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312 results on '"Pitkänen, Esa"'

1. Single-cell transcriptomes identify patient-tailored therapies for selective co-inhibition of cancer clones

Author

Ianevski, Aleksandr, Nader, Kristen, Driva, Kyriaki, Senkowski, Wojciech, Bulanova, Daria, Moyano-Galceran, Lidia, Ruokoranta, Tanja, Kuusanmäki, Heikki, Ikonen, Nemo, Sergeev, Philipp, Vähä-Koskela, Markus, Giri, Anil K., Vähärautio, Anna, Kontro, Mika, Porkka, Kimmo, Pitkänen, Esa, Heckman, Caroline A., Wennerberg, Krister, and Aittokallio, Tero

Published
2024
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2. Mutation-Attention (MuAt): deep representation learning of somatic mutations for tumour typing and subtyping.

Author

Sanjaya, Prima, Maljanen, Katri, Katainen, Riku, Waszak, Sebastian, Aaltonen, Lauri, Stegle, Oliver, Korbel, Jan, and Pitkänen, Esa

Subjects
Cancer genomics, Deep learning, Deep neural networks, Machine learning, Molecular tumour subtyping, Precision cancer medicine, Somatic mutations, Tumour type prediction, Whole exome sequencing, Whole genome sequencing, Neoplasms, Humans, Deep Learning, Benchmarking, Mutation
Abstract

BACKGROUND: Cancer genome sequencing enables accurate classification of tumours and tumour subtypes. However, prediction performance is still limited using exome-only sequencing and for tumour types with low somatic mutation burden such as many paediatric tumours. Moreover, the ability to leverage deep representation learning in discovery of tumour entities remains unknown. METHODS: We introduce here Mutation-Attention (MuAt), a deep neural network to learn representations of simple and complex somatic alterations for prediction of tumour types and subtypes. In contrast to many previous methods, MuAt utilizes the attention mechanism on individual mutations instead of aggregated mutation counts. RESULTS: We trained MuAt models on 2587 whole cancer genomes (24 tumour types) from the Pan-Cancer Analysis of Whole Genomes (PCAWG) and 7352 cancer exomes (20 types) from the Cancer Genome Atlas (TCGA). MuAt achieved prediction accuracy of 89% for whole genomes and 64% for whole exomes, and a top-5 accuracy of 97% and 90%, respectively. MuAt models were found to be well-calibrated and perform well in three independent whole cancer genome cohorts with 10,361 tumours in total. We show MuAt to be able to learn clinically and biologically relevant tumour entities including acral melanoma, SHH-activated medulloblastoma, SPOP-associated prostate cancer, microsatellite instability, POLE proofreading deficiency, and MUTYH-associated pancreatic endocrine tumours without these tumour subtypes and subgroups being provided as training labels. Finally, scrunity of MuAt attention matrices revealed both ubiquitous and tumour-type specific patterns of simple and complex somatic mutations. CONCLUSIONS: Integrated representations of somatic alterations learnt by MuAt were able to accurately identify histological tumour types and identify tumour entities, with potential to impact precision cancer medicine.

Published
2023

3. Augment like there's no tomorrow: Consistently performing neural networks for medical imaging

Author

Pohjonen, Joona, Stürenberg, Carolin, Föhr, Atte, Randen-Brady, Reija, Luomala, Lassi, Lohi, Jouni, Pitkänen, Esa, Rannikko, Antti, and Mirtti, Tuomas

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition
Abstract

Deep neural networks have achieved impressive performance in a wide variety of medical imaging tasks. However, these models often fail on data not used during training, such as data originating from a different medical centre. How to recognize models suffering from this fragility, and how to design robust models are the main obstacles to clinical adoption. Here, we present general methods to identify causes for model generalisation failures and how to circumvent them. First, we use $\textit{distribution-shifted datasets}$ to show that models trained with current state-of-the-art methods are highly fragile to variability encountered in clinical practice, and then develop a $\textit{strong augmentation}$ strategy to address this fragility. Distribution-shifted datasets allow us to discover this fragility, which can otherwise remain undetected after validation against multiple external datasets. Strong augmentation allows us to train robust models achieving consistent performance under shifts from the training data distribution. Importantly, we demonstrate that strong augmentation yields biomedical imaging models which retain high performance when applied to real-world clinical data. Our results pave the way for the development and evaluation of reliable and robust neural networks in clinical practice., Comment: Code for the paper is available from https://www.github.com/jopo666/StrongAugment

Published
2022

4. A Unified Review of Deep Learning for Automated Medical Coding

Author

Ji, Shaoxiong, Sun, Wei, Li, Xiaobo, Dong, Hang, Taalas, Ara, Zhang, Yijia, Wu, Honghan, Pitkänen, Esa, and Marttinen, Pekka

Subjects
Computer Science - Computation and Language, Computer Science - Information Retrieval
Abstract

Automated medical coding, an essential task for healthcare operation and delivery, makes unstructured data manageable by predicting medical codes from clinical documents. Recent advances in deep learning and natural language processing have been widely applied to this task. However, deep learning-based medical coding lacks a unified view of the design of neural network architectures. This review proposes a unified framework to provide a general understanding of the building blocks of medical coding models and summarizes recent advanced models under the proposed framework. Our unified framework decomposes medical coding into four main components, i.e., encoder modules for text feature extraction, mechanisms for building deep encoder architectures, decoder modules for transforming hidden representations into medical codes, and the usage of auxiliary information. Finally, we introduce the benchmarks and real-world usage and discuss key research challenges and future directions., Comment: ACM Computing Surveys

Published
2022
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5. 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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6. Spectral decoupling allows training transferable neural networks in medical imaging

Author

Pohjonen, Joona, Stürenberg, Carolin, Rannikko, Antti, Mirtti, Tuomas, and Pitkänen, Esa

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Artificial Intelligence, Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning, Statistics - Machine Learning
Abstract

Many current neural networks for medical imaging generalise poorly to data unseen during training. Such behaviour can be caused by networks overfitting easy-to-learn, or statistically dominant, features while disregarding other potentially informative features. For example, indistinguishable differences in the sharpness of the images from two different scanners can degrade the performance of the network significantly. All neural networks intended for clinical practice need to be robust to variation in data caused by differences in imaging equipment, sample preparation and patient populations. To address these challenges, we evaluate the utility of spectral decoupling as an implicit bias mitigation method. Spectral decoupling encourages the neural network to learn more features by simply regularising the networks' unnormalised prediction scores with an L2 penalty, thus having no added computational costs. We show that spectral decoupling allows training neural networks on datasets with strong spurious correlations and increases networks' robustness for data distribution shifts. To validate our findings, we train networks with and without spectral decoupling to detect prostate cancer tissue slides and COVID-19 in chest radiographs. Networks trained with spectral decoupling achieve up to 9.5 percent point higher performance on external datasets. Our results show that spectral decoupling helps with generalisation issues associated with neural networks, and can be used to complement or replace computationally expensive explicit bias mitigation methods, such as stain normalization in histological images. We recommend using spectral decoupling as an implicit bias mitigation method in any neural network intended for clinical use., Comment: 10 pages, 7 figures and 2 tables

Published
2021
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7. 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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8. 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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10. 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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12. Molecular features encoded in the ctDNA reveal heterogeneity and predict outcome in high-risk aggressive B-cell lymphoma

Author

Meriranta, Leo, Alkodsi, Amjad, Pasanen, Annika, Lepistö, Maija, Mapar, Parisa, Blaker, Yngvild Nuvin, Jørgensen, Judit, Karjalainen-Lindsberg, Marja-Liisa, Fiskvik, Idun, Mikalsen, Lars Tore G., Autio, Matias, Björkholm, Magnus, Jerkeman, Mats, Fluge, Øystein, Brown, Peter, Jyrkkiö, Sirkku, Holte, Harald, Pitkänen, Esa, Ellonen, Pekka, and Leppä, Sirpa

Published
2022
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16. 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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17. 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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18. ArcheD, a residual neural network for prediction of cerebrospinal fluid amyloid‐beta from amyloid PET images.

