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Items: 1 to 50 of 193

1.

An enhanced genetic model of colorectal cancer progression history.

Yang L, Wang S, Lee JJ, Lee S, Lee E, Shinbrot E, Wheeler DA, Kucherlapati R, Park PJ.

Genome Biol. 2019 Aug 15;20(1):168. doi: 10.1186/s13059-019-1782-4.

2.

Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas.

Donehower LA, Soussi T, Korkut A, Liu Y, Schultz A, Cardenas M, Li X, Babur O, Hsu TK, Lichtarge O, Weinstein JN, Akbani R; Cancer Genome Atlas Network, Wheeler DA.

Cell Rep. 2019 Jul 30;28(5):1370-1384.e5. doi: 10.1016/j.celrep.2019.07.001.

3.

Framework for microRNA variant annotation and prioritization using human population and disease datasets.

Oak N, Ghosh R, Huang KL, Wheeler DA, Ding L, Plon SE.

Hum Mutat. 2019 Jan;40(1):73-89. doi: 10.1002/humu.23668. Epub 2018 Nov 8.

PMID:
30302893
4.

Gene expression profiling and immune cell-type deconvolution highlight robust disease progression and survival markers in multiple cohorts of CTCL patients.

Lefrançois P, Xie P, Wang L, Tetzlaff MT, Moreau L, Watters AK, Netchiporouk E, Provost N, Gilbert M, Ni X, Sasseville D, Wheeler DA, Duvic M, Litvinov IV.

Oncoimmunology. 2018 May 31;7(8):e1467856. doi: 10.1080/2162402X.2018.1467856. eCollection 2018.

5.

Rare Variants in Known Susceptibility Loci and Their Contribution to Risk of Lung Cancer.

Liu Y, Lusk CM, Cho MH, Silverman EK, Qiao D, Zhang R, Scheurer ME, Kheradmand F, Wheeler DA, Tsavachidis S, Armstrong G, Zhu D, Wistuba II, Chow CB, Behrens C, Pikielny CW, Neslund-Dudas C, Pinney SM, Anderson M, Kupert E, Bailey-Wilson J, Gaba C, Mandal D, You M, de Andrade M, Yang P, Field JK, Liloglou T, Davies M, Lissowska J, Swiatkowska B, Zaridze D, Mukeriya A, Janout V, Holcatova I, Mates D, Milosavljevic S, Scelo G, Brennan P, McKay J, Liu G, Hung RJ, Christiani DC, Schwartz AG, Amos CI, Spitz MR.

J Thorac Oncol. 2018 Oct;13(10):1483-1495. doi: 10.1016/j.jtho.2018.06.016. Epub 2018 Jul 4.

PMID:
29981437
6.

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.

7.

National Cancer Institute Biospecimen Evidence-Based Practices: Harmonizing Procedures for Nucleic Acid Extraction from Formalin-Fixed, Paraffin-Embedded Tissue.

Greytak SR, Engel KB, Zmuda E, Casas-Silva E, Guan P, Hoadley KA, Mungall AJ, Wheeler DA, Doddapaneni HV, Moore HM.

Biopreserv Biobank. 2018 Aug;16(4):247-250. doi: 10.1089/bio.2018.0046. Epub 2018 Jun 19. No abstract available.

8.

Integrated Molecular Characterization of Testicular Germ Cell Tumors.

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; Cancer Genome Atlas Research Network, Akbani R, Wheeler DA, Laird PW, Nathanson KL, Cortessis VK, Hoadley KA.

Cell Rep. 2018 Jun 12;23(11):3392-3406. doi: 10.1016/j.celrep.2018.05.039.

9.

Chemistry-First Approach for Nomination of Personalized Treatment in Lung Cancer.

