Genetic Ancestry Correlates with Somatic Differences in a Real-World Clinical Cancer Sequencing Cohort. Arora K, Tran TN, Kemel Y, Mehine M, Liu YL, Nandakumar S, Smith SA, Brannon AR, Ostrovnaya I, Stopsack KH, Razavi P, Safonov A, Rizvi HA, Hellmann MD, Vijai J, Reynolds TC, Fagin JA, Carrot-Zhang J, Offit K, Solit DB, Ladanyi M, Schultz N, Zehir A, Brown CL, Stadler ZK, Chakravarty D, Bandlamudi C, Berger MF.  Cancer Discov. 2022 Nov 2;12(11):2552-2565. doi: 10.1158/2159-8290.CD-22-0312.

The context-specific role of germline pathogenicity in tumorigenesis. Srinivasan P, Bandlamudi C, Jonsson P, Kemel Y, Chavan SS, Richards AL, Penson AV, Bielski CM, Fong C, Syed A, Jayakumaran G, Prasad M, Hwee J, Sumer SO, de Bruijn I, Li X, Gao J, Schultz N, Cambria R, Galle J, Mukherjee S, Vijai J, Cadoo KA, Carlo MI, Walsh MF, Mandelker D, Ceyhan-Birsoy O, Shia J, Zehir A, Ladanyi M, Hyman DM, Zhang L, Offit K, Robson ME, Solit DB, Stadler ZK, Berger MF, Taylor BS.  Nat Genet. 2021 Nov;53(11):1577-1585. doi: 10.1038/s41588-021-00949-1. Epub 2021 Nov 5.

Noninvasive Detection of Polyclonal Acquired Resistance to FGFR Inhibition in Patients With Cholangiocarcinoma Harboring FGFR2 Alterations. Varghese AM, Patel J, Janjigian YY, Meng F, Selcuklu SD, Iyer G, Houck-Loomis B, Harding JJ, O’Reilly EM, Abou-Alfa GK, Lowery MA, Berger MF.  JCO Precis Oncol. 2021 Jan 8;5:PO.20.00178. doi: 10.1200/PO.20.00178.

Development of Genome-Derived Tumor Type Prediction to Inform Clinical Cancer Care. Penson A, Camacho N, Zheng Y, Varghese AM, Al-Ahmadie H, Razavi P, Chandarlapaty S, Vallejo CE, Vakiani E, Gilewski T, Rosenberg JE, Shady M, Tsui DWY, Reales DN, Abeshouse A, Syed A, Zehir A, Schultz N, Ladanyi M, Solit DB, Klimstra DS, Hyman DM, Taylor BS, Berger MF. JAMA Oncol. 2019 Nov 14.

Tumour lineage shapes BRCA-mediated phenotypes. Jonsson P, Bandlamudi C, Cheng ML, Srinivasan P, Chavan SS, Friedman ND, Rosen EY, Richards AL, Bouvier N, Selcuklu SD, Bielski CM, Abida W, Mandelker D, Birsoy O, Zhang L, Zehir A, Donoghue MTA, Baselga J, Offit K, Scher HI, O’Reilly EM, Stadler ZK, Schultz N, Socci ND, Viale A, Ladanyi M, Robson ME, Hyman DM, Berger MF, Solit DB, Taylor BS. Nature. 2019 Jul;571(7766):576-579.

Tracking tumour evolution in glioma through liquid biopsies of cerebrospinal fluid. Miller AM, Shah RH, Pentsova EI, Pourmaleki M, Briggs S, Distefano N, Zheng Y, Skakodub A, Mehta SA, Campos C, Hsieh WY, Selcuklu SD, Ling L, Meng F, Jing X, Samoila A, Bale TA, Tsui DWY, Grommes C, Viale A, Souweidane MM, Tabar V, Brennan CW, Reiner AS, Rosenblum M, Panageas KS, DeAngelis LM, Young RJ, Berger MF*, Mellinghoff IK*. Nature. 2019 Jan;565(7741):654-658.

Widespread Selection for Oncogenic Mutant Allele Imbalance in Cancer. Bielski CM, Donoghue MTA, Gadiya M, Hanrahan AJ, Won HH, Chang MT, Jonsson P, Penson AV, Gorelick A, Harris C, Schram AM, Syed A, Zehir A, Chapman PB, Hyman DM, Solit DB, Shannon K, Chandarlapaty S, Berger MF, Taylor BS. Cancer Cell. 2018; 34(5):852-862.e4.

Microsatellite Instability Is Associated With the Presence of Lynch Syndrome Pan-Cancer. Latham A, Srinivasan P, Kemel Y, Shia J, Bandlamudi C, Mandelker D, Middha S, Hechtman J, Zehir A, Dubard-Gault M, Tran C, Stewart C, Sheehan M, Penson A, DeLair D, Yaeger R, Vijai J, Mukherjee S, Galle J, Dickson MA, Janjigian Y, O’Reilly EM, Segal N, Saltz LB, Reidy-Lagunes D, Varghese AM, Bajorin D, Carlo MI, Cadoo K, Walsh MF, Weiser M, Aguilar JG, Klimstra DS, Diaz LA Jr, Baselga J, Zhang L, Ladanyi M, Hyman DM, Solit DB, Robson ME, Taylor BS, Offit K, Berger MF, Stadler ZK. Journal of Clinical Oncology. 2018; JCO1800283.

Genome doubling shapes the evolution and prognosis of advanced cancers. Bielski CM, Zehir A, Penson AV, Donoghue MTA, Chatila W, Armenia J, Chang MT, Schram AM, Jonsson P, Bandlamudi C, Razavi P, Iyer G, Robson ME, Stadler ZK, Schultz N, Baselga J, Solit DB, Hyman DM, Berger MF, Taylor BS. Nature Genetics. 2018; 50(8):1189-1195.

Plasma DNA-Based Molecular Diagnosis, Prognostication, and Monitoring of Patients with EWSR1 Fusion-Positive Sarcomas. Shukla NN, Patel JA, Magnan H, Zehir A, You D, Tang J, Meng F, Samoila A, Slotkin EK, Ambati SR, Chou AJ, Wexler LH, Meyers PA, Peerschke EI, Viale A, Berger MF, Ladanyi M. JCO Precision Oncology. 2017 Nov.CD-22-0312. PMID: 36048199

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; 21(3):374-382.e4.

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 DF, Yao J, 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 AN, Shukla N, 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. Nature Medicine. 2017; 23(6):703-713.

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. Journal of Clinical Oncology. 2016; 34(20):2404-15.

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 Oncology. 2016; 2(1):104-11.

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. The Journal of Molecular Diagnostics. 2015; 17(3):251-64.

Convergent loss of PTEN leads to clinical resistance to a PI(3)Kα inhibitor. Juric D, Castel P, Griffith M, Griffith OL, Won HH, Ellis H, Ebbesen SH, Ainscough BJ, Ramu A, Iyer G, Shah RH, Huynh T, Mino-Kenudson M, Sgroi D, Isakoff S, Thabet A, Elamine L, Solit DB, Lowe SW, Quadt C, Peters M, Derti A, Schegel R, Huang A, Mardis ER, Berger MF, Baselga J, Scaltriti M. Nature. 2015; 518(7538):240-4.

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 Biology. 2014; 15(8):454.

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. Nature Genetics. 2014; 46(5):424-6.

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. Nature Genetics. 2013; 45(12):1439-45.

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; 485(7399):502-6.

High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing. Wagle N*, 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 Discovery. 2012; 2(1):82-93.

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, Sougnez C, 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; 470(7333):214-20.