Nancy J. Cox, Ph.D.
Professor and Section Chief, Section of Genetic Medicine, Department of Medicine
Professor, Department of Human Genetics
Member: Computation Institute; Committee on Genetics, Genomics, and Systems Biology; Committee on Molecular Medicine; Committee on Cancer Biology
Ph.D. in Human Genetics from Yale University, 1982
B.S. in biology from the University of Notre Dame, 1978
KCBD 3220F 900 E 57th Street University of Chicago Chicago, IL 60637 USA
Phone: (773)-834-1001
Fax: (773) 702-2567
 

Research Description

The Cox Lab conducts research to identify and characterize the genetic component to common diseases and complex human traits.   Our lab is computational and “dry” rather than a traditional molecular genetics (“wet”) laboratory.  We develop methods to analyze and integrate a wide variety of data types and then apply these methods to analyze data from many different diseases and phenotypes.  For example, we are currently funded to analyze RNAseq data generated through the GTEx (Genotype-Tissue Expression) project (http://commonfund.nih.gov/GTEx/), as well as sequence data generated through the 1000 Genomes Project.  Our lab was the first to show that the genetic variation associated with complex human phenotypes is much more likely than expected to be variation that is also associated with mRNA levels for human transcripts1 – i.e. that SNPs associated with human diseases are also likely to be eQTLs (expression quantitative trait loci).  More recently, we have also shown that SNPs associated with microRNA levels2 and alternative splicing are over-represented among SNPs associated with human diseases3.  We are utilizing this information to develop new gene-based methods for genome association analysis that allow us to place more weight on genetic variation for which we have prior evidence of function.

We work extensively in pharmacogenomics on research projects designed to identify the genetic basis of response to chemotherapeutic agents and adverse events4.  We also have a long history of conducting research on the genetics of type 2 diabetes5, and are currently analyzing sequence data generated for the T2DGENES project – more than 10,000 exomes, and 600 whole genomes (60X coverage).  We are also part of the University of Chicago Conte Center, focused on applying new approaches to understand the genetic basis of autism, bipolar disorder and schizophrenia.6,7 I lead the analytic group for the International Tourette Syndrome Consortium, where we are conducting analyses for both GWAS (genome-wide association studies)8, and sequencing studies.  We are also working on breast cancer using both GWAS and sequence data, and have had recent success in characterizing genetic risk factors for mesothelioma9.

 

Selected Publications

Genetic factors affecting gene transcription and catalytic activity of UDP-glucuronosyltransferases in human liver.
Liu W, Ramirez J, Gamazon ER, Mirkov S, Chen P, Wu K, Sun C, Cox NJ, Cook E Jr, Das S, Ratain MJ
(2014 Oct) Hum Mol Genet. 2014 Oct 15;23(20):5558-69. doi: 10.1093/hmg/ddu268. Epub 2014 May 30. 24879639 (Full Text)

pRRophetic: An R Package for Prediction of Clinical Chemotherapeutic Response from Tumor Gene Expression Levels.
Geeleher P, Cox N, Huang RS
(2014) PLoS One. 2014 Sep 17;9(9):e107468. doi: 10.1371/journal.pone.0107468. eCollection 2014. 25229481 (Full Text)

Integrative analyses of genetic variation, epigenetic regulation, and the transcriptome to elucidate the biology of platinum sensitivity.
LaCroix B, Gamazon ER, Lenkala D, Im HK, Geeleher P, Ziliak D, Cox NJ, Huang RS
(2014) BMC Genomics. 2014 Apr 16;15:292. doi: 10.1186/1471-2164-15-292. 24739237 (Full Text)

Genome-wide Interrogation of Longitudinal FEV1 in Children with Asthma.
Wu K, Gamazon ER, Im HK, Geeleher P, White SR, Solway J, Clemmer GL, Weiss ST, Tantisira KG, Cox NJ, Ratain MJ, Huang RS
(2014 Sep) Am J Respir Crit Care Med. 2014 Sep 15;190(6):619-27. doi: 10.1164/rccm.201403-0460OC. 25221879

