Microbiology, QR1-502
Abstract

Abstract Background Microbial anaerobic digestion (AD) is used as a waste treatment process to degrade complex organic compounds into methane. The archaeal and bacterial taxa involved in AD are well known, whereas composition of the fungal community in the process has been less studied. The present study aimed to reveal the composition of archaeal, bacterial and fungal communities in response to increasing organic loading in mesophilic and thermophilic AD processes by applying 454 amplicon sequencing technology. Furthermore, a DNA microarray method was evaluated in order to develop a tool for monitoring the microbiological status of AD. Results The 454 sequencing showed that the diversity and number of bacterial taxa decreased with increasing organic load, while archaeal i.e. methanogenic taxa remained more constant. The number and diversity of fungal taxa increased during the process and varied less in composition with process temperature than bacterial and archaeal taxa, even though the fungal diversity increased with temperature as well. Evaluation of the microarray using AD sample DNA showed correlation of signal intensities with sequence read numbers of corresponding target groups. The sensitivity of the test was found to be about 1%. Conclusions The fungal community survives in anoxic conditions and grows with increasing organic loading, suggesting that Fungi may contribute to the digestion by metabolising organic nutrients for bacterial and methanogenic groups. The microarray proof of principle tests suggest that the method has the potential for semiquantitative detection of target microbial groups given that comprehensive sequence data is available for probe design.

Published
2012
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