Publications

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2018
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, Monnat RJ, Xiao Y, Wang C. Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas. Cell Rep. 2018 ;23(1):239-254.e6.
Shen H, Shih J, Hollern DP, Wang L, Bowlby R, Tickoo SK, Thorsson V, Mungall AJ, Newton Y, Hegde AM, Armenia J, Sánchez-Vega F, Pluta J, Pyle LC, Mehra R, Reuter VE, Godoy G, Jones J, Shelley CS, Feldman DR, Vidal DO, Lessel D, Kulis T, Cárcano FM, Leraas KM, Lichtenberg TM, Brooks D, Cherniack AD, Cho J, Heiman DI, Kasaian K, Liu M, Noble MS, Xi L, Zhang H, Zhou W, ZenKlusen JC, Hutter CM, Felau I, Zhang J, Schultz N, Getz G, Meyerson M, Stuart JM, Akbani R, Wheeler DA, Laird PW, Nathanson KL, Cortessis VK, Hoadley KA. Integrated Molecular Characterization of Testicular Germ Cell Tumors. Cell Rep. 2018 ;23(11):3392-3406.
Greytak SR, Engel KB, Zmuda E, Casas-Silva E, Guan P, Hoadley KA, Mungall AJ, Wheeler DA, Doddapaneni H, Moore HM. National Cancer Institute Biospecimen Evidence-Based Practices: Harmonizing Procedures for Nucleic Acid Extraction from Formalin-Fixed, Paraffin-Embedded Tissue. Biopreserv Biobank. 2018 ;16(4):247-250.
Ding L, Bailey MH, Porta-Pardo E, Thorsson V, Colaprico A, Bertrand D, Gibbs DL, Weerasinghe A, Huang K-L, 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 JClaude, Hoadley KA, Wendl MC, Shmulevich L, Lazar AJ, Wheeler DA, Getz G. Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics. Cell. 2018 ;173(2):305-320.e10.
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 DA, Ding L. Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines. Cell Syst. 2018 ;6(3):271-281.e7.
2017
Chakraborty R, Hampton OA, Abhyankar H, Zinn DJ, Grimes A, Skull B, Eckstein O, Mahmood N, Wheeler DA, López-Terrada D, Peters TL, Hicks JM, Elghetany T, Krance R, Poulikakos PI, Merad M, McClain KL, Allen CE, Parsons DW. Activating MAPK1 (ERK2) mutation in an aggressive case of disseminated juvenile xanthogranuloma. Oncotarget. 2017 ;8(28):46065-46070.
Moss TJ, Qi Y, Xi L, Peng B, Kim T-B, Ezzedine NE, Mosqueda ME, Guo CC, Czerniak BA, Ittmann M, Wheeler DA, Lerner SP, Matin SF. Comprehensive Genomic Characterization of Upper Tract Urothelial Carcinoma. Eur Urol. 2017 ;72(4):641-649.
Goschzik T, Gessi M, Dreschmann V, Gebhardt U, Wang L, Yamaguchi S, Wheeler DA, Lauriola L, Lau CC, Müller HL, Pietsch T. Genomic Alterations of Adamantinomatous and Papillary Craniopharyngioma. J Neuropathol Exp Neurol. 2017 ;76(2):126-134.
Sumazin P, Chen Y, Treviño LR, Sarabia SF, Hampton OA, Patel K, Mistretta T-A, Zorman B, Thompson P, Heczey A, Comerford S, Wheeler DA, Chintagumpala M, Meyers R, Rakheja D, Finegold MJ, Tomlinson G, D Parsons W, López-Terrada D. Genomic analysis of hepatoblastoma identifies distinct molecular and prognostic subgroups. Hepatology. 2017 ;65(1):104-121.
