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1. Pushing the boundaries of rare disease diagnostics with the help of the first Undiagnosed Hackathon

Author

Delgado-Vega, Angelica Maria, Cederroth, Helene, Taylan, Fulya, Ekholm, Katja, Ek, Marlene, Thonberg, Håkan, Jemt, Anders, Nilsson, Daniel, Eisfeldt, Jesper, Bilgrav Saether, Kristine, Höijer, Ida, Akgun-Dogan, Ozlem, Asano, Yui, Barakat, Tahsin Stefan, Batkovskyte, Dominyka, Baynam, Gareth, Bodamer, Olaf, Chetruengchai, Wanna, Corcoran, Pádraic, Couse, Madeline, Danis, Daniel, Demidov, German, Dohi, Eisuke, Erhardsson, Mattias, Fernandez-Luna, Luis, Fujiwara, Toyofumi, Garg, Neha, Giugliani, Roberto, Gonzaga-Jauregui, Claudia, Grigelioniene, Giedre, Groza, Tudor, Gunnarsson, Cecilia, Hammarsjö, Anna, Hammond, Charles Kumi, Hatirnaz Ng, Özden, Hesketh, Sirisha, Hettiarachchi, Dineshani, Johansson Soller, Maria, Kirmani, Umn Ahmed, Kjellberg, Martin, Kvarnung, Malin, Kvlividze, Oleg, Lagerstedt-Robinson, Kristina, Lasko, Paul, Lassmann, Timo, Lau, Lynette Y. S., Laurie, Steven, Lim, Weng Khong, Liu, Zhandong, Lysenkova Wiklander, Mariya, Makay, Prince, Maiga, Alassane Baneye, Maya-González, Carolina, Meyn, M. Stephen, Neethiraj, Ramprasad, Nigro, Vincenzo, Nordgren, Felix, Nordlund, Jessica, Orrsjö, Sara, Ottosson, Jesper, Ozbek, Ugur, Özdemir, Özkan, Partin, Clyde, Pearce, David A., Peck, Raquel, Pedersen, Annie, Pettersson, Maria, Pongpanich, Monnat, Posada de la Paz, Manuel, Ramani, Arun, Romero, Juan Andres, Romero, Vanessa I., Rosenquist, Richard, Saw, Aung Min, Spencer, Matthew, Stattin, Eva-Lena, Srichomthong, Chalurmpon, Tapia-Paez, Isabel, Taruscio, Domenica, Taylor, Julie P., Tkemaladze, Tinatin, Tully, Ian, Tümer, Zeynep, van Zelst-Stams, Wendy A. G., Verloes, Alain, Västerviga, Emma, Wang, Sailan, Yang, Rachel, Yamamoto, Shinya, Yépez, Vicente A., Zhang, Qing, Shotelersuk, Vorasuk, Wiafe, Samuel Agyei, Alanay, Yasemin, Botto, Lorenzo D., Kirmani, Salman, Lumaka, Aimé, Palmer, Elizabeth Emma, Puri, Ratna Dua, Wirta, Valtteri, Lindstrand, Anna, Buske, Orion J., Cederroth, Mikk, and Nordgren, Ann

Published
2024
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2. Epigenome-wide analysis across the development span of pediatric acute lymphoblastic leukemia: backtracking to birth

Author

Ghantous, Akram, Nusslé, Semira Gonseth, Nassar, Farah J., Spitz, Natalia, Novoloaca, Alexei, Krali, Olga, Nickels, Eric, Cahais, Vincent, Cuenin, Cyrille, Roy, Ritu, Li, Shaobo, Caron, Maxime, Lam, Dilys, Fransquet, Peter Daniel, Casement, John, Strathdee, Gordon, Pearce, Mark S., Hansen, Helen M., Lee, Hwi-Ho, Lee, Yong Sun, de Smith, Adam J., Sinnett, Daniel, Håberg, Siri Eldevik, McKay, Jill A., Nordlund, Jessica, Magnus, Per, Dwyer, Terence, Saffery, Richard, Wiemels, Joseph Leo, Munthe-Kaas, Monica Cheng, and Herceg, Zdenko

Published
2024
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4. Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative.

Author

Butler-Laporte, Guillaume, Povysil, Gundula, Kosmicki, Jack, Cirulli, Elizabeth, Drivas, Theodore, Furini, Simone, Saad, Chadi, Schmidt, Axel, Olszewski, Pawel, Korotko, Urszula, Quinodoz, Mathieu, Çelik, Elifnaz, Kundu, Kousik, Walter, Klaudia, Jung, Junghyun, Stockwell, Amy, Sloofman, Laura, Jordan, Daniel, Thompson, Ryan, Del Valle, Diane, Simons, Nicole, Cheng, Esther, Sebra, Robert, Schadt, Eric, Kim-Schulze, Seunghee, Gnjatic, Sacha, Merad, Miriam, Buxbaum, Joseph, Beckmann, Noam, Charney, Alexander, Przychodzen, Bartlomiej, Chang, Timothy, Pottinger, Tess, Shang, Ning, Brand, Fabian, Fava, Francesca, Mari, Francesca, Chwialkowska, Karolina, Niemira, Magdalena, Pula, Szymon, Baillie, J, Stuckey, Alex, Salas, Antonio, Bello, Xabier, Pardo-Seco, Jacobo, Gómez-Carballa, Alberto, Rivero-Calle, Irene, Martinón-Torres, Federico, Ganna, Andrea, Karczewski, Konrad, Veerapen, Kumar, Bourgey, Mathieu, Bourque, Guillaume, Eveleigh, Robert, Forgetta, Vincenzo, Morrison, David, Langlais, David, Lathrop, Mark, Mooser, Vincent, Nakanishi, Tomoko, Frithiof, Robert, Hultström, Michael, Lipcsey, Miklos, Marincevic-Zuniga, Yanara, Nordlund, Jessica, Schiabor Barrett, Kelly, Lee, William, Bolze, Alexandre, White, Simon, Riffle, Stephen, Tanudjaja, Francisco, Sandoval, Efren, Neveux, Iva, Dabe, Shaun, Casadei, Nicolas, Motameny, Susanne, Alaamery, Manal, Massadeh, Salam, Aljawini, Nora, Almutairi, Mansour, Arabi, Yaseen, Alqahtani, Saleh, Al Harthi, Fawz, Almutairi, Amal, Alqubaishi, Fatima, Alotaibi, Sarah, Binowayn, Albandari, Alsolm, Ebtehal, El Bardisy, Hadeel, Fawzy, Mohammad, Cai, Fang, Soranzo, Nicole, Butterworth, Adam, Geschwind, Daniel, Arteaga, Stephanie, Stephens, Alexis, Butte, Manish, Boutros, Paul, Yamaguchi, Takafumi, and Tao, Shu

