Charles Lee, PhD

Publications

• Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, La
  21293372
• Setlur SR, Ihm C, Tchinda J, Shams S, Werner L, Cho EK, Thompson C, Phillips K, Rassenti LZ, Kipps TJ, Neuberg D, Freedman AS, Lee C, Brown JR.Comparison of familial and sporadic chronic lymphocytic leukaemia using high resolution array comparative genomi
  20812997
• Ordulu Z, Dal Cin P, Chong WW, Choy KW, Lee C, Muto MG, Quade BJ, Morton CC.Disseminated peritoneal leiomyomatosis after laparoscopic supracervical hysterectomy with characteristic molecular cytogenetic findings of uterine leiomyoma.Genes Chromosomes Canc
  20842731
• Ligon AH, Morton CC, Bieber FR, Fletcher JA, Giersch AB, Kantarci S, Leach N, Lee C, Sandstrom M, Weremowicz S, Xiao S, Dal Cin P.Reporting of diagnostic cytogenetic results.Curr Protoc Hum Genet. 2010 Oct;Appendix 1:1D.1-23.
  20891028
• , Altshuler DM, Gibbs RA, Peltonen L, Altshuler DM, Gibbs RA, Peltonen L, Dermitzakis E, Schaffner SF, Yu F, Peltonen L, Dermitzakis E, Bonnen PE, Altshuler DM, Gibbs RA, de Bakker PI, Deloukas P, Gabriel SB, Gwilliam R, Hunt S, Inouye M, Jia X, Palotie
  20811451
• Mellott JG, Van der Gucht E, Lee CC, Carrasco A, Winer JA, Lomber SG.Areas of cat auditory cortex as defined by neurofilament proteins expressing SMI-32.Hear Res. 2010 Aug;267(1-2):119-36.
  20430082
• Lee CC, Winer JA.Convergence of thalamic and cortical pathways in cat auditory cortex.Hear Res. 2010 May 26.
  20576491
• Pang AW, Macdonald JR, Pinto D, Wei J, Rafiq MA, Conrad DF, Park H, Hurles ME, Lee C, Venter JC, Kirkness EF, Levy S, Feuk L, Scherer SW.Towards a comprehensive structural variation map of an individual human genome.Genome Biol. 2010 May 19;11(5):R52.
  20482838
• Sholl LM, Xiao Y, Joshi V, Yeap BY, Cioffredi LA, Jackman DM, Lee C, Jänne PA, Lindeman NI.EGFR mutation is a better predictor of response to tyrosine kinase inhibitors in non-small cell lung carcinoma than FISH, CISH, and immunohistochemistry.Am J Clin
  20472851
• Conrad DF, Bird C, Blackburne B, Lindsay S, Mamanova L, Lee C, Turner DJ, Hurles ME.Mutation spectrum revealed by breakpoint sequencing of human germline CNVs.Nat Genet. 2010 May;42(5):385-91.
  20364136
• Park H, Kim JI, Ju YS, Gokcumen O, Mills RE, Kim S, Lee S, Suh D, Hong D, Kang HP, Yoo YJ, Shin JY, Kim HJ, Yavartanoo M, Chang YW, Ha JS, Chong W, Hwang GR, Darvishi K, Kim H, Yang SJ, Yang KS, Kim H, Hurles ME, Scherer SW, Carter NP, Tyler-Smith C, Lee
  20364138
• Ercan D, Zejnullahu K, Yonesaka K, Xiao Y, Capelletti M, Rogers A, Lifshits E, Brown A, Lee C, Christensen JG, Kwiatkowski DJ, Engelman JA, Jänne PA.Amplification of EGFR T790M causes resistance to an irreversible EGFR inhibitor.Oncogene. 2010 Apr 22;29(
  20118985
• , Craddock N, Hurles ME, Cardin N, Pearson RD, Plagnol V, Robson S, Vukcevic D, Barnes C, Conrad DF, Giannoulatou E, Holmes C, Marchini JL, Stirrups K, Tobin MD, Wain LV, Yau C, Aerts J, Ahmad T, Andrews TD, Arbury H, Attwood A, Auton A, Ball SG, Balmfor
  20360734
• Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews TD, Barnes C, Campbell P, Fitzgerald T, Hu M, Ihm CH, Kristiansson K, Macarthur DG, Macdonald JR, Onyiah I, Pang AW, Robson S, Stirrups K, Valsesia A, Walter K, Wei J, , Tyler-Smi
  19812545
• Lee C, Scherer SW.The clinical context of copy number variation in the human genome.Expert Rev Mol Med. 2010;12:e8. Review.