Author

Tagmazian, Arina A., Schwarz, Claudia, Lange, Catharina, Pitkänen, Esa, and Vuoksimaa, Eero

Subjects
CEREBROSPINAL fluid, POSITRON emission tomography, CONVOLUTIONAL neural networks, LIMBIC system, PARIETAL lobe, AMYLOID
Abstract

Detection and measurement of amyloid‐beta (Aβ) in the brain is a key factor for early identification and diagnosis of Alzheimer's disease (AD). We aimed to develop a deep learning model to predict Aβ cerebrospinal fluid (CSF) concentration directly from amyloid PET images, independent of tracers, brain reference regions or preselected regions of interest. We used 1870 Aβ PET images and CSF measurements to train and validate a convolutional neural network ("ArcheD"). We evaluated the ArcheD performance in relation to episodic memory and the standardized uptake value ratio (SUVR) of cortical Aβ. We also compared the brain region's relevance for the model's CSF prediction within clinical‐based and biological‐based classifications. ArcheD‐predicted Aβ CSF values correlated with measured Aβ CSF values (r = 0.92; q < 0.01), SUVR (rAV45 = −0.64, rFBB = −0.69; q < 0.01) and episodic memory measures (0.33 < r < 0.44; q < 0.01). For both classifications, cerebral white matter significantly contributed to CSF prediction (q < 0.01), specifically in non‐symptomatic and early stages of AD. However, in late‐stage disease, the brain stem, subcortical areas, cortical lobes, limbic lobe and basal forebrain made more significant contributions (q < 0.01). Considering cortical grey matter separately, the parietal lobe was the strongest predictor of CSF amyloid levels in those with prodromal or early AD, while the temporal lobe played a more crucial role for those with AD. In summary, ArcheD reliably predicted Aβ CSF concentration from Aβ PET scans, offering potential clinical utility for Aβ level determination. [ABSTRACT FROM AUTHOR]

Published
2024
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22. S175: SINGLE-CELL ANALYSIS REVEALS SOMATIC TP53 MUTATIONS EMERGE IN EARLY PROGENITOR CELLS BUT BECOME ENRICHED IN THE ERYTHROID LINEAGE IN ERCC6L2 DISEASE

Author

Langohr, Laura, primary, Kaaja, Ilse, additional, Douglas, Suvi, additional, Räisänen, Tuulia, additional, Adhikari, Sadiksha, additional, Vähä-Koskela, Markus, additional, Heckman, Caroline, additional, Lahtela, Jenni, additional, Wartiovaara-Kautto, Ulla, additional, Pitkänen, Esa, additional, and Kilpivaara, Outi, additional

Published
2023
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23. 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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25. Teaching an algorithm to identify cancer from sequence data

Author

Turunen, Ari, Pitkänen, Esa, and Nyrönen, Tommi

Subjects
Deep learning, Cancer research, DNA sequencing, ELIXIR
Abstract

Deep learning has revolutionised cancer research. Deep neural networks can automatically detect features within a patient’s sample data that can be used to identify cancers. In the future, learning algorithms will be able to identify potential early-stage cancers from a blood sample. Esa Pitkänen and his research group at theInstitute for Molecular Medicine Finland(FIMM) are developing a new generation of deep-learning algorithms.

Published
2023
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26. Retrotransposon insertions can initiate colorectal cancer and are associated with poor survival

Author

Cajuso, Tatiana, Sulo, Päivi, Tanskanen, Tomas, Katainen, Riku, Taira, Aurora, Hänninen, Ulrika A., Kondelin, Johanna, Forsström, Linda, Välimäki, Niko, Aavikko, Mervi, Kaasinen, Eevi, Ristimäki, Ari, Koskensalo, Selja, Lepistö, Anna, Renkonen-Sinisalo, Laura, Seppälä, Toni, Kuopio, Teijo, Böhm, Jan, Mecklin, Jukka-Pekka, Kilpivaara, Outi, Pitkänen, Esa, Palin, Kimmo, and Aaltonen, Lauri A.

Published
2019
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27. Supplementary Table 1 from Comprehensive Evaluation of Protein Coding Mononucleotide Microsatellites in Microsatellite-Unstable Colorectal Cancer

Author

Kondelin, Johanna, primary, Gylfe, Alexandra E., primary, Lundgren, Sofie, primary, Tanskanen, Tomas, primary, Hamberg, Jiri, primary, Aavikko, Mervi, primary, Palin, Kimmo, primary, Ristolainen, Heikki, primary, Katainen, Riku, primary, Kaasinen, Eevi, primary, Taipale, Minna, primary, Taipale, Jussi, primary, Renkonen-Sinisalo, Laura, primary, Järvinen, Heikki, primary, Böhm, Jan, primary, Mecklin, Jukka-Pekka, primary, Vahteristo, Pia, primary, Tuupanen, Sari, primary, Aaltonen, Lauri A., primary, and Pitkänen, Esa, primary

Published
2023
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28. Supplementary Table 3 from Comprehensive Evaluation of Protein Coding Mononucleotide Microsatellites in Microsatellite-Unstable Colorectal Cancer

Author

Kondelin, Johanna, primary, Gylfe, Alexandra E., primary, Lundgren, Sofie, primary, Tanskanen, Tomas, primary, Hamberg, Jiri, primary, Aavikko, Mervi, primary, Palin, Kimmo, primary, Ristolainen, Heikki, primary, Katainen, Riku, primary, Kaasinen, Eevi, primary, Taipale, Minna, primary, Taipale, Jussi, primary, Renkonen-Sinisalo, Laura, primary, Järvinen, Heikki, primary, Böhm, Jan, primary, Mecklin, Jukka-Pekka, primary, Vahteristo, Pia, primary, Tuupanen, Sari, primary, Aaltonen, Lauri A., primary, and Pitkänen, Esa, primary

Published
2023
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29. Supplementary Table 4 from Comprehensive Evaluation of Protein Coding Mononucleotide Microsatellites in Microsatellite-Unstable Colorectal Cancer

Author

Kondelin, Johanna, primary, Gylfe, Alexandra E., primary, Lundgren, Sofie, primary, Tanskanen, Tomas, primary, Hamberg, Jiri, primary, Aavikko, Mervi, primary, Palin, Kimmo, primary, Ristolainen, Heikki, primary, Katainen, Riku, primary, Kaasinen, Eevi, primary, Taipale, Minna, primary, Taipale, Jussi, primary, Renkonen-Sinisalo, Laura, primary, Järvinen, Heikki, primary, Böhm, Jan, primary, Mecklin, Jukka-Pekka, primary, Vahteristo, Pia, primary, Tuupanen, Sari, primary, Aaltonen, Lauri A., primary, and Pitkänen, Esa, primary

Published
2023
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30. Supplementary Table 2 from Comprehensive Evaluation of Protein Coding Mononucleotide Microsatellites in Microsatellite-Unstable Colorectal Cancer

Author

Kondelin, Johanna, primary, Gylfe, Alexandra E., primary, Lundgren, Sofie, primary, Tanskanen, Tomas, primary, Hamberg, Jiri, primary, Aavikko, Mervi, primary, Palin, Kimmo, primary, Ristolainen, Heikki, primary, Katainen, Riku, primary, Kaasinen, Eevi, primary, Taipale, Minna, primary, Taipale, Jussi, primary, Renkonen-Sinisalo, Laura, primary, Järvinen, Heikki, primary, Böhm, Jan, primary, Mecklin, Jukka-Pekka, primary, Vahteristo, Pia, primary, Tuupanen, Sari, primary, Aaltonen, Lauri A., primary, and Pitkänen, Esa, primary

Published
2023
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31. Supplementary Table 5 from Comprehensive Evaluation of Protein Coding Mononucleotide Microsatellites in Microsatellite-Unstable Colorectal Cancer

Author

Kondelin, Johanna, primary, Gylfe, Alexandra E., primary, Lundgren, Sofie, primary, Tanskanen, Tomas, primary, Hamberg, Jiri, primary, Aavikko, Mervi, primary, Palin, Kimmo, primary, Ristolainen, Heikki, primary, Katainen, Riku, primary, Kaasinen, Eevi, primary, Taipale, Minna, primary, Taipale, Jussi, primary, Renkonen-Sinisalo, Laura, primary, Järvinen, Heikki, primary, Böhm, Jan, primary, Mecklin, Jukka-Pekka, primary, Vahteristo, Pia, primary, Tuupanen, Sari, primary, Aaltonen, Lauri A., primary, and Pitkänen, Esa, primary

Published
2023
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32. Supplementary Table 6 from Comprehensive Evaluation of Protein Coding Mononucleotide Microsatellites in Microsatellite-Unstable Colorectal Cancer

Author

Kondelin, Johanna, primary, Gylfe, Alexandra E., primary, Lundgren, Sofie, primary, Tanskanen, Tomas, primary, Hamberg, Jiri, primary, Aavikko, Mervi, primary, Palin, Kimmo, primary, Ristolainen, Heikki, primary, Katainen, Riku, primary, Kaasinen, Eevi, primary, Taipale, Minna, primary, Taipale, Jussi, primary, Renkonen-Sinisalo, Laura, primary, Järvinen, Heikki, primary, Böhm, Jan, primary, Mecklin, Jukka-Pekka, primary, Vahteristo, Pia, primary, Tuupanen, Sari, primary, Aaltonen, Lauri A., primary, and Pitkänen, Esa, primary

Published
2023
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33. Supplementary Figures 1-19, supplementary methods and extended literature evaluation of the candidate genes from Comprehensive Evaluation of Protein Coding Mononucleotide Microsatellites in Microsatellite-Unstable Colorectal Cancer

