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Items: 1 to 50 of 184

1.

Genomically annotated risk model for advanced renal-cell carcinoma: a retrospective cohort study.

Voss MH, Reising A, Cheng Y, Patel P, Marker M, Kuo F, Chan TA, Choueiri TK, Hsieh JJ, Hakimi AA, Motzer RJ.

Lancet Oncol. 2018 Nov 8. pii: S1470-2045(18)30648-X. doi: 10.1016/S1470-2045(18)30648-X. [Epub ahead of print]

PMID:
30416077
2.

Development of Tumor Mutation Burden as an Immunotherapy Biomarker: Utility for the Oncology Clinic.

Chan TA, Yarchoan M, Jaffee E, Swanton C, Quezada SA, Stenzinger A, Peters S.

Ann Oncol. 2018 Nov 5. doi: 10.1093/annonc/mdy495. [Epub ahead of print]

PMID:
30395155
3.

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.

4.

ATRX, DAXX or MEN1 mutant pancreatic neuroendocrine tumors are a distinct alpha-cell signature subgroup.

Chan CS, Laddha SV, Lewis PW, Koletsky MS, Robzyk K, Da Silva E, Torres PJ, Untch BR, Li J, Bose P, Chan TA, Klimstra DS, Allis CD, Tang LH.

Nat Commun. 2018 Oct 12;9(1):4158. doi: 10.1038/s41467-018-06498-2.

5.

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.

PMID:
30268436
6.

The hallmarks of successful anticancer immunotherapy.

Galluzzi L, Chan TA, Kroemer G, Wolchok JD, López-Soto A.

Sci Transl Med. 2018 Sep 19;10(459). pii: eaat7807. doi: 10.1126/scitranslmed.aat7807. Review.

PMID:
30232229
7.

Integrated Genomic Analysis of Hürthle Cell Cancer Reveals Oncogenic Drivers, Recurrent Mitochondrial Mutations, and Unique Chromosomal Landscapes.

Ganly I, Makarov V, Deraje S, Dong Y, Reznik E, Seshan V, Nanjangud G, Eng S, Bose P, Kuo F, Morris LGT, Landa I, Carrillo Albornoz PB, Riaz N, Nikiforov YE, Patel K, Umbricht C, Zeiger M, Kebebew E, Sherman E, Ghossein R, Fagin JA, Chan TA.

Cancer Cell. 2018 Aug 13;34(2):256-270.e5. doi: 10.1016/j.ccell.2018.07.002.

PMID:
30107176
8.

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.

9.

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.

10.

Phosphatidylinositol-3-Kinase Mutations Are Associated With Increased Local Failure in Brain Metastases Treated With Radiation.

Lockney NA, Wang DG, Pei X, Goldman DA, Zhang Z, Lin A, Chan TA, Yamada Y, Beal K, Yang TJ.

Int J Radiat Oncol Biol Phys. 2018 Jul 15;101(4):833-844. doi: 10.1016/j.ijrobp.2018.03.032. Epub 2018 Mar 29.

PMID:
29976496
11.

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.

12.

Update on Tumor Neoantigens and Their Utility: Why It Is Good to Be Different.

Lee CH, Yelensky R, Jooss K, Chan TA.

Trends Immunol. 2018 Jul;39(7):536-548. doi: 10.1016/j.it.2018.04.005. Epub 2018 May 8. Review.

PMID:
29751996
13.

Multicenter Phase IB Trial of Carboxyamidotriazole Orotate and Temozolomide for Recurrent and Newly Diagnosed Glioblastoma and Other Anaplastic Gliomas.

Omuro A, Beal K, McNeill K, Young RJ, Thomas A, Lin X, Terziev R, Kaley TJ, DeAngelis LM, Daras M, Gavrilovic IT, Mellinghoff I, Diamond EL, McKeown A, Manne M, Caterfino A, Patel K, Bavisotto L, Gorman G, Lamson M, Gutin P, Tabar V, Chakravarty D, Chan TA, Brennan CW, Garrett-Mayer E, Karmali RA, Pentsova E.

J Clin Oncol. 2018 Jun 10;36(17):1702-1709. doi: 10.1200/JCO.2017.76.9992. Epub 2018 Apr 23.

PMID:
29683790
14.

Tobacco Smoking-Associated Alterations in the Immune Microenvironment of Squamous Cell Carcinomas.

Desrichard A, Kuo F, Chowell D, Lee KW, Riaz N, Wong RJ, Chan TA, Morris LGT.

