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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, Ng PK, 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 Apr 5;173(2):371-385.e18. doi: 10.1016/j.cell.2018.02.060. Erratum in: Cell. 2018 Aug 9;174(4):1034-1035.


Advances in immuno-oncology biomarkers for gastroesophageal cancer: Programmed death ligand 1, microsatellite instability, and beyond.

Lin EM, Gong J, Klempner SJ, Chao J.

World J Gastroenterol. 2018 Jul 7;24(25):2686-2697. doi: 10.3748/wjg.v24.i25.2686. Review.


Pan-cancer analysis of copy number changes in programmed death-ligand 1 (PD-L1, CD274) - associations with gene expression, mutational load, and survival.

Budczies J, Bockmayr M, Denkert C, Klauschen F, Gröschel S, Darb-Esfahani S, Pfarr N, Leichsenring J, Onozato ML, Lennerz JK, Dietel M, Fröhling S, Schirmacher P, Iafrate AJ, Weichert W, Stenzinger A.

Genes Chromosomes Cancer. 2016 Aug;55(8):626-39. doi: 10.1002/gcc.22365. Epub 2016 May 30.


DNA mismatch repair deficiency in surgically resected lung adenocarcinoma: Microsatellite instability analysis using the Promega panel.

Takamochi K, Takahashi F, Suehara Y, Sato E, Kohsaka S, Hayashi T, Kitano S, Uneno T, Kojima S, Takeuchi K, Mano H, Suzuki K.

Lung Cancer. 2017 Aug;110:26-31. doi: 10.1016/j.lungcan.2017.05.016. Epub 2017 May 21.


Landscape of Tumor Mutation Load, Mismatch Repair Deficiency, and PD-L1 Expression in a Large Patient Cohort of Gastrointestinal Cancers.

Salem ME, Puccini A, Grothey A, Raghavan D, Goldberg RM, Xiu J, Korn WM, Weinberg BA, Hwang JJ, Shields AF, Marshall JL, Philip PA, Lenz HJ.

Mol Cancer Res. 2018 May;16(5):805-812. doi: 10.1158/1541-7786.MCR-17-0735. Epub 2018 Mar 9.


Why is immunotherapy effective (or not) in patients with MSI/MMRD tumors?

Nebot-Bral L, Coutzac C, Kannouche PL, Chaput N.

Bull Cancer. 2019 Feb;106(2):105-113. doi: 10.1016/j.bulcan.2018.08.007. Epub 2018 Oct 17. Review.


Cancer Driver Log (CanDL): Catalog of Potentially Actionable Cancer Mutations.

Damodaran S, Miya J, Kautto E, Zhu E, Samorodnitsky E, Datta J, Reeser JW, Roychowdhury S.

J Mol Diagn. 2015 Sep;17(5):554-9. doi: 10.1016/j.jmoldx.2015.05.002.


Cancer driver mutation prediction through Bayesian integration of multi-omic data.

Wang Z, Ng KS, Chen T, Kim TB, Wang F, Shaw K, Scott KL, Meric-Bernstam F, Mills GB, Chen K.

PLoS One. 2018 May 8;13(5):e0196939. doi: 10.1371/journal.pone.0196939. eCollection 2018.


Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics.

Ding L, Bailey MH, Porta-Pardo E, Thorsson V, Colaprico A, Bertrand D, Gibbs DL, Weerasinghe A, Huang KL, Tokheim C, Cortés-Ciriano I, Jayasinghe R, Chen F, Yu L, Sun S, Olsen C, Kim J, Taylor AM, Cherniack AD, Akbani R, Suphavilai C, Nagarajan N, Stuart JM, Mills GB, Wyczalkowski MA, Vincent BG, Hutter CM, Zenklusen JC, Hoadley KA, Wendl MC, Shmulevich L, Lazar AJ, Wheeler DA, Getz G; Cancer Genome Atlas Research Network.