Author

Kondelin, Johanna, primary, Gylfe, Alexandra E., primary, Lundgren, Sofie, primary, Tanskanen, Tomas, primary, Hamberg, Jiri, primary, Aavikko, Mervi, primary, Palin, Kimmo, primary, Ristolainen, Heikki, primary, Katainen, Riku, primary, Kaasinen, Eevi, primary, Taipale, Minna, primary, Taipale, Jussi, primary, Renkonen-Sinisalo, Laura, primary, Järvinen, Heikki, primary, Böhm, Jan, primary, Mecklin, Jukka-Pekka, primary, Vahteristo, Pia, primary, Tuupanen, Sari, primary, Aaltonen, Lauri A., primary, and Pitkänen, Esa, primary

Published
2023
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34. Supplementary Table 7 from Comprehensive Evaluation of Protein Coding Mononucleotide Microsatellites in Microsatellite-Unstable Colorectal Cancer

Author

Kondelin, Johanna, primary, Gylfe, Alexandra E., primary, Lundgren, Sofie, primary, Tanskanen, Tomas, primary, Hamberg, Jiri, primary, Aavikko, Mervi, primary, Palin, Kimmo, primary, Ristolainen, Heikki, primary, Katainen, Riku, primary, Kaasinen, Eevi, primary, Taipale, Minna, primary, Taipale, Jussi, primary, Renkonen-Sinisalo, Laura, primary, Järvinen, Heikki, primary, Böhm, Jan, primary, Mecklin, Jukka-Pekka, primary, Vahteristo, Pia, primary, Tuupanen, Sari, primary, Aaltonen, Lauri A., primary, and Pitkänen, Esa, primary

Published
2023
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39. Additional file 2 of Mutation-Attention (MuAt): deep representation learning of somatic mutations for tumour typing and subtyping

Author

Sanjaya, Prima, Maljanen, Katri, Katainen, Riku, Waszak, Sebastian M., Aaltonen, Lauri A., Stegle, Oliver, Korbel, Jan O., and Pitkänen, Esa

Abstract

Additional file 2: Figure S1. Architecture of MuAt. Figure S2. Top-1, top-3 and top-5 accuracy, precision, recall and F1 scores of MuAt models trained with different mutation types in PCAWG and TCGA data. Figure S3. Transfer learning performance. Figure S4. MuAt model performance with and without the attention module in PCAWG data with different combinations of mutation types. Figure S5. Confusion matrix of MuAt in TCGA data. Figure S6. Calibration curve of MuAt trained with PCAWG. Figure S7. Confusion matrix for MuAt and DNN in the independent ICGC dataset. Figure S8. Confusion matrix for MuAt and DNN trained on PCAWG in GEL. Figure S9. Confusion matrix for MuAt trained on PCAWG in GEL. Figure S10. Confusion matrix for MuAt and DNN in the Katainen et al dataset. Figure S11. Linear association of PCAWG driver events with MuAt tumour-level feature principal components. Figure S12. Prostate cancers with SPOP driver events. Figure S13. MuAt tumour-level feature UMAP showing medulloblastomas in the PCAWG dataset. Figure S14. Pancreatic endocrine tumours of four patients clustering with kidney cancers in MuAt tumour-level feature UMAP. Figure S15. MuAt SNV+pos tumour level features on PCAWG and GEL. Figure S16. A clustered heatmap of MuAt tumour-level feature in each PCAWG tumours. Figure S17. Association of MuAt tumour-level features with mutation counts by type. Figure S18. Association of MuAt PCAWG model tumour-level features with COSMIC mutational signatures. Figure S19. Variance in the number of mutations attributed to signaturesexplained by MuAt tumour-level features. Figure S20. Mean attention values of genomic positions per tumour type in the MuAt PCAWG model.

Published
2023
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40. A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns

Author

Jiao, Wei, Atwal, Gurnit, Polak, Paz, Karlic, Rosa, Cuppen, Edwin, Al-Shahrour, Fatima, Bailey, Peter J, Biankin, Andrew V, Boutros, Paul C, Campbell, Peter J, Chang, David K, Cooke, Susanna L, Deshpande, Vikram, Faltas, Bishoy M, Faquin, William C, Garraway, Levi, Getz, Gad, Grimmond, Sean M, Haider, Syed, Hoadley, Katherine A, Kaiser, Vera B, Kato, Mamoru, Kübler, Kirsten, Lazar, Alexander J, Li, Constance H, Louis, David N, Margolin, Adam, Martin, Sancha, Nahal-Bose, Hardeep K, Nielsen, G Petur, Nik-Zainal, Serena, Omberg, Larsson, P’ng, Christine, Perry, Marc D, Rheinbay, Esther, Rubin, Mark A, Semple, Colin A, Sgroi, Dennis C, Shibata, Tatsuhiro, Siebert, Reiner, Smith, Jaclyn, Stein, Lincoln D, Stobbe, Miranda D, Sun, Ren X, Thai, Kevin, Wright, Derek W, Wu, Chin-Lee, Yuan, Ke, Zhang, Junjun, Danyi, Alexandra, de Ridder, Jeroen, van Herpen, Carla, Lolkema, Martijn P, Steeghs, Neeltje, Morris, Quaid D, Aaltonen, Lauri A, Abascal, Federico, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J, Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C, Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B, Ally, Adrian, Alsop, Kathryn, Alvarez, Eva G, Amary, Fernanda, Amin, Samirkumar B, Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J, Ang, Yeng, Antonello, Davide, Anur, Pavana, Aparicio, Samuel, Appelbaum, Elizabeth L, Arai, Yasuhito, Aretz, Axel, Arihiro, Koji, Ariizumi, Shun-ichi, Armenia, Joshua, Arnould, Laurent, Asa, Sylvia, Assenov, Yassen, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, Bader, Gary D, Baez-Ortega, Adrian, Bailey, Matthew H, Balasundaram, Miruna, Balu, Saianand, Bandopadhayay, Pratiti, Banks, Rosamonde E, Barbi, Stefano, Barbour, Andrew P, Barenboim, Jonathan, Barnholtz-Sloan, Jill, Barr, Hugh, Barrera, Elisabet, Bartlett, John, Bartolome, Javier, Bassi, Claudio, Bathe, Oliver F, Baumhoer, Daniel, Bavi, Prashant, Baylin, Stephen B, Bazant, Wojciech, Beardsmore, Duncan, Beck, Timothy A, Behjati, Sam, Behren, Andreas, Niu, Beifang, Bell, Cindy, Beltran, Sergi, Benz, Christopher, Berchuck, Andrew, Bergmann, Anke K, Bergstrom, Erik N, Berman, Benjamin P, Berney, Daniel M, Bernhart, Stephan H, Beroukhim, Rameen, Berrios, Mario, Bersani, Samantha, Bertl, Johanna, Betancourt, Miguel, Bhandari, Vinayak, Bhosle, Shriram G, Bieg, Matthias, Bigner, Darell, Binder, Hans, Birney, Ewan, Birrer, Michael, Biswas, Nidhan K, Bjerkehagen, Bodil, Bodenheimer, Tom, Boice, Lori, Bonizzato, Giada, De Bono, Johann S, Boot, Arnoud, Bootwalla, Moiz S, Borg, Ake, Borkhardt, Arndt, Boroevich, Keith A, Borozan, Ivan, Borst, Christoph, Bosenberg, Marcus, Bosio, Mattia, Boultwood, Jacqueline, Bourque, Guillaume, Bova, G Steven, Bowen, David T, Bowlby, Reanne, Bowtell, David DL, Boyault, Sandrine, Boyce, Rich, Boyd, Jeffrey, Brazma, Alvis, Brennan, Paul, Brewer, Daniel S, Brinkman, Arie B, Bristow, Robert G, Broaddus, Russell R, Brock, Jane E, Brock, Malcolm, Broeks, Annegien, Brooks, Angela N, Brooks, Denise, Brors, Benedikt, Brunak, Søren, Bruxner, Timothy JC, Bruzos, Alicia L, Buchanan, Alex, Buchhalter, Ivo, Buchholz, Christiane, Bullman, Susan, Burke, Hazel, Burkhardt, Birgit, Burns, Kathleen H, Busanovich, John, Bustamante, Carlos D, Butler, Adam P, Butte, Atul J, Byrne, Niall J, Børresen-Dale, Anne-Lise, Caesar-Johnson, Samantha J, Cafferkey, Andy, Cahill, Declan, Calabrese, Claudia, Caldas, Carlos, Calvo, Fabien, Camacho, Niedzica, Campo, Elias, Cantù, Cinzia, Cao, Shaolong, Carey, Thomas E, Carlevaro-Fita, Joana, Carlsen, Rebecca, Cataldo, Ivana, Cazzola, Mario, Cebon, Jonathan, Cerfolio, Robert, Chadwick, Dianne E, Chakravarty, Dimple, Chalmers, Don, Chan, Calvin Wing Yiu, Chan, Kin, Chan-Seng-Yue, Michelle, Chandan, Vishal S, Chanock, Stephen J, Chantrill, Lorraine A, Chateigner, Aurélien, Chatterjee, Nilanjan, Chayama, Kazuaki, Chen, Hsiao-Wei, Chen, Jieming, Chen, Ken, Chen, Yiwen, Chen, Zhaohong, Cherniack, Andrew D, Chien, Jeremy, Chiew, Yoke-Eng, Chin, Suet-Feung, Cho, Juok, Cho, Sunghoon, Choi, Jung Kyoon, Choi, Wan, Chomienne, Christine, Chong, Zechen, Choo, Su Pin, Chou, Angela, Christ, Angelika N, Christie, Elizabeth L, Chuah, Eric, Cibulskis, Carrie, Cibulskis, Kristian, Cingarlini, Sara, Clapham, Peter, Claviez, Alexander, Cleary, Sean, Cloonan, Nicole, Cmero, Marek, Collins, Colin C, Connor, Ashton A, Cooper, Colin S, Cope, Leslie, Corbo, Vincenzo, Cordes, Matthew G, Cordner, Stephen M, Cortés-Ciriano, Isidro, Covington, Kyle, Cowin, Prue A, Craft, Brian, Craft, David, Creighton, Chad J, Cun, Yupeng, Curley, Erin, Cutcutache, Ioana, Czajka, Karolina, Czerniak, Bogdan, Dagg, Rebecca A, Danilova, Ludmila, Davi, Maria Vittoria, Davidson, Natalie R, Davies, Helen, Davis, Ian J, Davis-Dusenbery, Brandi N, Dawson, Kevin J, De La Vega, Francisco M, De Paoli-Iseppi, Ricardo, Defreitas, Timothy, Dei Tos, Angelo P, Delaneau, Olivier, Demchok, John A, Demeulemeester, Jonas, Demidov, German M, Demircioğlu, Deniz, Dennis, Nening M, Denroche, Robert E, Dentro, Stefan C, Desai, Nikita, Deshwar, Amit G, Desmedt, Christine, Deu-Pons, Jordi, Dhalla, Noreen, Dhani, Neesha C, Dhingra, Priyanka, Dhir, Rajiv, DiBiase, Anthony, Diamanti, Klev, Ding, Li, Ding, Shuai, Dinh, Huy Q, Dirix, Luc, Doddapaneni, HarshaVardhan, Donmez, Nilgun, Dow, Michelle T, Drapkin, Ronny, Drechsel, Oliver, Drews, Ruben M, Serge, Serge, Dudderidge, Tim, Dueso-Barroso, Ana, Dunford, Andrew J, Dunn, Michael, Dursi, Lewis Jonathan, Duthie, Fraser R, Dutton-Regester, Ken, Eagles, Jenna, Easton, Douglas F, Edmonds, Stuart, Edwards, Paul A, Edwards, Sandra E, Eeles, Rosalind A, Ehinger, Anna, Eils, Juergen, Eils, Roland, El-Naggar, Adel, Eldridge, Matthew, Ellrott, Kyle, Erkek, Serap, Escaramis, Georgia, Espiritu, Shadrielle