  20211047
• Turke AB, Zejnullahu K, Wu YL, Song Y, Dias-Santagata D, Lifshits E, Toschi L, Rogers A, Mok T, Sequist L, Lindeman NI, Murphy C, Akhavanfard S, Yeap BY, Xiao Y, Capelletti M, Iafrate AJ, Lee C, Christensen JG, Engelman JA, Jänne PA.Preexistence and clon
  20129249
• Setlur SR, Chen CX, Hossain RR, Ha JS, Van Doren VE, Stenzel B, Steiner E, Oldridge D, Kitabayashi N, Banerjee S, Chen JY, Schäfer G, Horninger W, Lee C, Rubin MA, Klocker H, Demichelis F.Genetic variation of genes involved in dihydrotestosterone metabol
  20056642
• Rhodes J, Amsterdam A, Sanda T, Moreau LA, McKenna K, Heinrichs S, Ganem NJ, Ho KW, Neuberg DS, Johnston A, Ahn Y, Kutok JL, Hromas R, Wray J, Lee C, Murphy C, Radtke I, Downing JR, Fleming MD, MacConaill LE, Amatruda JF, Gutierrez A, Galinsky I, Stone RM
  19704007
• Gökçümen O, Lee C.Copy number variants (CNVs) in primate species using array-based comparative genomic hybridization.Methods. 2009 Sep;49(1):18-25. Review.
  19545629
• Kim JI, Ju YS, Park H, Kim S, Lee S, Yi JH, Mudge J, Miller NA, Hong D, Bell CJ, Kim HS, Chung IS, Lee WC, Lee JS, Seo SH, Yun JY, Woo HN, Lee H, Suh D, Lee S, Kim HJ, Yavartanoo M, Kwak M, Zheng Y, Lee MK, Park H, Kim JY, Gokcumen O, Mills RE, Zaranek AW
  19587683
• Demichelis F,Setlur SR,Beroukhim R,Perner S,Korbel JO,Lafargue CJ,Pflueger D,Pina C,Hofer MD,Sboner A,Svensson MA,Rickman DS,Urban A,Snyder M,Meyerson M,Lee C,Gerstein MB,Kuefer R,Rubin MA.Distinct genomic aberrations associated with ERG rearranged prosta
  19156837
• Freeman JL,Ceol C,Feng H,Langenau DM,Belair C,Stern HM,Song A,Paw BH,Look AT,Zhou Y,Zon LI,Lee C.Construction and application of a zebrafish array comparative genomic hybridization platform.Genes Chromosomes Cancer. 2009 Feb;48(2):155-70.
  18973135
• Ionita-Laza I,Rogers AJ,Lange C,Raby BA,Lee C.Genetic association analysis of copy-number variation (CNV) in human disease pathogenesis.Genomics. 2009 Jan;93(1):22-6. Review.
  18822366
• Korn JM, Kuruvilla FG, McCarroll SA, Wysoker A, Nemesh J, Cawley S, Hubbell E, Veitch J, Collins PJ, Darvishi K, Lee C, Nizzari MM, Gabriel SB, Purcell S, Daly MJ, Altshuler D.Integrated genotype calling and association analysis of SNPs, common copy numbe
  18776909
• Perry GH, Yang F, Marques-Bonet T, Murphy C, Fitzgerald T, Lee AS, Hyland C, Stone AC, Hurles ME, Tyler-Smith C, Eichler EE, Carter NP, Lee C, Redon R.Copy number variation and evolution in humans and chimpanzees.Genome Res. 2008 Nov;18(11):1698-710.
  18775914
• Xue Y,Sun D,Daly A,Yang F,Zhou X,Zhao M,Huang N,Zerjal T,Lee C,Carter NP,Hurles ME,Tyler-Smith C.Adaptive evolution of UGT2B17 copy-number variation.Am J Hum Genet. 2008 Sep;83(3):337-46.
