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A Comprehensive Cancer Center Designated by the National Cancer Institute

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Project 4

Nancy Cox, PhD

  • *Gamazon ER, Zhang W, Huang RS, Dolan ME, Cox NJ. A pharmacogene database enhanced by the 1000 Genomes Project. Pharmacogenet Genomics 19:829-32, 2009.  PMC2935084
  • *Huang RS, Chen P, Wisel S, Duan S, Zhang W, Cook EH, Das S, Cox NJ, Dolan ME. Population-specific GSTM1 copy number variation. Hum Mol Genet 18:366-72, 2009.  PMC2722188
  • *Gamazon ER, Zhang W, Konkashbaev A, Duan S, Kistner EO, Nicolae DL, Dolan ME, Cox NJ. SCAN: SNP and copy number annotation. Bioinformatics 26:259-62, 2010.  PMC2852202
  • *Gamazon ER, Zhang W, Dolan ME, Cox NJ. Comprehensive survey of SNPs in the Affymetrix exon array using the 1000 Genomes dataset. PLoS One 5:e9366, 2010.  PMC2826392
  • *Nicolae DL, Gamazon E, Zhang W, Duan S, Dolan ME, Cox NJ. Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genet 6:e1000888, 2010.  PMC2848547
  • *Gamazon ER, Huang RS, Cox NJ, Dolan ME. Chemotherapeutic drug susceptibility associated SNPs are enriched in expression quantitative trait loci. Proc Natl Acad Sci 107:9287-92, 2010.  PMC2889115
  • *Gamazon ER, Im HK, Duan S, Lussier YA, Cox NJ, Dolan ME, Zhang W. Exprtarget: an integrative approach to predicting human microRNA targets. PLoS One 5:e13534, 2010.  PMC2958831
  • *Chen SH, Pei D, Yang W, Cheng C, Jeha S, Cox NJ, Evans WE, Pui CH, Relling MV. Genetic variations in GRIA1 on chromosome 5q33 related to asparaginase hypersensitivity. Clin Pharmacol Ther 88:191-6, 2010.  PMC3000799
  • *Stark AL, Zhang W, O’Donnell PH, Beiswanger CM, Huang RS, Cox NJ, Dolan ME. Population differences in rate of proliferation of international HapMap cell lines. Am J Hum Genet 87:829-33, 2010.  PMC2997375
  • *Gamazon ER, Duan S, Zhang W, Huang RS, Kistner EO, Dolan ME, Cox NJ. PACdb: a database for cell-based pharmacogenomics. Pharmacogenet Genomics 20:269-73, 2010.  PMC2914089
  • *Gamazon ER, Nicolae DL, Cox NJ. A study of CNVs as trait-associated polymorphisms and as expression quantitative  trait loci. PLoS Genet 7:e1001292, 2011.  PMC3033384
  • *Wheeler HE, Gorsic LK, Welsh M, Stark AL, Gamazon ER, Cox NJ, Dolan ME. Genome-wide local ancestry approach identifies genes and variants associated with chemotherapeutic susceptibility in African Americans. PLoS One 6:e21920, 2011.  PMC3130766
  • *Gamazon ER, Im HK, O’Donnell PH, Ziliak D, Stark AL, Cox NJ, Dolan ME, Huang RS. Comprehensive evaluation of the contribution of X chromosome genes to platinum sensitivity. Mol Cancer Ther 10:472-80, 2011.  PMC3079551
  • *Gamazon ER, Huang RS, Dolan ME, Cox NJ. Copy number polymorphisms and anticancer pharmacogenomics. Genome Biol 12:R46, 2011.  PMC3219969
  • *Ziliak D, O’Donnell PH, Im HK, Gamazon ER, Chen P, Delaney S, Shukla S, Das S, Cox NJ, Vokes EE, Cohen EE, Dolan ME, Huang RS. Germline polymorphisms discovered via a cell-based genome-wide approach predict platinum response in head and neck cancers. Transl Res 157:265-72, 2011.  PMC3079878