McMillan EA, Ryu MJ, Diep CH, Mendiratta S, Clemenceau JR, Vaden RM, Kim JH, Motoyaji T, Covington KR, Peyton M, Huffman K, Wu X, Girard L, Sung Y, Chen PH, Mallipeddi PL, Lee JY, Hanson J, Voruganti S, Yu Y, Park S, Sudderth J, DeSevo C, Muzny DM, Doddapaneni H, Gazdar A, Gibbs RA, Hwang TH, Heymach JV, Wistuba I, Coombes KR, Williams NS, Wheeler DA, MacMillan JB, Deberardinis RJ, Roth MG, Posner BA, Minna JD, Kim HS, White MA.

Cell. 2018 May 3;173(4):864-878.e29. doi: 10.1016/j.cell.2018.03.028. Epub 2018 Apr 19.

10.

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.

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 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.

12.

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.

13.

Genetic Mechanisms of Immune Evasion in Colorectal Cancer.

Grasso CS, Giannakis M, Wells DK, Hamada T, Mu XJ, Quist M, Nowak JA, Nishihara R, Qian ZR, Inamura K, Morikawa T, Nosho K, Abril-Rodriguez G, Connolly C, Escuin-Ordinas H, Geybels MS, Grady WM, Hsu L, Hu-Lieskovan S, Huyghe JR, Kim YJ, Krystofinski P, Leiserson MDM, Montoya DJ, Nadel BB, Pellegrini M, Pritchard CC, Puig-Saus C, Quist EH, Raphael BJ, Salipante SJ, Shin DS, Shinbrot E, Shirts B, Shukla S, Stanford JL, Sun W, Tsoi J, Upfill-Brown A, Wheeler DA, Wu CJ, Yu M, Zaidi SH, Zaretsky JM, Gabriel SB, Lander ES, Garraway LA, Hudson TJ, Fuchs CS, Ribas A, Ogino S, Peters U.

Cancer Discov. 2018 Jun;8(6):730-749. doi: 10.1158/2159-8290.CD-17-1327. Epub 2018 Mar 6.

14.

SVachra: a tool to identify genomic structural variation in mate pair sequencing data containing inward and outward facing reads.

Hampton OA, English AC, Wang M, Salerno WJ, Liu Y, Muzny DM, Han Y, Wheeler DA, Worley KC, Lupski JR, Gibbs RA.

BMC Genomics. 2017 Oct 3;18(Suppl 6):691. doi: 10.1186/s12864-017-4021-y.

15.

Corrigendum: Whole-genome landscape of pancreatic neuroendocrine tumours.

Scarpa A, Chang DK, Nones K, Corbo V, Patch AM, 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, Fink JL, Newell F, Waddell N, Holmes O, Kazakoff SH, Leonard C, Wood S, Xu Q, Hiriyur Nagaraj S, Amato E, Dalai I, Bersani S, Cataldo I, Dei Tos AP, Capelli P, Vittoria Davì M, 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 MC, 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; Australian Pancreatic Cancer Genome Initiative, Khanna KK, Gill AJ, Wheeler DA, Gibbs RA, Musgrove EA, Bassi C, Tortora G, Pederzoli P, Pearson JV, Waddell N, Biankin AV, Grimmond SM.

Nature. 2017 Oct 26;550(7677):548. doi: 10.1038/nature24026. Epub 2017 Sep 27.

PMID:
28953865
16.

Analysis of Genomes and Transcriptomes of Hepatocellular Carcinomas Identifies Mutations and Gene Expression Changes in the Transforming Growth Factor-β Pathway.

Chen J, Zaidi S, Rao S, Chen JS, Phan L, Farci P, Su X, Shetty K, White J, Zamboni F, Wu X, Rashid A, Pattabiraman N, Mazumder R, Horvath A, Wu RC, Li S, Xiao C, Deng CX, Wheeler DA, Mishra B, Akbani R, Mishra L.

Gastroenterology. 2018 Jan;154(1):195-210. doi: 10.1053/j.gastro.2017.09.007. Epub 2017 Sep 15.

17.

A Children's Oncology Group and TARGET initiative exploring the genetic landscape of Wilms tumor.

