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Genomes for Kids: The Scope of Pathogenic Mutations in Pediatric Cancer Revealed by Comprehensive DNA and RNA Sequencing.
Newman S, Nakitandwe J, Kesserwan CA, Azzato EM, Wheeler DA, Rusch M, Shurtleff S, Hedges DJ, Hamilton KV, Foy SG, Edmonson MN, Thrasher A, Bahrami A, Orr BA, Klco JM, Gu J, Harrison LW, Wang L, Clay MR, Ouma A, Silkov A, Liu Y, Zhang Z, Liu Y, Brady SW, Zhou X, Chang TC, Pande M, Davis E, Becksfort J, Patel A, Wilkinson MR, Rahbarinia D, Kubal M, Maciaszek JL, Pastor V, Knight J, Gout AM, Wang J, Gu Z, Mullighan CG, McGee RB, Quinn EA, Nuccio R, Mostafavi R, Gerhardt EL, Taylor LM, Valdez JM, Hines-Dowell SJ, Pappo AS, Robinson G, Johnson LM, Pui CH, Ellison DW, Downing JR, Zhang J, Nichols KE. Newman S, et al. Among authors: liu y. Cancer Discov. 2021 Dec 1;11(12):3008-3027. doi: 10.1158/2159-8290.CD-20-1631. Cancer Discov. 2021. PMID: 34301788 Free PMC article.
Deregulation of DUX4 and ERG in acute lymphoblastic leukemia.
Zhang J, McCastlain K, Yoshihara H, Xu B, Chang Y, Churchman ML, Wu G, Li Y, Wei L, Iacobucci I, Liu Y, Qu C, Wen J, Edmonson M, Payne-Turner D, Kaufmann KB, Takayanagi SI, Wienholds E, Waanders E, Ntziachristos P, Bakogianni S, Wang J, Aifantis I, Roberts KG, Ma J, Song G, Easton J, Mulder HL, Chen X, Newman S, Ma X, Rusch M, Gupta P, Boggs K, Vadodaria B, Dalton J, Liu Y, Valentine ML, Ding L, Lu C, Fulton RS, Fulton L, Tabib Y, Ochoa K, Devidas M, Pei D, Cheng C, Yang J, Evans WE, Relling MV, Pui CH, Jeha S, Harvey RC, Chen IL, Willman CL, Marcucci G, Bloomfield CD, Kohlschmidt J, Mrózek K, Paietta E, Tallman MS, Stock W, Foster MC, Racevskis J, Rowe JM, Luger S, Kornblau SM, Shurtleff SA, Raimondi SC, Mardis ER, Wilson RK, Dick JE, Hunger SP, Loh ML, Downing JR, Mullighan CG; St. Jude Children's Research Hospital–Washington University Pediatric Cancer Genome Project. Zhang J, et al. Among authors: liu y. Nat Genet. 2016 Dec;48(12):1481-1489. doi: 10.1038/ng.3691. Epub 2016 Oct 24. Nat Genet. 2016. PMID: 27776115 Free PMC article.
The whole-genome landscape of medulloblastoma subtypes.