  18760392
• Koivunen JP,Mermel C,Zejnullahu K,Murphy C,Lifshits E,Holmes AJ,Choi HG,Kim J,Chiang D,Thomas R,Lee J,Richards WG,Sugarbaker DJ,Ducko C,Lindeman N,Marcoux JP,Engelman JA,Gray NS,Lee C,Meyerson M,Janne PA.EML4-ALK fusion gene and efficacy of an ALK kinase
  18594010
• Perry GH, Ben-Dor A, Tsalenko A, Sampas N, Rodriguez-Revenga L, Tran CW, Scheffer A, Steinfeld I, Tsang P, Yamada NA, Park HS, Kim JI, Seo JS, Yakhini Z, Laderman S, Bruhn L, Lee C.The fine-scale and complex architecture of human copy-number variation.Am
  18304495
• Van Vlierberghe P, van Grotel M, Tchinda J, Lee C, Beverloo HB, van der Spek PJ, Stubbs A, Cools J, Nagata K, Fornerod M, Buijs-Gladdines J, Horstmann M, van Wering ER, Soulier J, Pieters R, Meijerink JP.The recurrent SET-NUP214 fusion as a new HOXA activ
  18299449
• Lee C, Morton CC.Structural genomic variation and personalized medicine.N Engl J Med. 2008 Feb 14;358(7):740-1.
  18272898
• Ionita-Laza I, Perry GH, Raby BA, Klanderman B, Lee C, Laird NM, Weiss ST, Lange C.On the analysis of copy-number variations in genome-wide association studies: a translation of the family-based association test.Genet Epidemiol. 2008 Apr;32(3):273-84.
  18228561
• Lee AS, Gutierrez-Arcelus M, Perry GH, Vallender EJ, Johnson WE, Miller GM, Korbel JO, Lee C.Analysis of copy number variation in the rhesus macaque genome identifies candidate loci for evolutionary and human disease studies.Hum Mol Genet. 2008 Apr 15;17(
  18180252
• O'Neil J, Tchinda J, Gutierrez A, Moreau L, Maser RS, Wong KK, Li W, McKenna K, Liu XS, Feng B, Neuberg D, Silverman L, DeAngelo DJ, Kutok JL, Rothstein R, DePinho RA, Chin L, Lee C, Look AT.Alu elements mediate MYB gene tandem duplication in human T-
  18070937
• Perry GH, Dominy NJ, Claw KG, Lee AS, Fiegler H, Redon R, Werner J, Villanea FA, Mountain JL, Misra R, Carter NP, Lee C, Stone AC.Diet and the evolution of human amylase gene copy number variation.Nat Genet. 2007 Oct;39(10):1256-60.
  17828263
• Lee C, Iafrate AJ, Brothman AR.Copy number variations and clinical cytogenetic diagnosis of constitutional disorders.Nat Genet. 2007 Jul;39(7 Suppl):S48-54. Review.
  17597782
• Scherer SW, Lee C, Birney E, Altshuler DM, Eichler EE, Carter NP, Hurles ME, Feuk L.Challenges and standards in integrating surveys of structural variation.Nat Genet. 2007 Jul;39(7 Suppl):S7-15. Review.
  17597783
• Ganapathi KA, Austin KM, Lee CS, Dias A, Malsch MM, Reed R, Shimamura A.The human Shwachman-Diamond syndrome protein, SBDS, associates with ribosomal RNA.Blood. 2007 Sep 1;110(5):1458-65.
  17475909
• Demichelis F, Fall K, Perner S, Andrén O, Schmidt F, Setlur SR, Hoshida Y, Mosquera JM, Pawitan Y, Lee C, Adami HO, Mucci LA, Kantoff PW, Andersson SO, Chinnaiyan AM, Johansson JE, Rubin MA.TMPRSS2:ERG gene fusion associated with lethal prostate cancer in
  17237811
• Engelman JA, Zejnullahu K, Mitsudomi T, Song Y, Hyland C, Park JO, Lindeman N, Gale CM, Zhao X, Christensen J, Kosaka T, Holmes AJ, Rogers AM, Cappuzzo F, Mok T, Lee C, Johnson BE, Cantley LC, Jänne PA.MET Amplification Leads to Gefitinib Resistance in Lu
  17463250
• , Eichler EE, Nickerson DA, Altshuler D, Bowcock AM, Brooks LD, Carter NP, Church DM, Felsenfeld A, Guyer M, Lee C, Lupski JR, Mullikin JC, Pritchard JK, Sebat J, Sherry ST, Smith D, Valle D, Waterston RH.Completing the map of human genetic variation.Natu
  17495918
• Lee CR, Bottone FG, Krahn JM, Li L, Mohrenweiser HW, Cook ME, Petrovich RM, Bell DA, Eling TE, Zeldin DC.Identification and functional characterization of polymorphisms in human cyclooxygenase-1 (PTGS1).Pharmacogenet Genomics. 2007 Feb;17(2):145-60.
