Subra Kugathasan, MD


Pediatrics & Human Genetics

Marcus Professor

Pediatric Gastroenterology

Scientific Director

Children's Healthcare of Atlanta Combined Center for Pediatric Inflammatory Bowel Disease

Phone: 404-727-4542



Dr Kugathasan’s research goal is to further extend novel genetic discoveries in inflammatory bowel disease (IBD), in particular common and rare susceptibility variants that are the cause of very early onset IBD. In addition, he has been investigating the immunogenetic mechanisms that underlie this chronic intestinal inflammation in children and adults with IBD. He is the principal investigator of a large 40 sites, multicenter research network where thousands of incident cases of early onset IBD are being enrolled. DNA, serum and intestinal biopsy materials are being banked to identify modifier genes, environmental and microbial factors that can be used to stratify the risk of complicated disease and surgery in IBD. As a clinician and an inflammatory bowel disease specialist, he also serves as scientific director of the inflammatory bowel disease program at Children’s Health Care of Atlanta and sees pediatric patients with inflammatory bowel disease, (both Crohn’s disease and ulcerative colitis) at Emory Children’s Center and Egleston Children’s hospital.

Dr. Kugathasan received his medical degree from Srilanka. After pediatric residency in Sinal Hospital of Baltimore, he completed his pediatric gastroenterology fellowship at Case Western Reserve University. His research training was in mucosal immunology at under the mentorship of Dr Fiocchi. In 2002, he received the Physician of the year award from Crohn’s and Colitis Foundation of America.  He was the recipient of the prestigious young clinical investigator award from the society of North American Pediatric Gastrenterology & Nutrition (NASPGHAN) and junior physician investigator award from American Federation for Medical Research (AFMR). He has served as a co-chair for pediatric affairs of Crohn’s and Colitis foundation of America. He moved to Emory University in 2008, and has been appointed as a Marcus Professor of Pediatric Gastroenterology / Inflammatory bowel disease.

Research Interests

Inflammatory bowel disease (IBD), which includes Crohn’s disease (CD) and ulcerative colitis (UC), is estimated to affect approximately 1.2 million Americans. IBD is a destructive, life-long, chronic inflammatory disorder which results in gastrointestinal bleeding, weight loss and poor quality of life. IBD affects all races and onset of the disease is usually in children and young adults. Familial, twin and linkage studies suggest that CD is highly heritable.

To determine and identify genetic associations in very young onset IBD in comparison to those found in older patients with adult onset disease. In particular, to identify high effect, highly penetrant but rare variants that cannot be identified by genome wide association studies.

To identify susceptibility and modifying factors and perform Genotype – serotype – bacteriotype - gene expression studies in carefully and prospectively identified incident cases of early onset IBD.  

Genome wide association studies to determine common SNPs / loci and copy number variants in African Americans with IBD. Replication studies in African Americans show that the major genetic variants that were found in Caucasians with IBD are not associated with African Americans. 

Use of the latest generation sequencing technologies to comprehensively  identify IBD - predisposing causal variants in order to fully characterize the physical scale of various genetic associations in IBD. Performing targeted sequencing in susceptibility loci found African Americans and Caucasians in parallel is another focus on interest. 


Wang K, Baldassano R, Zhang H, Qu HQ, Imielinski M, Kugathasan S., et al: Comparative genetic analysis of inflammatory bowel disease and type 1 diabetes implicates multiple loci with opposite effects. Hum Mol Genet. 2010 May 15;19(10):2059-67.

Imielinski M, Baldassano RN, Griffiths A, Russell RK, Annese V, Dubinsky M, Kugathasan al Common variants at five new loci associated with early-onset inflammatory bowel disease .Nat Genet. 2009 Dec;41(12):1335-40.

Wang K, Zhang H, Kugathasan S., Annese V, Bradfield JP, Russell RK, Sleiman PM, Imielinski M, Glessner J, Hou C, Wilson DC, Walters T, Kim C, Frackelton EC, Lionetti P, Barabino A, Van Limbergen J, Guthery S, Denson L, Piccoli D, Li M, Dubinsky M, Silverberg M, Griffiths A, Grant SF, Satsangi J, Baldassano R, Hakonarson H: Diverse genome-wide association studies associate the IL12/IL23 pathway with Crohn Disease.  Am J Hum Genet. 2009 Mar;84(3):399-405.

Kugathasan S., Baldassano RN, Bradfield JP, Sleiman PM, Imielinski M, Guthery SL, Cucchiara S, Kim CE, Frackelton EC, Annaiah K, Glessner JT, Santa E, Willson T, Eckert AW, Bonkowski E, Shaner JL, Smith RM, Otieno FG, Peterson N, Abrams DJ, Chiavacci RM, Grundmeier R, Mamula P, Tomer G, Piccoli DA, Monos DS, Annese V, Denson LA, Grant SF, Hakonarson H: Loci on 20q13 and 21q22 are associated with pediatric-onset inflammatory bowel disease. Nat Genet. 2008 Oct;40(10):1211-5.

Peterson N, Guthery S, Denson L, Lee J, Saeed S, Prahalad S, Biank V, Ehlert R, Tomer G, G rand R, Rudolph C, Kugathasan S:  Genetic variants in the autophagy pathway contribute to paediatric Crohn's disease. Gut. 2008 Sep;57(9):1336-7.

Kugathasan S., Collins N, Maresso K, Hoffmann RG, Stephens M, Werlin SL, Rudolph C, Broeckel U: CARD15 gene mutations and risk for early surgery in pediatric-onset Crohn's disease. Clin Gastroenterol Hepatol.  2004 Nov;2(11):1003-9.