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The Michael Berger Lab: Publications

View a full listing of Michael F. Berger’s journal articles.


Therapy-Related Clonal Hematopoiesis in Patients with Non-hematologic Cancers Is Common and Associated with Adverse Clinical Outcomes. Coombs CC, Zehir A, Devlin SM, Kishtagari A, Syed A, Jonsson P, Hyman DM, Solit DB, Robson ME, Baselga J, Arcila ME, Ladanyi M, Tallman MS, Levine RL, Berger MF. Cell Stem Cell. 2017 Sep 7;21(3):374-382.e4. doi: 10.1016/j.stem.2017.07.010. Epub 2017 Aug 10.

Mutation Detection in Patients With Advanced Cancer by Universal Sequencing of Cancer-Related Genes in Tumor and Normal DNA vs Guideline-Based Germline Testing. Mandelker D, Zhang L, Kemel Y, Stadler ZK, Joseph V, Zehir A, Pradhan N, Arnold A, Walsh MF, Li Y, Balakrishnan AR, Syed A, Prasad M, Nafa K, Carlo MI, Cadoo KA, Sheehan M, Fleischut MH, Salo-Mullen E, Trottier M, Lipkin SM, Lincoln A, Mukherjee S, Ravichandran V, Cambria R, Galle J, Abida W, Arcila ME, Benayed R, Shah R, Yu K, Bajorin DF, Coleman JA, Leach SD, Lowery MA, Garcia-Aguilar J, Kantoff PW, Sawyers CL, Dickler MN, Saltz L, Motzer RJ, O’Reilly EM, Scher HI, Baselga J, Klimstra DS1, Solit DB, Hyman DM, Berger MF, Ladanyi M, Robson ME, Offit K. JAMA. 2017 Sep 5;318(9):825-835. doi: 10.1001/jama.2017.11137.

Clinical and molecular characterization of patients with cancer of unknown primary in the modern era. Varghese AM, Arora A, Capanu M, Camacho N, Won HH, Zehir A, Gao J, Chakravarty D, Schultz N, Klimstra DS, Ladanyi M, Hyman DM, Solit DB, Berger MF, Saltz LB. Ann Oncol. 2017 Dec 1;28(12):3015-3021. doi: 10.1093/annonc/mdx545.

Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Zehir A, Benayed R, Shah RH, Syed A, Middha S, Kim HR, Srinivasan P, Gao J, Chakravarty D, Devlin SM, Hellmann MD, Barron DA, Schram AM, Hameed M, Dogan S, Ross DS, Hechtman JF, DeLair DF1, Yao J1, Mandelker DL, Cheng DT, Chandramohan R, Mohanty AS, Ptashkin RN, Jayakumaran G, Prasad M, Syed MH, Rema AB, Liu ZY, Nafa K, Borsu L, Sadowska J, Casanova J, Bacares R, Kiecka IJ, Razumova A, Son JB, Stewart L, Baldi T, Mullaney KA, Al-Ahmadie H, Vakiani E, Abeshouse AA, Penson AV, Jonsson P, Camacho N, Chang MT, Won HH, Gross BE, Kundra R, Heins ZJ, Chen HW, Phillips S, Zhang H, Wang J, Ochoa A, Wills J, Eubank M, Thomas SB, Gardos SM, Reales DN, Galle J, Durany R, Cambria R, Abida W, Cercek A, Feldman DR, Gounder MM, Hakimi AA, Harding JJ, Iyer G, Janjigian YY, Jordan EJ, Kelly CM, Lowery MA, Morris LGT, Omuro AM, Raj N, Razavi P, Shoushtari AN4, Shukla N11, Soumerai TE, Varghese AM, Yaeger R, Coleman J, Bochner B, Riely GJ, Saltz LB, Scher HI, Sabbatini PJ, Robson ME, Klimstra DS, Taylor BS, Baselga J, Schultz N, Hyman DM, Arcila ME, Solit DB, Ladanyi M, Berger MF. Nat Med. 2017 Jun;23(6):703-713. doi: 10.1038/nm.4333. Epub 2017 May 8.