Cross-Disorder Genome-Wide Analyses Suggest a Complex Genetic Relationship Between Tourette's Syndrome and OCD.
Yu D, Mathews CA, Scharf JM, Neale BM, Davis LK, Gamazon ER, Derks EM, Evans P, Edlund CK, Crane J, Fagerness JA, Osiecki L, Gallagher P, Gerber G, Haddad S, Illmann C, McGrath LM, Mayerfeld C, Arepalli S, Barlassina C, Barr CL, Bellodi L, Benarroch F, Berrio GB, Bienvenu OJ, Black DW, Bloch MH, Brentani H, Bruun RD, Budman CL, Camarena B, Campbell DD, Cappi C, Silgado JC, Cavallini MC, Chavira DA, Chouinard S, Cook EH, Cookson MR, Coric V, Cullen B, Cusi D, Delorme R, Denys D, Dion Y, Eapen V, Egberts K, Falkai P, Fernandez T, Fournier E, Garrido H, Geller D, Gilbert D, Girard SL, Grabe HJ, Grados MA, Greenberg BD, Gross-Tsur V, Grunblatt E, Hardy J, Heiman GA, Hemmings SM, Herrera LD, Hezel DM, Hoekstra PJ, Jankovic J, Kennedy JL, King RA, Konkashbaev AI, Kremeyer B, Kurlan R, Lanzagorta N, Leboyer M, Leckman JF, Lennertz L, Liu C, Lochner C, Lowe TL, Lupoli S, Macciardi F, Maier W, Manunta P, Marconi M, McCracken JT, Mesa Restrepo SC, Moessner R, Moorjani P, Morgan J, Muller H, Murphy DL, Naarden AL, Nurmi E, Ochoa WC, Ophoff RA, Pakstis AJ, Pato MT, Pato CN, Piacentini J, Pittenger C, Pollak Y, Rauch SL, Renner T, Reus VI, Richter MA, Riddle MA, Robertson MM, Romero R, Rosario MC, Rosenberg D, Ruhrmann S, Sabatti C, Salvi E, Sampaio AS, Samuels J, Sandor P, Service SK, Sheppard B, Singer HS, Smit JH, Stein DJ, Strengman E, Tischfield JA, Turiel M, Valencia Duarte AV, Vallada H, Veenstra-VanderWeele J, Walitza S, Wang Y, Weale M, Weiss R, Wendland JR, Westenberg HG, Shugart YY, Hounie AG, Miguel EC, Nicolini H, Wagner M, Ruiz-Linares A, Cath DC, McMahon W, Posthuma D, Oostra BA, Nestadt G, Rouleau GA, Purcell S, Jenike MA, Heutink P, Hanna GL, Conti DV, Arnold PD, Freimer NB, Stewart SE, Knowles JA, Cox NJ, Pauls DL
(2014 Aug) Am J Psychiatry. 2014 Aug 26. doi: 10.1176/appi.ajp.2014.13101306. 25158072

Genetic association signal near NTN4 in Tourette syndrome.
Paschou P, Yu D, Gerber G, Evans P, Tsetsos F, Davis LK, Karagiannidis I, Chaponis J, Gamazon E, Mueller-Vahl K, Stuhrmann M, Schloegelhofer M, Stamenkovic M, Hebebrand J, Noethen M, Nagy P, Barta C, Tarnok Z, Rizzo R, Depienne C, Worbe Y, Hartmann A, Cath DC, Budman CL, Sandor P, Barr C, Wolanczyk T, Singer H, Chou IC, Grados M, Posthuma D, Rouleau GA, Aschauer H, Freimer NB, Pauls DL, Cox NJ, Mathews CA, Scharf JM
(2014 Aug) Ann Neurol. 2014 Aug;76(2):310-5. doi: 10.1002/ana.24215. Epub 2014 Jul 21. 25042818 (Full Text)

