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1. Pathway level subtyping identifies a slow-cycling biological phenotype associated with poor clinical outcomes in colorectal cancer

Author

Malla, Sudhir B., Byrne, Ryan M., Lafarge, Maxime W., Corry, Shania M., Fisher, Natalie C., Tsantoulis, Petros K., Mills, Megan L., Ridgway, Rachel A., Lannagan, Tamsin R. M., Najumudeen, Arafath K., Gilroy, Kathryn L., Amirkhah, Raheleh, Maguire, Sarah L., Mulholland, Eoghan J., Belnoue-Davis, Hayley L., Grassi, Elena, Viviani, Marco, Rogan, Emily, Redmond, Keara L., Sakhnevych, Svetlana, McCooey, Aoife J., Bull, Courtney, Hoey, Emily, Sinevici, Nicoleta, Hall, Holly, Ahmaderaghi, Baharak, Domingo, Enric, Blake, Andrew, Richman, Susan D., Isella, Claudio, Miller, Crispin, Bertotti, Andrea, Trusolino, Livio, Loughrey, Maurice B., Kerr, Emma M., Tejpar, Sabine, Maughan, Timothy S., Lawler, Mark, Campbell, Andrew D., Leedham, Simon J., Koelzer, Viktor H., Sansom, Owen J., and Dunne, Philip D.

Published
2024
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2. Author Correction: Pathway level subtyping identifies a slow-cycling biological phenotype associated with poor clinical outcomes in colorectal cancer

Author

Malla, Sudhir B., Byrne, Ryan M., Lafarge, Maxime W., Corry, Shania M., Fisher, Natalie C., Tsantoulis, Petros K., Mills, Megan L., Ridgway, Rachel A., Lannagan, Tamsin R. M., Najumudeen, Arafath K., Gilroy, Kathryn L., Amirkhah, Raheleh, Maguire, Sarah L., Mulholland, Eoghan J., Belnoue-Davis, Hayley L., Grassi, Elena, Viviani, Marco, Rogan, Emily, Redmond, Keara L., Sakhnevych, Svetlana, McCooey, Aoife J., Bull, Courtney, Hoey, Emily, Sinevici, Nicoleta, Hall, Holly, Ahmaderaghi, Baharak, Domingo, Enric, Blake, Andrew, Richman, Susan D., Isella, Claudio, Miller, Crispin, Bertotti, Andrea, Trusolino, Livio, Loughrey, Maurice B., Kerr, Emma M., Tejpar, Sabine, Maughan, Timothy S., Lawler, Mark, Campbell, Andrew D., Leedham, Simon J., Koelzer, Viktor H., Sansom, Owen J., and Dunne, Philip D.

Published
2024
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6. Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts.

Author

Woo, Xing, Giordano, Jessica, Srivastava, Anuj, Zhao, Zi-Ming, Lloyd, Michael, de Bruijn, Roebi, Suh, Yun-Suhk, Patidar, Rajesh, Chen, Li, Scherer, Sandra, Bailey, Matthew, Yang, Chieh-Hsiang, Cortes-Sanchez, Emilio, Xi, Yuanxin, Wang, Jing, Wickramasinghe, Jayamanna, Kossenkov, Andrew, Rebecca, Vito, Sun, Hua, Mashl, R, Davies, Sherri, Jeon, Ryan, Frech, Christian, Randjelovic, Jelena, Rosains, Jacqueline, Galimi, Francesco, Bertotti, Andrea, Lafferty, Adam, OFarrell, Alice, Modave, Elodie, Lambrechts, Diether, Ter Brugge, Petra, Serra, Violeta, Marangoni, Elisabetta, El Botty, Rania, Kim, Hyunsoo, Kim, Jong-Il, Yang, Han-Kwang, Lee, Charles, Dean, Dennis, Davis-Dusenbery, Brandi, Evrard, Yvonne, Doroshow, James, Welm, Alana, Welm, Bryan, Lewis, Michael, Fang, Bingliang, Roth, Jack, Meric-Bernstam, Funda, Herlyn, Meenhard, Davies, Michael, Ding, Li, Li, Shunqiang, Govindan, Ramaswamy, Isella, Claudio, Moscow, Jeffrey, Trusolino, Livio, Byrne, Annette, Jonkers, Jos, Bult, Carol, Medico, Enzo, and Chuang, Jeffrey