MG, Estivill, Xavier, Etemadmoghadam, Dariush, Eyfjord, Jorunn E, Fan, Daiming, Fan, Yu, Farcas, Claudiu, Fassan, Matteo, Fatima, Aquila, Favero, Francesco, Fayzullaev, Nodirjon, Felau, Ina, Fereday, Sian, Ferguson, Martin L, Ferretti, Vincent, Feuerbach, Lars, Field, Matthew A, Fink, J Lynn, Finocchiaro, Gaetano, Fisher, Cyril, Fittall, Matthew W, Fitzgerald, Anna, Fitzgerald, Rebecca C, Flanagan, Adrienne M, Fleshner, Neil E, Flicek, Paul, Foekens, John A, Fong, Kwun M, Fonseca, Nuno A, Foster, Christopher S, Fox, Natalie S, Fraser, Michael, Frazer, Scott, Frenkel-Morgenstern, Milana, Friedman, William, Frigola, Joan, Fronick, Catrina C, Fujimoto, Akihiro, Fujita, Masashi, Fukayama, Masashi, Fulton, Lucinda A, Fulton, Robert S, Furuta, Mayuko, Futreal, P Andrew, Füllgrabe, Anja, Gabriel, Stacey B, Gallinger, Steven, Gambacorti-Passerini, Carlo, Gao, Jianjiong, Gao, Shengjie, Garred, Øystein, Garrison, Erik, Garsed, Dale W, Gehlenborg, Nils, Gelpi, Josep LL, George, Joshy, Gerhard, Daniela S, Gerhauser, Clarissa, Gershenwald, Jeffrey E, Gerstein, Mark, Gerstung, Moritz, Ghori, Mohammed, Ghossein, Ronald, Giama, Nasra H, Gibbs, Richard A, Gibson, Bob, Gill, Anthony J, Gill, Pelvender, Giri, Dilip D, Glodzik, Dominik, Gnanapragasam, Vincent J, Goebler, Maria Elisabeth, Goldman, Mary J, Gomez, Carmen, Gonzalez, Santiago, Gonzalez-Perez, Abel, Gordenin, Dmitry A, Gossage, James, Gotoh, Kunihito, Govindan, Ramaswamy, Grabau, Dorthe, Graham, Janet S, Grant, Robert C, Green, Anthony R, Green, Eric, Greger, Liliana, Grehan, Nicola, Grimaldi, Sonia, Grossman, Robert L, Grundhoff, Adam, Gundem, Gunes, Guo, Qianyun, Gupta, Manaswi, Gupta, Shailja, Gut, Ivo G, Gut, Marta, Göke, Jonathan, Ha, Gavin, Haake, Andrea, Haan, David, Haas, Siegfried, Haase, Kerstin, Haber, James E, Habermann, Nina, Hach, Faraz, Hama, Natsuko, Hamdy, Freddie C, Hamilton, Anne, Hamilton, Mark P, Han, Leng, Hanna, George B, Hansmann, Martin, Haradhvala, Nicholas J, Harismendy, Olivier, Harliwong, Ivon, Harmanci, Arif O, Harrington, Eoghan, Hasegawa, Takanori, Haussler, David, Hawkins, Steve, Hayami, Shinya, Hayashi, Shuto, Hayes, D Neil, Hayes, 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Deurzen, Carolien HM, van de Vijver, Marc J, Veer, L van’t, and von Mering, Christian

Subjects
Human Biology & Physiology, Ecology,Evolution & Ethology, Tumour Biology, Genetics & Genomics, Structural Biology & Biophysics, Computational & Systems Biology
Abstract

In cancer, the primary tumour’s organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we train a deep learning classifier to predict cancer type based on patterns of somatic passenger mutations detected in whole genome sequencing (WGS) of 2606 tumours representing 24 common cancer types produced by the PCAWG Consortium. Our classifier achieves an accuracy of 91% on held-out tumor samples and 88% and 83% respectively on independent primary and metastatic samples, roughly double the accuracy of trained pathologists when presented with a metastatic tumour without knowledge of the primary. Surprisingly, adding information on driver mutations reduced accuracy. Our results have clinical applicability, underscore how patterns of somatic passenger mutations encode the state of the cell of origin, and can inform future strategies to detect the source of circulating tumour DNA.

Published
2023
Full Text
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42. Combined burden and functional impact tests for cancer driver discovery using DriverPower

Author

Shuai, Shimin, Abascal, Federico, Amin, Samirkumar B, Bader, Gary D, Bandopadhayay, Pratiti, Barenboim, Jonathan, Beroukhim, Rameen, Bertl, Johanna, Boroevich, Keith A, Brunak, Søren, Campbell, Peter J, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Chen, Ken, Choi, Jung Kyoon, Deu-Pons, Jordi, Dhingra, Priyanka, Diamanti, Klev, Feuerbach, Lars, Fink, J Lynn, Fonseca, Nuno A, Frigola, Joan, Gambacorti-Passerini, Carlo, Garsed, Dale W, Gerstein, Mark, Getz, Gad, Guo, Qianyun, Gut, Ivo G, Haan, David, Hamilton, Mark P, Haradhvala, Nicholas J, Harmanci, Arif O, Helmy, Mohamed, Herrmann, Carl, Hess, Julian M, Hobolth, Asger, Hodzic, Ermin, Hong, Chen, Hornshøj, Henrik, Isaev, Keren, Izarzugaza, Jose MG, Johnson, Rory, Johnson, Todd A, Juul, Malene, Juul, Randi Istrup, Kahles, Andre, Kahraman, Abdullah, Kellis, Manolis, Khurana, Ekta, Kim, Jaegil, Kim, Jong K, Kim, Youngwook, Komorowski, Jan, Korbel, Jan O, Kumar, Sushant, Lanzós, Andrés, Larsson, Erik, Lawrence, Michael S, Lee, Donghoon, Lehmann, Kjong-Van, Li, Shantao, Li, Xiaotong, Lin, Ziao, Liu, Eric Minwei, Lochovsky, Lucas, Lou, Shaoke, Madsen, Tobias, Marchal, Kathleen, Martincorena, Iñigo, Martinez-Fundichely, Alexander, Maruvka, Yosef E, McGillivray, Patrick D, Meyerson, William, Muiños, Ferran, Mularoni, Loris, Nakagawa, Hidewaki, Nielsen, Morten Muhlig, Paczkowska, Marta, Park, Keunchil, Park, Kiejung, Pedersen, Jakob Skou, Pons, Tirso, Pulido-Tamayo, Sergio, Raphael, Benjamin J, Reimand, Jüri, Reyes-Salazar, Iker, Reyna, Matthew A, Rheinbay, Esther, Rubin, Mark A, Rubio-Perez, Carlota, Sahinalp, S Cenk, Saksena, Gordon, Salichos, Leonidas, Sander, Chris, Schumacher, Steven E, Shackleton, Mark, Shapira, Ofer, Shen, Ciyue, Shrestha, Raunak, Sidiropoulos, Nikos, Sieverling, Lina, Sinnott-Armstrong, Nasa, Stein, Lincoln D, Stuart, Joshua M, Tamborero, David, Tiao, Grace, Tsunoda, Tatsuhiko, Umer, Husen M, Uusküla-Reimand, Liis, Valencia, Alfonso, Vazquez, Miguel, Verbeke, Lieven PC, Wadelius, 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Subjects
Human Biology & Physiology, Ecology,Evolution & Ethology, Tumour Biology, Genetics & Genomics, Structural Biology & Biophysics, Computational & Systems Biology
Abstract