Copy number variation in obsessive-compulsive disorder and tourette syndrome: a cross-disorder study.
McGrath LM, Yu D, Marshall C, Davis LK, Thiruvahindrapuram B, Li B, Cappi C, Gerber G, Wolf A, Schroeder FA, Osiecki L, O'Dushlaine C, Kirby A, Illmann C, Haddad S, Gallagher P, Fagerness JA, Barr CL, Bellodi L, Benarroch F, Bienvenu OJ, Black DW, Bloch MH, Bruun RD, Budman CL, Camarena B, Cath DC, Cavallini MC, Chouinard S, Coric V, Cullen B, Delorme R, Denys D, Derks EM, Dion Y, Rosario MC, Eapen V, Evans P, Falkai P, Fernandez TV, Garrido H, Geller D, Grabe HJ, Grados MA, Greenberg BD, Gross-Tsur V, Grunblatt E, Heiman GA, Hemmings SM, Herrera LD, Hounie AG, Jankovic J, Kennedy JL, King RA, Kurlan R, Lanzagorta N, Leboyer M, Leckman JF, Lennertz L, Lochner C, Lowe TL, Lyon GJ, Macciardi F, Maier W, McCracken JT, McMahon W, Murphy DL, Naarden AL, Neale BM, Nurmi E, Pakstis AJ, Pato MT, Pato CN, Piacentini J, Pittenger C, Pollak Y, Reus VI, Richter MA, Riddle M, Robertson MM, Rosenberg D, Rouleau GA, Ruhrmann S, Sampaio AS, Samuels J, Sandor P, Sheppard B, Singer HS, Smit JH, Stein DJ, Tischfield JA, Vallada H, Veenstra-VanderWeele J, Walitza S, Wang Y, Wendland JR, Shugart YY, Miguel EC, Nicolini H, Oostra BA, Moessner R, Wagner M, Ruiz-Linares A, Heutink P, Nestadt G, Freimer N, Petryshen T, Posthuma D, Jenike MA, Cox NJ, Hanna GL, Brentani H, Scherer SW, Arnold PD, Stewart SE, Mathews CA, Knowles JA, Cook EH, Pauls DL, Wang K, Scharf JM
(2014 Aug) J Am Acad Child Adolesc Psychiatry. 2014 Aug;53(8):910-9. doi: 10.1016/j.jaac.2014.04.022. Epub 2014 Jun 24. 25062598

Poly-omic prediction of complex traits: OmicKriging.
Wheeler HE, Aquino-Michaels K, Gamazon ER, Trubetskoy VV, Dolan ME, Huang RS, Cox NJ, Im HK
(2014 Jul) Genet Epidemiol. 2014 Jul;38(5):402-15. doi: 10.1002/gepi.21808. Epub 2014 May 2. 24799323 (Full Text)

Re: Concordance between CYP2D6 genotypes obtained from tumor-derived and germline DNA.
Goetz MP, Brauch H, Ratain MJ, Cox NJ, Nakamura Y, Weinshilboum R, Ingle JN
(2014 May) J Natl Cancer Inst. 2014 Apr 3;106(5). pii: dju063. doi: 10.1093/jnci/dju063. 24700804

Genetic variation associated with euphorigenic effects of d-amphetamine is associated with diminished risk for schizophrenia and attention deficit hyperactivity disorder.
Hart AB, Gamazon ER, Engelhardt BE, Sklar P, Kahler AK, Hultman CM, Sullivan PF, Neale BM, Faraone SV, de Wit H, Cox NJ, Palmer AA
(2014 Apr) Proc Natl Acad Sci U S A. 2014 Apr 22;111(16):5968-73. doi: 10.1073/pnas.1318810111. Epub 2014 Apr 7. 24711425 (Full Text)

Genome-wide association study of Tourette's syndrome.
Scharf JM, Yu D, Mathews CA, Neale BM, Stewart SE, Fagerness JA, Evans P, Gamazon E, Edlund CK, Service SK, Tikhomirov A, Osiecki L, Illmann C, Pluzhnikov A, Konkashbaev A, Davis LK, Han B, Crane J, Moorjani P, Crenshaw AT, Parkin MA, Reus VI, Lowe TL, Rangel-Lugo M, Chouinard S, Dion Y, Girard S, Cath DC, Smit JH, King RA, Fernandez TV, Leckman JF, Kidd KK, Kidd JR, Pakstis AJ, State MW, Herrera LD, Romero R, Fournier E, Sandor P, Barr CL, Phan N, Gross-Tsur V, Benarroch F, Pollak Y, Budman CL, Bruun RD, Erenberg G, Naarden AL, Lee PC, Weiss N, Kremeyer B, Berrio GB, Campbell DD, Cardona Silgado JC, Ochoa WC, Mesa Restrepo SC, Muller H, Valencia Duarte AV, Lyon GJ, Leppert M, Morgan J, Weiss R, Grados MA, Anderson K, Davarya S, Singer H, Walkup J, Jankovic J, Tischfield JA, Heiman GA, Gilbert DL, Hoekstra PJ, Robertson MM, Kurlan R, Liu C, Gibbs JR, Singleton A, Hardy J, Strengman E, Ophoff RA, Wagner M, Moessner R, Mirel DB, Posthuma D, Sabatti C, Eskin E, Conti DV, Knowles JA, Ruiz-Linares A, Rouleau GA, Purcell S, Heutink P, Oostra BA, McMahon WM, Freimer NB, Cox NJ, Pauls DL
(2013 Jun) Mol Psychiatry. 2013 Jun;18(6):721-8. doi: 10.1038/mp.2012.69. Epub 2012 Aug 14. 22889924 (Full Text)

