Preprint

• Kubler K, Karlic R, ,… , Foulkes WD*, Polak P*, Getz G*. Tumor mutational landscape is a record of the pre-malignant state. bioRxiv

Peer-reviewed publications

 2021

• Ahuno ST, Doebley A-L, Ahearn TU, Yarney J, Titiloye N, Hamel N, Adjei E, Joe-Nat Clegg- Lamptey J-N, Edusei L, Awuah B, Song X, Vanderpuye V, Abubakar M, Duggan M, Stover D, Nyarko K, Bartlett JMS, Aitpillah F, Ansong D,  Gardner KL, Boateng FA, Bowcock AM, Caldas C, Foulkes WD, Beatrice WS,  Wiafe-Addai, Garcia-Closas M, Kwarteng A, Ha G*, Figueroa JD*, Polak P*. Circulating tumor DNA is readily detectable among Ghanaian breast cancer patients supporting non-invasive cancer genomic studies in Africa. medRxiv, 2020. npj Precision Oncology (in press) 
• Foulkes WD , Polak P. Li-Fraumeni Syndrome in the Cancer Genomics EraJNCI: Journal of the National Cancer Institute (in press)
• Matis  TS, Zayed N , Labraki B,  de la Durantaye M,  Matis  TA , Valenzuela  JC, Hamel  N , Atayan A, Rivera BP, Tabach Y, Tonin PN, , Orthwein A, Mes-Masson A-M, El-Haffaf ZE , Foulkes WD , and Polak P. Current gene panels account for nearly all homologous recombination repair-associated multiple-case breast cancer families (in press) 
• Singh H, Ha K, Hornick JL, Madha S, Cejas P, Jajoo K, Singh P, Polak P, Lee H, Shivdasani RA. Hybrid stomach-intestinal chromatin states underlie human Barrett’s metaplasia. Gastroenterology. 2021 Jun 3:S0016-5085(21)03084-5. doi: 10.1053/j.gastro.2021.05.057. Online ahead of print. PMID: 34090884 
• Sigel K, Zhou M, Park YA, Mutetwa T, Nadkarni G, Yeh C, Polak P, Sigel C, Conroy T, Juzyna B, Ychou M, Fojo T, Wisnivesky JP, Bates SE. Gemcitabine plus nab-paclitaxel versus FOLFIRINOX for unresected pancreatic cancer: Comparative effectiveness and evaluation of tumor growth in veterans. Semin Oncol. 2021 Feb 23:S0093-7754(21)00006-3. doi: 10.1053/j.seminoncol.2021.02.001. Online ahead of print. PMID: 33714591

2020

• Wang Y, Park JYP, Pacis A, Denroche RE, Jang GH, Zhang A, Cuggia A, Domecq C,    Monlong J, Raitses-Gurevich M, Grant RC, Borgida A, Holter S, Stossel C, Bu S, Masoomian M, Lungu IM, Bartlett JMS, Wilson JM, Gao ZH, Riazalhosseini Y, Asselah J, Bouganim N, Cabrera T, Boucher LM, Valenti D, Biagi J, Greenwood CMT, Polak P, Foulkes WD, Golan T, O’Kane GM, Fischer SE, Knox JJ, Gallinger S, Zogopoulos G. A Preclinical Trial and Molecularly Annotated Patient Cohort Identify Predictive Biomarkers in Homologous Recombination-deficient Pancreatic Cancer. Clin Cancer Res. 2020 Oct 15;26(20):5462-5476 PMID: 32816949.

• Mutetwa T, Foulkes WD, Polak P.Olaparib for Metastatic Castration-Resistant Prostate Cancer. The New England Journal of Medicine 2020. PMID: 383(9)890.

• Hughley R, Karlic R, Himanshu J, Turnbull C, Foulkes WD, Polak P. Etiologic Index – A Case-Only Measure of BRCA1/2-Associated Cancer Risk.  The New England Journal of Medicine. 2020. PMID: 32668122.

