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A Comprehensive Cancer Center Designated by the National Cancer Institute

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Genomics, Analytics, and Informatics Core: Breast SPORE-Related Publications

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 cellbased 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.

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

 

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