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Items: 1 to 20 of 337

1.

Precision oncogenomics.

Ferreira-Gonzalez A, Mardis ER.

Cold Spring Harb Mol Case Stud. 2019 Apr 1;5(2). pii: a004150. doi: 10.1101/mcs.a004150. Print 2019 Apr. No abstract available.

2.

Detection of neoantigen-specific T cells following a personalized vaccine in a patient with glioblastoma.

Johanns TM, Miller CA, Liu CJ, Perrin RJ, Bender D, Kobayashi DK, Campian JL, Chicoine MR, Dacey RG, Huang J, Fritsch EF, Gillanders WE, Artyomov MN, Mardis ER, Schreiber RD, Dunn GP.

Oncoimmunology. 2019 Jan 25;8(4):e1561106. doi: 10.1080/2162402X.2018.1561106. eCollection 2019.

3.

No evidence that G6PD deficiency affects the efficacy or safety of daunorubicin in acute lymphoblastic leukemia induction therapy.

Robinson KM, Yang W, Karol SE, Kornegay N, Jay D, Cheng C, Choi JK, Campana D, Pui CH, Wood B, Borowitz MJ, Gastier-Foster J, Larsen EC, Winick N, Carroll WL, Loh ML, Raetz EA, Hunger SP, Devidas M, Mardis ER, Fulton RS, Relling MV, Jeha S.

Pediatr Blood Cancer. 2019 Jun;66(6):e27681. doi: 10.1002/pbc.27681. Epub 2019 Mar 7.

PMID:
30848065
4.

The Clonal Evolution of Metastatic Osteosarcoma as Shaped by Cisplatin Treatment.

Brady SW, Ma X, Bahrami A, Satas G, Wu G, Newman S, Rusch M, Putnam DK, Mulder HL, Yergeau DA, Edmonson MN, Easton J, Alexandrov LB, Chen X, Mardis ER, Wilson RK, Downing JR, Pappo AS, Raphael BJ, Dyer MA, Zhang J.

Mol Cancer Res. 2019 Apr;17(4):895-906. doi: 10.1158/1541-7786.MCR-18-0620. Epub 2019 Jan 16.

PMID:
30651371
5.

Association of Tumor Microenvironment T-cell Repertoire and Mutational Load with Clinical Outcome after Sequential Checkpoint Blockade in Melanoma.

Yusko E, Vignali M, Wilson RK, Mardis ER, Hodi FS, Horak C, Chang H, Woods DM, Robins H, Weber J.

Cancer Immunol Res. 2019 Mar;7(3):458-465. doi: 10.1158/2326-6066.CIR-18-0226. Epub 2019 Jan 11.

PMID:
30635271
6.

Accounting for proximal variants improves neoantigen prediction.

Hundal J, Kiwala S, Feng YY, Liu CJ, Govindan R, Chapman WC, Uppaluri R, Swamidass SJ, Griffith OL, Mardis ER, Griffith M.

Nat Genet. 2019 Jan;51(1):175-179. doi: 10.1038/s41588-018-0283-9. Epub 2018 Dec 3.

PMID:
30510237
7.

Next-Generation Sequencing Technologies.

McCombie WR, McPherson JD, Mardis ER.

Cold Spring Harb Perspect Med. 2018 Nov 26. pii: a036798. doi: 10.1101/cshperspect.a036798. [Epub ahead of print]

PMID:
30478097
8.

Author Correction: The prognostic effects of somatic mutations in ER-positive breast cancer.

Griffith OL, Spies NC, Anurag M, Griffith M, Luo J, Tu D, Yeo B, Kunisaki J, Miller CA, Krysiak K, Hundal J, Ainscough BJ, Skidmore ZL, Campbell K, Kumar R, Fronick C, Cook L, Snider JE, Davies S, Kavuri SM, Chang EC, Magrini V, Larson DE, Fulton RS, Liu S, Leung S, Voduc D, Bose R, Dowsett M, Wilson RK, Nielsen TO, Mardis ER, Ellis MJ.