• Foulkes WD, Polak P. Bilateral Tumors – Inherited or Acquired? The New England Journal of Medicine. 2020 Jul 16;383(3):280-282.PMID: 32668120.

• Sanford JA, Nogiec CD, Lindholm ME, Adkins JN, Amar D, Dasari S, Drugan JK, Fernández FM, Radom-Aizik S, Schenk S, Snyder MP, Tracy RP, Vanderboom P, Trappe S, Walsh MJ; Molecular Transducers of Physical Activity Consortium.Molecular Transducers of Physical Activity Consortium (MoTrPAC): Mapping the Dynamic Responses to Exercise. Cell. 2020 Jun 25;181(7):1464-1474. doi: 10.1016/j.cell.2020.06.004. PMID: 32589957 Review.

• Koga Y, Song H, Chalmers ZR, Newberg J, Kim E, Carrot-Zhang J, Piou D, Polak P, Abdulkadir SA, Ziv E, Meyerson M, Frampton GM, Campbell JD, Huang FW. Genomic Profiling of Prostate Cancers from Men with African and European Ancestry. Clin Cancer Res. 2020 Jul 10. doi: 10.1158/1078-0432.CCR-19-4112. Online ahead of print. PMID: 32651179

• Sigel K, Swartz T, Golden E, Paranjpe I, Somani S, Richter F, De Freitas JK, Miotto R, Zhao S, Polak P, Mutetwa T, Factor S, Mehandru S, Mullen M, Cossarini F, Bottinger E, Fayad Z, Merad M, Gnjatic S, Aberg J, Charney A, Nadkarni G, Glicksberg BS. Covid-19 and People with HIV Infection: Outcomes for Hospitalized Patients in New York City. Clin Infect Dis. 2020 Jun 28:ciaa880. doi: 10.1093/cid/ciaa880. Online ahead of print. PMID: 32594164

• Ha K, Fujita M, Karlić R, Yang S, Xue R, Zhang C, Bai F, Zhang N, Hoshida Y,Polak P, Nakagawa H, Kim HG, Lee H.   (2020) Somatic mutation landscape reveals differential variability of cell-of-origin for primary liver cancer.   Heliyon;6(2):e03350

• Pan-cancer analysis of whole genomes. (2020) ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium.  Nature.578(7793):82-93.

• Jiao W*, Atwal G*, Polak P*, Karlic R, Cuppen E; PCAWG Tumor Subtypes and Clinical Translation Working Group, Danyi A, de Ridder J, van Herpen C, Lolkema MP, Steeghs N, Getz G, Morris Q, Stein LD; PCAWG Consortium. (2020). A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns. Nature Communication. 2020 Feb 5;11(1):728.

2019

• Yizhak K, Aguet F, Kim J, Hess JM, Kübler K, Grimsby J, Frazer R, Zhang H, Haradhvala NJ, Rosebrock D, Livitz D, Li X, Arich-Landkof E, Shoresh N, Stewart C, Segrè AV, Branton PA, Polak P, Ardlie KG, Getz G. (2019) RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues. Science. 7;364(6444).

• Castellsagué E, Li R, Aligue R, González S, Sanz J, Martin E, Velasco À, Capellá G, Stewart CJR, Vidal A, Majewski J, Rivera B, Polak P, Matias-Guiu X, Brunet J, Foulkes WD. (2019) Novel POLE pathogenic germline variants in a family with multiple primary tumors results in distinct mutational signatures.  Human Mutation. 40(1):36-41. doi: 10.1002/humu.23676.

2018

• 30) Miao D, Margolis CA, Vokes NI, Liu D, Taylor-Weiner A, Wankowicz SM, Adeegbe D, Keliher D, Schilling B, Tracy A, Manos M, Chau NG, Hanna GJ, Polak P, Rodig SJ, Signoretti S, Sholl LM, Engelman JA, Getz G, Jänne PA, Haddad RI, Choueiri TK, Barbie DA, Haq R, Awad MM, Schadendorf D, Hodi FS, Bellmunt J, Wong KK, Hammerman P, Van Allen EM. (2018) Genomic correlates of response to immune checkpoint blockade in microsatellite-stable solid tumors. Nature Genetics. 1271-1281. doi: 10.1038/s41588-018-0200-2.