Northcott PA, Buchhalter I, Morrissy AS, Hovestadt V, Weischenfeldt J, Ehrenberger T, Gröbner S, Segura-Wang M, Zichner T, Rudneva VA, Warnatz HJ, Sidiropoulos N, Phillips AH, Schumacher S, Kleinheinz K, Waszak SM, Erkek S, Jones DTW, Worst BC, Kool M, Zapatka M, Jäger N, Chavez L, Hutter B, Bieg M, Paramasivam N, Heinold M, Gu Z, Ishaque N, Jäger-Schmidt C, Imbusch CD, Jugold A, Hübschmann D, Risch T, Amstislavskiy V, Gonzalez FGR, Weber UD, Wolf S, Robinson GW, Zhou X, Wu G, Finkelstein D, Liu Y, Cavalli FMG, Luu B, Ramaswamy V, Wu X, Koster J, Ryzhova M, Cho YJ, Pomeroy SL, Herold-Mende C, Schuhmann M, Ebinger M, Liau LM, Mora J, McLendon RE, Jabado N, Kumabe T, Chuah E, Ma Y, Moore RA, Mungall AJ, Mungall KL, Thiessen N, Tse K, Wong T, Jones SJM, Witt O, Milde T, Von Deimling A, Capper D, Korshunov A, Yaspo ML, Kriwacki R, Gajjar A, Zhang J, Beroukhim R, Fraenkel E, Korbel JO, Brors B, Schlesner M, Eils R, Marra MA, Pfister SM, Taylor MD, Lichter P. Northcott PA, et al. Among authors: liu y. Nature. 2017 Jul 19;547(7663):311-317. doi: 10.1038/nature22973. Nature. 2017. PMID: 28726821 Free PMC article.
The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions.
Bolouri H, Farrar JE, Triche T Jr, Ries RE, Lim EL, Alonzo TA, Ma Y, Moore R, Mungall AJ, Marra MA, Zhang J, Ma X, Liu Y, Liu Y, Auvil JMG, Davidsen TM, Gesuwan P, Hermida LC, Salhia B, Capone S, Ramsingh G, Zwaan CM, Noort S, Piccolo SR, Kolb EA, Gamis AS, Smith MA, Gerhard DS, Meshinchi S. Bolouri H, et al. Among authors: liu y. Nat Med. 2018 Jan;24(1):103-112. doi: 10.1038/nm.4439. Epub 2017 Dec 11. Nat Med. 2018. PMID: 29227476 Free PMC article.
The landscape of genomic alterations across childhood cancers.
Gröbner SN, Worst BC, Weischenfeldt J, Buchhalter I, Kleinheinz K, Rudneva VA, Johann PD, Balasubramanian GP, Segura-Wang M, Brabetz S, Bender S, Hutter B, Sturm D, Pfaff E, Hübschmann D, Zipprich G, Heinold M, Eils J, Lawerenz C, Erkek S, Lambo S, Waszak S, Blattmann C, Borkhardt A, Kuhlen M, Eggert A, Fulda S, Gessler M, Wegert J, Kappler R, Baumhoer D, Burdach S, Kirschner-Schwabe R, Kontny U, Kulozik AE, Lohmann D, Hettmer S, Eckert C, Bielack S, Nathrath M, Niemeyer C, Richter GH, Schulte J, Siebert R, Westermann F, Molenaar JJ, Vassal G, Witt H; ICGC PedBrain-Seq Project; ICGC MMML-Seq Project; Burkhardt B, Kratz CP, Witt O, van Tilburg CM, Kramm CM, Fleischhack G, Dirksen U, Rutkowski S, Frühwald M, von Hoff K, Wolf S, Klingebiel T, Koscielniak E, Landgraf P, Koster J, Resnick AC, Zhang J, Liu Y, Zhou X, Waanders AJ, Zwijnenburg DA, Raman P, Brors B, Weber UD, Northcott PA, Pajtler KW, Kool M, Piro RM, Korbel JO, Schlesner M, Eils R, Jones DTW, Lichter P, Chavez L, Zapatka M, Pfister SM. Gröbner SN, et al. Among authors: liu y. Nature. 2018 Mar 15;555(7696):321-327. doi: 10.1038/nature25480. Epub 2018 Feb 28. Nature. 2018. PMID: 29489754
Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours.
