Publications in Embedded Genomics

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EMR and IBD – depression and anxiety
January 2013

Similar Risk of Depression and Anxiety Following Surgery or Hospitalization for Crohn’s Disease and Ulcerative Colitis, Ananthakrishnan AN, Gainer VS, Cai T, Perez RG, Cheng SC, Savova G, Chen P, Szolovits P, Xia Z, De Jager PL, Shaw S, Churchill S, Karlson EW, Kohane I, Perlis RH, Plenge RM, Murphy SN, Liao KP. Am J Gastroenterol. 2013 Jan 22. doi: 10.1038/ajg.2012.471. [Epub ahead of print] PMID: 23337479

IBD-related surgery or hospitalization is associated with a significant risk for depression and anxiety, with a similar magnitude of risk in both diseases.

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EMR and IBD – surgery and psychiatric disease
January 2013

Psychiatric co-morbidity is associated with increased risk of surgery in Crohn’s disease, Ananthakrishnan AN, Gainer VS, Perez RG, Cai T, Cheng SC, Savova G, Chen P, Szolovits P, Xia Z, De Jager PL, Shaw SY, Churchill S, Karlson EW, Kohane I, Perlis RH, Plenge RM, Murphy SN, Liao KP. Aliment Pharmacol Ther. 2013 Feb;37(4):445-54. doi: 10.1111/apt.12195. Epub 2013 Jan 7. PMID: 23289600

Depressive disorder or generalised anxiety is associated with a modestly increased risk of surgery in patients with Crohn’s disease. Interventions addressing this may improve patient outcomes.


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Autoantibodies and autoimmune risk alleles
December 2012

Autoantibodies, autoimmune risk alleles and clinical associations in rheumatoid arthritis cases and non-RA controls in the electronic medical records.  Liao KP, Kurreeman F, Li G, Duclos G, Murphy S, P RG, Cai T, Gupta N, Gainer V, Schur P, Cui J, Denny JC, Szolovits P, Churchill S, Kohane I, Karlson EW, Plenge RM. Arthritis Rheum. 2012 Dec 10. doi: 10.1002/art.37801. [Epub ahead of print] PMID: 23233247

We used i2b2 samples to demonstrate that autoimmune risk alleles influence the production of clinical autoantibodies (ANA, TPO, CCP, tTP) in both RA cases and non-RA controls.

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i2b2 paper on IBD
April 2012

Predictors of severe outcomes associated with Clostridium difficile infection in patients with inflammatory bowel disease, Ananthakrishnan AN, Guzman-Perez R, Gainer V, Cai T, Churchill S, Kohane I, Plenge RM, Murphy S. Aliment Pharmacol Ther. 2012 Apr;35(7):789-95. PMID: 22360370

Using EMR data in a virtual cohort of IBD patients, we identify clinical predictors of severe gastrointestinal infection.

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Multi-ethnic genetic study of RA risk
March 2012

Use of a Multiethnic Approach to Identify Rheumatoid-Arthritis-Susceptibility Loci, 1p36 and 17q12, Kurreeman FA, Stahl EA, Okada Y, Liao K, Diogo D, Raychaudhuri S, Freudenberg J, Kochi Y, Patsopoulos NA, Gupta N; CLEAR investigators, Sandor C, Bang SY, Lee HS, Padyukov L, Suzuki A, Siminovitch K, Worthington J, Gregersen PK, Hughes LB, Reynolds RJ, Bridges SL Jr, Bae SC, Yamamoto K, Plenge RM. Am J Hum Genet. 2012 Mar 9;90(3):524-32. PMID: 22365150

Using samples from i2b2, CLEAR (African Americans), Japan, and Korea, we demonstrate that a multi-ethnic approach is a power strategy to discover new RA risk loci.

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EMR portability
February 2012

Portability of an algorithm to identify rheumatoid arthritis in electronic health records. Carroll RJ, Thompson WK, Eyler AE, Mandelin AM, Cai T, Zink RM, Pacheco JA, Boomershine CS, Lasko TA, Xu H, Karlson EW, Perez RG, Gainer VS, Murphy SN, Ruderman EM, Pope RM, Plenge RM, Kho AN, Liao KP, Denny JC. J Am Med Inform Assoc. 2012 Feb 28. PMID: 22374935

We demonstrate portability of our EMR algorithm to define RA virtual cohorts across institutions.

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Genetic studies in EMR cohort
January 2011

Genetic Basis of Autoantibody Positive and Negative Rheumatoid Arthritis Risk in a Multi-ethnic Cohort Derived from Electronic Health Records. Kurreeman F, Liao K, Chibnik L, Hickey B, Stahl E, Gainer V, Li G, Bry L, Mahan S, Ardlie K, Thomson B, Szolovits P, Churchill S, Murphy SN, Cai T, Raychaudhuri S, Kohane I, Karlson E, Plenge RM. Am J Hum Genet. 2011;88(1):57-69. PMID: 21211616

We use our i2b2 samples to demonstrate that most RA risk alleles are shared across individuals of distinct geographic ancestry.  We also show that a GRS in samples derived from EMR data is identical to a GRS from traditional cohorts.

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Chronic fatigue in i2b2
November 2010

Xenotropic murine leukemia virus-related virus prevalence in patients with chronic fatigue syndrome or chronic immunomodulatory conditions. Henrich TJ, Li JZ, Felsenstein D, Kotton CN, Plenge RM, Pereyra F, Marty FM, Lin NH, Grazioso P, Crochiere DM, Eggers D, Kuritzkes DR, Tsibris AM.  J Infect Dis. 2010 Nov 15;202(10):1478-81. PMID: 20936980

We used i2b2 samples to show that XMLV-related virus was not associated with chronic fatigue syndrome.

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i2b2 EMR algorithm for RA
August 2010

Electronic medical records for discovery research in rheumatoid arthritis. Liao KP, Cai T, Gainer V, Goryachev S, Zeng-Treitler Q, Raychaudhuri S, Szolovits P, Churchill S, Murphy S, Kohane I, Karlson EW, Plenge RM.  Arthritis Care Res. 2010 Aug;62(8):1120-7. PMID: 20235204

This manuscript, the first to come out of our i2b2 project, describes how we mined EMR data to define a virtual cohort of RA patients at Partners HealthCare.

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