Germline Variants in Targeted Tumor Sequencing Using Matched Normal DNA. Schrader KA, Cheng DT, Joseph V, Prasad M, Walsh M, Zehir A, Ni A, Thomas T, Benayed R, Ashraf A, Lincoln A, Arcila M, Stadler Z, Solit D, Hyman DM, Zhang L, Klimstra D, Ladanyi M, Offit K, Berger M, Robson M. JAMA Oncol. 2016 Jan;2(1):104-11. doi: 10.1001/jamaoncol.2015.5208.

Evaluating Cancer of the Central Nervous System Through Next-Generation Sequencing of Cerebrospinal Fluid. Pentsova EI, Shah RH, Tang J, Boire A, You D, Briggs S, Omuro A, Lin X, Fleisher M, Grommes C, Panageas KS, Meng F, Selcuklu SD, Ogilvie S, Distefano N, Shagabayeva L, Rosenblum M, DeAngelis LM, Viale A, Mellinghoff IK, Berger MF. J Clin Oncol. 2016 Jul 10;34(20):2404-15. doi: 10.1200/JCO.2016.66.6487. Epub 2016 May 9.

Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT): A Hybridization Capture-Based Next-Generation Sequencing Clinical Assay for Solid Tumor Molecular Oncology. Cheng DT, Mitchell TN, Zehir A, Shah RH, Benayed R, Syed A, Chandramohan R, Liu ZY, Won HH, Scott SN, Brannon AR, O’Reilly C, Sadowska J, Casanova J, Yannes A, Hechtman JF, Yao J, Song W, Ross DS, Oultache A, Dogan S, Borsu L, Hameed M, Nafa K, Arcila ME, Ladanyi M, Berger MF. J Mol Diagn. 2015 May;17(3):251-64. doi: 10.1016/j.jmoldx.2014.12.006. Epub 2015 Mar 20.

Comparative sequencing analysis reveals high genomic concordance between matched primary and metastatic colorectal cancer lesions. Brannon AR, Vakiani E, Sylvester BE, Scott SN, McDermott G, Shah RH, Kania K, Viale A, Oschwald DM, Vacic V, Emde AK, Cercek A, Yaeger R, Kemeny NE, Saltz LB, Shia J, D’Angelica MI, Weiser MR, Solit DB, Berger MF. Genome Biol. 2014 Aug 28;15(8):454. doi: 10.1186/s13059-014-0454-7.

Advancing clinical oncology through genome biology and technology. Varghese AM, Berger MF. Genome Biol. 2014 Aug 7;15(8):427. doi: 10.1186/s13059-014-0427-x.

Recurrent SMARCA4 mutations in small cell carcinoma of the ovary.  Jelinic P, Mueller JJ, Olvera N, Dao F, Scott SN, Shah R, Gao J, Schultz N, Gonen M, Soslow RA, Berger MF, Levine DA. Nat Genet. 2014 May;46(5):424-6. doi: 10.1038/ng.2922. Epub 2014 Mar 23.

 Tumor genetic analyses of patients with metastatic renal cell carcinoma and extended benefit from mTOR inhibitor therapy.  Voss MH, Hakimi AA, Pham CG, Brannon AR, Chen YB, Cunha LF, Akin O, Liu H, Takeda S, Scott SN, Socci ND, Viale A, Schultz N, Sander C, Reuter VE, Russo P, Cheng EH, Motzer RJ, Berger MF, Hsieh JJ. Clin Cancer Res. 2014 Apr 1;20(7):1955-64. do: 10.1158/1078-0432.CCR-13-2345. Epub 2014 Mar 12.

ESR1 ligand-binding domain mutations in hormone-resistant breast cancer. Toy W, Shen Y, Won H, Green B, Sakr RA, Will M, Li Z, Gala K, Fanning S, King TA, Hudis C, Chen D, Taran T, Hortobagyi G, Greene G, Berger M, Baselga J, Chandarlapaty S. Nat Genet. 2013 Dec;45(12):1439-45. doi: 10.1038/ng.2822. Epub 2013 Nov 3.

Detecting somatic genetic alterations in tumor specimens by exon capture and massively parallel sequencing. Won HH, Scott SN, Brannon AR, Shah RH, Berger MF. J Vis Exp. 2013 Oct 18;(80):e50710. doi: 10.3791/50710.