Subjects
Animals, DNA Copy Number Variations, Databases, Genetic, Gene Expression Regulation, Neoplastic, Humans, Mice, Neoplasm Metastasis, Polymorphism, Single Nucleotide, Exome Sequencing, Xenograft Model Antitumor Assays
Abstract

Patient-derived xenografts (PDXs) are resected human tumors engrafted into mice for preclinical studies and therapeutic testing. It has been proposed that the mouse host affects tumor evolution during PDX engraftment and propagation, affecting the accuracy of PDX modeling of human cancer. Here, we exhaustively analyze copy number alterations (CNAs) in 1,451 PDX and matched patient tumor (PT) samples from 509 PDX models. CNA inferences based on DNA sequencing and microarray data displayed substantially higher resolution and dynamic range than gene expression-based inferences, and they also showed strong CNA conservation from PTs through late-passage PDXs. CNA recurrence analysis of 130 colorectal and breast PT/PDX-early/PDX-late trios confirmed high-resolution CNA retention. We observed no significant enrichment of cancer-related genes in PDX-specific CNAs across models. Moreover, CNA differences between patient and PDX tumors were comparable to variations in multiregion samples within patients. Our study demonstrates the lack of systematic copy number evolution driven by the PDX mouse host.

Published
2021

10. Supplementary Figure 1 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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11. Supplementary Table 1 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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12. Supplementary Table 8 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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13. Supplementary Table 5 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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14. Supplementary Figure 5 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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15. Supplementary Table 2 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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16. Supplementary Table 9 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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17. Supplementary Table 7 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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18. Supplementary Figure 6 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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19. Supplementary Table 3 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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20. Supplementary Methods 1 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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21. Supplementary Figure 3 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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22. Supplementary Table 6 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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23. Supplementary Figure 2 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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24. Supplementary Table 4 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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25. Supplementary Figure 4 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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26. Data from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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27. The EurOPDX Data Portal: an open platform for patient-derived cancer xenograft data sharing and visualization

Author

Dudová, Zdenka, Conte, Nathalie, Mason, Jeremy, Stuchlík, Dalibor, Peša, Radim, Halmagyi, Csaba, Perova, Zinaida, Mosaku, Abayomi, Thorne, Ross, Follette, Alex, Pivarč, Ľuboslav, Šašinka, Radim, Usman, Muhammad, Neuhauser, Steven, Begley, Dale A., Krupke, Debra M., Frassà, Massimiliano, Fiori, Alessandro, Corsi, Riccardo, Vezzadini, Luca, Isella, Claudio, Bertotti, Andrea, Bult, Carol, Parkinson, Helen, Medico, Enzo, Meehan, Terrence, and Křenek, Aleš

Published
2022
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28. Effective drug combinations in breast, colon and pancreatic cancer cells

Author

Jaaks, Patricia, Coker, Elizabeth A., Vis, Daniel J., Edwards, Olivia, Carpenter, Emma F., Leto, Simonetta M., Dwane, Lisa, Sassi, Francesco, Lightfoot, Howard, Barthorpe, Syd, van der Meer, Dieudonne, Yang, Wanjuan, Beck, Alexandra, Mironenko, Tatiana, Hall, Caitlin, Hall, James, Mali, Iman, Richardson, Laura, Tolley, Charlotte, Morris, James, Thomas, Frances, Lleshi, Ermira, Aben, Nanne, Benes, Cyril H., Bertotti, Andrea, Trusolino, Livio, Wessels, Lodewyk, and Garnett, Mathew J.

Published
2022
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29. Chromatin Velocity reveals epigenetic dynamics by single-cell profiling of heterochromatin and euchromatin

Author

Tedesco, Martina, Giannese, Francesca, Lazarević, Dejan, Giansanti, Valentina, Rosano, Dalia, Monzani, Silvia, Catalano, Irene, Grassi, Elena, Zanella, Eugenia R., Botrugno, Oronza A., Morelli, Leonardo, Panina Bordignon, Paola, Caravagna, Giulio, Bertotti, Andrea, Martino, Gianvito, Aldrighetti, Luca, Pasqualato, Sebastiano, Trusolino, Livio, Cittaro, Davide, and Tonon, Giovanni

Published
2022
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30. PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models