Farshidfar F, Zheng S, Gingras M-C, Newton Y, Shih J, A Robertson G, Hinoue T, Hoadley KA, Gibb EA, Roszik J, Covington KR, Wu C-C, Shinbrot E, Stransky N, Hegde A, Yang JDong, Reznik E, Sadeghi S, Pedamallu CSekhar, Ojesina AI, Hess JM, J Auman T, Rhie SK, Bowlby R, Borad MJ, Zhu AX, Stuart JM, Sander C, Akbani R, Cherniack AD, Deshpande V, Mounajjed T, Foo WChin, Torbenson MS, Kleiner DE, Laird PW, Wheeler DA, McRee AJ, Bathe OF, Andersen JB, Bardeesy N, Roberts LR, Kwong LN. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles. Cell Rep. 2017 ;18(11):2780-2794.
Gao B, Huang C, Kernstine K, Pelekanou V, Kluger Y, Jiang T, Peters-Hall JR, Coquelin M, Girard L, Zhang W, Huffman K, Oliver D, Kinose F, Haura E, Teer JK, Rix U, Le AT, Aisner DL, Varella-Garcia M, Doebele RC, Covington KR, Hampton OA, Doddapaneni H, Jayaseelan JC, Hu J, Wheeler DA, Shay JW, Rimm DL, Gazdar A, Minna JD. Non-malignant respiratory epithelial cells preferentially proliferate from resected non-small cell lung cancer specimens cultured under conditionally reprogrammed conditions. Oncotarget. 2017 ;8(7):11114-11126.
Hampton OA, English AC, Wang M, Salerno WJ, Liu Y, Muzny DM, Han Y, Wheeler DA, Worley KC, Lupski JR, Gibbs RA. SVachra: a tool to identify genomic structural variation in mate pair sequencing data containing inward and outward facing reads. BMC Genomics. 2017 ;18(Suppl 6):691.
Scarpa A, Chang DK, Nones K, Corbo V, Patch A-M, Bailey P, Lawlor RT, Johns AL, Miller DK, Mafficini A, Rusev B, Scardoni M, Antonello D, Barbi S, Sikora KO, Cingarlini S, Vicentini C, McKay S, Quinn MCJ, Bruxner TJC, Christ AN, Harliwong I, Idrisoglu S, McLean S, Nourse C, Nourbakhsh E, Wilson PJ, Anderson MJ, J Fink L, Newell F, Waddell N, Holmes O, Kazakoff SH, Leonard C, Wood S, Xu Q, Nagaraj SHiriyur, Amato E, Dalai I, Bersani S, Cataldo I, Tos APDei, Capelli P, Davì MVittoria, Landoni L, Malpaga A, Miotto M, Whitehall VLJ, Leggett BA, Harris JL, Harris J, Jones MD, Humphris J, Chantrill LA, Chin V, Nagrial AM, Pajic M, Scarlett CJ, Pinho A, Rooman I, Toon C, Wu J, Pinese M, Cowley M, Barbour A, Mawson A, Humphrey ES, Colvin EK, Chou A, Lovell JA, Jamieson NB, Duthie F, Gingras M-C, Fisher WE, Dagg RA, Lau LMS, Lee M, Pickett HA, Reddel RR, Samra JS, Kench JG, Merrett ND, Epari K, Nguyen NQ, Zeps N, Falconi M, Simbolo M, Butturini G, Van Buren G, Partelli S, Fassan M, Khanna KKum, Gill AJ, Wheeler DA, Gibbs RA, Musgrove EA, Bassi C, Tortora G, Pederzoli P, Pearson JV, Waddell N, Biankin AV, Grimmond SM. Whole-genome landscape of pancreatic neuroendocrine tumours. Nature. 2017 ;543(7643):65-71.
2016
Wang L, Wheeler DA, Prchal JT. Acquired uniparental disomy of chromosome 9p in hematologic malignancies. Exp Hematol. 2016 ;44(8):644-52.