Enrichment of cis-regulatory gene expression SNPs and methylation quantitative trait loci among bipolar disorder susceptibility variants.
Gamazon ER, Badner JA, Cheng L, Zhang C, Zhang D, Cox NJ, Gershon ES, Kelsoe JR, Greenwood TA, Nievergelt CM, Chen C, McKinney R, Shilling PD, Schork NJ, Smith EN, Bloss CS, Nurnberger JI, Edenberg HJ, Foroud T, Koller DL, Scheftner WA, Coryell W, Rice J, Lawson WB, Nwulia EA, Hipolito M, Byerley W, McMahon FJ, Schulze TG, Berrettini WH, Potash JB, Zandi PP, Mahon PB, McInnis MG, Zollner S, Zhang P, Craig DW, Szelinger S, Barrett TB, Liu C
(2013 Mar) Mol Psychiatry. 2013 Mar;18(3):340-6. doi: 10.1038/mp.2011.174. Epub 2012 Jan 3. 22212596 (Full Text)

Loci nominally associated with autism from genome-wide analysis show enrichment of brain expression quantitative trait loci but not lymphoblastoid cell line expression quantitative trait loci.
Davis LK, Gamazon ER, Kistner-Griffin E, Badner JA, Liu C, Cook EH, Sutcliffe JS, Cox NJ
(2012) Mol Autism. 2012 May 16;3(1):3. doi: 10.1186/2040-2392-3-3. 22591576 (Full Text)

Variants affecting exon skipping contribute to complex traits.

Lee, Y, Gamazon ER, Rebman E, Lee Y, Lee, S, Dolan ME, Cox NJ, Lussier YA

(2012) PLoS genetics (in press)

Genetic architecture of microRNA expression: implications for the transcriptome and complex traits.
Gamazon ER, Ziliak D, Im HK, LaCroix B, Park DS, Cox NJ, Huang RS
(2012 Jun) Am J Hum Genet. 2012 Jun 8;90(6):1046-63. doi: 10.1016/j.ajhg.2012.04.023. Epub 2012 May 31. 22658545 (Full Text)

A genome-wide association study of overall survival in pancreatic cancer patients treated with gemcitabine in CALGB 80303.
Innocenti F, Owzar K, Cox NL, Evans P, Kubo M, Zembutsu H, Jiang C, Hollis D, Mushiroda T, Li L, Friedman P, Wang L, Glubb D, Hurwitz H, Giacomini KM, McLeod HL, Goldberg RM, Schilsky RL, Kindler HL, Nakamura Y, Ratain MJ
(2012 Jan) Clin Cancer Res. 2012 Jan 15;18(2):577-84. doi: 10.1158/1078-0432.CCR-11-1387. Epub 2011 Dec 5. 22142827 (Full Text)

Germline BAP1 mutations predispose to malignant mesothelioma.
Testa JR, Cheung M, Pei J, Below JE, Tan Y, Sementino E, Cox NJ, Dogan AU, Pass HI, Trusa S, Hesdorffer M, Nasu M, Powers A, Rivera Z, Comertpay S, Tanji M, Gaudino G, Yang H, Carbone M
(2011 Oct) Nat Genet. 2011 Aug 28;43(10):1022-5. doi: 10.1038/ng.912. 21874000 (Full Text)

Genome-wide association and meta-analysis in populations from Starr County, Texas, and Mexico City identify type 2 diabetes susceptibility loci and enrichment for expression quantitative trait loci in top signals.
Below JE, Gamazon ER, Morrison JV, Konkashbaev A, Pluzhnikov A, McKeigue PM, Parra EJ, Elbein SC, Hallman DM, Nicolae DL, Bell GI, Cruz M, Cox NJ, Hanis CL
(2011 Aug) Diabetologia. 2011 Aug;54(8):2047-55. doi: 10.1007/s00125-011-2188-3. Epub 2011 Jun 7. 21647700 (Full Text)

Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS.
Nicolae DL, Gamazon E, Zhang W, Duan S, Dolan ME, Cox NJ
(2010 Apr) PLoS Genet. 2010 Apr 1;6(4):e1000888. doi: 10.1371/journal.pgen.1000888. 20369019 (Full Text)