Genome sequencing identifies a basis for everolimus sensitivity. Iyer G, Hanrahan AJ, Milowsky MI, Al-Ahmadie H, Scott SN, Janakiraman M, Pirun M, Sander C, Socci ND, Ostrovnaya I, Viale A, Heguy A, Peng L, Chan TA, Bochner B, Bajorin DF, Berger MF, Taylor BS, Solit DB. Science. 2012 Oct 12;338(6104):221. doi: 10.1126/science.1226344. Epub 2012 Aug 23.

Melanoma genome sequencing reveals frequent PREX2 mutations. Berger MF, Hodis E, Heffernan TP, Deribe YL, Lawrence MS, Protopopov A, Ivanova E, Watson IR, Nickerson E, Ghosh P, Zhang H, Zeid R, Ren X, Cibulskis K, Sivachenko AY, Wagle N, Sucker A, Sougnez C, Onofrio R, Ambrogio L, Auclair D, Fennell T, Carter SL, Drier Y, Stojanov P, Singer MA, Voet D, Jing R, Saksena G, Barretina J, Ramos AH, Pugh TJ, Stransky N, Parkin M, Winckler W, Mahan S, Ardlie K, Baldwin J, Wargo J, Schadendorf D, Meyerson M, Gabriel SB, Golub TR, Wagner SN, Lander ES, Getz G, Chin L, Garraway LA. Nature. 2012 May 9;485(7399):502-6. doi: 10.1038/nature11071.

High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing. Wagle N1, Berger MF, Davis MJ, Blumenstiel B, Defelice M, Pochanard P, Ducar M, Van Hummelen P, Macconaill LE, Hahn WC, Meyerson M, Gabriel SB, Garraway LA.  Cancer Discov. 2012 Jan;2(1):82-93. doi: 10.1158/2159-8290.CD-11-0184. Epub 2011 Nov 7.

Dissecting therapeutic resistance to RAF inhibition in melanoma by tumor genomic profiling. Wagle N, Emery C, Berger MF, Davis MJ, Sawyer A, Pochanard P, Kehoe SM, Johannessen C, MacConaill LE, Hahn WC, Meyerson M, Garraway LA. J Clin Oncol. 2011 Mar 7. (Epub ahead of print).

The genomic complexity of primary human prostate cancer. Berger MF, Lawrence MS, Demichelis F, Drier Y, Cibulskis K, Sivachenko AY, Sboner A, Esgueva R, Pflueger D, SougnezC, Onofrio R, Carter SL, Park K, Habegger L, Ambrogio L, Fennell T, Parkin M, Saksena G, Voet D, Ramos AH, Pugh TJ, Wilkinson J, Fisher S, Winckler W, Mahan S, Ardlie K, Baldwin J, Simons JW, Kitabayashi N, MacDonald TY, Kantoff PW, Chin L, Gabriel SB, Gerstein MB, Golub TR, Meyerson M, Tewari A, Lander ES, Getz G, Rubin MA, Garraway LA. Nature. 2011 Feb 10;470(7333):214-20.

Integrative analysis of the melanoma transcriptome. Berger MF, Levin JZ, Vijayendran K, Sivachenko A, Adiconis X, Maguire J, Johnson LA, Robinson J, Verhaak RG, Sougnez C, Onofrio RC, Ziaugra L, Cibulskis K, Laine E, Barretina J, Winckler W, Fisher DE, Getz G, Meyerson M, Jaffe DB, Gabriel SB, Lander ES, Dummer R, Gnirke A, Nusbaum C, Garraway LA. Genome Research. 2010 Apr;20(4):413-27. Epub 2010 Feb 23.

Diversity and complexity in DNA recognition by transcription factors. Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, Chan ET, Metzler G, Vedenko A, Chen X, Kuznetsov H, Wang CF, Coburn D, Newburger DE, Morris Q, Hughes TR, Bulyk ML. Science. 2009 Jun 26;324(5935):1720-3. Epub 2009 May 14.

Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Berger MF, Badis G, Gehrke AR, Talukder S, Philippakis AA, Peña-Castillo L, Alleyne TM, Mnaimneh S, Botvinnik OB, Chan ET, Khalid F, Zhang W, Newburger D, Jaeger SA, Morris QD, Bulyk ML, Hughes TR. Cell. 2008 Jun 27;133(7):1266-76.

Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Berger MF, Philippakis AA, Qureshi AM, He FS, Estep PW 3rd, Bulyk ML. Nature Biotechnology. 2006 Nov;24(11):1429-35. Epub 2006 Sep 24.