Chakraborty R, Burke TM, Hampton OA, Zinn DJ, Lim KPhaik Har, Abhyankar H, Scull B, Kumar V, Kakkar N, Wheeler DA, Roy A, Poulikakos PI, Merad M, McClain KL, D Parsons W, Allen CE. Alternative genetic mechanisms of BRAF activation in Langerhans cell histiocytosis. Blood. 2016 ;128(21):2533-2537.
Gingras M-C, Covington KR, Chang DK, Donehower LA, Gill AJ, Ittmann MM, Creighton CJ, Johns AL, Shinbrot E, Dewal N, Fisher WE, Pilarsky C, Grützmann R, Overman MJ, Jamieson NB, Van Buren G, Drummond J, Walker K, Hampton OA, Xi L, Muzny DM, Doddapaneni H, Lee SL, Bellair M, Hu J, Han Y, Dinh HH, Dahdouli M, Samra JS, Bailey P, Waddell N, Pearson JV, Harliwong I, Wang H, Aust D, Oien KA, Hruban RH, Hodges SE, McElhany A, Saengboonmee C, Duthie FR, Grimmond SM, Biankin AV, Wheeler DA, Gibbs RA. Ampullary Cancers Harbor ELF3 Tumor Suppressor Gene Mutations and Exhibit Frequent WNT Dysregulation. Cell Rep. 2016 ;14(4):907-19.
Lanikova L, Babosova O, Swierczek S, Wang L, Wheeler DA, Divoky V, Korinek V, Prchal JT. Coexistence of gain-of-function JAK2 germ line mutations with JAK2V617F in polycythemia vera. Blood. 2016 ;128(18):2266-2270.
Zheng S, Cherniack AD, Dewal N, Moffitt RA, Danilova L, Murray BA, Lerario AM, Else T, Knijnenburg TA, Ciriello G, Kim S, Assie G, Morozova O, Akbani R, Shih J, Hoadley KA, Choueiri TK, Waldmann J, Mete O, A Robertson G, Wu H-T, Raphael BJ, Shao L, Meyerson M, Demeure MJ, Beuschlein F, Gill AJ, Sidhu SB, Almeida MQ, Fragoso MCBV, Cope LM, Kebebew E, Habra MA, Whitsett TG, Bussey KJ, Rainey WE, Asa SL, Bertherat J, Fassnacht M, Wheeler DA, Hammer GD, Giordano TJ, Verhaak RGW. Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma. Cancer Cell. 2016 ;29(5):723-36.
Chitsazzadeh V, Coarfa C, Drummond JA, Nguyen T, Joseph A, Chilukuri S, Charpiot E, Adelmann CH, Ching G, Nguyen TN, Nicholas C, Thomas VD, Migden M, MacFarlane D, Thompson E, Shen J, Takata Y, McNiece K, Polansky MA, Abbas HA, Rajapakshe K, Gower A, Spira A, Covington KR, Xiao W, Gunaratne P, Pickering C, Frederick M, Myers JN, Shen L, Yao H, Su X, Rapini RP, Wheeler DA, Hawk ET, Flores ER, Tsai KY. Cross-species identification of genomic drivers of squamous cell carcinoma development across preneoplastic intermediates. Nat Commun. 2016 ;7:12601.
van der Crabben SN, Hennus MP, McGregor GA, Ritter DI, Nagamani SCS, Wells OS, Harakalova M, Chinn IK, Alt A, Vondrova L, Hochstenbach R, van Montfrans JM, Terheggen-Lagro SW, van Lieshout S, van Roosmalen MJ, Renkens I, Duran K, Nijman IJ, Kloosterman WP, Hennekam E, Orange JS, van Hasselt PM, Wheeler DA, Palecek JJ, Lehmann AR, Oliver AW, Pearl LH, Plon SE, Murray JM, van Haaften G. Destabilized SMC5/6 complex leads to chromosome breakage syndrome with severe lung disease. J Clin Invest. 2016 ;126(8):2881-92.
