Search Results - "BECKSFORT, Jared"

Exploring genomic alteration in pediatric cancer using ProteinPaint by Zhou, Xin, Edmonson, Michael N, Wilkinson, Mark R, Patel, Aman, Wu, Gang, Liu, Yu, Li, Yongjin, Zhang, Zhaojie, Rusch, Michael C, Parker, Matthew, Becksfort, Jared, Downing, James R, Zhang, Jinghui

“…The pediatric data set consists of 27,188 validated somatic coding lesions acquired at diagnosis or relapse from 17 subtypes of pediatric cancer, 252…”
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Clinical cancer genomic profiling by three-platform sequencing of whole genome, whole exome and transcriptome by Rusch, Michael, Nakitandwe, Joy, Shurtleff, Sheila, Newman, Scott, Zhang, Zhaojie, Edmonson, Michael N., Parker, Matthew, Jiao, Yuannian, Ma, Xiaotu, Liu, Yanling, Gu, Jiali, Walsh, Michael F., Becksfort, Jared, Thrasher, Andrew, Li, Yongjin, McMurry, James, Hedlund, Erin, Patel, Aman, Easton, John, Yergeau, Donald, Vadodaria, Bhavin, Tatevossian, Ruth G., Raimondi, Susana, Hedges, Dale, Chen, Xiang, Hagiwara, Kohei, McGee, Rose, Robinson, Giles W., Klco, Jeffery M., Gruber, Tanja A., Ellison, David W., Downing, James R, Zhang, Jinghui

“…To evaluate the potential of an integrated clinical test to detect diverse classes of somatic and germline mutations relevant to pediatric oncology, we…”
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Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): a cloud-based platform for curating and classifying germline variants by Edmonson, Michael N, Patel, Aman N, Hedges, Dale J, Wang, Zhaoming, Rampersaud, Evadnie, Kesserwan, Chimene A, Zhou, Xin, Liu, Yanling, Newman, Scott, Rusch, Michael C, McLeod, Clay L, Wilkinson, Mark R, Rice, Stephen V, Soussi, Thierry, Taylor, J Paul, Benatar, Michael, Becksfort, Jared B, Nichols, Kim E, Robison, Leslie L, Downing, James R, Zhang, Jinghui

“…Variant interpretation in the era of massively parallel sequencing is challenging. Although many resources and guidelines are available to assist with this…”
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A hybrid method of correcting CBCT for proton range estimation with deep learning and deformable image registration by Uh, Jinsoo, Wang, Chuang, Jordan, Jacob A, Pirlepesov, Fakhriddin, Becksfort, Jared B, Ates, Ozgur, Krasin, Matthew J, Hua, Chia-Ho

“… This study aimed to develop a novel method for generating synthetic CT (sCT) from cone-beam CT (CBCT) of the abdomen/pelvis with bowel gas pockets to…”
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Pre- and Posttherapy Risk Factors for Vasculopathy in Pediatric Patients With Craniopharyngioma Treated With Surgery and Proton Radiation Therapy by Lucas, Jr, John T, Faught, Austin M, Hsu, Chih Yang, Wilson, Lydia J, Guo, Yian, Li, Yimei, Khan, Raja, Becksfort, Jared B, LeVine, David A, Ismael, Yousef, Darrow, Kaleb, Moskvin, Vadim P, Pirlepesov, Fakhriddin, Klimo, Paul, Elijovich, Lucas, Indelicato, Daniel J, Boop, Fredrick A, Merchant, Thomas E

“…Vasculopathy (VAS) is a significant complication associated with radiation therapy in patients treated for brain tumors. We studied the type, location,…”
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Tyrosine kinome sequencing of pediatric acute lymphoblastic leukemia: a report from the Children's Oncology Group TARGET Project by Loh, Mignon L, Zhang, Jinghui, Harvey, Richard C, Roberts, Kathryn, Payne-Turner, Debbie, Kang, Huining, Wu, Gang, Chen, Xiang, Becksfort, Jared, Edmonson, Michael, Buetow, Kenneth H, Carroll, William L, Chen, I-Ming, Wood, Brent, Borowitz, Michael J, Devidas, Meenakshi, Gerhard, Daniela S, Bowman, Paul, Larsen, Eric, Winick, Naomi, Raetz, Elizabeth, Smith, Malcolm, Downing, James R, Willman, Cheryl L, Mullighan, Charles G, Hunger, Stephen P