Subjects
Humans, Exome, Genome-Wide Association Study, COVID-19, Genetic Predisposition to Disease, Toll-Like Receptor 7, SARS-CoV-2
Abstract

Host genetics is a key determinant of COVID-19 outcomes. Previously, the COVID-19 Host Genetics Initiative genome-wide association study used common variants to identify multiple loci associated with COVID-19 outcomes. However, variants with the largest impact on COVID-19 outcomes are expected to be rare in the population. Hence, studying rare variants may provide additional insights into disease susceptibility and pathogenesis, thereby informing therapeutics development. Here, we combined whole-exome and whole-genome sequencing from 21 cohorts across 12 countries and performed rare variant exome-wide burden analyses for COVID-19 outcomes. In an analysis of 5,085 severe disease cases and 571,737 controls, we observed that carrying a rare deleterious variant in the SARS-CoV-2 sensor toll-like receptor TLR7 (on chromosome X) was associated with a 5.3-fold increase in severe disease (95% CI: 2.75-10.05, p = 5.41x10-7). This association was consistent across sexes. These results further support TLR7 as a genetic determinant of severe disease and suggest that larger studies on rare variants influencing COVID-19 outcomes could provide additional insights.

Published
2022

5. Multimodal classification of molecular subtypes in pediatric acute lymphoblastic leukemia

Author

Krali, Olga, Marincevic-Zuniga, Yanara, Arvidsson, Gustav, Enblad, Anna Pia, Lundmark, Anders, Sayyab, Shumaila, Zachariadis, Vasilios, Heinäniemi, Merja, Suhonen, Janne, Oksa, Laura, Vepsäläinen, Kaisa, Öfverholm, Ingegerd, Barbany, Gisela, Nordgren, Ann, Lilljebjörn, Henrik, Fioretos, Thoas, Madsen, Hans O., Marquart, Hanne Vibeke, Flaegstad, Trond, Forestier, Erik, Jónsson, Ólafur G., Kanerva, Jukka, Lohi, Olli, Norén-Nyström, Ulrika, Schmiegelow, Kjeld, Harila, Arja, Heyman, Mats, Lönnerholm, Gudmar, Syvänen, Ann-Christine, and Nordlund, Jessica

Published
2023
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6. Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance

Author

Ren, Luyao, Duan, Xiaoke, Dong, Lianhua, Zhang, Rui, Yang, Jingcheng, Gao, Yuechen, Peng, Rongxue, Hou, Wanwan, Liu, Yaqing, Li, Jingjing, Yu, Ying, Zhang, Naixin, Shang, Jun, Liang, Fan, Wang, Depeng, Chen, Hui, Sun, Lele, Hao, Lingtong, Scherer, Andreas, Nordlund, Jessica, Xiao, Wenming, Xu, Joshua, Tong, Weida, Hu, Xin, Jia, Peng, Ye, Kai, Li, Jinming, Jin, Li, Hong, Huixiao, Wang, Jing, Fan, Shaohua, Fang, Xiang, Zheng, Yuanting, and Shi, Leming

Published
2023
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7. Genomic, transcriptomic and epigenomic sequencing data of the B-cell leukemia cell line REH

Author

Lysenkova Wiklander, Mariya, Övernäs, Elin, Lagensjö, Johanna, Raine, Amanda, Petri, Anna, Wiman, Ann-Christin, Ramsell, Jon, Marincevic-Zuniga, Yanara, Gezelius, Henrik, Martin, Tom, Bunikis, Ignas, Ekberg, Sara, Erlandsson, Rikard, Larsson, Pontus, Mosbech, Mai-Britt, Häggqvist, Susana, Hellstedt Kerje, Susanne, Feuk, Lars, Ameur, Adam, Liljedahl, Ulrika, and Nordlund, Jessica

Published
2023
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10. Next generation pan-cancer blood proteome profiling using proximity extension assay

Author

Álvez, María Bueno, Edfors, Fredrik, von Feilitzen, Kalle, Zwahlen, Martin, Mardinoglu, Adil, Edqvist, Per-Henrik, Sjöblom, Tobias, Lundin, Emma, Rameika, Natallia, Enblad, Gunilla, Lindman, Henrik, Höglund, Martin, Hesselager, Göran, Stålberg, Karin, Enblad, Malin, Simonson, Oscar E., Häggman, Michael, Axelsson, Tomas, Åberg, Mikael, Nordlund, Jessica, Zhong, Wen, Karlsson, Max, Gyllensten, Ulf, Ponten, Fredrik, Fagerberg, Linn, and Uhlén, Mathias

Published
2023
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14. Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing

Author

Xiao, Wenming, Ren, Luyao, Chen, Zhong, Fang, Li Tai, Zhao, Yongmei, Lack, Justin, Guan, Meijian, Zhu, Bin, Jaeger, Erich, Kerrigan, Liz, Blomquist, Thomas M., Hung, Tiffany, Sultan, Marc, Idler, Kenneth, Lu, Charles, Scherer, Andreas, Kusko, Rebecca, Moos, Malcolm, Xiao, Chunlin, Sherry, Stephen T., Abaan, Ogan D., Chen, Wanqiu, Chen, Xin, Nordlund, Jessica, Liljedahl, Ulrika, Maestro, Roberta, Polano, Maurizio, Drabek, Jiri, Vojta, Petr, Kõks, Sulev, Reimann, Ene, Madala, Bindu Swapna, Mercer, Timothy, Miller, Chris, Jacob, Howard, Truong, Tiffany, Moshrefi, Ali, Natarajan, Aparna, Granat, Ana, Schroth, Gary P., Kalamegham, Rasika, Peters, Eric, Petitjean, Virginie, Walton, Ashley, Shen, Tsai-Wei, Talsania, Keyur, Vera, Cristobal Juan, Langenbach, Kurt, de Mars, Maryellen, Hipp, Jennifer A., Willey, James C., Wang, Jing, Shetty, Jyoti, Kriga, Yuliya, Raziuddin, Arati, Tran, Bao, Zheng, Yuanting, Yu, Ying, Cam, Margaret, Jailwala, Parthav, Nguyen, Cu, Meerzaman, Daoud, Chen, Qingrong, Yan, Chunhua, Ernest, Ben, Mehra, Urvashi, Jensen, Roderick V., Jones, Wendell, Li, Jian-Liang, Papas, Brian N., Pirooznia, Mehdi, Chen, Yun-Ching, Seifuddin, Fayaz, Li, Zhipan, Liu, Xuelu, Resch, Wolfgang, Wang, Jingya, Wu, Leihong, Yavas, Gokhan, Miles, Corey, Ning, Baitang, Tong, Weida, Mason, Christopher E., Donaldson, Eric, Lababidi, Samir, Staudt, Louis M., Tezak, Zivana, Hong, Huixiao, Wang, Charles, and Shi, Leming

Published
2021
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15. Multi-modal single cell sequencing of B cells in primary Sjögren's Syndrome.

Author

Arvidsson, Gustav, Czarnewski, Paulo, Johansson, Alina, Raine, Amanda, Imgenberg-Kreuz, Juliana, Nordlund, Jessica, Nordmark, Gunnel, Syvänen, Ann-Christine, Arvidsson, Gustav, Czarnewski, Paulo, Johansson, Alina, Raine, Amanda, Imgenberg-Kreuz, Juliana, Nordlund, Jessica, Nordmark, Gunnel, and Syvänen, Ann-Christine

Abstract

OBJECTIVE: B cells are important in the pathogenesis of primary Sjögren's syndrome (pSS). Patients positive for SSA/SSB autoantibodies are more prone to systemic disease manifestations and adverse outcomes. We aimed to determine the role of B cell composition, gene expression and B cell receptor (BCR) usage in pSS subgroups stratified for SSA/SSB antibodies. METHODS: Over 230 000 B cells were isolated from peripheral blood of pSS patients (n = 6 SSA-, n = 8 SSA+ single positive and n = 10 SSA/SSB+ double positive) and four healthy controls, and processed for single cell RNA and VDJ sequencing. RESULTS: We show that SSA/SSB+ patients present the highest and lowest proportion of naïve and memory B cells respectively, and the highest upregulation of interferon-induced genes across all B cell subtypes. Differential usage of IGHV showed that IGHV1-69 and IGHV4-30-4 were more often used in all pSS subgroups compared with controls. Memory B cells from SSA/SSB+ patients displayed a higher proportion of cells with unmutated VDJ transcripts compared to other pSS patient groups and controls, indicating altered somatic hypermutation processes. Comparison with previous studies revealed heterogeneous clonotype pools, with little overlap in CDR3 sequences. Joint analysis using scRNA-seq and scVDJ-seq data allowed unsupervised stratification pSS patients, and identified novel parameters that correlated to disease manifestations and antibody status. CONCLUSION: We describe heterogeneity and molecular characteristics in B cells from pSS patients, providing clues to intrinsic differences in B cells that affect the phenotype and outcome, allowing stratification of pSS patients at improved resolution. This article is protected by copyright. All rights reserved.

Published
2024
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16. Comparison of high-throughput single-cell RNA-seq methods for ex vivo drug screening

Author

Gezelius, Henrik, Enblad, Anna Pia, Lundmark, Anders, Åberg, Martin, Blom, Kristin, Rudfeldt, Jakob, Raine, Amanda, Harila-Saari, Arja H., Rendo, Verónica, Heinaniemi, Merja, Andersson, Claes, Nordlund, Jessica, Gezelius, Henrik, Enblad, Anna Pia, Lundmark, Anders, Åberg, Martin, Blom, Kristin, Rudfeldt, Jakob, Raine, Amanda, Harila-Saari, Arja H., Rendo, Verónica, Heinaniemi, Merja, Andersson, Claes, and Nordlund, Jessica

Abstract

Functional precision medicine (FPM) aims to optimize patient-specific drug selection based on the unique characteristics of their cancer cells. Recent advancements in high throughput ex vivo drug profiling have accelerated interest in FPM. Here, we present a proof-of-concept study for an integrated experimental system that incorporates ex vivo treatment response with a single-cell gene expression output enabling barcoding of several drug conditions in one single-cell sequencing experiment. We demonstrate this through a proof-of-concept investigation focusing on the glucocorticoid-resistant acute lymphoblastic leukemia (ALL) E/R+ Reh cell line. Three different single-cell transcriptome sequencing (scRNA-seq) approaches were evaluated, each exhibiting high cell recovery and accurate tagging of distinct drug conditions. Notably, our comprehensive analysis revealed variations in library complexity, sensitivity (gene detection), and differential gene expression detection across the methods. Despite these differences, we identified a substantial transcriptional response to fludarabine, a highly relevant drug for treating high-risk ALL, which was consistently recapitulated by all three methods. These findings highlight the potential of our integrated approach for studying drug responses at the single-cell level and emphasize the importance of method selection in scRNA-seq studies. Finally, our data encompassing 27 327 cells are freely available to extend to future scRNA-seq methodological comparisons.