The discovery of driver mutations is one of the key motivations for cancer genome sequencing. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we describe DriverPower, a software package that uses mutational burden and functional impact evidence to identify driver mutations in coding and non-coding sites within cancer whole genomes. Using a total of 1373 genomic features derived from public sources, DriverPower’s background mutation model explains up to 93% of the regional variance in the mutation rate across multiple tumour types. By incorporating functional impact scores, we are able to further increase the accuracy of driver discovery. Testing across a collection of 2583 cancer genomes from the PCAWG project, DriverPower identifies 217 coding and 95 non-coding driver candidates. Comparing to six published methods used by the PCAWG Drivers and Functional Interpretation Working Group, DriverPower has the highest F1 score for both coding and non-coding driver discovery. This demonstrates that DriverPower is an effective framework for computational driver discovery.

Published
2023
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43. Integrative pathway enrichment analysis of multivariate omics data

Author

Paczkowska, Marta, Barenboim, Jonathan, Sintupisut, Nardnisa, Fox, Natalie S, Zhu, Helen, Abd-Rabbo, Diala, Mee, Miles W, Boutros, Paul C, Abascal, Federico, Amin, Samirkumar B, Bader, Gary D, Beroukhim, Rameen, Bertl, Johanna, Boroevich, Keith A, Brunak, Søren, Campbell, Peter J, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Chen, Ken, Choi, Jung Kyoon, Deu-Pons, Jordi, Dhingra, Priyanka, Diamanti, Klev, Feuerbach, Lars, Fink, J Lynn, Fonseca, Nuno A, Frigola, Joan, Gambacorti-Passerini, Carlo, Garsed, Dale W, Gerstein, Mark, Getz, Gad, Gonzalez-Perez, Abel, Guo, Qianyun, Gut, Ivo G, Haan, David, Hamilton, Mark P, Haradhvala, Nicholas J, Harmanci, Arif O, Helmy, Mohamed, Herrmann, Carl, Hess, Julian M, Hobolth, Asger, Hodzic, Ermin, Hong, Chen, Hornshøj, Henrik, Isaev, Keren, Izarzugaza, Jose MG, Johnson, Rory, Johnson, Todd A, Juul, Malene, Juul, Randi Istrup, Kahles, Andre, Kahraman, Abdullah, Kellis, Manolis, Khurana, Ekta, Kim, Jaegil, Kim, Jong K, Kim, Youngwook, Komorowski, Jan, Korbel, Jan O, Kumar, Sushant, Lanzós, Andrés, Lawrence, Michael S, Lee, Donghoon, Lehmann, Kjong-Van, Li, Shantao, Li, Xiaotong, Lin, Ziao, Liu, Eric Minwei, Lochovsky, Lucas, Lou, Shaoke, Madsen, Tobias, Marchal, Kathleen, Martincorena, Iñigo, Martinez-Fundichely, Alexander, Maruvka, Yosef E, McGillivray, Patrick D, Meyerson, William, Muiños, Ferran, Mularoni, Loris, Nakagawa, Hidewaki, Nielsen, Morten Muhlig, Park, Keunchil, Park, Kiejung, Pedersen, Jakob Skou, Pich, Oriol, Pons, Tirso, Pulido-Tamayo, Sergio, Raphael, Benjamin J, Reyes-Salazar, Iker, Reyna, Matthew A, Rheinbay, Esther, Rubin, Mark A, Rubio-Perez, Carlota, Sabarinathan, Radhakrishnan, Sahinalp, S Cenk, Saksena, Gordon, Salichos, Leonidas, Sander, Chris, Schumacher, Steven E, Shackleton, Mark, Shapira, Ofer, Shen, Ciyue, Shrestha, Raunak, Shuai, Shimin, Sidiropoulos, Nikos, Sieverling, Lina, Sinnott-Armstrong, Nasa, Stein, Lincoln D, Stuart, Joshua M, Tamborero, David, Tiao, Grace, Tsunoda, Tatsuhiko, Umer, Husen M, Uusküla-Reimand, Liis, Valencia, Alfonso, Vazquez, Miguel, Verbeke, Lieven PC, Wadelius, Claes, Wadi, Lina, Wang, Jiayin, Warrell, Jonathan, Waszak, Sebastian M, Weischenfeldt, Joachim, Wheeler, David A, Wu, Guanming, Yu, Jun, Zhang, Jing, Zhang, Xuanping, Zhang, Yan, Zhao, Zhongming, Zou, Lihua, von Mering, Christian, Reimand, Jüri, Aaltonen, Lauri A, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J, Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C, Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T, Al-Shahrour, Fatima, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B, Ally, Adrian, Alsop, Kathryn, Alvarez, Eva G, Amary, Fernanda, Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J, Ang, Yeng, Antonello, Davide, Anur, Pavana, Aparicio, Samuel, Appelbaum, Elizabeth L, Arai, Yasuhito, Aretz, Axel, Arihiro, Koji, Ariizumi, Shun-ichi, Armenia, Joshua, Arnould, Laurent, Asa, Sylvia, Assenov, Yassen, Atwal, Gurnit, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, Baez-Ortega, Adrian, Bailey, Matthew H, Bailey, Peter J, Balasundaram, Miruna, Balu, Saianand, Bandopadhayay, Pratiti, Banks, Rosamonde E, Barbi, Stefano, Barbour, Andrew P, Barnholtz-Sloan, Jill, Barr, Hugh, Barrera, Elisabet, Bartlett, John, Bartolome, Javier, Bassi, Claudio, Bathe, Oliver F, Baumhoer, Daniel, Bavi, Prashant, Baylin, Stephen B, Bazant, Wojciech, Beardsmore, Duncan, Beck, Timothy A, Behjati, Sam, Behren, Andreas, Niu, Beifang, Bell, Cindy, Beltran, Sergi, Benz, Christopher, Berchuck, Andrew, Bergmann, Anke K, Bergstrom, Erik N, Berman, Benjamin P, Berney, Daniel M, Bernhart, Stephan H, Berrios, Mario, Bersani, Samantha, Betancourt, Miguel, Bhandari, Vinayak, Bhosle, Shriram G, Biankin, Andrew V, Bieg, Matthias, Bigner, Darell, Binder, Hans, Birney, Ewan, Birrer, Michael, Biswas, Nidhan K, Bjerkehagen, Bodil, Bodenheimer, Tom, Boice, Lori, Bonizzato, Giada, De Bono, Johann S, Boot, Arnoud, Bootwalla, Moiz S, Borg, Ake, Borkhardt, Arndt, Borozan, Ivan, Borst, Christoph, Bosenberg, Marcus, Bosio, Mattia, Boultwood, Jacqueline, Bourque, Guillaume, Bova, G Steven, Bowen, David T, Bowlby, Reanne, Bowtell, David DL, Boyault, Sandrine, Boyce, Rich, Boyd, Jeffrey, Brazma, Alvis, Brennan, Paul, Brewer, Daniel S, Brinkman, Arie B, Bristow, Robert G, Broaddus, Russell R, Brock, Jane E, Brock, Malcolm, Broeks, Annegien, Brooks, Angela N, Brooks, Denise, Brors, Benedikt, Bruxner, Timothy JC, Bruzos, Alicia L, Buchanan, Alex, Buchhalter, Ivo, Buchholz, Christiane, Bullman, Susan, Burke, Hazel, Burkhardt, Birgit, Burns, Kathleen H, Busanovich, John, Bustamante, Carlos D, Butler, Adam P, Butte, Atul J, Byrne, Niall J, Børresen-Dale, Anne-Lise, Caesar-Johnson, Samantha J, Cafferkey, Andy, Cahill, Declan, Calabrese, Claudia, Caldas, Carlos, Calvo, Fabien, Camacho, Niedzica, Campo, Elias, Cantù, Cinzia, Cao, Shaolong, Carey, Thomas E, Carlsen, Rebecca, Cataldo, Ivana, Cazzola, Mario, Cebon, Jonathan, Cerfolio, Robert, Chadwick, Dianne E, Chalmers, Don, Chan, Kin, Chan-Seng-Yue, Michelle, Chandan, Vishal S, Chang, David K, Chanock, Stephen J, Chantrill, Lorraine A, Chateigner, Aurélien, Chatterjee, Nilanjan, Chayama, Kazuaki, Chen, Hsiao-Wei, Chen, Jieming, Chen, Yiwen, Chen, Zhaohong, Cherniack, Andrew D, Chien, Jeremy, Chiew, Yoke-Eng, Chin, Suet-Feung, Cho, Juok, Cho, Sunghoon, Choi, Wan, Chomienne, Christine, Chong, Zechen, Choo, Su Pin, Chou, Angela, Christ, Angelika N, Christie, Elizabeth L, Chuah, Eric, Cibulskis, Carrie, Cibulskis, Kristian, Cingarlini, Sara, Clapham, Peter, Claviez, Alexander, Cleary, Sean, Cloonan, Nicole, Cmero, Marek, Collins, Colin C, Connor, Ashton A, Cooke, Susanna L, Cooper, Colin S, Cope, Leslie, Corbo, Vincenzo, Cordes, Matthew G, Cordner, Stephen M, Cortés-Ciriano, Isidro, Covington, Kyle, Cowin, Prue A, Craft, Brian, Craft, David, Creighton, Chad J, Cun, Yupeng, Curley, Erin, Cutcutache, Ioana, Czajka, Karolina, Czerniak, Bogdan, Dagg, Rebecca A, Danilova, Ludmila, Davi, Maria Vittoria, Davidson, Natalie R, Davies, Helen, Davis, Ian J, Davis-Dusenbery, Brandi N, Dawson, Kevin J, De La Vega, Francisco M, De Paoli-Iseppi, Ricardo, Defreitas, Timothy, Dei Tos, Angelo P, Delaneau, Olivier, Demchok, John A, Demeulemeester, Jonas, Demidov, German M, Demircioğlu, Deniz, Dennis, Nening M, Denroche, Robert E, Dentro, Stefan C, Desai, Nikita, Deshpande, Vikram, Deshwar, Amit G, Desmedt, Christine, Dhalla, Noreen, Dhani, Neesha C, Dhir, Rajiv, DiBiase, Anthony, Ding, Li, Ding, Shuai, Dinh, Huy Q, Dirix, Luc, Doddapaneni, HarshaVardhan, Donmez, Nilgun, Dow, Michelle T, Drapkin, Ronny, Drechsel, Oliver, Drews, Ruben M, Serge, Serge, Dudderidge, Tim, Dueso-Barroso, Ana, Dunford, Andrew J, Dunn, Michael, Dursi, Lewis Jonathan, Duthie, Fraser R, Dutton-Regester, Ken, Eagles, Jenna, Easton, Douglas F, Edmonds, Stuart, Edwards, Paul A, Edwards, Sandra E, Eeles, Rosalind A, Ehinger, Anna, Eils, Juergen, Eils, Roland, El-Naggar, Adel, Eldridge, Matthew, Ellrott, Kyle, Erkek, Serap, Escaramis, Georgia, Espiritu, Shadrielle MG, Estivill, Xavier, Etemadmoghadam, Dariush, Eyfjord, Jorunn E, Faltas, Bishoy M, Fan, Daiming, Fan, Yu, Faquin, William C, Farcas, Claudiu, Fassan, Matteo, Fatima, Aquila, Favero, Francesco, Fayzullaev, Nodirjon, Felau, Ina, Fereday, Sian, Ferguson, Martin L, Ferretti, Vincent, Field, Matthew A, Finocchiaro, Gaetano, Fisher, Cyril, Fittall, Matthew