• Gopal RK, Kübler K, Calvo SE, Polak P, Livitz D, Rosebrock D, Sadow PM, Campbell B, Donovan SE, Amin S, Gigliotti BJ, Grabarek Z, Hess JM, Stewart C, Braunstein LZ, Arndt PF, Mordecai S, Shih AR, Chaves F, Zhan T, Lubitz CC, Kim J, Iafrate AJ, Wirth L, Parangi S, Leshchiner I, Daniels GH, Mootha VK, Dias-Santagata D, Getz G, McFadden DG. (2018) Widespread Chromosomal Losses and Mitochondrial DNA Alterations as Genetic Drivers in Hürthle Cell Carcinoma. Cancer Cell.;34(2):242-255.e5. doi: 10.1016/j.ccell.2018.06.013.

• Viswanathan SR, Ha G, Hoff AM, Wala JA, Carrot-Zhang J, Whelan CW, Haradhvala NJ, Freeman SS, Reed SC, Rhoades J, Polak P, Cipicchio M, Wankowicz SA, Wong A, Kamath T, Zhang Z, Gydush GJ, Rotem D; PCF/SU2C International Prostate Cancer Dream Team, Love JC, Getz G, Gabriel S, Zhang CZ, Dehm SM, Nelson PS, Van Allen EM, Choudhury AD, Adalsteinsson VA, Beroukhim R, Taplin ME, Meyerson M. (2018) Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing.  Cell.;174(2):433-447.e19. doi: 10.1016/j.cell.2018.05.036. Epub 2018 Jun 18.

• Rivera B, Polak P, Foulkes WD. (2018) Monogenic Diseases of DNA Repair. New England Journal Medicine. 378(5):491

•  Wardell CP, Fujita M, Yamada T, Simbolo M, Fassan M, Karlic R, Polak P, Kim J, Hatanaka Y, Maejima K, Lawlor RT, Nakanishi Y, Mitsuhashi T, Fujimoto A, Furuta M, Ruzzenente A, Conci S, Oosawa A, Sasaki-Oku A, Nakano K, Tanaka H, Yamamoto Y, Michiaki K, Kawakami Y, Aikata H, Ueno M, Hayami S, Gotoh K, Ariizumi SI, Yamamoto M, Yamaue H, Chayama K, Miyano S, Getz G, Scarpa A, Hirano S, Nakamura T, Nakagawa H.(2018) Genomic Characterization of Biliary Tract Cancers Identifies Driver Genes and Predisposing Mutations. Journal of Hepatology pii: S0168-8278(18)30021-7

2017

• Adalsteinsson VA, Ha G, Freeman SS, Choudhury AD, Stover DG, Parsons HA, Gydush G, Reed SC, Rotem D, Rhoades J, Loginov D, Livitz D, Rosebrock D, Leshchiner I, Kim J, Stewart C, Rosenberg M, Francis JM, Zhang CZ, Cohen O, Oh C, Ding H, Polak P, Lloyd M, Mahmud S, Helvie K, Merrill MS, Santiago RA, O’Connor EP, Jeong SH, Leeson R, Barry RM, Kramkowski JF, Zhang Z, Polacek L, Lohr JG, Schleicher M, Lipscomb E, Saltzman A, Oliver NM, Marini L, Waks AG, Harshman LC, Tolaney SM, Van Allen EM, Winer EP, Lin NU, Nakabayashi M, Taplin ME, Johannessen CM, Garraway LA, Golub TR, Boehm JS, Wagle N, Getz G, Love JC, Meyerson M. (2017) Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors. Nature Communication 8(1):1324