  • *Huang RS, Johnatty SE, Gamazon ER, Ziliak D, Duan S, Zhang W, Kistner EO, Chen P, Beesley J, Mi S, O’Donnell PH, Fraiman YS, Das S, Cox NJ, Macgregor S, Goode EL, Vierkant RA, Fridley BL, Hogdall E, Kjaer SK, Jensen A, Moysich KB, Grasela M, Odunsi K, Brown R, Paul J, Lambrechts D, Despierre E, Vergote I, Gross J, Karlan BY, deFazio A, Chenevix-Trench G, Australian Ovarian Cancer Study Group, Dolan ME. Platinum sensitivity-related germline polymorphism discovered via a cell-based approach and analysis of its association with outcome in ovarian cancer patients. Clin Cancer Res 17:5490-500, 2011.  PMC3160494
  • *Zheng Y, Ogundiran TO, Adebamowo C, Nathanson KL, Domchek SM, Rebbeck TR, Simon MS, John EM, Hennis A, Nemesure B, Wu SY, Leske MC, Ambs S, Niu Q, Zhang J, Cox NJ, Olopade OI, Huo D. Lack of association between common single nucleotide polymorphisms in the TERT-CLPTM1L locus and breast cancer in women of African ancestry. Breast Cancer Res Treat 132:341-5, 2012.
  • *Im HK, Gamazon ER, Stark AL, Huang RS, Cox NJ, Dolan ME. Mixed effects modeling of proliferation rates in cell-based models: consequence for pharmacogenomics and cancer. PLoS Genet 8:e1002525, 2012.  PMC3276560
  • *O’Donnell PH, Stark AL, Gamazon ER, Wheeler HE, McIlwee BE, Gorsic L, Im HK, Huang RS, Cox NJ, Dolan ME. Identification of novel germline polymorphisms governing capecitabine sensitivity. Cancer 118:4063-73, 2012.  PMC3413892
  • *Wheeler HE, Gamazon ER, Wing C, Njiaju UO, Njoku C, Baldwin RM, Owzar K, Jiang C, Watson D, Shterev I, Kubo M, Zembutsu H, Winer EP, Hudis CA, Shulman LN, Nakamura Y, Ratain MJ, Kroetz DL, Cox NJ, Dolan ME. Integration of cell line and clinical trial genome-wide analyses supports a polygenic architecture of paclitaxel-induced sensory peripheral neuropathy. Clin Cancer Res 19:491-9, 2013.  PMC3549006
  • *Wheeler HE, Gamazon ER, Stark AL, O’Donnell PH, Gorsic LK, Huang RS, Cox NJ, Dolan ME. Genome-wide meta-analysis identifies variants associated with platinating agent susceptibility across populations. Pharmacogenomics J 13:35-43, 2013.  PMC3370147
  • *Chen F, Chen GK, Stram DO, Millikan RC, Ambrosone CB, John EM, Bernstein L, Zheng W, Palmer JR, Hu JJ, Rebbeck TR, Ziegler RG, Nyante S, Bandera EV, Ingles SA, Press MF, Ruiz-Narvaez EA, Deming SL, Rodriguez-Gil JL, Demichele A, Chanock SJ, Blot W, Signorello L, Cai Q, Li G, Long J, Huo D, Zheng Y, Cox NJ, Olopade OI, Ogundiran TO, Adebamowo C, Nathanson KL, Domchek SM, Simon MS, Hennis A, Nemesure B, Wu SY, Leske MC, Ambs S, Hutter CM, Young A, Kooperberg C, Peters U, Rhie SK, Wan P, Sheng X, Pooler LC, Van Den Berg DJ, Le Marchand L, Kolonel LN, Henderson BE, Haiman CA. A genome-wide association study of breast cancer in women of African ancestry. Hum Genet 132:39–48, 2013.
  • *Zheng Y, Ogundiran TO, Falusi AG, Nathanson KL, John EM, Hennis AJ, Ambs S, Domchek SM, Rebbeck TR, Simon MS, Nemesure B, Wu SY, Leske MC, Odetunde A, Niu Q, Zhang J, Afolabi C, Gamazon ER, Cox NJ, Olopade CO, Olufunmilayo OI, Huo D. Fine-mapping of breast cancer genome-wide association studies loci in women of African ancestry identifies novel susceptibility markers. Carcinogenesis, Epub ahead of print, 2013.
  • *Gamazon E, Huang RS, Dolan ME, Cox N, Im HK. Integrative genomics: quantifying significance of phenotype-genotype relationships from multiple sources of high-throughput data. Frontiers Stat Genet Method, in press, 2013.