“…One recently identified subtype of pediatric B-precursor acute lymphoblastic leukemia (ALL) has been termed BCR-ABL1-like or Ph-like because of similarity of…”
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Comparative Analysis of Atlas and Neural Network Autosegmentation Methods for Pediatric Craniospinal Irradiation With the Development of a Knowledge-Based Quality Assurance Tool by Ates, Ozgur, Tsui, James Man Git, Wooten, Zachary, Hutcheson, Sydney, Zhang, Rico, Becksfort, Jared, Merchant, Thomas E., Hua, Chia-ho

“…This study aims to evaluate the performance of Atlas and neural network autosegmentation methods and develop a knowledge-based quality assurance (QA) tool for…”
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Revised clinical and molecular risk strata define the incidence and pattern of failure in medulloblastoma following risk-adapted radiotherapy and dose-intensive chemotherapy: results from a phase III multi-institutional study by Lucas, John T, Tinkle, Christopher L, Huang, Jie, Onar-Thomas, Arzu, Srinivasan, Sudharsan, Tumlin, Parker, Becksfort, Jared B, Klimo, Paul, Boop, Frederick A, Robinson, Giles W, Orr, Brent A, Harreld, Julie H, Krasin, Matthew J, Northcott, Paul A, Ellison, David W, Gajjar, Amar, Merchant, Thomas E

“…We characterize the patterns of progression across medulloblastoma (MB) clinical risk and molecular subgroups from SJMB03, a Phase III clinical trial. One…”
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Germline Mutations in Predisposition Genes in Pediatric Cancer by Zhang, Jinghui, Walsh, Michael F, Wu, Gang, Edmonson, Michael N, Gruber, Tanja A, Easton, John, Hedges, Dale, Ma, Xiaotu, Zhou, Xin, Yergeau, Donald A, Wilkinson, Mark R, Vadodaria, Bhavin, Chen, Xiang, McGee, Rose B, Hines-Dowell, Stacy, Nuccio, Regina, Quinn, Emily, Shurtleff, Sheila A, Rusch, Michael, Patel, Aman, Becksfort, Jared B, Wang, Shuoguo, Weaver, Meaghann S, Ding, Li, Mardis, Elaine R, Wilson, Richard K, Gajjar, Amar, Ellison, David W, Pappo, Alberto S, Pui, Ching-Hon, Nichols, Kim E, Downing, James R

“…A constitutive mutation in a cancer-susceptibility gene can have implications for clinical treatment and genetic counseling of family members. This study…”
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RB1 gene inactivation by chromothripsis in human retinoblastoma by McEvoy, Justina, Nagahawatte, Panduka, Finkelstein, David, Richards-Yutz, Jennifer, Valentine, Marcus, Ma, Jing, Mullighan, Charles, Song, Guangchun, Chen, Xiang, Wilson, Matthew, Brennan, Rachel, Pounds, Stanley, Becksfort, Jared, Huether, Robert, Lu, Charles, Fulton, Robert S, Fulton, Lucinda L, Hong, Xin, Dooling, David J, Ochoa, Kerri, Mardis, Elaine R, Wilson, Richard K, Easton, John, Zhang, Jinghui, Downing, James R, Ganguly, Arupa, Dyer, Michael A

“…Retinoblastoma is a rare childhood cancer of the developing retina. Most retinoblastomas initiate with biallelic inactivation of the RB1 gene through diverse…”
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Contrasting roles of histone 3 lysine 27 demethylases in acute lymphoblastic leukaemia by Ntziachristos, Panagiotis, Tsirigos, Aristotelis, Welstead, G. Grant, Trimarchi, Thomas, Bakogianni, Sofia, Xu, Luyao, Loizou, Evangelia, Holmfeldt, Linda, Strikoudis, Alexandros, King, Bryan, Mullenders, Jasper, Becksfort, Jared, Nedjic, Jelena, Paietta, Elisabeth, Tallman, Martin S., Rowe, Jacob M., Tonon, Giovanni, Satoh, Takashi, Kruidenier, Laurens, Prinjha, Rab, Akira, Shizuo, Van Vlierberghe, Pieter, Ferrando, Adolfo A., Jaenisch, Rudolf, Mullighan, Charles G., Aifantis, Iannis

