Multi-omic machine learning predictor of breast cancer therapy response
Sammut, Stephen-John, Crispin-Ortuzar, Mireia, Chin, Suet-Feung, Provenzano, Elena, Bardwell, Helen A., Ma, Wenxin, Cope, Wei, Dariush, Ali, Dawson, Sarah-Jane, Abraham, Jean E., Dunn, Janet, Hiller, Louise, Thomas, Jeremy, Cameron, David A., Bartlett, John M. S., Hayward, Larry, Pharoah, Paul D., Markowetz, Florian, Rueda, Oscar M., Earl, Helena M., Caldas, Carlos
Published in Nature (London) (27.01.2022)
Published in Nature (London) (27.01.2022)
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Journal Article
Dynamics of breast-cancer relapse reveal late-recurring ER-positive genomic subgroups
Rueda, Oscar M., Sammut, Stephen-John, Seoane, Jose A., Chin, Suet-Feung, Caswell-Jin, Jennifer L., Callari, Maurizio, Batra, Rajbir, Pereira, Bernard, Bruna, Alejandra, Ali, H. Raza, Provenzano, Elena, Liu, Bin, Parisien, Michelle, Gillett, Cheryl, McKinney, Steven, Green, Andrew R., Murphy, Leigh, Purushotham, Arnie, Ellis, Ian O., Pharoah, Paul D., Rueda, Cristina, Aparicio, Samuel, Caldas, Carlos, Curtis, Christina
Published in Nature (London) (01.03.2019)
Published in Nature (London) (01.03.2019)
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Journal Article
Personalized circulating tumor DNA analysis to detect residual disease after neoadjuvant therapy in breast cancer
McDonald, Bradon R, Contente-Cuomo, Tania, Sammut, Stephen-John, Odenheimer-Bergman, Ahuva, Ernst, Brenda, Perdigones, Nieves, Chin, Suet-Feung, Farooq, Maria, Mejia, Rosa, Cronin, Patricia A, Anderson, Karen S, Kosiorek, Heidi E, Northfelt, Donald W, McCullough, Ann E, Patel, Bhavika K, Weitzel, Jeffrey N, Slavin, Thomas P, Caldas, Carlos, Pockaj, Barbara A, Murtaza, Muhammed
Published in Science translational medicine (07.08.2019)
Published in Science translational medicine (07.08.2019)
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Journal Article
The molecular landscape of Asian breast cancers reveals clinically relevant population-specific differences
Pan, Jia-Wern, Zabidi, Muhammad Mamduh Ahmad, Ng, Pei-Sze, Meng, Mei-Yee, Hasan, Siti Norhidayu, Sandey, Bethan, Sammut, Stephen-John, Yip, Cheng-Har, Rajadurai, Pathmanathan, Rueda, Oscar M., Caldas, Carlos, Chin, Suet-Feung, Teo, Soo-Hwang
Published in Nature communications (22.12.2020)
Published in Nature communications (22.12.2020)
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Journal Article
DNA methylation landscapes of 1538 breast cancers reveal a replication-linked clock, epigenomic instability and cis-regulation
Batra, Rajbir Nath, Lifshitz, Aviezer, Vidakovic, Ana Tufegdzic, Chin, Suet-Feung, Sati-Batra, Ankita, Sammut, Stephen-John, Provenzano, Elena, Ali, H. Raza, Dariush, Ali, Bruna, Alejandra, Murphy, Leigh, Purushotham, Arnie, Ellis, Ian, Green, Andrew, Garrett-Bakelman, Francine E., Mason, Chris, Melnick, Ari, Aparicio, Samuel A. J. R., Rueda, Oscar M., Tanay, Amos, Caldas, Carlos
Published in Nature communications (13.09.2021)
Published in Nature communications (13.09.2021)
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Journal Article
Comparison of tumor‐informed and tumor‐naïve sequencing assays for ctDNA detection in breast cancer
Santonja, Angela, Cooper, Wendy N, Eldridge, Matthew D, Edwards, Paul A W, Morris, James A, Edwards, Abigail R, Zhao, Hui, Heider, Katrin, Couturier, Dominique‐Laurent, Vijayaraghavan, Aadhitthya, Mennea, Paulius, Ditter, Emma‐Jane, Smith, Christopher G, Boursnell, Chris, Manzano García, Raquel, Rueda, Oscar M, Beddowes, Emma, Biggs, Heather, Sammut, Stephen‐John, Rosenfeld, Nitzan, Caldas, Carlos, Abraham, Jean E, Gale, Davina
Published in EMBO molecular medicine (07.06.2023)
Published in EMBO molecular medicine (07.06.2023)
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Journal Article
The Genomic and Immune Landscapes of Lethal Metastatic Breast Cancer
De Mattos-Arruda, Leticia, Sammut, Stephen-John, Ross, Edith M., Bashford-Rogers, Rachael, Greenstein, Erez, Markus, Havell, Morganella, Sandro, Teng, Yvonne, Maruvka, Yosef, Pereira, Bernard, Rueda, Oscar M., Chin, Suet-Feung, Contente-Cuomo, Tania, Mayor, Regina, Arias, Alexandra, Ali, H. Raza, Cope, Wei, Tiezzi, Daniel, Dariush, Aliakbar, Dias Amarante, Tauanne, Reshef, Dan, Ciriaco, Nikaoly, Martinez-Saez, Elena, Peg, Vicente, Ramon y Cajal, Santiago, Cortes, Javier, Vassiliou, George, Getz, Gad, Nik-Zainal, Serena, Murtaza, Muhammed, Friedman, Nir, Markowetz, Florian, Seoane, Joan, Caldas, Carlos
Published in Cell reports (Cambridge) (28.05.2019)
