Publications

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2021
Wheeler DA, Takebe N, Hinoue T, Hoadley KA, Cardenas MF, Hamilton AM, Laird PW, Wang L, Johnson A, Dewal N, Miller V, Piñeyro D, de Moura MCastro, Esteller M, Shen H, Zenklusen JClaude, Tarnuzzer R, McShane LM, Tricoli JV, Williams PM, Lubensky I, O'Sullivan-Coyne G, Kohn EC, Little RF, White J, Malik S, Harris L, Weil C, Chen AP, Karlovich C, Rodgers B, Shankar L, Jacobs P, Nolan T, Hu J, Muzny DM, Doddapaneni H, Korchina V, Gastier-Foster J, Bowen J, Leraas K, Edmondson EF, Doroshow JH, Conley BA, S Ivy P, Staudt LM. Molecular Features of Cancers Exhibiting Exceptional Responses to Treatment. Cancer Cell. 2021 ;39(1):38-53.e7.
Maniakas A, Henderson YC, Hei H, Peng S, Chen Y, Jiang Y, Ji S, Cardenas M, Chiu Y, Bell D, Williams MD, Hofmann M-C, Scherer SE, Wheeler DA, Busaidy NL, Dadu R, Wang JR, Cabanillas ME, Zafereo M, Johnson FM, Lai SY. Novel Anaplastic Thyroid Cancer PDXs and Cell Lines: Expanding Preclinical Models of Genetic Diversity. J Clin Endocrinol Metab. 2021 ;106(11):e4652-e4665.
Gingras M-C, Sabo A, Cardenas M, Rana A, Dhingra S, Meng Q, Hu J, Muzny DM, Doddapaneni H, Perez L, Korchina V, Nessner C, Liu X, Chao H, Goss J, Gibbs RA. Sequencing of a central nervous system tumor demonstrates cancer transmission in an organ transplant. Life Sci Alliance. 2021 ;4(9).
Gou X, Anurag M, Lei JT, Kim B-J, Singh P, Seker S, Fandino D, Han A, Rehman S, Hu J, Korchina V, Doddapaneni H, Dobrolecki LE, Mitsiades N, Lewis MT, Welm AL, Li S, Lee AV, Robinson DR, Foulds CE, Ellis MJ. Transcriptional Reprogramming Differentiates Active from Inactive ESR1 Fusions in Endocrine Therapy-Refractory Metastatic Breast Cancer. Cancer Res. 2021 ;81(24):6259-6272.
Swierkowska J, Karolak JA, Gambin T, Rydzanicz M, Frajdenberg A, Mrugacz M, Podfigurna-Musielak M, Stankiewicz P, Lupski JR, Gajecka M. Variants in FLRT3 and SLC35E2B identified using exome sequencing in seven high myopia families from Central Europe. Adv Med Sci. 2021 ;66(1):192-198.
2020
A Khan B, Gadot R, Shetty A, Bayley JC, Hadley CC, Cardenas MF, Jalali A, Harmanci AS, Harmanci AO, Wheeler DA, Klisch TJ, Patel AJ. Identification of novel fusion transcripts in meningioma. J Neurooncol. 2020 ;149(2):219-230.
2019
Agha G, Mendelson MM, Ward-Caviness CK, Joehanes R, Huan T, Gondalia R, Salfati E, Brody JA, Fiorito G, Bressler J, Chen BH, Ligthart S, Guarrera S, Colicino E, Just AC, Wahl S, Gieger C, Vandiver AR, Tanaka T, Hernandez DG, Pilling LC, Singleton AB, Sacerdote C, Krogh V, Panico S, Tumino R, Li Y, Zhang G, Stewart JD, Floyd JS, Wiggins KL, Rotter JI, Multhaup M, Bakulski K, Horvath S, Tsao PS, Absher DM, Vokonas P, Hirschhorn J, M Fallin D, Liu C, Bandinelli S, Boerwinkle E, Dehghan A, Schwartz JD, Psaty BM, Feinberg AP, Hou L, Ferrucci L, Sotoodehnia N, Matullo G, Peters A, Fornage M, Assimes TL, Whitsel EA, Levy D, Baccarelli AA. Blood Leukocyte DNA Methylation Predicts Risk of Future Myocardial Infarction and Coronary Heart Disease. Circulation. 2019 ;140(8):645-657.
de Vries PS, Sabater-Lleal M, Huffman JE, Marten J, Song C, Pankratz N, Bartz TM, de Haan HG, Delgado GE, Eicher JD, Martinez-Perez A, Ward-Caviness CK, Brody JA, Chen M-H, de Maat MPM, Frånberg M, Gill D, Kleber ME, Rivadeneira F, Soria JManuel, Tang W, Tofler GH, Uitterlinden AG, Vlieg Avan Hylcka, Seshadri S, Boerwinkle E, Davies NM, Giese A-K, M Ikram K, Kittner SJ, McKnight B, Psaty BM, Reiner AP, Sargurupremraj M, Taylor KD, Fornage M, Hamsten A, Marz W, Rosendaal FR, Souto JCarlos, Dehghan A, Johnson AD, Morrison AC, O'Donnell CJ, Smith NL. A genome-wide association study identifies new loci for factor VII and implicates factor VII in ischemic stroke etiology. Blood. 2019 ;133(9):967-977.