W, Fitzgerald, Anna, Fitzgerald, Rebecca C, Flanagan, Adrienne M, Fleshner, Neil E, Flicek, Paul, Foekens, John A, Fong, Kwun M, Foster, Christopher S, Fraser, Michael, Frazer, Scott, Frenkel-Morgenstern, Milana, Friedman, William, Fronick, Catrina C, Fujimoto, Akihiro, Fujita, Masashi, Fukayama, Masashi, Fulton, Lucinda A, Fulton, Robert S, Furuta, Mayuko, Futreal, P Andrew, Füllgrabe, Anja, Gabriel, Stacey B, Gallinger, Steven, Gao, Jianjiong, Gao, Shengjie, Garraway, Levi, Garred, Øystein, Garrison, Erik, Gehlenborg, Nils, Gelpi, Josep LL, George, Joshy, Gerhard, Daniela S, Gerhauser, Clarissa, Gershenwald, Jeffrey E, Gerstung, Moritz, Ghori, Mohammed, Ghossein, Ronald, Giama, Nasra H, Gibbs, Richard A, Gibson, Bob, Gill, Anthony J, Gill, Pelvender, Giri, Dilip D, Glodzik, Dominik, Gnanapragasam, Vincent J, Goebler, Maria Elisabeth, Goldman, Mary J, Gomez, Carmen, Gonzalez, Santiago, Gordenin, Dmitry A, Gossage, James, Gotoh, Kunihito, Govindan, Ramaswamy, Grabau, Dorthe, Graham, Janet S, Grant, Robert C, Green, Anthony R, Green, Eric, Greger, Liliana, Grehan, Nicola, Grimaldi, Sonia, Grimmond, Sean M, Grossman, Robert L, Grundhoff, Adam, Gundem, Gunes, Gupta, Manaswi, Gupta, Shailja, Gut, Marta, Göke, Jonathan, Ha, Gavin, Haake, Andrea, Haas, Siegfried, Haase, Kerstin, Haber, James E, Habermann, Nina, Hach, Faraz, Haider, Syed, Hama, Natsuko, Hamdy, Freddie C, Hamilton, Anne, Han, Leng, Hanna, George B, Hansmann, Martin, Harismendy, Olivier, Harliwong, Ivon, Harrington, Eoghan, Hasegawa, Takanori, Haussler, David, Hawkins, Steve, Hayami, Shinya, Hayashi, Shuto, Hayes, D Neil, Hayes, Stephen J, Hayward, Nicholas K, Hazell, Steven, He, Yao, Heath, Allison P, Heath, Simon C, Hedley, David, Hegde, Apurva M, Heiman, David I, Heinold, Michael C, Heins, Zachary, Heisler, Lawrence E, Hellstrom-Lindberg, Eva, Heo, Seong Gu, Hepperla, Austin J, Heredia-Genestar, José María, Hersey, Peter, Hilmarsdottir, Holmfridur, Hinton, Jonathan, Hirano, Satoshi, Hiraoka, Nobuyoshi, Hoadley, Katherine A, Hoell, Jessica I, Hoffmann, Steve, Hofmann, Oliver, Holbrook, Andrea, Holik, Aliaksei Z, Hollingsworth, Michael A, Holmes, Oliver, Holt, Robert A, Hong, Eun Pyo, Hong, Jongwhi H, Hooijer, Gerrit K, Hosoda, Fumie, Hou, Yong, Hovestadt, Volker, Howat, William, Hoyle, Alan P, Hruban, Ralph H, Hu, Jianhong, Hu, Taobo, Hua, Xing, Huang, Kuan-lin, Huang, Mei, Huang, Mi Ni, Huang, Vincent, Huang, Yi, Huber, Wolfgang, Hudson, Thomas J, Hummel, Michael, Hung, Jillian A, Huntsman, David, Hupp, Ted R, Huse, Jason, Huska, Matthew R, Hutter, Barbara, Hutter, Carolyn M, Hübschmann, Daniel, Iacobuzio-Donahue, Christine A, Imbusch, Charles David, Imielinski, Marcin, Imoto, Seiya, Isaacs, William B, Ishikawa, Shumpei, Iskar, Murat, Islam, SM Ashiqul, Ittmann, Michael, Ivkovic, Sinisa, Jacquemier, Jocelyne, Jakrot, Valerie, Jamieson, Nigel B, Jang, Gun Ho, Jang, Se Jin, Jayaseelan, Joy C, Jayasinghe, Reyka, Jefferys, Stuart R, Jegalian, Karine, Jennings, Jennifer L, Jeon, Seung-Hyup, Jerman, Lara, Ji, Yuan, Jiao, Wei, Johansson, Peter A, Johns, Amber L, Johns, Jeremy, Jolly, Clemency, Joly, Yann, Jonasson, Jon G, Jones, Corbin D, Jones, David R, Jones, David TW, Jones, Nic, Jones, Steven JM, Jonkers, Jos, Ju, Young Seok, Juhl, Hartmut, Jung, Jongsun, Juul, Sissel, Jäger, Natalie, Kabbe, Rolf, Kaiser, Vera B, Kakavand, Hojabr, Kalimuthu, Sangeetha, von Kalle, Christof, Kang, Koo Jeong, Karaszi, Katalin, Karlan, Beth, Karlić, Rosa, Karsch, Dennis, Kasaian, Katayoon, Kassahn, Karin S, Katai, Hitoshi, Kato, Mamoru, Katoh, Hiroto, Kawakami, Yoshiiku, Kay, Jonathan D, Kazakoff, Stephen H, Kazanov, Marat D, Keays, Maria, Kebebew, Electron, Kefford, Richard F, Kench, James G, Kennedy, Catherine J, Kerssemakers, Jules NA, Khoo, David, Khoo, Vincent, Khuntikeo, Narong, Kilpinen, Helena, Kim, Hark Kyun, Kim, Hyung-Lae, Kim, Hyung-Yong, Kim, Hyunghwan, Kim, Jihoon, King, Tari A, Klapper, Wolfram, Kleinheinz, Kortine, Klimczak, Leszek J, Knappskog, Stian, Kneba, Michael, Knoppers, Bartha M, Koh, Youngil, Komura, Daisuke, Komura, Mitsuhiro, Kong, Gu, Kool, Marcel, Korchina, Viktoriya, Korshunov, Andrey, Koscher, Michael, Koster, Roelof, Kote-Jarai, Zsofia, Koures, Antonios, Kovacevic, Milena, Kremeyer, Barbara, Kretzmer, Helene, Kreuz, Markus, Krishnamurthy, Savitri, Kube, Dieter, Kumar, Kiran, Kumar, Pardeep, Kumar, Yogesh, Kundra, Ritika, Kübler, Kirsten, Küppers, Ralf, Lagergren, Jesper, Lai, Phillip H, Laird, Peter W, Lakhani, Sunil R, Lalansingh, Christopher M, Lalonde, Emilie, Lamaze, Fabien C, Lambert, Adam, Lander, Eric, Landgraf, Pablo, Landoni, Luca, Langerød, Anita, Larsimont, Denis, Larsson, Erik, Lathrop, Mark, Lau, Loretta MS, Lawerenz, Chris, Lawlor, Rita T, Lazar, Alexander J, Lazic, Ana Mijalkovic, Le, Xuan, Lee, Darlene, Lee, Eunjung Alice, Lee, Hee Jin, Lee, Jake June-Koo, Lee, Jeong-Yeon, Lee, Juhee, Lee, Ming Ta Michael, Lee-Six, Henry, Lehrach, Hans, Lenze, Dido, Leonard, Conrad R, Leongamornlert, Daniel A, Leshchiner, Ignaty, Letourneau, Louis, Letunic, Ivica, Levine, Douglas A, Lewis, Lora, Ley, Tim, Li, Chang, Li, Constance H, Li, Haiyan Irene, Li, Jun, Li, Lin, Li, Siliang, Li, Xiaobo, Li, Xinyue, Li, Yilong, Liang, Han, Liang, Sheng-Ben, Lichter, Peter, Lin, Pei, Linehan, WM, Lingjærde, Ole Christian, Liu, Dongbing, Liu, Fei-Fei Fei, Liu, Fenglin, Liu, Jia, Liu, Xingmin, Livingstone, Julie, Livitz, Dimitri, Livni, Naomi, Loeffler, Markus, Long, Georgina V, Lopez-Guillermo, Armando, Louis, David N, Lovat, Laurence B, Lu, Yiling, Lu, Yong-Jie, Lu, Youyong, Luchini, Claudio, Lungu, Ilinca, Luo, Xuemei, Luxton, Hayley J, Lynch, Andy G, Lype, Lisa, López, Cristina, López-Otín, Carlos, Z, Eric, Ma, Yussanne, MacGrogan, Gaetan, MacRae, Shona, Macintyre, Geoff, Maejima, Kazuhiro, Mafficini, Andrea, Maglinte, Dennis T, Maitra, Arindam, Majumder, Partha P, Malcovati, Luca, Malikic, Salem, Malleo, Giuseppe, Mann, Graham J, Mantovani-Löffler, Luisa, Marchegiani, Giovanni, Mardis, Elaine R, Margolin, Adam A, Marin, Maximillian G, Markowetz, Florian, Markowski, Julia, Marks, Jeffrey, Marques-Bonet, Tomas, Marra, Marco A, Marsden, Luke, Martens, John WM, Martin, Sancha, Martin-Subero, Jose I, Mashl, R Jay, Massie, Charlie E, Matthew, Thomas J, Matthews, Lucy, Mayer, Erik, Mayes, Simon, Mayo, Michael, Mbabaali, Faridah, McCune, Karen, McDermott, Ultan, McLellan, Michael D, McPherson, John D, McPherson, John R, McPherson, Treasa A, Meier, Samuel R, Meng, Alice, Meng, Shaowu, Menzies, Andrew, Merrett, Neil D, Merson, Sue, Meyerson, Matthew, Mieczkowski, Piotr A, Mihaiescu, George L, Mijalkovic, Sanja, Mikkelsen, Tom, Milella, Michele, Mileshkin, Linda, Miller, Christopher A, Miller, David K, Miller, Jessica K, Mills, Gordon B, Milovanovic, Ana, Minner, Sarah, Miotto, Marco, Arnau, Gisela Mir, Mirabello, Lisa, Mitchell, Chris, Mitchell, Thomas J, Miyano, Satoru, Miyoshi, Naoki, Mizuno, Shinichi, Molnár-Gábor, Fruzsina, Moore, Malcolm J, Moore, Richard A, Morganella, Sandro, Morris, Quaid D, Morrison, Carl, Mose, Lisle E, Moser, Catherine D, Mungall, Andrew J, Mungall, Karen, Musgrove, Elizabeth A, Mustonen, Ville, Mutch, David, Muyas, Francesc, Muzny, Donna M, Muñoz, Alfonso, Myers, Jerome, Myklebost, Ola, Möller, Peter, Nagae, Genta, Nagrial, Adnan M, Nahal-Bose, Hardeep K, Nakagama, Hitoshi, Nakamura, Hiromi, Nakamura, Toru, Nakano, Kaoru, Nandi, Tannistha, Nangalia, Jyoti, Nastic, Mia, Navarro, Arcadi, Navarro, Fabio CP, Neal, David E, Nettekoven, Gerd, Newell, Felicity, Newhouse, Steven J, Newton, Yulia, Ng, Alvin Wei Tian, Ng, Anthony, Nicholson, Jonathan, Nicol, David, Nie, Yongzhan, Nielsen, G Petur, Nik-Zainal, Serena, Noble, Michael S, Nones, Katia, Northcott, Paul A, Notta, Faiyaz, O’Connor, Brian D, O’Donnell, Peter, O’Donovan, Maria, O’Meara, Sarah, O’Neill, Brian Patrick, O’Neill, J Robert, Ocana, David, Ochoa, Angelica, Oesper, Layla, Ogden, Christopher, Ohdan, Hideki, Ohi, Kazuhiro, Ohno-Machado, Lucila, Oien, Karin A, Ojesina, Akinyemi I, Ojima, Hidenori, Okusaka, Takuji, Omberg, Larsson, Ong, Choon Kiat, Ossowski, Stephan, Ott, German, Ouellette, BF Francis, P’ng, Christine, Paiella, Salvatore, Pairojkul, Chawalit, Pajic, Marina, Pan-Hammarström, Qiang, Papaemmanuil, Elli, Papatheodorou, Irene, Paramasivam, Nagarajan, Park, Ji Wan, Park, Joong-Won, Park, Peter J, Parker, Joel S, Parsons, Simon L, Pass, Harvey, Pasternack, Danielle, Pastore, Alessandro, Patch, Ann-Marie, Pauporté, Iris, Pea, Antonio, Pearson, John V, Pedamallu, Chandra Sekhar, Pederzoli, Paolo, 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Vijver, Marc J, and Veer, L van’t