Published
2024
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17. Refining risk prediction in pediatric acute lymphoblastic leukemia through DNA methylation profiling

Author

Orgueira, Adrian Mosquera, Krali, Olga, Miguez, Carlos Perez, Raindo, Andres Peleteiro, Arias, Jose Angel Diaz, Perez, Marta Sonia Gonzalez, Encinas, Manuel Mateo Perez, Sanmartin, Manuel Fernandez, Sinnet, Daniel, Heyman, Mats, Lönnerholm, Gudmar, Noren-Nyström, Ulrika, Schmiegelow, Kjeld, Nordlund, Jessica, Orgueira, Adrian Mosquera, Krali, Olga, Miguez, Carlos Perez, Raindo, Andres Peleteiro, Arias, Jose Angel Diaz, Perez, Marta Sonia Gonzalez, Encinas, Manuel Mateo Perez, Sanmartin, Manuel Fernandez, Sinnet, Daniel, Heyman, Mats, Lönnerholm, Gudmar, Noren-Nyström, Ulrika, Schmiegelow, Kjeld, and Nordlund, Jessica

Abstract

Acute lymphoblastic leukemia (ALL) is the most prevalent cancer in children, and despite considerable progress in treatment outcomes, relapses still pose significant risks of mortality and long-term complications. To address this challenge, we employed a supervised machine learning technique, specifically random survival forests, to predict the risk of relapse and mortality using array-based DNA methylation data from a cohort of 763 pediatric ALL patients treated in Nordic countries. The relapse risk predictor (RRP) was constructed based on 16 CpG sites, demonstrating c-indexes of 0.667 and 0.677 in the training and test sets, respectively. The mortality risk predictor (MRP), comprising 53 CpG sites, exhibited c-indexes of 0.751 and 0.754 in the training and test sets, respectively. To validate the prognostic value of the predictors, we further analyzed two independent cohorts of Canadian (n = 42) and Nordic (n = 384) ALL patients. The external validation confirmed our findings, with the RRP achieving a c-index of 0.667 in the Canadian cohort, and the RRP and MRP achieving c-indexes of 0.529 and 0.621, respectively, in an independent Nordic cohort. The precision of the RRP and MRP models improved when incorporating traditional risk group data, underscoring the potential for synergistic integration of clinical prognostic factors. The MRP model also enabled the definition of a risk group with high rates of relapse and mortality. Our results demonstrate the potential of DNA methylation as a prognostic factor and a tool to refine risk stratification in pediatric ALL. This may lead to personalized treatment strategies based on epigenetic profiling., Adrián Mosquera Orgueira and Olga Krali contributed equally to this work.

Published
2024
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18. BCP neoplasms : same or different?

Author

Nordlund, Jessica and Nordlund, Jessica

Abstract

In this issue of Blood, Kroeze et al1 provide an in-depth analysis of the genomic and transcriptomic landscape of pediatric B-cell precursor lymphoblastic lymphoma (BCP-LBL). Pediatric B-cell precursor malignancies present in 2 distinct forms: BCP acute lymphoblastic leukemia (BCP-ALL), predominantly affecting the bone marrow and blood, and the less common BCP-LBL, characterized by its origin in extramedullary tissues and presentation as a solid tumor rather than widespread bone marrow involvement (see figure). Despite their morphologic and immunophenotypic similarities, most studies to date have focused on BCP-ALL, leaving BCP-LBL relatively understudied.

Published
2024
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19. A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing

Author

Lysenkova, Mariya, Arvidsson, Gustav, Bunikis, Ignas, Lundmark, Anders, Raine, Amanda, Marincevic-Zuniga, Yanara, Gezelius, Henrik, Bremer, Anna, Feuk, Lars, Ameur, Adam, Nordlund, Jessica, Lysenkova, Mariya, Arvidsson, Gustav, Bunikis, Ignas, Lundmark, Anders, Raine, Amanda, Marincevic-Zuniga, Yanara, Gezelius, Henrik, Bremer, Anna, Feuk, Lars, Ameur, Adam, and Nordlund, Jessica

Published
2024
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20. Immune cells lacking Y chromosome show dysregulation of autosomal gene expression

Author

Dumanski, Jan P., Halvardson, Jonatan, Davies, Hanna, Rychlicka-Buniowska, Edyta, Mattisson, Jonas, Moghadam, Behrooz Torabi, Nagy, Noemi, Węglarczyk, Kazimierz, Bukowska-Strakova, Karolina, Danielsson, Marcus, Olszewski, Paweł, Piotrowski, Arkadiusz, Oerton, Erin, Ambicka, Aleksandra, Przewoźnik, Marcin, Bełch, Łukasz, Grodzicki, Tomasz, Chłosta, Piotr L., Imreh, Stefan, Giedraitis, Vilmantas, Kilander, Lena, Nordlund, Jessica, Ameur, Adam, Gyllensten, Ulf, Johansson, Åsa, Józkowicz, Alicja, Siedlar, Maciej, Klich-Rączka, Alicja, Jaszczyński, Janusz, Enroth, Stefan, Baran, Jarosław, Ingelsson, Martin, Perry, John R. B., Ryś, Janusz, and Forsberg, Lars A.