Cogné B, Ehresmann S, Beauregard-Lacroix E, Rousseau J, Besnard T, Garcia T, Petrovski S, Avni S, McWalter K, Blackburn PR, Sanders SJ, Uguen K, Harris J, Cohen JS, Blyth M, Lehman A, Berg J, Li MH, Kini U, Joss S, von der Lippe C, Gordon CT, Humberson JB, Robak L, Scott DA, Sutton VR, Skraban CM, Johnston JJ, Poduri A, Nordenskjöld M, Shashi V, Gerkes EH, Bongers EMHF, Gilissen C, Zarate YA, Kvarnung M, Lally KP, Kulch PA, Daniels B, Hernandez-Garcia A, Stong N, McGaughran J, Retterer K, Tveten K, Sullivan J, Geisheker MR, Stray-Pedersen A, Tarpinian JM, Klee EW, Sapp JC, Zyskind J, Holla ØL, Bedoukian E, Filippini F, Guimier A, Picard A, Busk ØL, Punetha J, Pfundt R, Lindstrand A, Nordgren A, Kalb F, Desai M, Ebanks AHarmon, Jhangiani SN, Dewan T, Akdemir ZHCoban, Telegrafi A, Zackai EH, Begtrup A, Song X, Toutain A, Wentzensen IM, Odent S, Bonneau D, Latypova X, Deb W, Redon S, Bilan F, Legendre M, Troyer C, Whitlock K, Caluseriu O, Murphree MI, Pichurin PN, Agre K, Gavrilova R, Rinne T, Park M, Shain C, Heinzen EL, Xiao R, Amiel J, Lyonnet S, Isidor B, Biesecker LG, Lowenstein D, Posey JE, Denommé-Pichon A-S, Férec C, Yang X-J, Rosenfeld JA, Gilbert-Dussardier B, Audebert-Bellanger S, Redon R, Stessman HAF, Nellaker C, Yang Y, Lupski JR, Goldstein DB, Eichler EE, Bolduc F, Bézieau S, Küry S, Campeau PM. Missense Variants in the Histone Acetyltransferase Complex Component Gene TRRAP Cause Autism and Syndromic Intellectual Disability. Am J Hum Genet. 2019 ;104(3):530-541.
Patel AJ, Wan Y-W, Al-Ouran R, Revelli J-P, Cardenas MF, Oneissi M, Xi L, Jalali A, Magnotti JF, Muzny DM, Doddapaneni H, Sebastian S, Heck KA, J Goodman C, Gopinath SP, Liu Z, Rao G, Plon SE, Yoshor D, Wheeler DA, Zoghbi HY, Klisch TJ. Molecular profiling predicts meningioma recurrence and reveals loss of DREAM complex repression in aggressive tumors. Proc Natl Acad Sci U S A. 2019 ;116(43):21715-21726.
Oswiecimska J, Dawidziuk M, Gambin T, Ziora K, Marek M, Rzonca S, D. Guilbride L, Jhangiani SN, Obuchowicz A, Sikora A, Lupski JR, Wiszniewski W, Gawlinski P. A Patient with Berardinelli-Seip Syndrome, Novel Splicesite Mutation and Concomitant Development of Non-diabetic Polyneuropathy. J Clin Res Pediatr Endocrinol. 2019 ;11(3):319-326.
2018
Berger AC, Korkut A, Kanchi RS, Hegde AM, Lenoir W, Liu W, Liu Y, Fan H, Shen H, Ravikumar V, Rao A, Schultz A, Li X, Sumazin P, Williams C, Mestdagh P, Gunaratne PH, Yau C, Bowlby R, A Robertson G, Tiezzi DG, Wang C, Cherniack AD, Godwin AK, Kuderer NM, Rader JS, Zuna RE, Sood AK, Lazar AJ, Ojesina AI, Adebamowo C, Adebamowo SN, Baggerly KA, Chen T-W, Chiu H-S, Lefever S, Liu L, MacKenzie K, Orsulic S, Roszik J, Shelley CSimon, Song Q, Vellano CP, Wentzensen N, Weinstein JN, Mills GB, Levine DA, Akbani R. A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers. Cancer Cell. 2018 ;33(4):690-705.e9.