  17301694
• Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, Thorne N, Redon R, Bird CP, de Grassi A, Lee C, Tyler-Smith C, Carter N, Scherer SW, Tavaré S, Deloukas P, Hurles ME, Dermitzakis ET.Relative impact of nucleotide and copy number variation on gene e
  17289997
• Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, Cho EK, Dallaire S, Freeman JL, Gonzalez JR, Gratacos M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marshall CR, Mei R, Montgomery L, Nishimura
  17122850
• Khaja R, Zhang J, MacDonald JR, He Y, Joseph-George AM, Wei J, Rafiq MA, Qian C, Shago M, Pantano L, Aburatani H, Jones K, Redon R, Hurles M, Armengol L, Estivill X, Mural RJ, Lee C, Scherer SW, Feuk L.Genome assembly comparison identifies structural vari
  17115057
• Tchinda J, Lee C.Detecting copy number variation in the human genome using comparative genomic hybridization.Biotechniques. 2006 Oct;41(4):385, 387, 389 passim.
  17068952
• Freeman JL, Perry GH, Feuk L, Redon R, McCarroll SA, Altshuler DM, Aburatani H, Jones KW, Tyler-Smith C, Hurles ME, Carter NP, Scherer SW, Lee C.Copy number variation: New insights in genome diversity.Genome Res. 2006 Aug;16(8):949-61. Review.
  16809666
• Perry GH, Tchinda J, McGrath SD, Zhang J, Picker SR, Cáceres AM, Iafrate AJ, Tyler-Smith C, Scherer SW, Eichler EE, Stone AC, Lee C.Hotspots for copy number variation in chimpanzees and humans.Proc Natl Acad Sci U S A. 2006 May 23;103(21):8006-11.
  16702545
• Yan CT, Kaushal D, Murphy M, Zhang Y, Datta A, Chen C, Monroe B, Mostoslavsky G, Coakley K, Gao Y, Mills KD, Fazeli AP, Tepsuporn S, Hall G, Mulligan R, Fox E, Bronson R, De Girolami U, Lee C, Alt FW.XRCC4 suppresses medulloblastomas with recurrent transl
  16670198
• Nadeau JH, Lee C.Genetics: copies count.Nature. 2006 Feb 16;439(7078):798-9.
  16482142
• McCarroll SA, Hadnott TN, Perry GH, Sabeti PC, Zody MC, Barrett JC, Dallaire S, Gabriel SB, Lee C, Daly MJ, Altshuler DM,.Common deletion polymorphisms in the human genome.Nat Genet. 2006 Jan;38(1):86-92.
  16468122
• Ouahchi K, Lindeman N, Lee C.Copy number variants and pharmacogenomics.Pharmacogenomics. 2006 Jan;7(1):25-9.
  16354122
• Tomlins SA, Rhodes DR, Perner S, Dhanasekaran SM, Mehra R, Sun XW, Varambally S, Cao X, Tchinda J, Kuefer R, Lee C, Montie JE, Shah RB, Pienta KJ, Rubin MA, Chinnaiyan AM.Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer.Sc
  16254181
• Shepard JL, Amatruda JF, Stern HM, Subramanian A, Finkelstein D, Ziai J, Finley KR, Pfaff KL, Hersey C, Zhou Y, Barut B, Freedman M, Lee C, Spitsbergen J, Neuberg D, Weber G, Golub TR, Glickman JN, Kutok JL, Aster JC, Zon LI.A zebrafish bmyb mutation caus
  16150706
• Garraway LA, Widlund HR, Rubin MA, Getz G, Berger AJ, Ramaswamy S, Beroukhim R, Milner DA, Granter SR, Du J, Lee C, Wagner SN, Li C, Golub TR, Rimm DL, Meyerson ML, Fisher DE, Sellers WR.Integrative genomic analyses identify MITF as a lineage survival onc
  16001072
• Lee C.Vive la difference!.Nat Genet. 2005 Jul;37(7):660-1.
  15990882
• Jeon Y, Bekiranov S, Karnani N, Kapranov P, Ghosh S, MacAlpine D, Lee C, Hwang DS, Gingeras TR, Dutta A.Temporal profile of replication of human chromosomes.Proc Natl Acad Sci U S A. 2005 May 3;102(18):6419-24.
