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Allison Ashley-Koch, PhD

Simon G. Gregory, PhD

Elizabeth R. Hauser, PhD

Michael A. Hauser, PhD

Yi-Ju Li, PhD

Yutao Liu, PhD

Svati H. Shah, MD, MHS

Michelle P. Winn, MD

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Core Faculty

Simon G. Gregory, PhD Simon G. Gregory, PhD, is an Associate Professor in the Section of Medical Genetics, Department of Medicine. Dr. Gregory's research applies the experience he gained from leading the mapping of the mouse genome and sequencing human chromosome 1 for the Human Genome Project to elucidating the molecular mechanisms underlying multi-factorial diseases. His primary area of research involves the identification of the genetic, genomic and epigenetic factors that give rise to the development of chronic complex disease. Dr Gregory is director of the Duke Epigenetics and Epigenomics Program, and director of the Duke Bioinformatics Workshop, a forum for researchers to gain in-depth experience of using publicly available molecular genomics databases.

BSc, Royal Melbourne Institute of Technology, Melbourne, Australia
PhD, Wellcome Trust Sanger Institute, Hinxton, United Kingdom

Dr. Gregory's laboratory is involved in several group-based and collaborative research projects.

Multiple Sclerosis: In 2007 Dr Gregory and his collaborators identified the first MS gene outside of the MHC to be associated with the disease. The finding forms the basis of ongoing functional research to identify the mechanism by which the cytokine receptor (IL7R) is implicated in the disease. This work is being achieved through close collaboration with the lab of Dr Mariano Garcia Blanco and Dr Lisa Barcellos at University of California, Berkeley and involves assessing T cell signaling of IL7 in MS patients, understanding the mechanism of IL7R splicing, and the construction of an IL7R mouse model of the disease. Dr Gregory is also Principal Investigator of the MS-MURDOCK study. The study is currently developing a 1,000 patient multiple sclerosis collection that is independent of subtype with the aims of understanding the mechanisms associated with MS development and progression, and the generation of multi-omic biomarkers to facilitate reclassification of the disease.

Cardiovascular Disease: It is estimated that every one in four deaths in the US is attributable to heart disease and the health burden is believed to be greater than $100 billion annually. Dr. Gregory is collaborating with Drs. Svati Shah, Bill Kraus and Elizabeth Hauser to identify the genetic architecture of the disease using Duke's unique CATHGEN cohort via GWAS and candidate gene association studies, metabolomic profiling with Dr. Chris Newgard, and transcriptomic and epigenomic approaches. The latter, profiling the methylome of cardiovascular disease, also forms the basis of collaboration with cardiologists Drs. Svati Shah, Asad Shah and G. Chad Hughes to identify DNA methylation and gene expression differences during bi- and tricuspid aorta development.

Neural Tube Defects: NTDs encompass a variety of aberrant developmental phenotypes, including spina bifida and anencephaly. Dr. Gregory is collaborating with Drs. Allison Ashley-Koch, Janee Van Waes (Creighton University) and Ron Riley (USDA) to identify the genetic causes of NTD through environmental exposure to fumonisin in Guatemala. The Gregory lab is also using next-generation sequencing to identify causal mutations in genetically loaded NTD families, and DNA methylome profiling techniques to establish the role of environmentally labile epigenetic marks in the development of NTDs within discordant monozygotic twins.

Chiari Malformation: Chiari malformation is the downward displacement of the cerebellar tonsils into the central nervous system causing a variety of neurological symptoms including headaches, fatigue, dizziness, nausea, and, in severe cases, paralysis. The Gregory lab is collaborating with Dr Allison Ashley-Koch to identify the genetic causes of the disorder, i.e. whether herniation of the tonsils results from a cramped posterior fossa or via tethering of the spinal cord.

Autism: Recent CDC estimates suggest that autism affects more than one in 88 children in the US. Dr Gregory's group is using several approaches to not only understand the genetic and epigenetic mechanisms underlying autism, but also how children can be treated to improve their symptoms, and the events at the time of birth that may lead the development of the disorder. Together with Professor Emeritus of Pediatrics
Dr. G. Robert Delong, Dr Gregory is investigating how epigenetic factors within a multigenerational family can lead to the development of the disorder and how the identification of compound genetic risk factors in psychosocial families by exome sequencing may lead to the development of autism. The effect of genomic repeats in autism cases is being explored in collaboration with Dr Jay Shendure of Washington University. Dr Gregory is also an investigator with the SOARS consortium headed by Dr Lin Sikich at the University of North Carolina. This exciting new clinical trial will assess the efficacy of nasally delivered oxytocin to ameliorate some of the core deficits of autism. The Gregory lab's role in the consortium is to develop epigenetic and expression biomarkers of oxytocin response. Finally, the Gregory lab is collaborating with Dr Marie Lynn Miranda at the University of Michigan and Dr Chad Grotegut at the Duke University Medical Center to understand how events at birth, particularly induced and or augmented births, may lead to the development of autism.