Gadd S, Huff V, Walz AL, Ooms AHAG, Armstrong AE, Gerhard DS, Smith MA, Auvil JMG, Meerzaman D, Chen QR, Hsu CH, Yan C, Nguyen C, Hu Y, Hermida LC, Davidsen T, Gesuwan P, Ma Y, Zong Z, Mungall AJ, Moore RA, Marra MA, Dome JS, Mullighan CG, Ma J, Wheeler DA, Hampton OA, Ross N, Gastier-Foster JM, Arold ST, Perlman EJ.

Nat Genet. 2017 Oct;49(10):1487-1494. doi: 10.1038/ng.3940. Epub 2017 Aug 21.

18.

Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles.

Farshidfar F, Zheng S, Gingras MC, Newton Y, Shih J, Robertson AG, Hinoue T, Hoadley KA, Gibb EA, Roszik J, Covington KR, Wu CC, Shinbrot E, Stransky N, Hegde A, Yang JD, Reznik E, Sadeghi S, Pedamallu CS, Ojesina AI, Hess JM, Auman JT, Rhie SK, Bowlby R, Borad MJ; Cancer Genome Atlas Network, Zhu AX, Stuart JM, Sander C, Akbani R, Cherniack AD, Deshpande V, Mounajjed T, Foo WC, Torbenson MS, Kleiner DE, Laird PW, Wheeler DA, McRee AJ, Bathe OF, Andersen JB, Bardeesy N, Roberts LR, Kwong LN.

Cell Rep. 2017 Jun 27;19(13):2878-2880. doi: 10.1016/j.celrep.2017.06.008. No abstract available.

19.

Comprehensive Genomic Characterization of Upper Tract Urothelial Carcinoma.

Moss TJ, Qi Y, Xi L, Peng B, Kim TB, Ezzedine NE, Mosqueda ME, Guo CC, Czerniak BA, Ittmann M, Wheeler DA, Lerner SP, Matin SF.

Eur Urol. 2017 Oct;72(4):641-649. doi: 10.1016/j.eururo.2017.05.048. Epub 2017 Jun 7.

PMID:
28601352
20.

Activating MAPK1 (ERK2) mutation in an aggressive case of disseminated juvenile xanthogranuloma.

Chakraborty R, Hampton OA, Abhyankar H, Zinn DJ, Grimes A, Skull B, Eckstein O, Mahmood N, Wheeler DA, Lopez-Terrada D, Peters TL, Hicks JM, Elghetany T, Krance R, Poulikakos PI, Merad M, McClain KL, Allen CE, Parsons DW.

Oncotarget. 2017 Jul 11;8(28):46065-46070. doi: 10.18632/oncotarget.17521.

21.

Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles.

Farshidfar F, Zheng S, Gingras MC, Newton Y, Shih J, Robertson AG, Hinoue T, Hoadley KA, Gibb EA, Roszik J, Covington KR, Wu CC, Shinbrot E, Stransky N, Hegde A, Yang JD, Reznik E, Sadeghi S, Pedamallu CS, Ojesina AI, Hess JM, Auman JT, Rhie SK, Bowlby R, Borad MJ; Cancer Genome Atlas Network, Zhu AX, Stuart JM, Sander C, Akbani R, Cherniack AD, Deshpande V, Mounajjed T, Foo WC, Torbenson MS, Kleiner DE, Laird PW, Wheeler DA, McRee AJ, Bathe OF, Andersen JB, Bardeesy N, Roberts LR, Kwong LN.

Cell Rep. 2017 Mar 14;18(11):2780-2794. doi: 10.1016/j.celrep.2017.02.033. Erratum in: Cell Rep. 2017 Jun 27;19(13):2878-2880.

22.

Whole-genome landscape of pancreatic neuroendocrine tumours.