Published in Cell reports (Cambridge) (28.05.2019)
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Journal Article
Computational approach to discriminate human and mouse sequences in patient-derived tumour xenografts
Callari, Maurizio, Batra, Ankita Sati, Batra, Rajbir Nath, Sammut, Stephen-John, Greenwood, Wendy, Clifford, Harry, Hercus, Colin, Chin, Suet-Feung, Bruna, Alejandra, Rueda, Oscar M, Caldas, Carlos
Published in BMC genomics (05.01.2018)
Published in BMC genomics (05.01.2018)
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Journal Article
Intersect-then-combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers
Callari, Maurizio, Sammut, Stephen-John, De Mattos-Arruda, Leticia, Bruna, Alejandra, Rueda, Oscar M, Chin, Suet-Feung, Caldas, Carlos
Published in Genome medicine (18.04.2017)
Published in Genome medicine (18.04.2017)
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Journal Article
Next Generation-Targeted Amplicon Sequencing (NG-TAS): an optimised protocol and computational pipeline for cost-effective profiling of circulating tumour DNA
Gao, Meiling, Callari, Maurizio, Beddowes, Emma, Sammut, Stephen-John, Grzelak, Marta, Biggs, Heather, Jones, Linda, Boumertit, Abdelhamid, Linn, Sabine C, Cortes, Javier, Oliveira, Mafalda, Baird, Richard, Chin, Suet-Feung, Caldas, Carlos
Published in Genome medicine (04.01.2019)
Published in Genome medicine (04.01.2019)
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Journal Article
The temporal mutational and immune tumour microenvironment remodelling of HER2-negative primary breast cancers
De Mattos-Arruda, Leticia, Cortes, Javier, Blanco-Heredia, Juan, Tiezzi, Daniel G., Villacampa, Guillermo, Gonçalves-Ribeiro, Samuel, Paré, Laia, Souza, Carla Anjos, Ortega, Vanesa, Sammut, Stephen-John, Cusco, Pol, Fasani, Roberta, Chin, Suet-Feung, Perez-Garcia, Jose, Dienstmann, Rodrigo, Nuciforo, Paolo, Villagrasa, Patricia, Rubio, Isabel T., Prat, Aleix, Caldas, Carlos
Published in NPJ breast cancer (07.06.2021)
Published in NPJ breast cancer (07.06.2021)
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Journal Article
The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes
Pereira, Bernard, Chin, Suet-Feung, Rueda, Oscar M, Vollan, Hans-Kristian Moen, Provenzano, Elena, Bardwell, Helen A, Pugh, Michelle, Jones, Linda, Russell, Roslin, Sammut, Stephen-John, Tsui, Dana W Y, Liu, Bin, Dawson, Sarah-Jane, Abraham, Jean, Northen, Helen, Peden, John F, Mukherjee, Abhik, Turashvili, Gulisa, Green, Andrew R, McKinney, Steve, Oloumi, Arusha, Shah, Sohrab, Rosenfeld, Nitzan, Murphy, Leigh, Bentley, David R, Ellis, Ian O, Purushotham, Arnie, Pinder, Sarah E, Børresen-Dale, Anne-Lise, Earl, Helena M, Pharoah, Paul D, Ross, Mark T, Aparicio, Samuel, Caldas, Carlos
Published in Nature communications (10.05.2016)
Published in Nature communications (10.05.2016)
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Journal Article
A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer Compounds
Bruna, Alejandra, Rueda, Oscar M., Greenwood, Wendy, Batra, Ankita Sati, Callari, Maurizio, Batra, Rajbir Nath, Pogrebniak, Katherine, Sandoval, Jose, Cassidy, John W., Tufegdzic-Vidakovic, Ana, Sammut, Stephen-John, Jones, Linda, Provenzano, Elena, Baird, Richard, Eirew, Peter, Hadfield, James, Eldridge, Matthew, McLaren-Douglas, Anne, Barthorpe, Andrew, Lightfoot, Howard, O’Connor, Mark J., Gray, Joe, Cortes, Javier, Baselga, Jose, Marangoni, Elisabetta, Welm, Alana L., Aparicio, Samuel, Serra, Violeta, Garnett, Mathew J., Caldas, Carlos
Published in Cell (22.09.2016)
Published in Cell (22.09.2016)
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Journal Article
AACR Project GENIE: 100,000 Cases and Beyond
Pugh, Trevor J, Bell, Jonathan L, Bruce, Jeff P, Doherty, Gary J, Galvin, Matthew, Green, Michelle F, Hunter-Zinck, Haley, Kumari, Priti, Lenoue-Newton, Michele L, Li, Marilyn M, Lindsay, James, Mazor, Tali, Ovalle, Andrea, Sammut, Stephen-John, Schultz, Nikolaus, Yu, Thomas V, Sweeney, Shawn M, Bernard, Brady
Published in Cancer discovery (02.09.2022)
Published in Cancer discovery (02.09.2022)
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Journal Article
Predictability of B cell clonal persistence and immunosurveillance in breast cancer
Sammut, Stephen-John, Galson, Jacob D., Minter, Ralph, Sun, Bo, Chin, Suet-Feung, De Mattos-Arruda, Leticia, Finch, Donna K., Schätzle, Sebastian, Dias, Jorge, Rueda, Oscar M., Seoane, Joan, Osbourn, Jane, Caldas, Carlos, Bashford-Rogers, Rachael J. M.