• Maruvka YE, Mouw KW, Karlic R, Parasuraman P, Kamburov A, Polak P, Haradhvala NJ, Hess JM, Rheinbay E, Brody Y, Koren A, Braunstein LZ, D’Andrea A, Lawrence MS, Bass A, Bernards A, Michor F, Getz G. (2017) Analysis of somatic microsatellite indels identifies driver events in human tumors. Nature Biotechnology 35(10):951-959

• Polak P*, Kim J*, Braunstein LZ*, Tao G., Karlic R., Rosebrock D., Livitz D., Kübler K., Mouw KW., Haradhvala NJ., Kamburov A, Maruvka YE., Leshchiner I., Lander ES., Golub TR., Zick A.,  Lawrence MS., Haber DA, Laird PW, Shen H., Ellisen LW., D’Andrea A., Chanock SJ., Foulkes WD and Getz G  (2017) A mutational signature reveals alterations underlying deficient homologous recombination repair in breast cancer.  Nature Genetics 49(10):1476-1486 *Equal contribution

• Cancer Genome Atlas Research Network (Polak P) Integrated genomic characterization of oesophageal carcinoma. Nature 2017 12;541(7636):169-175.

2016

• Kim J.*, Mouw KW. *, Polak P.*, Braunstein LZ., Kamburov A., Kwiatkowski D., Rosenberg JE., Van Allen EM., D’Andrea A., Getz G., (2016) Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors.   Nature Genetics 48, 600–606  *Equal contribution
• Haradhvala, N.*, Polak P.*, Koren A., Stojanov P., Covington K., Shinbrot E., Hess J., Rheinbay, E., Kim J., Maruvka, Y., Braunstein LZ., Wheeler D., Lawrence M., Getz G. (2016) Mutational strand asymmetries in cancer genomes reveal Mechanisms of DNA Damage and repair. Cell 164(3):538-49  *Equal contribution

2015

• Kazanov MD, Roberts SA, Polak P, Stamatoyannopoulos J, Klimczak LJ, Gordenin DA, Sunyaev SR. (2015) APOBEC-Induced Cancer Mutations Are Uniquely Enriched in Early-Replicating, Gene-Dense, and Active Chromatin Regions. Cell Reports. 10;13(6):1103-1109.

• Kasar S., Jaegil K., Improgo R., Tiao G., Polak P, Lawrence MS., Kiezun A., Fernandes S., Bahl S., Sougnez C., Gabriel S., Lander ES., Haesook K., Getz G., Brown JR (2015) Whole-genome sequencing reveals two Activation-Induced Cytidine Deaminase signatures during Indolent Chronic Lymphocytic Leukemia evolution.  Nature Communications 6: 8866

• Kamburov A., Lawrence MS., Polak P, Leshchiner I., Lage K, Golub TR., Lander ES, Getz G. (2015) Comprehensive assessment of cancer missense mutation clustering in protein structures. Proc Natl Acad Sci U S A. 112(40): E5486-95

• Francioli LC. *, Polak P.*, Koren A.*, Menelaou A., Chun S., Renkens I., Genome of the Netherlands Consortium, van Duijn CN., Swertz M., Wijmenga C., van Ommen G., Slagboom PE., Boomsma DI., Ye K., Guryev G., Arndt PF., Kloosterman, WP., de Bakker PIW., Sunyaev, SR. (2015) Genome-wide patterns and properties of de novo mutations in humans.  Nature Genetics 47(7):822-826. *Equal contribution

• Polak, P, * Karlic, R*., Koren, A., Thurman, B., Sandstrom, Lawrence, M. S., R., Reynolds, A., Rynes, E., Vlahovicek, K., Stamatoyannopoulos, J., Sunyaev, S. (2015) Cell-of-origin chromatin organization shapes the mutational landscape of cancer.  Nature 518(7539):360-364. *Equal contribution

• Roadmap Epigenomics Consortium (2015) Integrative analysis of 111 reference human epigenomes. Nature 518(7539):317-330.