Fuchs Endothelial Corneal Dystrophy: FECD a slow progressing degenerative disease of the cornea that usually affects both eyes, is slightly more common in women than in men, and usually impacts visual acuity in the 50s and 60s. Dr Gregory is collaborating with Dr Yi-Ju Li and Dr. Gordon Klintworth to understand the genetic basis of the disease. The Duke FECD team has accumulated an FECD collection of over 1400 individuals and is considered one of the largest such collections in the country.

Osteoarthritis: Osteoarthritis (OA) is the most prevalent form of arthritis world-wide. According to the recent Global Burden of Disease 2010 Project, OA is a leading cause of disability globally and the fastest increasing major health condition. The Gregory lab is currently pursuing two collaborations to understand the development and progression of OA. The first is with Duke researchers Drs. Virgina Kraus and Elizabeth Hauser to profile the epigenetic and transcriptomic changes associated with primary tissue in the development of osteoarthritic knees while the second collaboration with Dr Fashid Guilak is aimed at identifying the epigenetic mechanisms associated with diet induced changes of mouse stem cells in the development of obesity and OA.

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Dr. Gregory is member of the graduate faculty of the Computational Biology and Bioinformatics, Molecular Genetics and Microbiology and University Program in Genetics and Genomics Duke programs.

Current Lab Members

Former Lab Members

Stephanie Arvai

Rachel Cote PhD (UNC Chapel Hill)

Joshua Beaver

Christina Sheedy PhD (Duke UPGG Program)

Megan Chryst-Ladd

Matthew Schemmel (Illumia)

Elizabeth Grass

Josh Virgadamo (U.S. Navy)

Nick White PhD

Jessica Johnson (Mt. Sinai Medical Center)


Jennifer Doss (Duke UPGG Program)


Shera Watson (Duke Cardiology)


Aaron Towers (Duke UPGG Program)

Current Trainees
Deidre Krupp - Duke MGM Graduate Program
Laura Bergamaschi PhD - Post Doctoral Fellow

Former Trainees
Mollie Minear PhD - UPGG Graduate Program (Duke GELP - Post Doctoral Fellow)
Christina Markunas PhD - UPGG Graduate Program (NIEHS - Post Doctoral Fellow)
Jessica Connelly PhD - Post Doctoral Fellow (University of Virginia - Faculty)
Beth Sutton PhD - Post Doctoral Fellow (Campbell University - Faculty)
Jama Purser MD - Clinical Fellow

Current and Past High School and Pre-Baccalaureate Trainees
Hailey Gosnell - NCSM
Drew Harrelson - NCSM
Cynthia Rouf - NCSU
Nicole Joy - Duke University
Lauren Vaughan - Duke University
Angeline Luong - Duke University
Hunter Nisonoff - Duke University
Thomas Boyle - Duke University
Allison Dorogi - Duke University
Jaret (Mac) Karnuta - Duke University
Seth Newman - Washington University
Aisha Venugopal - UNC, Chapel Hill

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Selected Publications

Gregory SG, Barlow KF, McLay KE, Kaul R, Swarbreck D, Dunham A, Scott CE, et al. The DNA sequence and biological annotation of human chromosome 1. Nature. 2006 May 18;441(7091):315-21. PMID: 16710414

Connelly JJ, Wang T, Cox JE, Haynes C, Wang L, Shah SH, Crosslin DR, Hale AB, Nelson S, Crossman DC, Granger CB, Haines JL, Jones CJH, Vance JM, Goldschmidt-Clermont PJ, Kraus WE, Hauser ER, Gregory SG. GATA2 is associated with familial early onset coronary artery disease. PLoS Genetics 2006 2(8). PMCID: PMC1557786..