  15845769
• Klaassens M, van Dooren M, Eussen HJ, Douben H, den Dekker AT, Lee C, Donahoe PK, Galjaard RJ, Goemaere N, de Krijger RR, Wouters C, Wauters J, Oostra BA, Tibboel D, de Klein A.Congenital diaphragmatic hernia and chromosome 15q26: determination of a candi
  15750894
• Patton EE, Widlund HR, Kutok JL, Kopani KR, Amatruda JF, Murphey RD, Berghmans S, Mayhall EA, Traver D, Fletcher CD, Aster JC, Granter SR, Look AT, Lee C, Fisher DE, Zon LI.BRAF mutations are sufficient to promote nevi formation and cooperate with p53 in
  15694309
• Lee C, Smith A.Molecular cytogenetic methodologies and a bacterial artificial chromosome (BAC) probe panel resource for genomic analyses in zebrafish.Methods Cell Biol. 2004;77:241-54.
  15602915
• Roberts AE, Irons MB, Kimonis VE, Mulliken JB, Morton CC, Lee C, Listewnik M.Description of a case of distal 2p trisomy by array-based comparative genomic hybridization: a high resolution genome-wide investigation for chromosomal aneuploidy in a single as
  15372522
• Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C.Detection of large-scale variation in the human genome.Nat Genet. 2004 Aug 01;19:1-3.
• Poss KD, Nechiporuk A, Stringer KF, Lee C, Keating MT.Germ cell aneuploidy in zebrafish with mutations in the mitotic checkpoint gene mps1.Genes Dev. 2004 Jul 1;18(13):1527-32.
  15231734
• Dettori T, Frau DV, Garcia JL, Pierantoni G, Lee C, Hernandez JM, Fusco A, Morton CC, Vanni R.Comprehensive conventional and molecular cytogenetic characterization of B-CPAP, a human papillary thyroid carcinoma-derived cell line.Cancer Genet Cytogenet. 20
  15172756
• Rooney S, Sekiguchi J, Whitlow S, Eckersdorff M, Manis JP, Lee C, Ferguson DO, Alt FW.Artemis and p53 cooperate to suppress oncogenic N-myc amplification in progenitor B cells.Proc Natl Acad Sci U S A. 2004 Feb 24;101(8):2410-5.
  14983023
• Paw BH, Davidson AJ, Zhou Y, Li R, Pratt SJ, Lee C, Trede NS, Brownlie A, Donovan A, Liao EC, Ziai JM, Drejer AH, Guo W, Kim CH, Gwynn B, Peters LL, Chernova MN, Alper SL, Zapata A, Wickramasinghe SN, Lee MJ, Lux SE, Fritz A, Postlethwait JH, Zon LI.Cell-
• Zhu C, Mills KD, Ferguson DO, Lee C, Manis J, Fleming J, Gao Y, Morton CC, Alt FW.Unrepaired DNA breaks in p53-deficient cells lead to oncogenic gene amplification subsequent to translocations.Cell. 2002;109:811-821.
• Sharpless NE, Ferguson DO, O'Hagan RC, Castrillon DH, Lee C, Farazi PA, Alson S, Fleming J, Morton CC, Frank K, Chin L, Alt FW, DePinho RA.Impaired nonhomologous end-joining provokes soft tissue sarcomas harboring chromosomal translocations, amplifica
  11779495
• Lee C, Murray MF, Miron PM, Marsden D, Irons M, Wilkins-Haug LE, Morton CC.Clinical picture: Multicolour karyotyping.Lancet. 2001 Apr 21;357(9264):1240.
  11458963
• Li YC, Lee C, Sanoudou D, Hseu TH, Li SY, Lin CC, Hsu TH.Interstitial colocalization of two cervid satellite DNAs involved in the genesis of the Indian muntjac karyotype.Chromosome Res. 2000;8(5):363-73.
  10997777
• Lee C, Stanyon R, Lin CC, Ferguson-Smith MA.Conservation of human gamma-X centromeric satellite DNA among primates with an autosomal localization in certain Old World monkeys.Chromosome Res. 1999;7(1):43-7.
  10219731
• Lee C, Lin CC.Conservation of a 31-bp bovine subrepeat in centromeric satellite DNA monomers of Cervus elaphus and other cervid species.Chromosome Res. 1996 Sep;4(6):427-35.
  8889241
• Lee C, Li X, Jabs EW, Court D, Lin CC.Human gamma X satellite DNA: an X chromosome specific centromeric DNA sequence.Chromosoma. 1995 Nov;104(2):103-12.
  8585987
• Lin CC, Sasi R, Lee C, Fan YS, Court D.Isolation and identification of a novel tandemly repeated DNA sequence in the centromeric region of human chromosome 8.Chromosoma. 1993 May;102(5):333-9.
  7916664