Published in Nature immunology (01.05.2024)
Published in Nature immunology (01.05.2024)
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Journal Article
Prognostic Value of MammaPrint® in Invasive Lobular Breast Cancer
Beumer, Inès J., Persoon, Marion, Witteveen, Anke, Dreezen, Christa, Chin, Suet-Feung, Sammut, Stephen-John, Snel, Mireille, Caldas, Carlos, Linn, Sabine, van 't Veer, Laura J., Bernards, Rene, Glas, Annuska M.
Published in Biomarker Insights (01.01.2016)
Published in Biomarker Insights (01.01.2016)
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Journal Article
Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers
Chin, Suet-Feung, Santonja, Angela, Grzelak, Marta, Ahn, Soomin, Sammut, Stephen-John, Clifford, Harry, Rueda, Oscar M., Pugh, Michelle, Goldgraben, Mae A., Bardwell, Helen A., Cho, Eun Yoon, Provenzano, Elena, Rojo, Federico, Alba, Emilio, Caldas, Carlos
Published in Experimental and molecular pathology (01.06.2018)
Published in Experimental and molecular pathology (01.06.2018)
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Journal Article
Big data in cancer genomics
Maia, Ana-Teresa, Sammut, Stephen-John, Jacinta-Fernandes, Ana, Chin, Suet-Feung
Published in Current opinion in systems biology (01.08.2017)
Published in Current opinion in systems biology (01.08.2017)
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Journal Article
Erratum: The somatic mutation profiles of 2,433 breast cancers refine their genomic and transcriptomic landscapes
Pereira, Bernard, Chin, Suet-Feung, Rueda, Oscar M., Vollan, Hans-Kristian Moen, Provenzano, Elena, Bardwell, Helen A., Pugh, Michelle, Jones, Linda, Russell, Roslin, Sammut, Stephen-John, Tsui, Dana W. Y., Liu, Bin, Dawson, Sarah-Jane, Abraham, Jean, Northen, Helen, Peden, John F., Mukherjee, Abhik, Turashvili, Gulisa, Green, Andrew R., McKinney, Steve, Oloumi, Arusha, Shah, Sohrab, Rosenfeld, Nitzan, Murphy, Leigh, Bentley, David R., Ellis, Ian O., Purushotham, Arnie, Pinder, Sarah E., Børresen-Dale, Anne-Lise, Earl, Helena M., Pharoah, Paul D., Ross, Mark T., Aparicio, Samuel, Caldas, Carlos
Published in Nature communications (06.06.2016)
Published in Nature communications (06.06.2016)
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Journal Article
The somatic mutation profiles of 2,433 breast cancers refine their genomic and transcriptomic landscapes
Pereira, Bernard, Chin, Suet-Feung, Rueda, Oscar M., Vollan, Hans-Kristian Moen, Provenzano, Elena, Bardwell, Helen A., Pugh, Michelle, Jones, Linda, Russell, Roslin, Sammut, Stephen-John, Tsui, Dana W. Y., Liu, Bin, Dawson, Sarah-Jane, Abraham, Jean, Northen, Helen, Peden, John F., Mukherjee, Abhik, Turashvili, Gulisa, Green, Andrew R., McKinney, Steve, Oloumi, Arusha, Shah, Sohrab, Rosenfeld, Nitzan, Murphy, Leigh, Bentley, David R., Ellis, Ian O., Purushotham, Arnie, Pinder, Sarah E., Børresen-Dale, Anne-Lise, Earl, Helena M., Pharoah, Paul D., Ross, Mark T., Aparicio, Samuel, Caldas, Carlos
Published in Nature communications (10.05.2016)
Published in Nature communications (10.05.2016)
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