M. Eileen Dolan, PhD

  • Huang RS, Duan S, Kistner EO, Hartford CM, Dolan ME. Genetic variants associated with carboplatin-induced cytotoxicity in cell lines derived from Africans. Mol Cancer Ther 7:3038-46, 2008.  PMC2743011
  • Zhang W, Huang RS, Dolan ME. Cell-based models for discovery of pharmacogenomic markers of anticancer agent toxicity. Trends Cancer Res 4:1-13, 2008.  PMC3076057
  • *Huang RS, Chen P, Wisel S, Duan S, Zhang W, Cook EH, Das S, Cox NJ, Dolan ME. Population-specific GSTM1 copy number variation. Hum Mol Genet 18:366-72, 2009.  PMC2722188
  • *Shukla SJ, Duan S, Wu X, Badner JA, Kasza K, Dolan ME. Whole-genome approach implicates CD44 in cellular resistance to carboplatin. Hum Genomics 3:128-42, 2009.  PMC2683878
  • O’Donnell PH, Dolan ME. Cancer pharmacoethnicity: ethnic differences in susceptibility to the effects of chemotherapy. Clin Cancer Res 15:4806-14, 2009.  PMC2774468
  • Zhang W, Dolan ME. Use of cell lines in the investigation of pharmacogenetic loci. Curr Pharm Des 15:3782-95, 2009.  PMC2782819
  • *Welsh M, Mangravite L, Medina MW, Tantisira K, Zhang W, Huang RS, McLeod H, Dolan ME. Pharmacogenomic discovery using cell-based models. Pharmacol Rev 61:413-29, 2009.  PMC2802425
  • Pinto N, Ludeman SM, Dolan ME. Drug focus: pharmacogenetic studies related to cyclophosphamide-based therapy. Pharmacogenomics 10:1897-903, 2009. PMC2820268
  • *Duan S, Mi S, Zhang W, Dolan ME. Comprehensive analysis of the impact of SNPs and CNVs on human microRNAs and their regulatory genes. RNA Biol 6:412-25, 2009.  PMC2783774
  • *Gamazon ER, Zhang W, Huang RS, Dolan ME, Cox NJ. A pharmacogene database enhanced by the 1000 genomes project. Pharmacogenet Genomics 19:829-32, 2009.  PMC2935084
  • Zhang W, Dolan ME. Impact of the 1000 genomes project on the next wave of pharmacogenomic discovery. Pharmacogenomics 1:249-56, 2010. PMC2833269
  • Huang RS, Dolan ME. Approaches to discovery of pharmacogenomic markers in oncology: 2000-2010-2020. Pharmacogenomics 11:471-4, 2010.  PMC2864525
  • *Nicolae DL, Gamazon E, Zhang W, Duan S, Dolan ME, Cox NJ. Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genet 6:e1000888, 2010.  PMC2848547
  • *Gamazon ER, Zhang W, Dolan ME, Cox NJ. Comprehensive survey of SNPs in the affymetrix exon array using the 1000 genomes dataset. PLoS One 5:e9366, 2010.  PMC2826392
  • *Gamazon ER, Zhang W, Konkashbaev A, Duan S, Kistner EO, Nicolae DL, Dolan ME, Cox NJ. SCAN: SNP and copy number annotation. Bioinformatics 26:259-62, 2010.  PMC2852202
  • *Gamazon ER, Duan S, Zhang W, Huang RS, Kistner EO, Dolan ME, Cox NJ. PACdb: a database for cell-based pharmacogenomics. Pharmacogenet Genomics 20:269-73, 2010.  PMC2914089
  • O'Donnell PH, Gamazon E, Zhang W, Stark AL, Kistner-Griffin EO, Huang RS, Dolan ME. Population differences in platinum toxicity as a means to identify novel genetic susceptibility variants. Pharmacogenet Genomics 20:327-37, 2010.  PMC2908307