Scarpa A, Chang DK, Nones K, Corbo V, Patch AM, 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 MC, Bruxner TJ, Christ AN, Harliwong I, Idrisoglu S, McLean S, Nourse C, Nourbakhsh E, Wilson PJ, Anderson MJ, Fink JL, Newell F, Waddell N, Holmes O, Kazakoff SH, Leonard C, Wood S, Xu Q, Nagaraj SH, Amato E, Dalai I, Bersani S, Cataldo I, Dei Tos AP, Capelli P, Davì MV, Landoni L, Malpaga A, Miotto M, Whitehall VL, 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 MC, Fisher WE, Dagg RA, Lau LM, 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; Australian Pancreatic Cancer Genome Initiative, Khanna KK, Gill AJ, Wheeler DA, Gibbs RA, Musgrove EA, Bassi C, Tortora G, Pederzoli P, Pearson JV, Waddell N, Biankin AV, Grimmond SM.

Nature. 2017 Mar 2;543(7643):65-71. doi: 10.1038/nature21063. Epub 2017 Feb 15. Erratum in: Nature. 2017 Sep 27;:.

PMID:
28199314
23.

SMARCA4-inactivating mutations increase sensitivity to Aurora kinase A inhibitor VX-680 in non-small cell lung cancers.

Tagal V, Wei S, Zhang W, Brekken RA, Posner BA, Peyton M, Girard L, Hwang T, Wheeler DA, Minna JD, White MA, Gazdar AF, Roth MG.

Nat Commun. 2017 Jan 19;8:14098. doi: 10.1038/ncomms14098.

24.

Genomic Alterations of Adamantinomatous and Papillary Craniopharyngioma.

Goschzik T, Gessi M, Dreschmann V, Gebhardt U, Wang L, Yamaguchi S, Wheeler DA, Lauriola L, Lau CC, Müller HL, Pietsch T.

J Neuropathol Exp Neurol. 2017 Feb 1;76(2):126-134. doi: 10.1093/jnen/nlw116.

PMID:
28069929
25.

Non-malignant respiratory epithelial cells preferentially proliferate from resected non-small cell lung cancer specimens cultured under conditionally reprogrammed conditions.

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 HV, Jayaseelan JC, Hu J, Wheeler DA, Shay JW, Rimm DL, Gazdar A, Minna JD.

Oncotarget. 2017 Feb 14;8(7):11114-11126. doi: 10.18632/oncotarget.14366.

26.

Coexistence of gain-of-function JAK2 germ line mutations with JAK2V617F in polycythemia vera.

Lanikova L, Babosova O, Swierczek S, Wang L, Wheeler DA, Divoky V, Korinek V, Prchal JT.

Blood. 2016 Nov 3;128(18):2266-2270. Epub 2016 Sep 19. No abstract available.

27.

Genomic analysis of hepatoblastoma identifies distinct molecular and prognostic subgroups.

Sumazin P, Chen Y, Treviño LR, Sarabia SF, Hampton OA, Patel K, Mistretta TA, Zorman B, Thompson P, Heczey A, Comerford S, Wheeler DA, Chintagumpala M, Meyers R, Rakheja D, Finegold MJ, Tomlinson G, Parsons DW, López-Terrada D.

Hepatology. 2017 Jan;65(1):104-121. doi: 10.1002/hep.28888. Epub 2016 Nov 29.

PMID:
27775819
28.

Renal cell carcinoma harboring somatic TSC2 mutations in a child with methylmalonic acidemia.

Potter SL, Venkatramani R, Wenderfer S, Graham BH, Vasudevan SA, Sher A, Wu H, Wheeler DA, Yang Y, Eng CM, Gibbs RA, Roy A, Plon SE, Parsons DW.

Pediatr Blood Cancer. 2017 May;64(5). doi: 10.1002/pbc.26286. Epub 2016 Oct 17.

29.

Alternative genetic mechanisms of BRAF activation in Langerhans cell histiocytosis.

Chakraborty R, Burke TM, Hampton OA, Zinn DJ, Lim KP, Abhyankar H, Scull B, Kumar V, Kakkar N, Wheeler DA, Roy A, Poulikakos PI, Merad M, McClain KL, Parsons DW, Allen CE.