Gregory SG, Schmidt S, Seth P, Oksenberg JR et al. Interleukin 7 receptor a chain (IL7R) shows allelic and functional association with multiple sclerosis. Nat Genet. 2007, Sep;39(9):1083-91

The International Multiple Sclerosis Genetics Consortium. Risk Alleles for Multiple Sclerosis Identified by a Genomewide Study. NEJM 2007 357:851-862 . PMID: 17660530

J.J. Connelly, S.H. Shah, J.F. Doss, S. Gadson, S. Nelson, D.R. Crosslin, A.B. Hale, X. Lou, T. Wang, C. Haynes, D. Seo, D.C. Crossman, V. Mooser, C.B. Granger, C.J.H. Jones, W.E. Kraus, E.R. Hauser and S.G. Gregory. Genetic and functional association of FAM5C with myocardial infarction.. BMC Medical Genetics 2008, 9:33 (22 Apr 2008). PMCID: PMC2382879

Stamm DS, Siegel DG, Mehltretter L, Connelly JJ, Trott A, Ellis N, Zismann V, Stephan DA, George TM, Vekemans M, Ashley-Koch A, Gilbert J, Gregory SG, Speer MC. Refinement of 2q and 7p Loci in a Large Multiplex NTD Family. Birth Defects Res A Clin Mol Teratol. 2008 Jun;82(6):441-52. PMCID: PMC2712757.

Gregory SG, Connelly JJ, Towers AJ, Johnson J, Biscocho D, Markunas CA, et al. Genomic and epigenetic evidence for oxytocin receptor deficiency in autism. BMC Med. 2009 Oct 22;7(1):62. PMID: 19845972. PMCID: PMC2774338

Minear MA, Crosslin DR, Sutton BS, Connelly JJ, NelsonSC, Gadson-Watson S, Wang T, Seo D, Vance JM, Sketch MH Jr, Haynes C, Goldschmidt-Clermont PJ, Shah SH, Kraus WE, Hauser ER, Gregory SG. Polymorphic variants in tenascin-C (TNC) are associated with atherosclerosis and coronary artery disease. Hum Genet. 2011 Jun;129(6):641-54. Epub 2011 Feb 5.PMID: 21298289. PMCID: PMC3576662

Hara MR, Kovacs JJ, Whalen EJ, Rajagopal S, Strachan RT, Grant W, Towers AJ, Williams B, Lam CM, Xiao K, Shenoy SK, Gregory SG, Ahn S, Duckett DR, Lefkowitz RJ. A stress response pathway regulates DNA damage through β(2)-adrenoreceptors and β-arrestin-1. Nature. 2011 Aug 21;477(7364):349-53. PMID: 21857681. PMCID: PMC3628753

Lin N, Di C, Bortoff K, Fu J, Truszkowski P, Killela P, Duncan C, McLendon R, Bigner D, Gregory S, Adamson DC. Deletion or Epigenetic Silencing of AJAP1 on 1p36 in Glioblastoma. Mol Cancer Res. 2012 Feb;10(2):208-17. PMID: 22241217. PMCID: PMC3288240

Krupp DR, Xu PT, Thomas S, Dellinger A, Etchevers HC, Vekemans M, Gilbert JR, Speer MC, Ashley-Koch AE, Gregory SG. Transcriptome profiling of genes involved in neural tube closure during human embryonic development using long serial analysis of gene expression (long-SAGE). Birth Defects Res A Clin Mol Teratol. 2012 Sep;94(9):683-92. doi: 10.1002/bdra.23040. Epub 2012 Jul 18. PMCID: PMC3438356 [Available on 2013/9/1]

Evsyukova I, Bradrick SS, Gregory SG, Garcia-Blanco MA. Cleavage and polyadenylation specificity factor 1 (CPSF1) regulates alternative splicing of interleukin 7 receptor (IL7R) exon 6. RNA. 2013 Jan;19(1):103-15. doi: 10.1261/rna.035410.112. Epub 2012 Nov 14. PMID: 23151878; PMCID: PMC3527722.

Simon G. Gregory, Rebecca Anthopolos, Claire Osgood, Chad A. Grotegut, and Marie Lynn Miranda. Association of autism with induced or augmented childbirth in North Carolina Birth Record (1990-1998) and Education Research (1997-2007) Databases. JAMA Pediatr. 2013;167(10):959-966. doi:10.1001/jamapediatrics.2013.2904

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Contact at:
Duke Molecular Physiology Institute
300 N. Duke Street, DUMC 104775
Durham, 27701, NC
Tel: (919) 684-0726
Fax: (919) 684-0924

Director, Genomics Core Laboratory
David H. Murdock Research Institute
150 Research Campus Drive
Kannapolis, NC 28081
(888) 545-6598

E-mail: simon.gregory@duke.edu

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