Ma X, Liu Y, Liu Y, Alexandrov LB, Edmonson MN, Gawad C, Zhou X, Li Y, Rusch MC, Easton J, Huether R, Gonzalez-Pena V, Wilkinson MR, Hermida LC, Davis S, Sioson E, Pounds S, Cao X, Ries RE, Wang Z, Chen X, Dong L, Diskin SJ, Smith MA, Guidry Auvil JM, Meltzer PS, Lau CC, Perlman EJ, Maris JM, Meshinchi S, Hunger SP, Gerhard DS, Zhang J. Ma X, et al. Among authors: liu y. Nature. 2018 Mar 15;555(7696):371-376. doi: 10.1038/nature25795. Epub 2018 Feb 28. Nature. 2018. PMID: 29489755 Free PMC article.
Clinical cancer genomic profiling by three-platform sequencing of whole genome, whole exome and transcriptome.
Rusch M, Nakitandwe J, Shurtleff S, Newman S, Zhang Z, Edmonson MN, Parker M, Jiao Y, Ma X, Liu Y, Gu J, Walsh MF, Becksfort J, Thrasher A, Li Y, McMurry J, Hedlund E, Patel A, Easton J, Yergeau D, Vadodaria B, Tatevossian RG, Raimondi S, Hedges D, Chen X, Hagiwara K, McGee R, Robinson GW, Klco JM, Gruber TA, Ellison DW, Downing JR, Zhang J. Rusch M, et al. Among authors: liu y. Nat Commun. 2018 Sep 27;9(1):3962. doi: 10.1038/s41467-018-06485-7. Nat Commun. 2018. PMID: 30262806 Free PMC article.
Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): a cloud-based platform for curating and classifying germline variants.
Edmonson MN, Patel AN, Hedges DJ, Wang Z, Rampersaud E, Kesserwan CA, Zhou X, Liu Y, Newman S, Rusch MC, McLeod CL, Wilkinson MR, Rice SV, Soussi T, Taylor JP, Benatar M, Becksfort JB, Nichols KE, Robison LL, Downing JR, Zhang J. Edmonson MN, et al. Among authors: liu y. Genome Res. 2019 Sep;29(9):1555-1565. doi: 10.1101/gr.250357.119. Epub 2019 Aug 22. Genome Res. 2019. PMID: 31439692 Free PMC article.
Therapy-induced mutations drive the genomic landscape of relapsed acute lymphoblastic leukemia.
Li B, Brady SW, Ma X, Shen S, Zhang Y, Li Y, Szlachta K, Dong L, Liu Y, Yang F, Wang N, Flasch DA, Myers MA, Mulder HL, Ding L, Liu Y, Tian L, Hagiwara K, Xu K, Zhou X, Sioson E, Wang T, Yang L, Zhao J, Zhang H, Shao Y, Sun H, Sun L, Cai J, Sun HY, Lin TN, Du L, Li H, Rusch M, Edmonson MN, Easton J, Zhu X, Zhang J, Cheng C, Raphael BJ, Tang J, Downing JR, Alexandrov LB, Zhou BS, Pui CH, Yang JJ, Zhang J. Li B, et al. Among authors: liu y. Blood. 2020 Jan 2;135(1):41-55. doi: 10.1182/blood.2019002220. Blood. 2020. PMID: 31697823 Free PMC article.
MYCN amplification and ATRX mutations are incompatible in neuroblastoma.
Zeineldin M, Federico S, Chen X, Fan Y, Xu B, Stewart E, Zhou X, Jeon J, Griffiths L, Nguyen R, Norrie J, Easton J, Mulder H, Yergeau D, Liu Y, Wu J, Van Ryn C, Naranjo A, Hogarty MD, Kamiński MM, Valentine M, Pruett-Miller SM, Pappo A, Zhang J, Clay MR, Bahrami A, Vogel P, Lee S, Shelat A, Sarthy JF, Meers MP, George RE, Mardis ER, Wilson RK, Henikoff S, Downing JR, Dyer MA. Zeineldin M, et al. Among authors: liu y. Nat Commun. 2020 Feb 14;11(1):913. doi: 10.1038/s41467-020-14682-6. Nat Commun. 2020. PMID: 32060267 Free PMC article.
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