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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: patel a. 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.
Germline Mutations in Predisposition Genes in Pediatric Cancer.
Zhang J, Walsh MF, Wu G, Edmonson MN, Gruber TA, Easton J, Hedges D, Ma X, Zhou X, Yergeau DA, Wilkinson MR, Vadodaria B, Chen X, McGee RB, Hines-Dowell S, Nuccio R, Quinn E, Shurtleff SA, Rusch M, Patel A, Becksfort JB, Wang S, Weaver MS, Ding L, Mardis ER, Wilson RK, Gajjar A, Ellison DW, Pappo AS, Pui CH, Nichols KE, Downing JR. Zhang J, et al. Among authors: patel a. N Engl J Med. 2015 Dec 10;373(24):2336-2346. doi: 10.1056/NEJMoa1508054. Epub 2015 Nov 18. N Engl J Med. 2015. PMID: 26580448 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: patel a. Nat Commun. 2018 Sep 27;9(1):3962. doi: 10.1038/s41467-018-06485-7. Nat Commun. 2018. PMID: 30262806 Free PMC article.
St. Jude Cloud: A Pediatric Cancer Genomic Data-Sharing Ecosystem.
McLeod C, Gout AM, Zhou X, Thrasher A, Rahbarinia D, Brady SW, Macias M, Birch K, Finkelstein D, Sunny J, Mudunuri R, Orr BA, Treadway M, Davidson B, Ard TK, Chiao A, Swistak A, Wiggins S, Foy S, Wang J, Sioson E, Wang S, Michael JR, Liu Y, Ma X, Patel A, Edmonson MN, Wilkinson MR, Frantz AM, Chang TC, Tian L, Lei S, Islam SMA, Meyer C, Thangaraj N, Tater P, Kandali V, Ma S, Nguyen T, Serang O, McGuire I, Robison N, Gentry D, Tang X, Palmer LE, Wu G, Suh E, Tanner L, McMurry J, Lear M, Pappo AS, Wang Z, Wilson CL, Cheng Y, Meshinchi S, Alexandrov LB, Weiss MJ, Armstrong GT, Robison LL, Yasui Y, Nichols KE, Ellison DW, Bangur C, Mullighan CG, Baker SJ, Dyer MA, Miller G, Newman S, Rusch M, Daly R, Perry K, Downing JR, Zhang J. McLeod C, et al. Among authors: patel a. Cancer Discov. 2021 May;11(5):1082-1099. doi: 10.1158/2159-8290.CD-20-1230. Epub 2021 Jan 6. Cancer Discov. 2021. PMID: 33408242 Free PMC article.
CONSERTING: integrating copy-number analysis with structural-variation detection.
Chen X, Gupta P, Wang J, Nakitandwe J, Roberts K, Dalton JD, Parker M, Patel S, Holmfeldt L, Payne D, Easton J, Ma J, Rusch M, Wu G, Patel A, Baker SJ, Dyer MA, Shurtleff S, Espy S, Pounds S, Downing JR, Ellison DW, Mullighan CG, Zhang J. Chen X, et al. Among authors: patel a, patel s. Nat Methods. 2015 Jun;12(6):527-30. doi: 10.1038/nmeth.3394. Epub 2015 May 4. Nat Methods. 2015. PMID: 25938371 Free PMC article.
Exploring genomic alteration in pediatric cancer using ProteinPaint.
Zhou X, Edmonson MN, Wilkinson MR, Patel A, Wu G, Liu Y, Li Y, Zhang Z, Rusch MC, Parker M, Becksfort J, Downing JR, Zhang J. Zhou X, et al. Among authors: patel a. Nat Genet. 2016 Jan;48(1):4-6. doi: 10.1038/ng.3466. Nat Genet. 2016. PMID: 26711108 Free PMC article. No abstract available.
Genetic Risk for Subsequent Neoplasms Among Long-Term Survivors of Childhood Cancer.
Wang Z, Wilson CL, Easton J, Thrasher A, Mulder H, Liu Q, Hedges DJ, Wang S, Rusch MC, Edmonson MN, Levy S, Lanctot JQ, Caron E, Shelton K, Currie K, Lear M, Patel A, Rosencrance C, Shao Y, Vadodaria B, Yergeau D, Sapkota Y, Brooke RJ, Moon W, Rampersaud E, Ma X, Chang TC, Rice SV, Pepper C, Zhou X, Chen X, Chen W, Jones A, Boone B, Ehrhardt MJ, Krasin MJ, Howell RM, Phillips NS, Lewis C, Srivastava D, Pui CH, Kesserwan CA, Wu G, Nichols KE, Downing JR, Hudson MM, Yasui Y, Robison LL, Zhang J. Wang Z, et al. Among authors: patel a. J Clin Oncol. 2018 Jul 10;36(20):2078-2087. doi: 10.1200/JCO.2018.77.8589. Epub 2018 May 30. J Clin Oncol. 2018. PMID: 29847298 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: patel an. 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.
Enrichment of heterozygous germline RECQL4 loss-of-function variants in pediatric osteosarcoma.
Maciaszek JL, Oak N, Chen W, Hamilton KV, McGee RB, Nuccio R, Mostafavi R, Hines-Dowell S, Harrison L, Taylor L, Gerhardt EL, Ouma A, Edmonson MN, Patel A, Nakitandwe J, Pappo AS, Azzato EM, Shurtleff SA, Ellison DW, Downing JR, Hudson MM, Robison LL, Santana V, Newman S, Zhang J, Wang Z, Wu G, Nichols KE, Kesserwan CA. Maciaszek JL, et al. Among authors: patel a. Cold Spring Harb Mol Case Stud. 2019 Oct 23;5(5):a004218. doi: 10.1101/mcs.a004218. Print 2019 Oct. Cold Spring Harb Mol Case Stud. 2019. PMID: 31604778 Free PMC article.
Estimated number of adult survivors of childhood cancer in United States with cancer-predisposing germline variants.
Wilson CL, Wang Z, Liu Q, Ehrhardt MJ, Mostafavi R, Easton J, Mulder H, Hedges DJ, Wang S, Rusch M, Edmonson M, Levy S, Lanctot JQ, Currie K, Lear M, Patel A, Sapkota Y, Brooke RJ, Moon W, Chang TC, Chen W, Kesserwan CA, Wu G, Nichols KE, Hudson MM, Zhang J, Robison LL, Yasui Y. Wilson CL, et al. Among authors: patel a. Pediatr Blood Cancer. 2020 Feb;67(2):e28047. doi: 10.1002/pbc.28047. Epub 2019 Nov 17. Pediatr Blood Cancer. 2020. PMID: 31736278 Free PMC article.
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