  • *Gamazon ER, Huang RS, Cox NJ, Dolan ME. Chemotherapeutic drug susceptibility associated SNPs are enriched in expression quantitative trait loci. Proc Natl Acad Sci USA 107:9287-92, 2010.  PMC2889115
  • Stark AL, Zhang W, Mi S, Duan S, O’Donnell PH, Huang RS, Dolan ME. Heritable and non-genetic factors as variables of pharmacologic phenotypes in lymphoblastoid cell lines. Pharmacogenomics J 10:505-12, 2010.  PMC2975793
  • *Gamazon ER, Im HK, Duan S, Lussier YA, Cox NJ, Dolan ME, Zhang W. Exprtarget: an integrative approach to predicting human microRNA targets. PLoS One 5:e13534, 2010.  PMC2958831
  • Zhang W, Dolan ME. Emerging role of microRNAs in drug response. Curr Opin Mol Ther 12:695-702, 2010.  PMC3233195
  • *Stark AL, Zhang W, O’Donnell PH, Beiswanger CM, Huang RS, Cox NJ, Dolan ME. Population differences in rate of proliferation of international HapMap cell lines. Am J Hum Genet 87:829-33, 2010.  PMC2997375
  • *Ziliak D, O’Donnell PH, Im HK, Gamazon ER, Chen P, Delaney S, Shukla S, Das S, Cox NJ, Vokes EE, Cohen EE, Dolan ME, Huang RS. Germline polymorphisms discovered via a cell-based genome-wide approach predict platinum response in head and neck cancers. Transl Res 157:265-72, 2011.  PMC3079878
  • *Gamazon ER, Im HK, O’Donnell PH, Ziliak D, Stark AL, Cox NJ, Dolan ME, Huang RS. Comprehensive evaluation of the contribution of X chromosome genes to platinum sensitivity. Mol Cancer Ther 10:472-80, 2011.  PMC3079551
  • Wen Y, Gorsic LK, Wheeler HE, Ziliak DM, Huang RS, Dolan ME. Chemotherapeutic-induced apoptosis: a phenotype for pharmacogenomics studies. Pharmacogenetics Genomics 21:476-88, 2011.  PMC3134538
  • *Gamazon ER, Huang RS, Dolan ME, Cox NJ. Copy number polymorphisms and anticancer pharmacogenomics. Genome Biol 12:R46, 2011.  PMC3219969
  • *Huang RS, Gamazon ER, Ziliak D, Wen Y, Im HK, Zhang W, Wing C, Duan S, Bleibel WK, Cox NJ, Dolan ME. Population differences in microRNA expression and biological implications. RNA Biol 8:692-701, 2011.  PMC3225983
  • *Huang RS, Johnatty SE, Gamazon ER, Ziliak D, Duan S, Zhang W, Kistner EO, Chen P, Beesley J, Mi S, O’Donnell PH, Fraiman YS, Das S, Cox NJ, Macgregor S, Goode EL, Vierkant RA, Fridley BL, Hogdall E, Kjaer SK, Jensen A, Moysich KB, Grasela M, Odunsi K, Brown R, Paul J, Lambrechts D, Despierre E, Vergote I, Gross J, Karlan BY, deFazio A, Chenevix-Trench G, Australian Ovarian Cancer Study Group, Dolan ME. Platinum sensitivity-related germline polymorphism discovered via a cell-based approach and analysis of its association with outcome in ovarian cancer patients. Clin Cancer Res 17:5490-500, 2011.  PMC3160494
  • *Wheeler HE, Gorsic LK, Welsh M, Stark AL, Gamazon ER, Cox NJ, Dolan ME. Genome-wide local ancestry approach identifies genes and variants associated with chemotherapeutic susceptibility in African Americans. PLoS One 6:e21920, 2011.  PMC3130766