Published
2021
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22. Refining risk prediction in pediatric Acute Lymphoblastic Leukemia through DNA methylation profiling

Author

Orgueira, Adrián Mosquera, primary, Krali, Olga, additional, Míguez, Carlos Pérez, additional, Raíndo, Andrés Peleteiro, additional, Arias, José Ángel Díaz, additional, Pérez, Marta Sonia González, additional, Encinas, Manuel Mateo Pérez, additional, Sanmartín, Manuel Fernández, additional, Sinnet, Daniel, additional, Heyman, Mats, additional, Lönnerholm, Gudmar, additional, Norén-Nyström, Ulrika, additional, Schmiegelow, Kjeld, additional, and Nordlund, Jessica, additional

Published
2023
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23. Author Correction: The SEQC2 epigenomics quality control (EpiQC) study

Author

Foox, Jonathan, Nordlund, Jessica, Lalancette, Claudia, Gong, Ting, Lacey, Michelle, Lent, Samantha, Langhorst, Bradley W., Ponnaluri, V. K. Chaithanya, Williams, Louise, Padmanabhan, Karthik Ramaswamy, Cavalcante, Raymond, Lundmark, Anders, Butler, Daniel, Mozsary, Christopher, Gurvitch, Justin, Greally, John M., Suzuki, Masako, Menor, Mark, Nasu, Masaki, Alonso, Alicia, Sheridan, Caroline, Scherer, Andreas, Bruinsma, Stephen, Golda, Gosia, Muszynska, Agata, Łabaj, Paweł P., Campbell, Matthew A., Wos, Frank, Raine, Amanda, Liljedahl, Ulrika, Axelsson, Tomas, Wang, Charles, Chen, Zhong, Yang, Zhaowei, Li, Jing, Yang, Xiaopeng, Wang, Hongwei, Melnick, Ari, Guo, Shang, Blume, Alexander, Franke, Vedran, de Caceres, Inmaculada Ibanez, Rodriguez-Antolin, Carlos, Rosas, Rocio, Davis, Justin Wade, Ishii, Jennifer, Megherbi, Dalila B., Xiao, Wenming, Liao, Will, Xu, Joshua, Hong, Huixiao, Ning, Baitang, Tong, Weida, Akalin, Altuna, Wang, Yunliang, Deng, Youping, and Mason, Christopher E.

Published
2021
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25. The SEQC2 epigenomics quality control (EpiQC) study

Author

Foox, Jonathan, Nordlund, Jessica, Lalancette, Claudia, Gong, Ting, Lacey, Michelle, Lent, Samantha, Langhorst, Bradley W., Ponnaluri, V. K. Chaithanya, Williams, Louise, Padmanabhan, Karthik Ramaswamy, Cavalcante, Raymond, Lundmark, Anders, Butler, Daniel, Mozsary, Christopher, Gurvitch, Justin, Greally, John M., Suzuki, Masako, Menor, Mark, Nasu, Masaki, Alonso, Alicia, Sheridan, Caroline, Scherer, Andreas, Bruinsma, Stephen, Golda, Gosia, Muszynska, Agata, Łabaj, Paweł P., Campbell, Matthew A., Wos, Frank, Raine, Amanda, Liljedahl, Ulrika, Axelsson, Tomas, Wang, Charles, Chen, Zhong, Yang, Zhaowei, Li, Jing, Yang, Xiaopeng, Wang, Hongwei, Melnick, Ari, Guo, Shang, Blume, Alexander, Franke, Vedran, Ibanez de Caceres, Inmaculada, Rodriguez-Antolin, Carlos, Rosas, Rocio, Davis, Justin Wade, Ishii, Jennifer, Megherbi, Dalila B., Xiao, Wenming, Liao, Will, Xu, Joshua, Hong, Huixiao, Ning, Baitang, Tong, Weida, Akalin, Altuna, Wang, Yunliang, Deng, Youping, and Mason, Christopher E.

Published
2021
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26. Whole genome and exome sequencing reference datasets from a multi-center and cross-platform benchmark study

Author

Zhao, Yongmei, Fang, Li Tai, Shen, Tsai-wei, Choudhari, Sulbha, Talsania, Keyur, Chen, Xiongfong, Shetty, Jyoti, Kriga, Yuliya, Tran, Bao, Zhu, Bin, Chen, Zhong, Chen, Wanqiu, Wang, Charles, Jaeger, Erich, Meerzaman, Daoud, Lu, Charles, Idler, Kenneth, Ren, Luyao, Zheng, Yuanting, Shi, Leming, Petitjean, Virginie, Sultan, Marc, Hung, Tiffany, Peters, Eric, Drabek, Jiri, Vojta, Petr, Maestro, Roberta, Gasparotto, Daniela, Kõks, Sulev, Reimann, Ene, Scherer, Andreas, Nordlund, Jessica, Liljedahl, Ulrika, Foox, Jonathan, Mason, Christopher E., Xiao, Chunlin, Hong, Huixiao, and Xiao, Wenming

Published
2021
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28. The proliferative history shapes the DNA methylome of B-cell tumors and predicts clinical outcome

Author

Duran-Ferrer, Martí, Clot, Guillem, Nadeu, Ferran, Beekman, Renée, Baumann, Tycho, Nordlund, Jessica, Marincevic-Zuniga, Yanara, Lönnerholm, Gudmar, Rivas-Delgado, Alfredo, Martín, Silvia, Ordoñez, Raquel, Castellano, Giancarlo, Kulis, Marta, Queirós, Ana C., Lee, Seung-Tae, Wiemels, Joseph, Royo, Romina, Puiggrós, Montserrat, Lu, Junyan, Giné, Eva, Beà, Sílvia, Jares, Pedro, Agirre, Xabier, Prosper, Felipe, López-Otín, Carlos, Puente, Xosé S., Oakes, Christopher C., Zenz, Thorsten, Delgado, Julio, López-Guillermo, Armando, Campo, Elías, and Martín-Subero, José Ignacio