J Natl Cancer Inst. 2018 Apr 11. doi: 10.1093/jnci/djy060. [Epub ahead of print]

PMID:
29659925
15.

Correction to: Genomics of NSCLC patients both affirm PD-L1 expression and predict their clinical responses to anti-PD-1 immunotherapy.

Brogden KA, Parashar D, Hallier AR, Braun T, Qian F, Rizvi NA, Bossler AD, Milhem MM, Chan TA, Abbasi T, Vali S.

BMC Cancer. 2018 Apr 12;18(1):413. doi: 10.1186/s12885-018-4200-5.

16.

The Immune Landscape of Cancer.

Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, Mose LE, Vo NS, Liu J, Liu Y, Rader J, Dhankani V, Reynolds SM, Bowlby R, Califano A, Cherniack AD, Anastassiou D, Bedognetti D, Rao A, Chen K, Krasnitz A, Hu H, Malta TM, Noushmehr H, Pedamallu CS, Bullman S, Ojesina AI, Lamb A, Zhou W, Shen H, Choueiri TK, Weinstein JN, Guinney J, Saltz J, Holt RA, Rabkin CE; Cancer Genome Atlas Research Network, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich L.

Immunity. 2018 Apr 17;48(4):812-830.e14. doi: 10.1016/j.immuni.2018.03.023. Epub 2018 Apr 5.

17.

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics.

Liu J, Lichtenberg T, Hoadley KA, Poisson LM, Lazar AJ, Cherniack AD, Kovatich AJ, Benz CC, Levine DA, Lee AV, Omberg L, Wolf DM, Shriver CD, Thorsson V; Cancer Genome Atlas Research Network, Hu H.

Cell. 2018 Apr 5;173(2):400-416.e11. doi: 10.1016/j.cell.2018.02.052.

18.

A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples.

Chen H, Li C, Peng X, Zhou Z, Weinstein JN; Cancer Genome Atlas Research Network, Liang H.

Cell. 2018 Apr 5;173(2):386-399.e12. doi: 10.1016/j.cell.2018.03.027.

19.

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.

20.

Pathogenic Germline Variants in 10,389 Adult Cancers.

Huang KL, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C, Paczkowska M, Reynolds S, Wyczalkowski MA, Oak N, Scott AD, Krassowski M, Cherniack AD, Houlahan KE, Jayasinghe R, Wang LB, Zhou DC, Liu D, Cao S, Kim YW, Koire A, McMichael JF, Hucthagowder V, Kim TB, Hahn A, Wang C, McLellan MD, Al-Mulla F, Johnson KJ; Cancer Genome Atlas Research Network, Lichtarge O, Boutros PC, Raphael B, Lazar AJ, Zhang W, Wendl MC, Govindan R, Jain S, Wheeler D, Kulkarni S, Dipersio JF, Reimand J, Meric-Bernstam F, Chen K, Shmulevich I, Plon SE, Chen F, Ding L.

Cell. 2018 Apr 5;173(2):355-370.e14. doi: 10.1016/j.cell.2018.03.039.

21.

Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation.

Malta TM, Sokolov A, Gentles AJ, Burzykowski T, Poisson L, Weinstein JN, Kamińska B, Huelsken J, Omberg L, Gevaert O, Colaprico A, Czerwińska P, Mazurek S, Mishra L, Heyn H, Krasnitz A, Godwin AK, Lazar AJ; Cancer Genome Atlas Research Network, Stuart JM, Hoadley KA, Laird PW, Noushmehr H, Wiznerowicz M.

Cell. 2018 Apr 5;173(2):338-354.e15. doi: 10.1016/j.cell.2018.03.034.

22.

Oncogenic Signaling Pathways in The Cancer Genome Atlas.

Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC, Dimitriadoy S, Liu DL, Kantheti HS, Saghafinia S, Chakravarty D, Daian F, Gao Q, Bailey MH, Liang WW, Foltz SM, Shmulevich I, Ding L, Heins Z, Ochoa A, Gross B, Gao J, Zhang H, Kundra R, Kandoth C, Bahceci I, Dervishi L, Dogrusoz U, Zhou W, Shen H, Laird PW, Way GP, Greene CS, Liang H, Xiao Y, Wang C, Iavarone A, Berger AH, Bivona TG, Lazar AJ, Hammer GD, Giordano T, Kwong LN, McArthur G, Huang C, Tward AD, Frederick MJ, McCormick F, Meyerson M; Cancer Genome Atlas Research Network, Van Allen EM, Cherniack AD, Ciriello G, Sander C, Schultz N.