Nat Commun. 2018 Nov 14;9(1):4850. doi: 10.1038/s41467-018-07407-3.

9.

A deep learning approach to automate refinement of somatic variant calling from cancer sequencing data.

Ainscough BJ, Barnell EK, Ronning P, Campbell KM, Wagner AH, Fehniger TA, Dunn GP, Uppaluri R, Govindan R, Rohan TE, Griffith M, Mardis ER, Swamidass SJ, Griffith OL.

Nat Genet. 2018 Dec;50(12):1735-1743. doi: 10.1038/s41588-018-0257-y. Epub 2018 Nov 5.

PMID:
30397337
10.

The Impact of Next-Generation Sequencing on Cancer Genomics: From Discovery to Clinic.

Mardis ER.

Cold Spring Harb Perspect Med. 2018 Nov 5. pii: a036269. doi: 10.1101/cshperspect.a036269. [Epub ahead of print]

PMID:
30397020
11.

Comprehensive Molecular Characterization of the Hippo Signaling Pathway in Cancer.

Wang Y, Xu X, Maglic D, Dill MT, Mojumdar K, Ng PK, Jeong KJ, Tsang YH, Moreno D, Bhavana VH, Peng X, Ge Z, Chen H, Li J, Chen Z, Zhang H, Han L, Du D, Creighton CJ, Mills GB; Cancer Genome Atlas Research Network, Camargo F, Liang H.

Cell Rep. 2018 Oct 30;25(5):1304-1317.e5. doi: 10.1016/j.celrep.2018.10.001.

12.

A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-β Superfamily.

Korkut A, Zaidi S, Kanchi RS, Rao S, Gough NR, Schultz A, Li X, Lorenzi PL, Berger AC, Robertson G, Kwong LN, Datto M, Roszik J, Ling S, Ravikumar V, Manyam G, Rao A, Shelley S, Liu Y, Ju Z, Hansel D, de Velasco G, Pennathur A, Andersen JB, O'Rourke CJ, Ohshiro K, Jogunoori W, Nguyen BN, Li S, Osmanbeyoglu HU, Ajani JA, Mani SA, Houseman A, Wiznerowicz M, Chen J, Gu S, Ma W, Zhang J, Tong P, Cherniack AD, Deng C, Resar L; Cancer Genome Atlas Research Network, Weinstein JN, Mishra L, Akbani R.

Cell Syst. 2018 Oct 24;7(4):422-437.e7. doi: 10.1016/j.cels.2018.08.010. Epub 2018 Sep 26.

13.

Recurrent WNT pathway alterations are frequent in relapsed small cell lung cancer.

Wagner AH, Devarakonda S, Skidmore ZL, Krysiak K, Ramu A, Trani L, Kunisaki J, Masood A, Waqar SN, Spies NC, Morgensztern D, Waligorski J, Ponce J, Fulton RS, Maggi LB Jr, Weber JD, Watson MA, O'Conor CJ, Ritter JH, Olsen RR, Cheng H, Mukhopadhyay A, Can I, Cessna MH, Oliver TG, Mardis ER, Wilson RK, Griffith M, Griffith OL, Govindan R.

Nat Commun. 2018 Sep 17;9(1):3787. doi: 10.1038/s41467-018-06162-9.

14.

The prognostic effects of somatic mutations in ER-positive breast cancer.

Griffith OL, Spies NC, Anurag M, Griffith M, Luo J, Tu D, Yeo B, Kunisaki J, Miller CA, Krysiak K, Hundal J, Ainscough BJ, Skidmore ZL, Campbell K, Kumar R, Fronick C, Cook L, Snider JE, Davies S, Kavuri SM, Chang EC, Magrini V, Larson DE, Fulton RS, Liu S, Leung S, Voduc D, Bose R, Dowsett M, Wilson RK, Nielsen TO, Mardis ER, Ellis MJ.

Nat Commun. 2018 Sep 4;9(1):3476. doi: 10.1038/s41467-018-05914-x. Erratum in: Nat Commun. 2018 Nov 14;9(1):4850.

15.