Jacobs DI, Fukumura K, Bainbridge MN, Armstrong GN, Tsavachidis S, Gu X, Doddapaneni H, Hu J, Jayaseelan JC, Muzny DM, Huse JT, Bondy ML. Elucidating the molecular pathogenesis of glioma: integrated germline and somatic profiling of a familial glioma case series. Neuro Oncol. 2018 ;20(12):1625-1633.
Hsieh JJ, Le V, Cao D, Cheng EH, Creighton CJ. Genomic classifications of renal cell carcinoma: a critical step towards the future application of personalized kidney cancer care with pan-omics precision. J Pathol. 2018 ;244(5):525-537.
Ge S, Xia X, Ding C, Zhen B, Zhou Q, Feng J, Yuan J, Chen R, Li Y, Ge Z, Ji J, Zhang L, Wang J, Li Z, Lai Y, Hu Y, Li Y, Li Y, Gao J, Chen L, Xu J, Zhang C, Jung SYun, Choi JMin, Jain A, Liu M, Song L, Liu W, Guo G, Gong T, Huang Y, Qiu Y, Huang W, Shi T, Zhu W, Wang Y, He F, Shen L, Qin J. A proteomic landscape of diffuse-type gastric cancer. Nat Commun. 2018 ;9(1):1012.
2017
Agarwala A, Pokharel Y, Saeed A, Sun W, Virani SS, Nambi V, Ndumele C, Shahar E, Heiss G, Boerwinkle E, Konety S, Hoogeveen RC, Ballantyne CM. The association of lipoprotein(a) with incident heart failure hospitalization: Atherosclerosis Risk in Communities study. Atherosclerosis. 2017 ;262:131-137.
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.
Chandrashekar DS, Bashel B, Balasubramanya SAkshaya Ho, Creighton CJ, Ponce-Rodriguez I, Chakravarthi BVSK, Varambally S. UALCAN: A Portal for Facilitating Tumor Subgroup Gene Expression and Survival Analyses. Neoplasia. 2017 ;19(8):649-658.
2016
Wang L, Wheeler DA, Prchal JT. Acquired uniparental disomy of chromosome 9p in hematologic malignancies. Exp Hematol. 2016 ;44(8):644-52.
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):723-736.
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.
A Hakimi A, Reznik E, Lee C-H, Creighton CJ, A Brannon R, Luna A, B Aksoy A, Liu EMinwei, Shen R, Lee W, Chen Y, Stirdivant SM, Russo P, Chen YBei, Tickoo SK, Reuter VE, Cheng EH, Sander C, Hsieh JJ. An Integrated Metabolic Atlas of Clear Cell Renal Cell Carcinoma. Cancer Cell. 2016 ;29(1):104-116.
2015
Seco CZazo, de Castro LSerrão, van Nierop JW, Morín M, Jhangiani S, Verver EJJ, Schraders M, Maiwald N, Wesdorp M, Venselaar H, Spruijt L, Oostrik J, Schoots J, van Reeuwijk J, Lelieveld SH, Huygen PLM, Insenser M, Admiraal RJC, Pennings RJE, Hoefsloot LH, Arias-Vásquez A, de Ligt J, Yntema HG, Jansen JH, Muzny DM, Huls G, van Rossum MM, Lupski JR, Moreno-Pelayo MAngel, Kunst HPM, Kremer H. Allelic Mutations of KITLG, Encoding KIT Ligand, Cause Asymmetric and Unilateral Hearing Loss and Waardenburg Syndrome Type 2. Am J Hum Genet. 2015 ;97(5):647-60.
Huemer M, Karall D, Schossig A, Abdenur JE, Jasmi FAl, Biagosch C, Distelmaier F, Freisinger P, Graham BH, Haack TB, Hauser N, Hertecant J, Ebrahimi-Fakhari D, Konstantopoulou V, Leydiker K, Lourenco CM, Scholl-Bürgi S, Wilichowski E, Wolf NI, Wortmann SB, Taylor RW, Mayr JA, Bonnen PE, Sperl W, Prokisch H, McFarland R. Clinical, morphological, biochemical, imaging and outcome parameters in 21 individuals with mitochondrial maintenance defect related to FBXL4 mutations. J Inherit Metab Dis. 2015 ;38(5):905-14.
Wang L, Ni X, Covington KR, Yang BY, Shiu J, Zhang X, Xi L, Meng Q, Langridge T, Drummond J, Donehower LA, Doddapaneni H, Muzny DM, Gibbs RA, Wheeler DA, Duvic M. Genomic profiling of Sézary syndrome identifies alterations of key T cell signaling and differentiation genes. Nat Genet. 2015 ;47(12):1426-34.