Cell. 2018 Apr 5;173(2):321-337.e10. doi: 10.1016/j.cell.2018.03.035.

23.

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.

24.

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer.

Hoadley KA, Yau C, Hinoue T, Wolf DM, Lazar AJ, Drill E, Shen R, Taylor AM, Cherniack AD, Thorsson V, Akbani R, Bowlby R, Wong CK, Wiznerowicz M, Sanchez-Vega F, Robertson AG, Schneider BG, Lawrence MS, Noushmehr H, Malta TM; Cancer Genome Atlas Network, Stuart JM, Benz CC, Laird PW.

Cell. 2018 Apr 5;173(2):291-304.e6. doi: 10.1016/j.cell.2018.03.022.

25.

Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas.

Liu Y, Sethi NS, Hinoue T, Schneider BG, Cherniack AD, Sanchez-Vega F, Seoane JA, Farshidfar F, Bowlby R, Islam M, Kim J, Chatila W, Akbani R, Kanchi RS, Rabkin CS, Willis JE, Wang KK, McCall SJ, Mishra L, Ojesina AI, Bullman S, Pedamallu CS, Lazar AJ, Sakai R; Cancer Genome Atlas Research Network, Thorsson V, Bass AJ, Laird PW.

Cancer Cell. 2018 Apr 9;33(4):721-735.e8. doi: 10.1016/j.ccell.2018.03.010. Epub 2018 Apr 2.

26.

lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer.

Wang Z, Yang B, Zhang M, Guo W, Wu Z, Wang Y, Jia L, Li S; Cancer Genome Atlas Research Network, Xie W, Yang D.

Cancer Cell. 2018 Apr 9;33(4):706-720.e9. doi: 10.1016/j.ccell.2018.03.006. Epub 2018 Apr 2.

27.

A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers.

Berger AC, Korkut A, Kanchi RS, Hegde AM, Lenoir W, Liu W, Liu Y, Fan H, Shen H, Ravikumar V, Rao A, Schultz A, Li X, Sumazin P, Williams C, Mestdagh P, Gunaratne PH, Yau C, Bowlby R, Robertson AG, Tiezzi DG, Wang C, Cherniack AD, Godwin AK, Kuderer NM, Rader JS, Zuna RE, Sood AK, Lazar AJ, Ojesina AI, Adebamowo C, Adebamowo SN, Baggerly KA, Chen TW, Chiu HS, Lefever S, Liu L, MacKenzie K, Orsulic S, Roszik J, Shelley CS, Song Q, Vellano CP, Wentzensen N; Cancer Genome Atlas Research Network, Weinstein JN, Mills GB, Levine DA, Akbani R.

Cancer Cell. 2018 Apr 9;33(4):690-705.e9. doi: 10.1016/j.ccell.2018.03.014. Epub 2018 Apr 2.

28.

Genomic and Functional Approaches to Understanding Cancer Aneuploidy.

Taylor AM, Shih J, Ha G, Gao GF, Zhang X, Berger AC, Schumacher SE, Wang C, Hu H, Liu J, Lazar AJ; Cancer Genome Atlas Research Network, Cherniack AD, Beroukhim R, Meyerson M.

Cancer Cell. 2018 Apr 9;33(4):676-689.e3. doi: 10.1016/j.ccell.2018.03.007. Epub 2018 Apr 2.

29.

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 Apr 3;23(1):313-326.e5. doi: 10.1016/j.celrep.2018.03.075. Erratum in: Cell Rep. 2018 Jun 19;23(12):3698.

30.

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context.

Chiu HS, Somvanshi S, Patel E, Chen TW, Singh VP, Zorman B, Patil SL, Pan Y, Chatterjee SS; Cancer Genome Atlas Research Network, Sood AK, Gunaratne PH, Sumazin P.

Cell Rep. 2018 Apr 3;23(1):297-312.e12. doi: 10.1016/j.celrep.2018.03.064.

31.

Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types.

Seiler M, Peng S, Agrawal AA, Palacino J, Teng T, Zhu P, Smith PG; Cancer Genome Atlas Research Network, Buonamici S, Yu L.

Cell Rep. 2018 Apr 3;23(1):282-296.e4. doi: 10.1016/j.celrep.2018.01.088.

32.

Systematic Analysis of Splice-Site-Creating Mutations in Cancer.