Subjects
Human Biology & Physiology, Ecology,Evolution & Ethology, Tumour Biology, Genetics & Genomics, Structural Biology & Biophysics, Computational & Systems Biology
Abstract

Multi-omics datasets represent distinct aspects of the central dogma of molecular biology. Such high-dimensional molecular profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple datasets using statistical data fusion, rationalizes contributing evidence and highlights associated genes. As part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we integrated genes with coding and non-coding mutations and revealed frequently mutated pathways and additional cancer genes with infrequent mutations. We also analyzed prognostic molecular pathways by integrating genomic and transcriptomic features of 1780 breast cancers and highlighted associations with immune response and anti-apoptotic signaling. Integration of ChIP-seq and RNA-seq data for master regulators of the Hippo pathway across normal human tissues identified processes of tissue regeneration and stem cell regulation. ActivePathways is a versatile method that improves systems-level understanding of cellular organization in health and disease through integration of multiple molecular datasets and pathway annotations.

Published
2023
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44. Pathway and network analysis of more than 2500 whole cancer genomes

Author

Reyna, Matthew A, Haan, David, Paczkowska, Marta, Verbeke, Lieven PC, Vazquez, Miguel, Kahraman, Abdullah, Pulido-Tamayo, Sergio, Barenboim, Jonathan, Wadi, Lina, Dhingra, Priyanka, Shrestha, Raunak, Getz, Gad, Lawrence, Michael S, Pedersen, Jakob Skou, Rubin, Mark A, Wheeler, David A, Brunak, Søren, Izarzugaza, Jose MG, Khurana, Ekta, Marchal, Kathleen, von Mering, Christian, Sahinalp, S Cenk, Valencia, Alfonso, Abascal, Federico, Amin, Samirkumar B, Bader, Gary D, Bandopadhayay, Pratiti, Beroukhim, Rameen, Bertl, Johanna, Boroevich, Keith A, Busanovich, John, Campbell, Peter J, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Chen, Ken, Choi, Jung Kyoon, Deu-Pons, Jordi, Diamanti, Klev, Feuerbach, Lars, Fink, J Lynn, Fonseca, Nuno A, Frigola, Joan, Gambacorti-Passerini, Carlo, Garsed, Dale W, Gerstein, Mark, Guo, Qianyun, Gut, Ivo G, Hamilton, Mark P, Haradhvala, Nicholas J, Harmanci, Arif O, Helmy, Mohamed, Herrmann, Carl, Hess, Julian M, Hobolth, Asger, Hodzic, 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Subjects
Human Biology & Physiology, Ecology,Evolution & Ethology, Tumour Biology, Genetics & Genomics, Structural Biology & Biophysics, Computational & Systems Biology
Abstract

The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding mutations, most notably TERT promoter mutations, have been reported. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancer across 38 tumor types, we perform multi-faceted pathway and network analyses of non-coding mutations across 2583 whole cancer genomes from 27 tumor types compiled by the ICGC/TCGA PCAWG project that was motivated by the success of pathway and network analyses in prioritizing rare mutations in protein-coding genes. While few non-coding genomic elements are recurrently mutated in this cohort, we identify 93 genes harboring non-coding mutations that cluster into several modules of interacting proteins. Among these are promoter mutations associated with reduced mRNA expression in TP53, TLE4, and TCF4. We find that biological processes had variable proportions of coding and non-coding mutations, with chromatin remodeling and proliferation pathways altered primarily by coding mutations, while developmental pathways, including Wnt and Notch, altered by both coding and non-coding mutations. RNA splicing is primarily altered by non-coding mutations in this cohort, and samples containing non-coding mutations in well-known RNA splicing factors exhibit similar gene expression signatures as samples with coding mutations in these genes. These analyses contribute a new repertoire of possible cancer genes and mechanisms that are altered by non-coding mutations and offer insights into additional cancer vulnerabilities that can be investigated for potential therapeutic treatments.

Published
2023
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45. Divergent mutational processes distinguish hypoxic and normoxic tumours

Author

Bhandari, Vinayak, Li, Constance H, Bristow, Robert G, Boutros, Paul C, Aaltonen, Lauri A, Abascal, Federico, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J, Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C, Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T, Al-Shahrour, Fatima, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B, Ally, Adrian, Alsop, Kathryn, Alvarez, Eva G, Amary, Fernanda, Amin, Samirkumar B, Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J, Ang, Yeng, Antonello, Davide, Anur, Pavana, Aparicio, Samuel, Appelbaum, Elizabeth L, Arai, Yasuhito, Aretz, Axel, Arihiro, Koji, Ariizumi, Shun-ichi, Armenia, Joshua, Arnould, Laurent, Asa, Sylvia, Assenov, Yassen, Atwal, Gurnit, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, Bader, Gary D, Baez-Ortega, Adrian, Bailey, Matthew H, Bailey, Peter J, Balasundaram, Miruna, Balu, Saianand, Bandopadhayay, Pratiti, Banks, Rosamonde E, 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Subjects
Human Biology & Physiology, Ecology,Evolution & Ethology, Tumour Biology, Genetics & Genomics, Structural Biology & Biophysics, Computational & Systems Biology
Abstract

Many primary tumours have low levels of molecular oxygen (hypoxia), and hypoxic tumours respond poorly to therapy. Pan-cancer molecular hallmarks of tumour hypoxia remain poorly understood, with limited comprehension of its associations with specific mutational processes, non-coding driver genes and evolutionary features. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we quantify hypoxia in 1188 tumours spanning 27 cancer types. Elevated hypoxia associates with increased mutational load across cancer types, irrespective of underlying mutational class. The proportion of mutations attributed to several mutational signatures of unknown aetiology directly associates with the level of hypoxia, suggesting underlying mutational processes for these signatures. At the gene level, driver mutations in TP53, MYC and PTEN are enriched in hypoxic tumours, and mutations in PTEN interact with hypoxia to direct tumour evolutionary trajectories. Overall, hypoxia plays a critical role in shaping the genomic and evolutionary landscapes of cancer.

Published
2023
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46. Genomic footprints of activated telomere maintenance mechanisms in cancer

Author

Sieverling, Lina, Hong, Chen, Koser, Sandra D, Ginsbach, Philip, Kleinheinz, Kortine, Hutter, Barbara, Braun, Delia M, Cortés-Ciriano, Isidro, Xi, Ruibin, Kabbe, Rolf, Park, Peter J, Eils, Roland, Schlesner, Matthias, Akdemir, Kadir C, Alvarez, Eva G, Baez-Ortega, Adrian, Beroukhim, Rameen, Boutros, Paul C, Bowtell, David DL, Brors, Benedikt, Burns, Kathleen H, Campbell, Peter J, Chan, Kin, Chen, Ken, Dueso-Barroso, Ana, Dunford, Andrew J, Edwards, Paul A, Estivill, Xavier, Etemadmoghadam, Dariush, Feuerbach, Lars, Fink, J Lynn, Frenkel-Morgenstern, Milana, Garsed, Dale W, Gerstein, Mark, Gordenin, Dmitry A, Haan, David, Haber, James E, Hess, Julian M, Imielinski, Marcin, Jones, David TW, Ju, Young Seok, Kazanov, Marat D, Klimczak, Leszek J, Koh, Youngil, Korbel, Jan O, Kumar, Kiran, Lee, Eunjung Alice, Lee, Jake June-Koo, Li, Yilong, Lynch, Andy G, Macintyre, Geoff, Markowetz, Florian, Martincorena, Iñigo, Martinez-Fundichely, Alexander, Meyerson, Matthew, Miyano, Satoru, Nakagawa, 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Christian

Subjects
Human Biology & Physiology, Ecology,Evolution & Ethology, Tumour Biology, Genetics & Genomics, Structural Biology & Biophysics, Computational & Systems Biology
Abstract

Cancers require telomere maintenance mechanisms for unlimited replicative potential. They achieve this through TERT activation or alternative telomere lengthening associated with ATRX or DAXX loss. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we dissect whole-genome sequencing data of over 2500 matched tumor-control samples from 36 different tumor types aggregated within the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium to characterize the genomic footprints of these mechanisms. While the telomere content of tumors with ATRX or DAXX mutations (ATRX/DAXXtrunc) is increased, tumors with TERT modifications show a moderate decrease of telomere content. One quarter of all tumor samples contain somatic integrations of telomeric sequences into non-telomeric DNA. This fraction is increased to 80% prevalence in ATRX/DAXXtrunc tumors, which carry an aberrant telomere variant repeat (TVR) distribution as another genomic marker. The latter feature includes enrichment or depletion of the previously undescribed singleton TVRs TTCGGG and TTTGGG, respectively. Our systematic analysis provides new insight into the recurrent genomic alterations associated with telomere maintenance mechanisms in cancer.

Published
2023
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50. Contribution of allelic imbalance to colorectal cancer

Author

Palin, Kimmo, Pitkänen, Esa, Turunen, Mikko, Sahu, Biswajyoti, Pihlajamaa, Päivi, Kivioja, Teemu, Kaasinen, Eevi, Välimäki, Niko, Hänninen, Ulrika A., Cajuso, Tatiana, Aavikko, Mervi, Tuupanen, Sari, Kilpivaara, Outi, van den Berg, Linda, Kondelin, Johanna, Tanskanen, Tomas, Katainen, Riku, Grau, Marta, Rauanheimo, Heli, Plaketti, Roosa-Maria, Taira, Aurora, Sulo, Päivi, Hartonen, Tuomo, Dave, Kashyap, Schmierer, Bernhard, Botla, Sandeep, Sokolova, Maria, Vähärautio, Anna, Gladysz, Kornelia, Ongen, Halit, Dermitzakis, Emmanouil, Bramsen, Jesper Bertram, Ørntoft, Torben Falck, Andersen, Claus Lindbjerg, Ristimäki, Ari, Lepistö, Anna, Renkonen-Sinisalo, Laura, Mecklin, Jukka-Pekka, Taipale, Jussi, and Aaltonen, Lauri A.

Published
2018
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