2014

• Koren A., Handsaker RE., Kamitaki N., Karlic R., Ghosh S., Polak P, Eggan K., McCarrol S.A. (2014) Genetic Variation in Human DNA Replication Timing Cell 159 (5) 1015-1026

• Francioli, LC., Genome of the Netherlands Project Consortium (Polak P.), De-Bakker, P. I. W. (2014) Whole-genome sequence variation, population structure and demographic history of the Netherlands    Nature Genetics 46, 818-825

• Polak, P*, Lawrence, MS.*, Haugen, E., Stoletzki Nm, Stojanov, P., Thurman, RE., Garraway, LA., Mirkin S., Getz, G., Stamatoyannopoulos JA., Sunyaev, SR. (2014) Reduced local mutation density in regulatory DNA of cancer genomes linked to DNA repair Nature Biotechnology 32, 71-75  *Equal contribution

2013

• Lawrence, MS.*, Stojanov P*., Polak P.*, Kryukov GV., Cibulskis K., Sivachenko A., Carter SL., Stewart C., Mermel CH., Roberts SA., Kiezun A., Hammerman PS., McKenna A., Drier Y., Zou, L., Ramos, A.H., Pugh TJ., Stransky N., Helman E., Kim J., Sougnez C., Ambrogio L., Nickerson E., Shefler E., Cortés ML., Auclair D., Saksena G., Voet D., Noble M., DiCara D, Lin P., Lichtenstein L., Heiman DI., Fennell T., Imielinski M., Hernandez B., Hodis E., Baca S., Dulak AM., Lohr J., Landau DA., Wu C., Melendez-Zajgla J., Hidalgo-Miranda A., Koren, A., McCarroll SA., Mora J., Lee, RS., Crompton B, Onofrio R., Parkin M., Winckler W., Ardlie K., Gabriel SB., Roberts CW., Biegel JA., Stegmaier K., Bass, AJ., Garraway LA., Meyerson,M., Golub, TR., Gordenin,DA., Sunyaev SR., Lander ES., Getz G. (2013)  Mutational heterogeneity in cancer and the search for new cancer-associated genes.  Nature 499 (7457):214-218.*Equal contribution4

2012

• Koren A, Polak P, Nemesh J, Michaelson JJ, Sebat J , Sunyaev SR, McCarroll SA. (2012) Differential relationship of DNA replication timing to different forms of human mutation and variation. American Journal of Human Genetics 91(6):1033-40

• Neale BM., Kou Y., Liu L., Ma’ayan A, Samocha KE., Sabo A., Lin CF., Stevens C., Wang LS., Makarov V., Polak P. et al. (2012)  Patterns and rates of exonic de novo mutations in autism spectrum disorders Nature 485 (7397) 242-245.

2011-2006

• Kim EB, Fang X, Fushan AA, Huang Z, Lobanov AV, Han L, Marino SM, Un X, Turanov AA, Yang P, Yim SH, Zhao X, Kasaikina MV, Stoletzki N, Peng C, Polak P et al. (2011) Genome sequencing reveals insights into physiology and longevity of the naked mole rat.  Nature 479 (7372) 223-7
• Polak P, R. Querfurth R., Arndt PF. (2010) The evolution of transcription-associated biases of mutations across vertebrates.  BMC Evolutionary Biology 10

• Polak P. and Arndt PF. (2009)  Long Range bi-directional strand asymmetries originate at CpG islands in the human genome Genome Biology and Evolution 2009, 189
• Polak P. and Arndt PF. (2008) Transcription induces strand-specific mutations at the 5′ end of human genes, Genome Research 18, 1216-1223.
• Polak P. and Wolansky, G. (2007) nThe Lazy Travelling Salesman Problem, Control, Optimization and Calculus of Variations 13, (3) 538-552
• Polak P. and E. Domany E., (2006) Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes.  BMC Genomics 7 p. 133
• Geva-Zatorsky N., Rosenfeld N., Itzkovitz S., Milo R., Sigal A., Dekel E., Yarnitzky T., Liron Y., Polak  P., Lahav G. and Alon,U. (2006) Oscillations and variability in the p53 system,  Molecular Systems Biology 2