Jayasinghe RG, Cao S, Gao Q, Wendl MC, Vo NS, Reynolds SM, Zhao Y, Climente-González H, Chai S, Wang F, Varghese R, Huang M, Liang WW, Wyczalkowski MA, Sengupta S, Li Z, Payne SH, Fenyö D, Miner JH, Walter MJ; Cancer Genome Atlas Research Network, Vincent B, Eyras E, Chen K, Shmulevich I, Chen F, Ding L.

Cell Rep. 2018 Apr 3;23(1):270-281.e3. doi: 10.1016/j.celrep.2018.03.052.

33.

Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers.

Peng X, Chen Z, Farshidfar F, Xu X, Lorenzi PL, Wang Y, Cheng F, Tan L, Mojumdar K, Du D, Ge Z, Li J, Thomas GV, Birsoy K, Liu L, Zhang H, Zhao Z, Marchand C, Weinstein JN; Cancer Genome Atlas Research Network, Bathe OF, Liang H.

Cell Rep. 2018 Apr 3;23(1):255-269.e4. doi: 10.1016/j.celrep.2018.03.077.

34.

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas.

Knijnenburg TA, Wang L, Zimmermann MT, Chambwe N, Gao GF, Cherniack AD, Fan H, Shen H, Way GP, Greene CS, Liu Y, Akbani R, Feng B, Donehower LA, Miller C, Shen Y, Karimi M, Chen H, Kim P, Jia P, Shinbrot E, Zhang S, Liu J, Hu H, Bailey MH, Yau C, Wolf D, Zhao Z, Weinstein JN, Li L, Ding L, Mills GB, Laird PW, Wheeler DA, Shmulevich I; Cancer Genome Atlas Research Network, Monnat RJ Jr, Xiao Y, Wang C.

Cell Rep. 2018 Apr 3;23(1):239-254.e6. doi: 10.1016/j.celrep.2018.03.076.

35.

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Gao Q, Liang WW, Foltz SM, Mutharasu G, Jayasinghe RG, Cao S, Liao WW, Reynolds SM, Wyczalkowski MA, Yao L, Yu L, Sun SQ; Fusion Analysis Working Group; Cancer Genome Atlas Research Network, Chen K, Lazar AJ, Fields RC, Wendl MC, Van Tine BA, Vij R, Chen F, Nykter M, Shmulevich I, Ding L.

Cell Rep. 2018 Apr 3;23(1):227-238.e3. doi: 10.1016/j.celrep.2018.03.050.

36.

Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types.

Ge Z, Leighton JS, Wang Y, Peng X, Chen Z, Chen H, Sun Y, Yao F, Li J, Zhang H, Liu J, Shriver CD, Hu H; Cancer Genome Atlas Research Network, Piwnica-Worms H, Ma L, Liang H.

Cell Rep. 2018 Apr 3;23(1):213-226.e3. doi: 10.1016/j.celrep.2018.03.047.

37.

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas.

Campbell JD, Yau C, Bowlby R, Liu Y, Brennan K, Fan H, Taylor AM, Wang C, Walter V, Akbani R, Byers LA, Creighton CJ, Coarfa C, Shih J, Cherniack AD, Gevaert O, Prunello M, Shen H, Anur P, Chen J, Cheng H, Hayes DN, Bullman S, Pedamallu CS, Ojesina AI, Sadeghi S, Mungall KL, Robertson AG, Benz C, Schultz A, Kanchi RS, Gay CM, Hegde A, Diao L, Wang J, Ma W, Sumazin P, Chiu HS, Chen TW, Gunaratne P, Donehower L, Rader JS, Zuna R, Al-Ahmadie H, Lazar AJ, Flores ER, Tsai KY, Zhou JH, Rustgi AK, Drill E, Shen R, Wong CK; Cancer Genome Atlas Research Network, Stuart JM, Laird PW, Hoadley KA, Weinstein JN, Peto M, Pickering CR, Chen Z, Van Waes C.

Cell Rep. 2018 Apr 3;23(1):194-212.e6. doi: 10.1016/j.celrep.2018.03.063.

38.

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images.

Saltz J, Gupta R, Hou L, Kurc T, Singh P, Nguyen V, Samaras D, Shroyer KR, Zhao T, Batiste R, Van Arnam J; Cancer Genome Atlas Research Network, Shmulevich I, Rao AUK, Lazar AJ, Sharma A, Thorsson V.

Cell Rep. 2018 Apr 3;23(1):181-193.e7. doi: 10.1016/j.celrep.2018.03.086.

39.

Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas.