  • *Wilke RA, Dolan ME. Genetics and variable drug response. JAMA 306:306-7, 2011.  PMC3539154 
  • *Innocenti F, Cox NJ, Dolan ME. The use of genomic information to optimize cancer chemotherapy. Semin Oncol 38:186-95, 2011.  PMC3076508
    Pinto N, Dolan ME. Clinically relevant genetic variations in drug metabolizing enzymes. Curr Drug Metab 12:487-97, 2011.  PMC3110519
  • *Im HK, Gamazon ER, Stark AL, Huang RS, Cox NJ, Dolan ME. Mixed effects modeling of proliferation rates in cell-based models: consequence for pharmacogenomics and cancer. PLoS Genet 8:e1002525, 2012.  PMC3276560
  • *O’Donnell PH, Stark AL, Gamazon ER, Wheeler HE, McIlwee BE, Gorsic L, Im HK, Huang RS, Cox NJ, Dolan ME. Identification of novel germline polymorphisms governing capecitabine sensitivity. Cancer 118:4063-73, 2012.  PMC3413892
  • *Njiaju UO, Gamazon ER, Gorsic LK, Delaney SM, Wheeler HE, Im HK, Dolan ME. Whole-genome studies identify solute carrier transporters in cellular susceptibility to paclitaxel. Pharmacogenet Genomics 22:498-507, 2012.  PMC3376193
  • *Leandro-Garcia LJ, Leskela S, Jara C, Green H, Avall-Lundqvist E, Wheeler HE, Dolan ME, Inglada-Perez L, Maliszewska A, de Cubas AA, Comino-Mendez I, Mancikova V, Cascon A, Robledo M, Rodriguez-Antona C. Regulatory polymorphisms in tubulin IIa are associated with paclitaxel-induced peripheral neuropathy. Clin Cancer Res 18:4441-8, 2012.
  • Wheeler HE, Dolan ME. Lymphoblastoid cell lines in pharmacogenomic discovery and clinical translation. Pharmacogenomics 13:55-70, 2012.  PMC3292907
  • *Bockhorn J, Dalton R, Nwachukwu C, Huang S, Prat A, Yee K, Chang YF, Huo D, Wen Y, Swanson KE, Qiu T, Lu J, Park SY, Dolan ME, Perou CM, Olopade OI, Clarke MF, Greene GL, Liu H. MicroRNA-30c inhibits human breast tumour chemotherapy resistance by regulating TWF1 and IL-11. Nat Commun 4:1393, 2013.
  • *Wheeler HE, Gamazon ER, Wing C, Njiaju UO, Njoku C, Baldwin RM, Owzar K, Jiang C, Watson D, Shterev I, Kubo M, Zembutsu H, Winer EP, Hudis CA, Shulman LN, Nakamura Y, Ratain MJ, Kroetz DL, Cox NJ, Dolan ME. Integration of cell line and clinical trial genome-wide analyses supports a polygenic architecture of paclitaxel-induced sensory peripheral neuropathy. Clin Cancer Res 19:491-9, 2013.  PMC3549006
  • *Wheeler HE, Gamazon ER, Stark AL, O’Donnell PH, Gorsic LK, Huang RS, Cox NJ, Dolan ME. Genome-wide meta-analysis identifies variants associated with platinating agent susceptibility across populations. Pharmacogenomics J 13:35-43, 2013.  PMC3370147
  • *Gamazon E, Huang RS, Dolan ME, Cox N, Im HK. Integrative genomics: quantifying significance of phenotype-genotype relationships from multiple sources of high-throughput data. Frontiers Stat Genet Method, in press, 2013.