Identification of Therapeutic Targets in Rhabdomyosarcoma through Integrated Genomic, Epigenomic, and Proteomic Analyses.

Stewart E, McEvoy J, Wang H, Chen X, Honnell V, Ocarz M, Gordon B, Dapper J, Blankenship K, Yang Y, Li Y, Shaw TI, Cho JH, Wang X, Xu B, Gupta P, Fan Y, Liu Y, Rusch M, Griffiths L, Jeon J, Freeman BB 3rd, Clay MR, Pappo A, Easton J, Shurtleff S, Shelat A, Zhou X, Boggs K, Mulder H, Yergeau D, Bahrami A, Mardis ER, Wilson RK, Zhang J, Peng J, Downing JR, Dyer MA; St. Jude Children's Research Hospital – Washington University Pediatric Cancer Genome Project.

Cancer Cell. 2018 Sep 10;34(3):411-426.e19. doi: 10.1016/j.ccell.2018.07.012. Epub 2018 Aug 23.

PMID:
30146332
16.

Oral Cavity Squamous Cell Carcinoma Xenografts Retain Complex Genotypes and Intertumor Molecular Heterogeneity.

Campbell KM, Lin T, Zolkind P, Barnell EK, Skidmore ZL, Winkler AE, Law JH, Mardis ER, Wartman LD, Adkins DR, Chernock RD, Griffith M, Uppaluri R, Griffith OL.

Cell Rep. 2018 Aug 21;24(8):2167-2178. doi: 10.1016/j.celrep.2018.07.058.

17.

Comprehensive Characterization of Cancer Driver Genes and Mutations.

Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Kwok-Shing Ng P, Jeong KJ, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortés-Ciriano I, Zhou DC, Liang WW, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H; MC3 Working Group; Cancer Genome Atlas Research Network, Lawrence MS, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding L.

Cell. 2018 Aug 9;174(4):1034-1035. doi: 10.1016/j.cell.2018.07.034. No abstract available.

18.

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients.

Kahles A, Lehmann KV, Toussaint NC, Hüser M, Stark SG, Sachsenberg T, Stegle O, Kohlbacher O, Sander C; Cancer Genome Atlas Research Network, Rätsch G.

Cancer Cell. 2018 Aug 13;34(2):211-224.e6. doi: 10.1016/j.ccell.2018.07.001. Epub 2018 Aug 2.

19.

Integrated Analysis of RNA and DNA from the Phase III Trial CALGB 40601 Identifies Predictors of Response to Trastuzumab-Based Neoadjuvant Chemotherapy in HER2-Positive Breast Cancer.

Tanioka M, Fan C, Parker JS, Hoadley KA, Hu Z, Li Y, Hyslop TM, Pitcher BN, Soloway MG, Spears PA, Henry LN, Tolaney S, Dang CT, Krop IE, Harris LN, Berry DA, Mardis ER, Winer EP, Hudis CA, Carey LA, Perou CM.

Clin Cancer Res. 2018 Nov 1;24(21):5292-5304. doi: 10.1158/1078-0432.CCR-17-3431. Epub 2018 Jul 23.

PMID:
30037817
20.

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma.

Ricketts CJ, De Cubas AA, Fan H, Smith CC, Lang M, Reznik E, Bowlby R, Gibb EA, Akbani R, Beroukhim R, Bottaro DP, Choueiri TK, Gibbs RA, Godwin AK, Haake S, Hakimi AA, Henske EP, Hsieh JJ, Ho TH, Kanchi RS, Krishnan B, Kwiatkowski DJ, Lui W, Merino MJ, Mills GB, Myers J, Nickerson ML, Reuter VE, Schmidt LS, Shelley CS, Shen H, Shuch B, Signoretti S, Srinivasan R, Tamboli P, Thomas G, Vincent BG, Vocke CD, Wheeler DA, Yang L, Kim WY, Robertson AG; Cancer Genome Atlas Research Network, Spellman PT, Rathmell WK, Linehan WM.

Cell Rep. 2018 Jun 19;23(12):3698. doi: 10.1016/j.celrep.2018.06.032. No abstract available.

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