Published
2020
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29. Evolutionary dynamics of 1,976 lymphoid malignancies predict clinical outcome

Author

Gabbutt, Calum, primary, Duran-Ferrer, Marti, additional, Grant, Heather, additional, Mallo, Diego, additional, Nadeu, Ferran, additional, Househam, Jacob, additional, Villamor, Neus, additional, Krali, Olga, additional, Nordlund, Jessica, additional, Zenz, Thorsten, additional, Campo, Elias, additional, Lopez-Guillermo, Armando, additional, Fitzgibbon, Jude, additional, Barnes, Chris P, additional, Shibata, Darryl, additional, Martin-Subero, Jose I, additional, and Graham, Trevor A, additional

Published
2023
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32. Contributors

Author

Ali, Muhammad, primary, Anwar, Zobia, additional, Asp, Patrik, additional, Bell, Douglas A, additional, Campbell, Mel, additional, Carlberg, Carsten, additional, Carless, Melanie A., additional, Chen, Xingqi, additional, Choudhury, Yashmin, additional, Coêlho, Marina de Castro, additional, Dalan, Emma, additional, Das, Raima, additional, Davis, Ryan R., additional, del Sol, Antonio, additional, Dzobo, Kevin, additional, Fenstermaker, Tyler K., additional, Ghosh, Sankar Kumar, additional, Grady, W.M., additional, Hausmann, Michael, additional, Hildenbrand, Georg, additional, Hofner, Manuela, additional, Horn, Bradley, additional, Hu, Guoku, additional, Ito, Masaki, additional, Izumiya, Yoshihiro, additional, Joshi, Anagha, additional, Jung, Sascha, additional, Jurkowska, Renata Z, additional, Jurkowski, Tomasz P, additional, Kishi, Yusuke, additional, Krainer, Julie, additional, Kumar, Ashish, additional, Kundu, Sharbadeb, additional, Laskar, Shaheen, additional, Lee, Jin-Ho, additional, Marina, Dunaeva, additional, Mazo, Alexander, additional, Montanera, Kaitlin N., additional, Nakabayashi, Kazuhiko, additional, Neary, Jennifer L., additional, Neme, Antonio, additional, Nöhammer, Christa, additional, Nordlund, Jessica, additional, de Oliveira, Naila Francis Paulo, additional, Pabinger, Stephan, additional, Paul, Amit, additional, Petruk, Svetlana, additional, Pulverer, Walter, additional, Rhee, Ho Sung, additional, Riddle, Nicole C., additional, Romanowska, Julia, additional, Schoelz, John M., additional, Seuter, Sabine, additional, Shibin, Sherin M., additional, Siomi, Haruhiko, additional, Tanić, Miljana, additional, Tepper, Clifford G., additional, Tian, Changhai, additional, Tollefsbol, Trygve O., additional, Tong, Jingjing, additional, Uchino, Haruto, additional, Viana Filho, José Maria Chagas, additional, Wan, Ma, additional, Wang, Zhihua, additional, Weinhäusel, Andreas, additional, Willbanks, A., additional, Williams, Graham, additional, Xie, Yinping, additional, Yamanaka, Soichiro, additional, and Yu, M., additional

Published
2020
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35. Feasibility to use whole-genome sequencing as a sole diagnostic method to detect genomic aberrations in pediatric B-cell acute lymphoblastic leukemia

Author

Rezayee, Fatemah, primary, Eisfeldt, Jesper, additional, Skaftason, Aron, additional, Öfverholm, Ingegerd, additional, Sayyab, Shumaila, additional, Syvänen, Ann Christine, additional, Maqbool, Khurram, additional, Lilljebjörn, Henrik, additional, Johansson, Bertil, additional, Olsson-Arvidsson, Linda, additional, Pietras, Christina Orsmark, additional, Staffas, Anna, additional, Palmqvist, Lars, additional, Fioretos, Thoas, additional, Cavelier, Lucia, additional, Fogelstrand, Linda, additional, Nordlund, Jessica, additional, Wirta, Valtteri, additional, Rosenquist, Richard, additional, and Barbany, Gisela, additional

Published
2023
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40. Multimodal Single-Cell Sequencing of B Cells in Primary Sjögren’s Syndrome.

Author

Arvidsson, Gustav, Czarnewski, Paulo, Johansson, Alina, Raine, Amanda, Imgenberg-Kreuz, Juliana, Nordlund, Jessica, Nordmark, Gunnel, and Syvänen, Ann-Christine

Subjects
RNA analysis, AUTOANTIBODIES, B cells, SEQUENCE analysis, IMMUNOGLOBULINS, GENETIC mutation, CELL receptors, MOLECULAR pathology, COMPARATIVE studies, GENE expression profiling, DESCRIPTIVE statistics, SJOGREN'S syndrome, PHENOTYPES
Abstract