Author

Meehan, Terrence F, Conte, Nathalie, Goldstein, Theodore, Inghirami, Giorgio, Murakami, Mark A, Brabetz, Sebastian, Gu, Zhiping, Wiser, Jeffrey A, Dunn, Patrick, Begley, Dale A, Krupke, Debra M, Bertotti, Andrea, Bruna, Alejandra, Brush, Matthew H, Byrne, Annette T, Caldas, Carlos, Christie, Amanda L, Clark, Dominic A, Dowst, Heidi, Dry, Jonathan R, Doroshow, James H, Duchamp, Olivier, Evrard, Yvonne A, Ferretti, Stephane, Frese, Kristopher K, Goodwin, Neal C, Greenawalt, Danielle, Haendel, Melissa A, Hermans, Els, Houghton, Peter J, Jonkers, Jos, Kemper, Kristel, Khor, Tin O, Lewis, Michael T, Lloyd, KC Kent, Mason, Jeremy, Medico, Enzo, Neuhauser, Steven B, Olson, James M, Peeper, Daniel S, Rueda, Oscar M, Seong, Je Kyung, Trusolino, Livio, Vinolo, Emilie, Wechsler-Reya, Robert J, Weinstock, David M, Welm, Alana, Weroha, S John, Amant, Frédéric, Pfister, Stefan M, Kool, Marcel, Parkinson, Helen, Butte, Atul J, and Bult, Carol J

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Cancer, Good Health and Well Being, Animals, Databases as Topic, Disease Models, Animal, Humans, Mice, Neoplasms, Patients, Xenograft Model Antitumor Assays, Oncology & Carcinogenesis, Biochemistry and cell biology, Oncology and carcinogenesis
Abstract

Patient-derived tumor xenograft (PDX) mouse models have emerged as an important oncology research platform to study tumor evolution, mechanisms of drug response and resistance, and tailoring chemotherapeutic approaches for individual patients. The lack of robust standards for reporting on PDX models has hampered the ability of researchers to find relevant PDX models and associated data. Here we present the PDX models minimal information standard (PDX-MI) for reporting on the generation, quality assurance, and use of PDX models. PDX-MI defines the minimal information for describing the clinical attributes of a patient's tumor, the processes of implantation and passaging of tumors in a host mouse strain, quality assurance methods, and the use of PDX models in cancer research. Adherence to PDX-MI standards will facilitate accurate search results for oncology models and their associated data across distributed repository databases and promote reproducibility in research studies using these models. Cancer Res; 77(21); e62-66. ©2017 AACR.

Published
2017

31. Heterogeneity and evolution of DNA mutation rates in microsatellite stable colorectal cancer

Author

Grassi, Elena, primary, Vurchio, Valentina, additional, Cresswell, George David, additional, Catalano, Irene, additional, Lupo, Barbara, additional, Sassi, Francesco, additional, Galimi, Francesco, additional, Borgato, Sofia, additional, Ferri, Martina, additional, Viviani, Marco, additional, Pompei, Simone, additional, Urgese, Gianvito, additional, Chen, Bingjie, additional, Zanella, Eugenia Rosalinda, additional, Cottino, Francesca, additional, Bardelli, Alberto, additional, Cosentino Lagormarsino, Marco, additional, Sottoriva, Andrea, additional, Trusolino, Livio, additional, and Bertotti, Andrea, additional

Published
2024
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32. Pathway level subtyping identifies a slow-cycling and transcriptionally lethargic biological phenotype associated with poor clinical outcomes in colon cancer independent of genetics

Author

Malla, Sudhir B, primary, Byrne, Ryan M, additional, Lafarge, Maxime, additional, Corry, Shania M, additional, Fisher, Natalie C, additional, Tsantoulis, Petros, additional, Campbell, Andrew, additional, Lannagan, Tamsin, additional, Najumudeen, Arafath K, additional, Gilroy, Kathryn, additional, Amirkhah, Raheleh, additional, Maguire, Sarah, additional, Mulholland, Eoghan, additional, Belnoue-Davis, Hayley L, additional, Grassi, Elena, additional, Viviani, Marco, additional, Rogan, Emily, additional, Redmond, Keara, additional, Sakhnevych, Svetlana, additional, McCooey, Aoife, additional, Bull, Courtney, additional, Hoey, Emily, additional, Sinevici, Nicoleta, additional, Hall, Holly, additional, Ahmaderaghi, Baharak, additional, Domingo, Enric, additional, Blake, Andrew, additional, Richman, Susan, additional, Isella, Claudio, additional, Miller, Crispin, additional, Bertotti, Andrea, additional, Trusolino, Livio, additional, Loughrey, Maurice, additional, Kerr, Emma, additional, Tejpar, Sabine, additional, Maughan, Tim, additional, Lawler, Mark, additional, Leedham, Simon J, additional, Koelzer, Viktor H, additional, Sansom, Owen J, additional, and Dunne, Philip D, additional