Gini Fleming, MD

  • Fleming GF, Ma CX, Huo D, Sattar H, Tretiakova M, Lin L, Hahn OM, Olopade FO, Nanda R, Hoffman PC, Naughton MJ, Pluard T, Conzen SD, Ellis MJ. Phase II trial of temsirolimus in patients with metastatic breast cancer. Breast Cancer Res Treat 136:355-63, 2012.

Peter H. O'Donnell, MD

  • O’Donnell PH, Dolan ME. Cancer pharmacoethnicity: ethnic differences in susceptibility to the effects of chemotherapy. Clin Cancer Res 15:4806-14, 2009.  PMC2774468
  • O'Donnell PH, Gamazon E, Zhang W, Stark AL, Kistner-Griffin EO, Huang RS, Dolan ME. Population differences in platinum toxicity as a means to identify novel genetic susceptibility variants. Pharmacogenet Genomics 20:327-37, 2010.  PMC2908307
  • Stark AL, Zhang W, Mi S, Duan S, O’Donnell PH, Huang RS, Dolan ME. Heritable and non-genetic factors as variables of pharmacologic phenotypes in lymphoblastoid cell lines. Pharmacogenomics J 10:505-12, 2010.  PMC2975793
  • *Stark AL, Zhang W, O’Donnell PH, Beiswanger CM, Huang RS, Cox NJ, Dolan ME. Population differences in rate of proliferation of international HapMap cell lines. Am J Hum Genet 87:829-33, 2010.  PMC2997375
  • *Ziliak D, O’Donnell PH, Im HK, Gamazon ER, Chen P, Delaney S, Shukla S, Das S, Cox NJ, Vokes EE, Cohen EE, Dolan ME, Huang RS. Germline polymorphisms discovered via a cell-based genome-wide approach predict platinum response in head and neck cancers. Transl Res 157:265-72, 2011.  PMC3079878
  • *Gamazon ER, Im HK, O’Donnell PH, Ziliak D, Stark AL, Cox NJ, Dolan ME, Huang RS. Comprehensive evaluation of the contribution of X chromosome genes to platinum sensitivity. Mol Cancer Ther 10:472-80, 2011.  PMC3079551
  • *Huang RS, Johnatty SE, Gamazon ER, Ziliak D, Duan S, Zhang W, Kistner EO, Chen P, Beesley J, Mi S, O’Donnell PH, Fraiman YS, Das S, Cox NJ, Macgregor S, Goode EL, Vierkant RA, Fridley BL, Hogdall E, Kjaer SK, Jensen A, Moysich KB, Grasela M, Odunsi K, Brown R, Paul J, Lambrechts D, Despierre E, Vergote I, Gross J, Karlan BY, deFazio A, Chenevix-Trench G, Australian Ovarian Cancer Study Group, Dolan ME. Platinum sensitivity-related germline polymorphism discovered via a cell-based approach and analysis of its association with outcome in ovarian cancer patients. Clin Cancer Res 17:5490-500, 2011.  PMC3160494
  • *O’Donnell PH, Stark AL, Gamazon ER, Wheeler HE, McIlwee BE, Gorsic L, Im HK, Huang RS, Cox NJ, Dolan ME. Identification of novel germline polymorphisms governing capecitabine sensitivity. Cancer 118:4063-73, 2012.  PMC3413892
  • *Wheeler HE, Gamazon ER, Stark AL, O’Donnell PH, Gorsic LK, Huang RS, Cox NJ, Dolan ME. Genome-wide meta-analysis identifies variants associated with platinating agent susceptibility across populations. Pharmacogenomics J 13:35-43, 2013.  PMC3370147 

Mark Ratain, MD

  • *Wheeler HE, Gamazon ER, Wing C, Njiaju UO, Njoku C, Baldwin RM, Owzar K, Jiang C, Watson D, Shterev I, Kubo M, Zembutsu H, Winer EP, Hudis CA, Shulman LN, Nakamura Y, Ratain MJ, Kroetz DL, Cox NJ, Dolan ME. Integration of cell line and clinical trial genome-wide analyses supports a polygenic architecture of paclitaxel-induced sensory peripheral neuropathy. Clin Cancer Res 19:491-9, 2013.  PMC3549006

* Result of collaboration within SPORE, with other SPORES, other funded NCI networks

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