Objective. B cells are important in the pathogenesis of primary Sjögren’s syndrome (pSS). Patients positive for Sjögren’s syndrome antigen A/Sjögren syndrome antigen B (SSA/SSB) autoantibodies are more prone to systemic disease manifestations and adverse outcomes. We aimed to determine the role of B cell composition, gene expression, and B cell receptor usage in pSS subgroups stratified for SSA/SSB antibodies. Methods. Over 230,000 B cells were isolated from peripheral blood of patients with pSS (n = 6 SSA−, n = 8 SSA+ single positive and n = 10 SSA/SSB+ double positive) and four healthy controls and processed for single-cell RNA sequencing (scRNA-seq) and single-cell variable, diversity, and joining (VDJ) gene sequencing (scVDJ-seq). Results. We show that SSA/SSB+ patients present the highest and lowest proportion of naïve and memory B cells, respectively, and the highest up-regulation of interferon-induced genes across all B cell subtypes. Differential usage of IGHV showed that IGHV1-69 and IGHV4-30-4 were more often used in all pSS subgroups compared with controls. Memory B cells from SSA/SSB+ patients displayed a higher proportion of cells with unmutated VDJ transcripts compared with other pSS patient groups and controls, indicating altered somatic hypermutation processes. Comparison with previous studies revealed heterogeneous clonotype pools, with little overlap in CDR3 sequences. Joint analysis using scRNA-seq and scVDJ-seq data allowed unsupervised stratification of patients with pSS and identified novel parameters that correlated to disease manifestations and antibody status. Conclusion. We describe heterogeneity and molecular characteristics in B cells from patients with pSS, providing clues to intrinsic differences in B cells that affect the phenotype and outcome and allowing stratification of patients with pSS at improved resolution. [ABSTRACT FROM AUTHOR]

Published
2024
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42. Genomic, transcriptomic and epigenomic sequencing data of the B- cell leukemia cell line REH

Author

Wiklander, Mariya Lysenkova, primary, Övernäs, Elin, additional, Lagensjö, Johanna, additional, Raine, Amanda, additional, Petri, Anna, additional, Wiman, Ann-Christine, additional, Ramsell, Jon, additional, Marincevic-Zuniga, Yanara, additional, Gezelius, Henrik, additional, Martin, Tom, additional, Bunikis, Ignas, additional, Ekberg, Sara, additional, Erlandsson, Rikard, additional, Larsson, Pontus, additional, Mosbech, Mai-Britt, additional, Häggkvist, Susana, additional, Kerje, Susanne Hellstedt, additional, Feuk, Lars, additional, Ameur, Adam, additional, Liljedahl, Ulrika, additional, and Nordlund, Jessica, additional

Published
2023
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43. Abstract LB362: Epigenome-wide DNA methylation alterations precede diagnosis since birth and affect prognosis of pediatric B-cell acute lymphoblastic leukemia

Author

Ghantous, Akram, primary, Nusslé, Semira Gonseth, additional, Nassar, Farah, additional, Spitz, Natalia, additional, Novoloaca, Alexei, additional, Krali, Olga, additional, Roy, Ritu, additional, Li, Shaobo, additional, Caron, Maxime, additional, Lam, Lilys, additional, Fransquet, Peter Daniel, additional, Casement, John, additional, Strathdee, John, additional, Pearce, Mark S., additional, Hansen, Helen M., additional, De Smith, Adam J., additional, Sinnett, Daniel, additional, Håberg, Siri Eldevik, additional, McKay, Jill, additional, Nordlund, Jessica, additional, Magnus, Per, additional, Dwyer, Terence, additional, Saffery, Richard, additional, Wiemels, Joseph Leo, additional, Munthe-Kaas, Monica Cheng, additional, and Herceg, Zdenko, additional

Published
2023
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45. Multimodal classification of molecular subtypes in pediatric acute lymphoblastic leukemia

Author

Krali, Olga, primary, Marincevic-Zuniga, Yanara, additional, Arvidsson, Gustav, additional, Enblad, Anna Pia, additional, Lundmark, Anders, additional, Sayyab, Shumaila, additional, Zachariadis, Vasilios, additional, Heinäniemi, Merja, additional, Suhonen, Janne, additional, Oksa, Laura, additional, Vepsäläinen, Kaisa, additional, Öfverholm, Ingegerd, additional, Barbany, Gisela, additional, Nordgren, Ann, additional, Lilljebjörn, Henrik, additional, Fioretos, Thoas, additional, Madsen, Hans O., additional, Marquart, Hanne Vibeke, additional, Flaegstad, Trond, additional, Forestier, Erik, additional, Jónsson, Ólafur G, additional, Kanerva, Jukka, additional, Lohi, Olli, additional, Norén-Nyström, Ulrika, additional, Schmiegelow, Kjeld, additional, Harila, Arja, additional, Heyman, Mats, additional, Lönnerholm, Gudmar, additional, Syvänen, Ann-Christine, additional, and Nordlund, Jessica, additional

Published
2023
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47. Feasibility to use whole-genome sequencing as a sole diagnostic method to detect genomic aberrations in pediatric B-cell acute lymphoblastic leukemia

Author

Rezayee, Fatemah, Eisfeldt, Jesper, Skaftason, Aron, Ofverholm, Ingegerd, Sayyab, Shumaila, Syvänen, Ann-Christine, Maqbool, Khurram, Lilljebjorn, Henrik, Johansson, Bertil, Olsson-Arvidsson, Linda, Pietras, Christina Orsmark, Staffas, Anna, Palmqvist, Lars, Fioretos, Thoas, Cavelier, Lucia, Fogelstrand, Linda, Nordlund, Jessica, Wirta, Valtteri, Rosenquist, Richard, Barbany, Gisela, Rezayee, Fatemah, Eisfeldt, Jesper, Skaftason, Aron, Ofverholm, Ingegerd, Sayyab, Shumaila, Syvänen, Ann-Christine, Maqbool, Khurram, Lilljebjorn, Henrik, Johansson, Bertil, Olsson-Arvidsson, Linda, Pietras, Christina Orsmark, Staffas, Anna, Palmqvist, Lars, Fioretos, Thoas, Cavelier, Lucia, Fogelstrand, Linda, Nordlund, Jessica, Wirta, Valtteri, Rosenquist, Richard, and Barbany, Gisela