Published
2024
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36. Quantifying single-cell ERK dynamics in colorectal cancer organoids reveals EGFR as an amplifier of oncogenic MAPK pathway signalling

Author

Ponsioen, Bas, Post, Jasmin B., Buissant des Amorie, Julian R., Laskaris, Dimitrios, van Ineveld, Ravian L., Kersten, Simone, Bertotti, Andrea, Sassi, Francesco, Sipieter, François, Cappe, Benjamin, Mertens, Sander, Verlaan-Klink, Ingrid, Boj, Sylvia F., Vries, Rob G. J., Rehmann, Holger, Vandenabeele, Peter, Riquet, Franck B., Trusolino, Livio, Bos, Johannes L., and Snippert, Hugo J. G.

Published
2021
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41. Phosphoproteomics of patient-derived xenographs identifies targets and markers associated with sensitivity and resistance to EGFR blockade in colorectal cancer

Author

Beekhof, Robin, primary, Bertotti, Andrea, additional, Böttger, Franziska, additional, Vurchio, Valentina, additional, Cottino, Francesca, additional, Zanella, Eugenia R., additional, Migliardi, Giorgia, additional, Viviani, Marco, additional, Grassi, Elena, additional, Lupo, Barbara, additional, Henneman, Alex A., additional, Knol, Jaco C., additional, Pham, Thang V., additional, de Goeij-de Haas, Richard, additional, Piersma, Sander R., additional, Labots, Mariette, additional, Verheul, Henk M.W., additional, Trusolino, Livio, additional, and Jimenez, Connie R., additional

Published
2023
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44. Rituximab Treatment Prevents Lymphoma Onset in Gastric Cancer Patient-Derived Xenografts

Author

Corso, Simona, Cargnelutti, Marilisa, Durando, Stefania, Menegon, Silvia, Apicella, Maria, Migliore, Cristina, Capeloa, Tania, Ughetto, Stefano, Isella, Claudio, Medico, Enzo, Bertotti, Andrea, Sassi, Francesco, Sarotto, Ivana, Casorzo, Laura, Pisacane, Alberto, Mangioni, Monica, Sottile, Antonino, Degiuli, Maurizio, Fumagalli, Uberto, Sgroi, Giovanni, Molfino, Sarah, De Manzoni, Giovanni, Rosati, Riccardo, De Simone, Michele, Marrelli, Daniele, Saragoni, Luca, Rausei, Stefano, Pallabazzer, Giovanni, Roviello, Franco, Cassoni, Paola, Sapino, Anna, Bass, Adam, and Giordano, Silvia

Published
2018
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45. Prioritization of cancer therapeutic targets using CRISPR–Cas9 screens

Author

Behan, Fiona M., Iorio, Francesco, Picco, Gabriele, Gonçalves, Emanuel, Beaver, Charlotte M., Migliardi, Giorgia, Santos, Rita, Rao, Yanhua, Sassi, Francesco, Pinnelli, Marika, Ansari, Rizwan, Harper, Sarah, Jackson, David Adam, McRae, Rebecca, Pooley, Rachel, Wilkinson, Piers, van der Meer, Dieudonne, Dow, David, Buser-Doepner, Carolyn, Bertotti, Andrea, Trusolino, Livio, Stronach, Euan A., Saez-Rodriguez, Julio, Yusa, Kosuke, and Garnett, Mathew J.