“…T-cell acute lymphoblastic leukaemia (T-ALL) is a haematological malignancy with a poor prognosis and no available targeted therapies; now two histone H3…”
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The genomic landscape of diffuse intrinsic pontine glioma and pediatric non-brainstem high-grade glioma by Wu, Gang, Diaz, Alexander K, Paugh, Barbara S, Rankin, Sherri L, Ju, Bensheng, Li, Yongjin, Zhu, Xiaoyan, Qu, Chunxu, Chen, Xiang, Zhang, Junyuan, Easton, John, Edmonson, Michael, Ma, Xiaotu, Lu, Charles, Nagahawatte, Panduka, Hedlund, Erin, Rusch, Michael, Pounds, Stanley, Lin, Tong, Onar-Thomas, Arzu, Huether, Robert, Kriwacki, Richard, Parker, Matthew, Gupta, Pankaj, Becksfort, Jared, Wei, Lei, Mulder, Heather L, Boggs, Kristy, Vadodaria, Bhavin, Yergeau, Donald, Russell, Jake C, Ochoa, Kerri, Fulton, Robert S, Fulton, Lucinda L, Jones, Chris, Boop, Frederick A, Broniscer, Alberto, Wetmore, Cynthia, Gajjar, Amar, Ding, Li, Mardis, Elaine R, Wilson, Richard K, Taylor, Michael R, Downing, James R, Ellison, David W, Zhang, Jinghui, Baker, Suzanne J

“…Suzanne Baker, Jinghui Zhang and colleagues report the identification of recurrent somatic mutations in the bone morphogenetic protein (BMP) receptor ACVR1 in…”
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Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and non-brainstem glioblastomas by GANG WU, BRONISCER, Alberto, JUNYUAN ZHANG, GAJJAR, Amar, DYER, Michael A, MULLIGHAN, Charles G, GILBERTSON, Richard J, MARDIS, Elaine R, WILSON, Richard K, DOWNING, James R, ELLISON, David W, JINGHUI ZHANG, MCEACHRON, Troy A, BAKER, Suzanne J, LU, Charles, PAUGH, Barbara S, BECKSFORT, Jared, CHUNXU QU, LI DING, HUETHER, Robert, PARKER, Matthew

“…Suzanne Baker and colleagues sequenced the whole genomes of seven pediatric brainstem glioblastomas and matched normal tissue. They found that 78% of diffuse…”
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Targetable Kinase-Activating Lesions in Ph-like Acute Lymphoblastic Leukemia by Roberts, Kathryn G, Li, Yongjin, Payne-Turner, Debbie, Harvey, Richard C, Yang, Yung-Li, Pei, Deqing, McCastlain, Kelly, Ding, Li, Lu, Charles, Song, Guangchun, Ma, Jing, Becksfort, Jared, Rusch, Michael, Chen, Shann-Ching, Easton, John, Cheng, Jinjun, Boggs, Kristy, Santiago-Morales, Natalia, Iacobucci, Ilaria, Fulton, Robert S, Wen, Ji, Valentine, Marcus, Cheng, Cheng, Paugh, Steven W, Devidas, Meenakshi, Chen, I-Ming, Reshmi, Shalini, Smith, Amy, Hedlund, Erin, Gupta, Pankaj, Nagahawatte, Panduka, Wu, Gang, Chen, Xiang, Yergeau, Donald, Vadodaria, Bhavin, Mulder, Heather, Winick, Naomi J, Larsen, Eric C, Carroll, William L, Heerema, Nyla A, Carroll, Andrew J, Grayson, Guy, Tasian, Sarah K, Moore, Andrew S, Keller, Frank, Frei-Jones, Melissa, Whitlock, James A, Raetz, Elizabeth A, White, Deborah L, Hughes, Timothy P, Guidry Auvil, Jaime M, Smith, Malcolm A, Marcucci, Guido, Bloomfield, Clara D, Mrózek, Krzysztof, Kohlschmidt, Jessica, Stock, Wendy, Kornblau, Steven M, Konopleva, Marina, Paietta, Elisabeth, Pui, Ching-Hon, Jeha, Sima, Relling, Mary V, Evans, William E, Gerhard, Daniela S, Gastier-Foster, Julie M, Mardis, Elaine, Wilson, Richard K, Loh, Mignon L, Downing, James R, Hunger, Stephen P, Willman, Cheryl L, Zhang, Jinghui, Mullighan, Charles G