Blood. 2016 Nov 24;128(21):2533-2537. Epub 2016 Oct 11.

30.

Significance of TP53 Mutation in Wilms Tumors with Diffuse Anaplasia: A Report from the Children's Oncology Group.

Ooms AH, Gadd S, Gerhard DS, Smith MA, Guidry Auvil JM, Meerzaman D, Chen QR, Hsu CH, Yan C, Nguyen C, Hu Y, Ma Y, Zong Z, Mungall AJ, Moore RA, Marra MA, Huff V, Dome JS, Chi YY, Tian J, Geller JI, Mullighan CG, Ma J, Wheeler DA, Hampton OA, Walz AL, van den Heuvel-Eibrink MM, de Krijger RR, Ross N, Gastier-Foster JM, Perlman EJ.

Clin Cancer Res. 2016 Nov 15;22(22):5582-5591. doi: 10.1158/1078-0432.CCR-16-0985. Epub 2016 Oct 4.

31.

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.

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 C, Roy A, Plon SE, Parsons DW.

Cold Spring Harb Mol Case Stud. 2016 Sep;2(5):a001057. doi: 10.1101/mcs.a001057.

32.

Cross-species identification of genomic drivers of squamous cell carcinoma development across preneoplastic intermediates.

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.

Nat Commun. 2016 Aug 30;7:12601. doi: 10.1038/ncomms12601.

33.

MuSE: accounting for tumor heterogeneity using a sample-specific error model improves sensitivity and specificity in mutation calling from sequencing data.

Fan Y, Xi L, Hughes DS, Zhang J, Zhang J, Futreal PA, Wheeler DA, Wang W.

Genome Biol. 2016 Aug 24;17(1):178. doi: 10.1186/s13059-016-1029-6.

34.

Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma.

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, Robertson AG, Wu HT, 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; Cancer Genome Atlas Research Network, Hammer GD, Giordano TJ, Verhaak RGW.

Cancer Cell. 2016 Aug 8;30(2):363. doi: 10.1016/j.ccell.2016.07.013. Epub 2016 Aug 8. No abstract available.

35.

Destabilized SMC5/6 complex leads to chromosome breakage syndrome with severe lung disease.

van der Crabben SN, Hennus MP, McGregor GA, Ritter DI, Nagamani SC, 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.

J Clin Invest. 2016 Aug 1;126(8):2881-92. doi: 10.1172/JCI82890. Epub 2016 Jul 18.

36.

SV-STAT accurately detects structural variation via alignment to reference-based assemblies.

Davis CF, Ritter DI, Wheeler DA, Wang H, Ding Y, Dugan SP, Bainbridge MN, Muzny DM, Rao PH, Man TK, Plon SE, Gibbs RA, Lau CC.

Source Code Biol Med. 2016 Jun 18;11:8. doi: 10.1186/s13029-016-0051-0. eCollection 2016.

37.

Mixed-phenotype acute leukemia (MPAL) exhibits frequent mutations in DNMT3A and activated signaling genes.

Eckstein OS, Wang L, Punia JN, Kornblau SM, Andreeff M, Wheeler DA, Goodell MA, Rau RE.

Exp Hematol. 2016 Aug;44(8):740-4. doi: 10.1016/j.exphem.2016.05.003. Epub 2016 May 18.

38.

Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma.

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, Robertson AG, Wu HT, 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; Cancer Genome Atlas Research Network, Hammer GD, Giordano TJ, Verhaak RGW.

Cancer Cell. 2016 May 9;29(5):723-736. doi: 10.1016/j.ccell.2016.04.002. Erratum in: Cancer Cell. 2016 Aug 8;30(2):363.

39.

ITD assembler: an algorithm for internal tandem duplication discovery from short-read sequencing data.

Rustagi N, Hampton OA, Li J, Xi L, Gibbs RA, Plon SE, Kimmel M, Wheeler DA.