Abstract

Introduction The suitability of whole-genome sequencing (WGS) as the sole method to detect clinically relevant genomic aberrations in B-cell acute lymphoblastic leukemia (ALL) was investigated with the aim of replacing current diagnostic methods. Methods For this purpose, we assessed the analytical performance of 150 bp paired-end WGS (90x leukemia/30x germline). A set of 88 retrospective B-cell ALL samples were selected to represent established ALL subgroups as well as ALL lacking stratifying markers by standard-of-care (SoC), so-called B-other ALL. Results Both the analysis of paired leukemia/germline (L/N)(n=64) as well as leukemia-only (L-only)(n=88) detected all types of aberrations mandatory in the current ALLTogether trial protocol, i.e., aneuploidies, structural variants, and focal copy-number aberrations. Moreover, comparison to SoC revealed 100% concordance and that all patients had been assigned to the correct genetic subgroup using both approaches. Notably, WGS could allocate 35 out of 39 B-other ALL samples to one of the emerging genetic subgroups considered in the most recent classifications of ALL. We further investigated the impact of high (90x; n=58) vs low (30x; n=30) coverage on the diagnostic yield and observed an equally perfect concordance with SoC; low coverage detected all relevant lesions. Discussion The filtration of the WGS findings with a short list of genes recurrently rearranged in ALL was instrumental to extract the clinically relevant information efficiently. Nonetheless, the detection of DUX4 rearrangements required an additional customized analysis, due to multiple copies of this gene embedded in the highly repetitive D4Z4 region. We conclude that the diagnostic performance of WGS as the standalone method was remarkable and allowed detection of all clinically relevant genomic events in the diagnostic setting of B-cell ALL.

Published
2023
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48. Increased MYB alternative promoter usage is associated with relapse in acute lymphoblastic leukemia

Author

Fehr, André, Arvidsson, Gustav, Nordlund, Jessica, Lönnerholm, Gudmar, Stenman, Göran, Andersson, Mattias K., Fehr, André, Arvidsson, Gustav, Nordlund, Jessica, Lönnerholm, Gudmar, Stenman, Göran, and Andersson, Mattias K.

Abstract

Therapy-resistant disease is a major cause of death in patients with acute lymphoblastic leukemia (ALL). Activation of the MYB oncogene is associated with ALL and leads to uncontrolled neoplastic cell proliferation and blocked differentiation. Here, we used RNA-seq to study the clinical significance of MYB expression and MYB alternative promoter (TSS2) usage in 133 pediatric ALLs. RNA-seq revealed that all cases analyzed overexpressed MYB and demonstrated MYB TSS2 activity. qPCR analyses confirmed the expression of the alternative MYB promoter also in seven ALL cell lines. Notably, high MYB TSS2 activity was significantly associated with relapse (p = 0.007). Moreover, cases with high MYB TSS2 usage showed evidence of therapy-resistant disease with increased expression of ABC multidrug resistance transporter genes (e.g., ABCA2, ABCB5, and ABCC10) and enzymes catalyzing drug degradation (e.g., CYP1A2, CYP2C9, and CYP3A5). Elevated MYB TSS2 activity was further associated with augmented KRAS signaling (p < 0.05) and decreased methylation of the conventional MYB promoter (p < 0.01). Taken together, our results suggest that MYB alternative promoter usage is a novel potential prognostic biomarker for relapse and therapy resistance in pediatric ALL.

Published
2023
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49. Mapping Chemo-Resistance Profiles of Pediatric Acute Leukemia through Integration of Ex-Vivo Drug Screens with Molecular Data

Author

Enblad, Anna Pia, Krali, Olga, Blom, Kristin, Andersson, Claes, Frost, Britt-marie, Palle, Josefine, Harila, Arja, Forestier, Erik, Kanerva, Jukka, Flægstad, Trond, Jónsson, Ólafur G, Schmiegelow, Kjeld, Heyman, Mats, Nygren, Peter, Larsson, Rolf, Lönnerholm, Gudmar, Nordlund, Jessica, Enblad, Anna Pia, Krali, Olga, Blom, Kristin, Andersson, Claes, Frost, Britt-marie, Palle, Josefine, Harila, Arja, Forestier, Erik, Kanerva, Jukka, Flægstad, Trond, Jónsson, Ólafur G, Schmiegelow, Kjeld, Heyman, Mats, Nygren, Peter, Larsson, Rolf, Lönnerholm, Gudmar, and Nordlund, Jessica

Abstract

ntroduction While novel approaches for treatment of acute lymphoblastic leukemia (ALL) in children have resulted in significant improvements in survival rates, survivors are faced with potentially life-long challenges as a result of the highly toxic treatment and the outcome for patients who relapse remains poor. The current risk-adapted treatment for ALL in children includes multiple drugs administered sequentially or in combination, with little variation in timing or intensity. Factors that affect varying treatment response between patients and cellular mechanisms that underly response to individual drugs are still under exploration. In this study, we investigate the relationship between ex-vivo drug resistance, transcriptomes, epigenomes and clinical outcome, with the aim of better understanding underlying determinants of treatment response. Methods Pediatric patients diagnosed with B-ALL between 1992 and 2008 in the Nordic countries were included in the study (n = 598). For these patients, ex-vivo drug response to ten clinically used drugs was determined using the fluorometric microculture cytotoxicity assay (FMCA). Clinical data, including follow-up information (overall survival and relapse free survival) was available for all patients. Additionally, DNA-methylation (450K array, n = 383) and gene expression profiling (RNA-seq, n = 119) was performed on a subset of diagnostic patient samples. The patients were stratified into low, medium and high resistance groups based on ex-vivo drug response. The low and high resistance groups were compared with regard to differentially methylated CpG sites or expressed genes associated with individual drug response profiles. Results Overall survival was significantly lower for patients with higher ex-vivo drug resistance to dexamethasone, doxorubicin and thioguanine compared to patients that displayed sensitivity to these drugs (p < 0.05). Similarly, relapse free survival was s

Published
2023

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