“…About 25% of young adults with ALL have Ph-like genotypes, which are associated with poor outcomes with conventional treatment. In this gene-expression study,…”
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The landscape of somatic mutations in infant MLL-rearranged acute lymphoblastic leukemias by Andersson, Anna K, Ma, Jing, Wang, Jianmin, Chen, Xiang, Gedman, Amanda Larson, Dang, Jinjun, Nakitandwe, Joy, Holmfeldt, Linda, Parker, Matthew, Easton, John, Huether, Robert, Kriwacki, Richard, Rusch, Michael, Wu, Gang, Li, Yongjin, Mulder, Heather, Raimondi, Susana, Pounds, Stanley, Kang, Guolian, Shi, Lei, Becksfort, Jared, Gupta, Pankaj, Payne-Turner, Debbie, Vadodaria, Bhavin, Boggs, Kristy, Yergeau, Donald, Manne, Jayanthi, Song, Guangchun, Edmonson, Michael, Nagahawatte, Panduka, Wei, Lei, Cheng, Cheng, Pei, Deqing, Sutton, Rosemary, Venn, Nicola C, Chetcuti, Albert, Rush, Amanda, Catchpoole, Daniel, Heldrup, Jesper, Fioretos, Thoas, Lu, Charles, Ding, Li, Pui, Ching-Hon, Shurtleff, Sheila, Mullighan, Charles G, Mardis, Elaine R, Wilson, Richard K, Gruber, Tanja A, Zhang, Jinghui, Downing, James R

“…Anna Andersson, Tanja Gruber, James Downing and colleagues report a genomic analysis of infant acute lymphoblastic leukemias with MLL rearrangements. They…”
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C11orf95–RELA fusions drive oncogenic NF-κB signalling in ependymoma by Parker, Matthew, Mohankumar, Kumarasamypet M., Punchihewa, Chandanamali, Weinlich, Ricardo, Dalton, James D., Li, Yongjin, Lee, Ryan, Tatevossian, Ruth G., Phoenix, Timothy N., Thiruvenkatam, Radhika, White, Elsie, Tang, Bo, Orisme, Wilda, Gupta, Kirti, Rusch, Michael, Chen, Xiang, Li, Yuxin, Nagahawhatte, Panduka, Hedlund, Erin, Finkelstein, David, Wu, Gang, Shurtleff, Sheila, Easton, John, Boggs, Kristy, Yergeau, Donald, Vadodaria, Bhavin, Mulder, Heather L., Becksfort, Jared, Gupta, Pankaj, Huether, Robert, Ma, Jing, Song, Guangchun, Gajjar, Amar, Merchant, Thomas, Boop, Frederick, Smith, Amy A., Ding, Li, Lu, Charles, Ochoa, Kerri, Zhao, David, Fulton, Robert S., Fulton, Lucinda L., Mardis, Elaine R., Wilson, Richard K., Downing, James R., Green, Douglas R., Zhang, Jinghui, Ellison, David W., Gilbertson, Richard J.