BMC Bioinformatics. 2016 Apr 27;17:188. doi: 10.1186/s12859-016-1031-8.

40.

Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma.

Chen F, Zhang Y, Şenbabaoğlu Y, Ciriello G, Yang L, Reznik E, Shuch B, Micevic G, De Velasco G, Shinbrot E, Noble MS, Lu Y, Covington KR, Xi L, Drummond JA, Muzny D, Kang H, Lee J, Tamboli P, Reuter V, Shelley CS, Kaipparettu BA, Bottaro DP, Godwin AK, Gibbs RA, Getz G, Kucherlapati R, Park PJ, Sander C, Henske EP, Zhou JH, Kwiatkowski DJ, Ho TH, Choueiri TK, Hsieh JJ, Akbani R, Mills GB, Hakimi AA, Wheeler DA, Creighton CJ.

Cell Rep. 2016 Mar 15;14(10):2476-89. doi: 10.1016/j.celrep.2016.02.024. Epub 2016 Mar 3.

41.

Genomic Profiling of Pediatric Acute Myeloid Leukemia Reveals a Changing Mutational Landscape from Disease Diagnosis to Relapse.

Farrar JE, Schuback HL, Ries RE, Wai D, Hampton OA, Trevino LR, Alonzo TA, Guidry Auvil JM, Davidsen TM, Gesuwan P, Hermida L, Muzny DM, Dewal N, Rustagi N, Lewis LR, Gamis AS, Wheeler DA, Smith MA, Gerhard DS, Meshinchi S.

Cancer Res. 2016 Apr 15;76(8):2197-205. doi: 10.1158/0008-5472.CAN-15-1015. Epub 2016 Mar 3.

42.

Genomic analyses identify molecular subtypes of pancreatic cancer.

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Pharmacogenetic characterization of naturally occurring germline NT5C1A variants to chemotherapeutic nucleoside analogs.

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Pharmacogenet Genomics. 2016 Jun;26(6):271-9. doi: 10.1097/FPC.0000000000000208.

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An open access pilot freely sharing cancer genomic data from participants in Texas.

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Sci Data. 2016 Feb 16;3:160010. doi: 10.1038/sdata.2016.10.

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Diagnostic Yield of Clinical Tumor and Germline Whole-Exome Sequencing for Children With Solid Tumors.

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JAMA Oncol. 2016 May 1;2(5):616-624. doi: 10.1001/jamaoncol.2015.5699.

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Mutational Strand Asymmetries in Cancer Genomes Reveal Mechanisms of DNA Damage and Repair.

Haradhvala NJ, Polak P, Stojanov P, Covington KR, Shinbrot E, Hess JM, Rheinbay E, Kim J, Maruvka YE, Braunstein LZ, Kamburov A, Hanawalt PC, Wheeler DA, Koren A, Lawrence MS, Getz G.

Cell. 2016 Jan 28;164(3):538-49. doi: 10.1016/j.cell.2015.12.050. Epub 2016 Jan 21.

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Ampullary Cancers Harbor ELF3 Tumor Suppressor Gene Mutations and Exhibit Frequent WNT Dysregulation.

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Cell Rep. 2016 Feb 2;14(4):907-919. doi: 10.1016/j.celrep.2015.12.005. Epub 2016 Jan 21.

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A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.

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Nat Commun. 2015 Dec 9;6:10001. doi: 10.1038/ncomms10001.

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Acquired uniparental disomy of chromosome 9p in hematologic malignancies.

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Exp Hematol. 2016 Aug;44(8):644-52. doi: 10.1016/j.exphem.2015.11.005. Epub 2015 Dec 2. Review.

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Clonal Dynamics In Vivo of Virus Integration Sites of T Cells Expressing a Safety Switch.

Chang EC, Liu H, West JA, Zhou X, Dakhova O, Wheeler DA, Heslop HE, Brenner MK, Dotti G.

Mol Ther. 2016 Apr;24(4):736-45. doi: 10.1038/mt.2015.217. Epub 2015 Dec 7.

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