D Parsons W, Roy A, Yang Y, Wang T, Scollon S, Bergstrom K, Kerstein RA, Gutierrez S, Petersen AK, Bavle A, Lin FY, López-Terrada DH, Monzon FA, M Hicks J, Eldin KW, Quintanilla NM, Adesina AM, Mohila CA, Whitehead W, Jea A, Vasudevan SA, Nuchtern JG, Ramamurthy U, McGuire AL, Hilsenbeck SG, Reid JG, Muzny DM, Wheeler DA, Berg SL, Chintagumpala MM, Eng CM, Gibbs RA, Plon SE. Diagnostic Yield of Clinical Tumor and Germline Whole-Exome Sequencing for Children With Solid Tumors. JAMA Oncol. 2016 ;.
Bailey P, Chang DK, Nones K, Johns AL, Patch A-M, Gingras M-C, Miller DK, Christ AN, Bruxner TJC, Quinn MC, Nourse C, L Murtaugh C, Harliwong I, Idrisoglu S, Manning S, Nourbakhsh E, Wani S, Fink L, Holmes O, Chin V, Anderson MJ, Kazakoff S, Leonard C, Newell F, Waddell N, Wood S, Xu Q, Wilson PJ, Cloonan N, Kassahn KS, Taylor D, Quek K, Robertson A, Pantano L, Mincarelli L, Sanchez LN, Evers L, Wu J, Pinese M, Cowley MJ, Jones MD, Colvin EK, Nagrial AM, Humphrey ES, Chantrill LA, Mawson A, Humphris J, Chou A, Pajic M, Scarlett CJ, Pinho AV, Giry-Laterriere M, Rooman I, Samra JS, Kench JG, Lovell JA, Merrett ND, Toon CW, Epari K, Nguyen NQ, Barbour A, Zeps N, Moran-Jones K, Jamieson NB, Graham JS, Duthie F, Oien K, Hair J, Grützmann R, Maitra A, Iacobuzio-Donahue CA, Wolfgang CL, Morgan RA, Lawlor RT, Corbo V, Bassi C, Rusev B, Capelli P, Salvia R, Tortora G, Mukhopadhyay D, Petersen GM, Munzy DM, Fisher WE, Karim SA, Eshleman JR, Hruban RH, Pilarsky C, Morton JP, Sansom OJ, Scarpa A, Musgrove EA, Bailey U-MHagbo, Hofmann O, Sutherland RL, Wheeler DA, Gill AJ, Gibbs RA, Pearson JV, Waddell N, Biankin AV, Grimmond SM. Genomic analyses identify molecular subtypes of pancreatic cancer. Nature. 2016 ;531(7592):47-52.
Farrar JE, Schuback HL, Ries RE, Wai D, Hampton OA, Treviño LR, Alonzo TA, Auvil JMGuidry, Davidsen TM, Gesuwan P, Hermida L, Muzny DM, Dewal N, Rustagi N, Lewis LR, Gamis AS, Wheeler DA, Smith MA, Gerhard DS, Meshinchi S. Genomic Profiling of Pediatric Acute Myeloid Leukemia Reveals a Changing Mutational Landscape from Disease Diagnosis to Relapse. Cancer Res. 2016 ;76(8):2197-205.
Lin FY, Bergstrom K, Person R, Bavle A, Ballester LY, Scollon S, Raesz-Martinez R, Jea A, Birchansky S, Wheeler DA, Berg SL, Chintagumpala MM, Adesina AM, Eng CM, Roy A, Plon SE, D Parsons W. Integrated tumor and germline whole-exome sequencing identifies mutations in MAPK and PI3K pathway genes in an adolescent with rosette-forming glioneuronal tumor of the fourth ventricle. Cold Spring Harb Mol Case Stud. 2016 ;2(5):a001057.
Rustagi N, Hampton OA, Li J, Xi L, Gibbs RA, Plon SE, Kimmel M, Wheeler DA. ITD assembler: an algorithm for internal tandem duplication discovery from short-read sequencing data. BMC Bioinformatics. 2016 ;17:188.