Way GP, Sanchez-Vega F, La K, Armenia J, Chatila WK, Luna A, Sander C, Cherniack AD, Mina M, Ciriello G, Schultz N; Cancer Genome Atlas Research Network, Sanchez Y, Greene CS.

Cell Rep. 2018 Apr 3;23(1):172-180.e3. doi: 10.1016/j.celrep.2018.03.046.

40.

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas.

Schaub FX, Dhankani V, Berger AC, Trivedi M, Richardson AB, Shaw R, Zhao W, Zhang X, Ventura A, Liu Y, Ayer DE, Hurlin PJ, Cherniack AD, Eisenman RN, Bernard B, Grandori C; Cancer Genome Atlas Network.

Cell Syst. 2018 Mar 28;6(3):282-300.e2. doi: 10.1016/j.cels.2018.03.003.

41.

Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines.

Ellrott K, Bailey MH, Saksena G, Covington KR, Kandoth C, Stewart C, Hess J, Ma S, Chiotti KE, McLellan M, Sofia HJ, Hutter C, Getz G, Wheeler D, Ding L; MC3 Working Group; Cancer Genome Atlas Research Network.

Cell Syst. 2018 Mar 28;6(3):271-281.e7. doi: 10.1016/j.cels.2018.03.002.

42.

Atrx inactivation drives disease-defining phenotypes in glioma cells of origin through global epigenomic remodeling.

Danussi C, Bose P, Parthasarathy PT, Silberman PC, Van Arnam JS, Vitucci M, Tang OY, Heguy A, Wang Y, Chan TA, Riggins GJ, Sulman EP, Lang F, Creighton CJ, Deneen B, Miller CR, Picketts DJ, Kannan K, Huse JT.

Nat Commun. 2018 Mar 13;9(1):1057. doi: 10.1038/s41467-018-03476-6.

43.

Genomics of NSCLC patients both affirm PD-L1 expression and predict their clinical responses to anti-PD-1 immunotherapy.

Brogden KA, Parashar D, Hallier AR, Braun T, Qian F, Rizvi NA, Bossler AD, Milhem MM, Chan TA, Abbasi T, Vali S.

BMC Cancer. 2018 Feb 27;18(1):225. doi: 10.1186/s12885-018-4134-y. Erratum in: BMC Cancer. 2018 Apr 12;18(1):413.

44.

ImmunoMap: A Bioinformatics Tool for T-cell Repertoire Analysis.

Sidhom JW, Bessell CA, Havel JJ, Kosmides A, Chan TA, Schneck JP.

Cancer Immunol Res. 2018 Feb;6(2):151-162. doi: 10.1158/2326-6066.CIR-17-0114. Epub 2017 Dec 20.

PMID:
29263161
45.

Merkel Cell Carcinoma Patients Presenting Without a Primary Lesion Have Elevated Markers of Immunity, Higher Tumor Mutation Burden, and Improved Survival.

Vandeven N, Lewis CW, Makarov V, Riaz N, Paulson KG, Hippe D, Bestick A, Doumani R, Marx T, Takagishi S, Chan TA, Choi J, Nghiem P.

Clin Cancer Res. 2018 Feb 15;24(4):963-971. doi: 10.1158/1078-0432.CCR-17-1678. Epub 2017 Dec 15.

PMID:
29246939
46.

Patient HLA class I genotype influences cancer response to checkpoint blockade immunotherapy.

Chowell D, Morris LGT, Grigg CM, Weber JK, Samstein RM, Makarov V, Kuo F, Kendall SM, Requena D, Riaz N, Greenbaum B, Carroll J, Garon E, Hyman DM, Zehir A, Solit D, Berger M, Zhou R, Rizvi NA, Chan TA.

Science. 2018 Feb 2;359(6375):582-587. doi: 10.1126/science.aao4572. Epub 2017 Dec 7.

47.

Mutant-IDH1-dependent chromatin state reprogramming, reversibility, and persistence.

Turcan S, Makarov V, Taranda J, Wang Y, Fabius AWM, Wu W, Zheng Y, El-Amine N, Haddock S, Nanjangud G, LeKaye HC, Brennan C, Cross J, Huse JT, Kelleher NL, Osten P, Thompson CB, Chan TA.

Nat Genet. 2018 Jan;50(1):62-72. doi: 10.1038/s41588-017-0001-z. Epub 2017 Nov 27.

PMID:
29180699
48.

Identification of unique neoantigen qualities in long-term survivors of pancreatic cancer.

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