“…Members of the nuclear factor-κB (NF-κB) family of transcriptional regulators are central mediators of the cellular inflammatory response. Although…”
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Genetic alterations in uncommon low-grade neuroepithelial tumors: BRAF, FGFR1, and MYB mutations occur at high frequency and align with morphology by Qaddoumi, Ibrahim, Orisme, Wilda, Wen, Ji, Santiago, Teresa, Gupta, Kirti, Dalton, James D., Tang, Bo, Haupfear, Kelly, Punchihewa, Chandanamali, Easton, John, Mulder, Heather, Boggs, Kristy, Shao, Ying, Rusch, Michael, Becksfort, Jared, Gupta, Pankaj, Wang, Shuoguo, Lee, Ryan P., Brat, Daniel, Peter Collins, V., Dahiya, Sonika, George, David, Konomos, William, Kurian, Kathreena M., McFadden, Kathryn, Serafini, Luciano Neder, Nickols, Hilary, Perry, Arie, Shurtleff, Sheila, Gajjar, Amar, Boop, Fredrick A., Klimo, Paul D., Mardis, Elaine R., Wilson, Richard K., Baker, Suzanne J., Zhang, Jinghui, Wu, Gang, Downing, James R., Tatevossian, Ruth G., Ellison, David W.

“…Low-grade neuroepithelial tumors (LGNTs) are diverse CNS tumors presenting in children and young adults, often with a history of epilepsy. While the genetic…”
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Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas by Zhang, Jinghui, Wu, Gang, Miller, Claudia P, Tatevossian, Ruth G, Dalton, James D, Tang, Bo, Orisme, Wilda, Punchihewa, Chandanamali, Parker, Matthew, Qaddoumi, Ibrahim, Boop, Fredrick A, Lu, Charles, Kandoth, Cyriac, Ding, Li, Lee, Ryan, Huether, Robert, Chen, Xiang, Hedlund, Erin, Nagahawatte, Panduka, Rusch, Michael, Boggs, Kristy, Cheng, Jinjun, Becksfort, Jared, Ma, Jing, Song, Guangchun, Li, Yongjin, Wei, Lei, Wang, Jianmin, Shurtleff, Sheila, Easton, John, Zhao, David, Fulton, Robert S, Fulton, Lucinda L, Dooling, David J, Vadodaria, Bhavin, Mulder, Heather L, Tang, Chunlao, Ochoa, Kerri, Mullighan, Charles G, Gajjar, Amar, Kriwacki, Richard, Sheer, Denise, Gilbertson, Richard J, Mardis, Elaine R, Wilson, Richard K, Downing, James R, Baker, Suzanne J, Ellison, David W

“…David Ellison and colleagues report whole-genome sequencing of pediatric low-grade gliomas, the most common pediatric brain tumor. They identify a range of…”
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Outcomes of children with BCR-ABL1–like acute lymphoblastic leukemia treated with risk-directed therapy based on the levels of minimal residual disease by Roberts, Kathryn G, Pei, Deqing, Campana, Dario, Payne-Turner, Debbie, Li, Yongjin, Cheng, Cheng, Sandlund, John T, Jeha, Sima, Easton, John, Becksfort, Jared, Zhang, Jinghui, Coustan-Smith, Elaine, Raimondi, Susana C, Leung, Wing H, Relling, Mary V, Evans, William E, Downing, James R, Mullighan, Charles G, Pui, Ching-Hon

“…BCR-ABL1–like acute lymphoblastic leukemia (ALL) is a recently identified B-cell ALL (B-ALL)subtype with poor outcome that exhibits a gene expression profile…”
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The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes by Huether, Robert, Dong, Li, Chen, Xiang, Wu, Gang, Parker, Matthew, Wei, Lei, Ma, Jing, Edmonson, Michael N., Hedlund, Erin K., Rusch, Michael C., Shurtleff, Sheila A., Mulder, Heather L., Boggs, Kristy, Vadordaria, Bhavin, Cheng, Jinjun, Yergeau, Donald, Song, Guangchun, Becksfort, Jared, Lemmon, Gordon, Weber, Catherine, Cai, Zhongling, Dang, Jinjun, Walsh, Michael, Gedman, Amanda L., Faber, Zachary, Easton, John, Gruber, Tanja, Kriwacki, Richard W., Partridge, Janet F., Ding, Li, Wilson, Richard K., Mardis, Elaine R., Mullighan, Charles G., Gilbertson, Richard J., Baker, Suzanne J., Zambetti, Gerard, Ellison, David W., Zhang, Jinghui, Downing, James R.

“…Studies of paediatric cancers have shown a high frequency of mutation across epigenetic regulators. Here we sequence 633 genes, encoding the majority of known…”
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