Cell. 2018 Apr 5;173(2):305-320.e10. doi: 10.1016/j.cell.2018.03.033.


What does PD-L1 positive or negative mean?

Ribas A, Hu-Lieskovan S.

J Exp Med. 2016 Dec 12;213(13):2835-2840. Epub 2016 Nov 30. Review.


Identification of druggable cancer driver genes amplified across TCGA datasets.

Chen Y, McGee J, Chen X, Doman TN, Gong X, Zhang Y, Hamm N, Ma X, Higgs RE, Bhagwat SV, Buchanan S, Peng SB, Staschke KA, Yadav V, Yue Y, Kouros-Mehr H.

PLoS One. 2014 May 29;9(5):e98293. doi: 10.1371/journal.pone.0098293. eCollection 2014. Erratum in: PLoS One. 2014;9(9):e107646.


Frequent mutations in acetylation and ubiquitination sites suggest novel driver mechanisms of cancer.

Narayan S, Bader GD, Reimand J.

Genome Med. 2016 May 12;8(1):55. doi: 10.1186/s13073-016-0311-2.


Characterization of immune regulatory molecules B7-H4 and PD-L1 in low and high grade endometrial tumors.

Bregar A, Deshpande A, Grange C, Zi T, Stall J, Hirsch H, Reeves J, Sathyanarayanan S, Growdon WB, Rueda BR.

Gynecol Oncol. 2017 Jun;145(3):446-452. doi: 10.1016/j.ygyno.2017.03.006. Epub 2017 Mar 25.


CanDrA: cancer-specific driver missense mutation annotation with optimized features.

Mao Y, Chen H, Liang H, Meric-Bernstam F, Mills GB, Chen K.

PLoS One. 2013 Oct 30;8(10):e77945. doi: 10.1371/journal.pone.0077945. eCollection 2013.


Potential Predictive Value of TP53 and KRAS Mutation Status for Response to PD-1 Blockade Immunotherapy in Lung Adenocarcinoma.

Dong ZY, Zhong WZ, Zhang XC, Su J, Xie Z, Liu SY, Tu HY, Chen HJ, Sun YL, Zhou Q, Yang JJ, Yang XN, Lin JX, Yan HH, Zhai HR, Yan LX, Liao RQ, Wu SP, Wu YL.

Clin Cancer Res. 2017 Jun 15;23(12):3012-3024. doi: 10.1158/1078-0432.CCR-16-2554. Epub 2016 Dec 30.


The Roles of microRNAs in Regulating the Expression of PD-1/PD-L1 Immune Checkpoint.

Wang Q, Lin W, Tang X, Li S, Guo L, Lin Y, Kwok HF.

Int J Mol Sci. 2017 Nov 27;18(12). pii: E2540. doi: 10.3390/ijms18122540. Review.


Clinicopathologic implications of immune classification by PD-L1 expression and CD8-positive tumor-infiltrating lymphocytes in stage II and III gastric cancer patients.

Koh J, Ock CY, Kim JW, Nam SK, Kwak Y, Yun S, Ahn SH, Park DJ, Kim HH, Kim WH, Lee HS.

Oncotarget. 2017 Apr 18;8(16):26356-26367. doi: 10.18632/oncotarget.15465.


Differences in histological features and PD-L1 expression between sporadic microsatellite instability and Lynch-syndrome-associated disease in Japanese patients with colorectal cancer.

Yamada R, Yamaguchi T, Iijima T, Wakaume R, Takao M, Koizumi K, Hishima T, Horiguchi SI.

Int J Clin Oncol. 2018 Jun;23(3):504-513. doi: 10.1007/s10147-018-1238-y. Epub 2018 Jan 11.


Clonal status of actionable driver events and the timing of mutational processes in cancer evolution.

McGranahan N, Favero F, de Bruin EC, Birkbak NJ, Szallasi Z, Swanton C.

Sci Transl Med. 2015 Apr 15;7(283):283ra54. doi: 10.1126/scitranslmed.aaa1408.

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