Published
2019
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46. CONNECTOR, fitting and clustering of longitudinal data to reveal a new risk stratification system

Author

Pernice, Simone, primary, Sirovich, Roberta, additional, Grassi, Elena, additional, Viviani, Marco, additional, Ferri, Martina, additional, Sassi, Francesco, additional, Alessandrì, Luca, additional, Tortarolo, Dora, additional, Calogero, Raffaele A, additional, Trusolino, Livio, additional, Bertotti, Andrea, additional, Beccuti, Marco, additional, Olivero, Martina, additional, and Cordero, Francesca, additional

Published
2023
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47. Abstract 4327: MSI cancer associated DNA (TA)n-dinucleotide repeat expansions and implications for Werner synthetic lethality

Author

Picco, Gabriele, primary, Bhosle, Shriram, additional, Kalyva, Maria, additional, Grassi, Elena, additional, Gibson, Freddy, additional, Saedi, Angham Al, additional, Vieira, Sara, additional, Sanders, Mathijs, additional, Trusolino, Livio, additional, Bertotti, Andrea, additional, Cortes-Ciriano, Isidro, additional, and Garnett, Mathew, additional

Published
2023
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48. Supplementary Figure S2 from Amplification of the MET Receptor Drives Resistance to Anti-EGFR Therapies in Colorectal Cancer

Author

Bardelli, Alberto, primary, Corso, Simona, primary, Bertotti, Andrea, primary, Hobor, Sebastijan, primary, Valtorta, Emanuele, primary, Siravegna, Giulia, primary, Sartore-Bianchi, Andrea, primary, Scala, Elisa, primary, Cassingena, Andrea, primary, Zecchin, Davide, primary, Apicella, Maria, primary, Migliardi, Giorgia, primary, Galimi, Francesco, primary, Lauricella, Calogero, primary, Zanon, Carlo, primary, Perera, Timothy, primary, Veronese, Silvio, primary, Corti, Giorgio, primary, Amatu, Alessio, primary, Gambacorta, Marcello, primary, Diaz, Luis A., primary, Sausen, Mark, primary, Velculescu, Victor E., primary, Comoglio, Paolo, primary, Trusolino, Livio, primary, Di Nicolantonio, Federica, primary, Giordano, Silvia, primary, and Siena, Salvatore, primary

Published
2023
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49. Supplementary Figure 3 from EGFR Blockade Reverts Resistance to KRASG12C Inhibition in Colorectal Cancer

Author

Amodio, Vito, primary, Yaeger, Rona, primary, Arcella, Pamela, primary, Cancelliere, Carlotta, primary, Lamba, Simona, primary, Lorenzato, Annalisa, primary, Arena, Sabrina, primary, Montone, Monica, primary, Mussolin, Benedetta, primary, Bian, Yu, primary, Whaley, Adele, primary, Pinnelli, Marika, primary, Murciano-Goroff, Yonina R., primary, Vakiani, Efsevia, primary, Valeri, Nicola, primary, Liao, Wei-Li, primary, Bhalkikar, Anuja, primary, Thyparambil, Sheeno, primary, Zhao, Hui-Yong, primary, de Stanchina, Elisa, primary, Marsoni, Silvia, primary, Siena, Salvatore, primary, Bertotti, Andrea, primary, Trusolino, Livio, primary, Li, Bob T., primary, Rosen, Neal, primary, Di Nicolantonio, Federica, primary, Bardelli, Alberto, primary, and Misale, Sandra, primary

Published
2023
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50. Supplementary Table 1 from A Molecularly Annotated Platform of Patient-Derived Xenografts (“Xenopatients”) Identifies HER2 as an Effective Therapeutic Target in Cetuximab-Resistant Colorectal Cancer

Author

Bertotti, Andrea, primary, Migliardi, Giorgia, primary, Galimi, Francesco, primary, Sassi, Francesco, primary, Torti, Davide, primary, Isella, Claudio, primary, Corà, Davide, primary, Di Nicolantonio, Federica, primary, Buscarino, Michela, primary, Petti, Consalvo, primary, Ribero, Dario, primary, Russolillo, Nadia, primary, Muratore, Andrea, primary, Massucco, Paolo, primary, Pisacane, Alberto, primary, Molinaro, Luca, primary, Valtorta, Emanuele, primary, Sartore-Bianchi, Andrea, primary, Risio, Mauro, primary, Capussotti, Lorenzo, primary, Gambacorta, Marcello, primary, Siena, Salvatore, primary, Medico, Enzo, primary, Sapino, Anna, primary, Marsoni, Silvia, primary, Comoglio, Paolo M., primary, Bardelli, Alberto, primary, and Trusolino, Livio, primary

Published
2023
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