Autoimmune diseases (AID) refer to destructive conditions involving an aberrant chronic activation of the adaptive immune system, where the immune cells instead of producing antibodies to attack foreign invaders, mistakenly attack the body’s own healthy cells. While autoimmune diseases are heterogeneous according to symptoms, lesion types, and prognosis, and are usually studied in isolation according to groups based on organ system; various autoimmunity diseases share similar immune effector mechanisms. Recent genetic studies suggest that many autoimmune and chronic autoinflammatory condi
Denny’s Group at Vandy
Breast cancer is the most common cancer and the second leading cause of cancer-related death among women in the U.S. Known breast cancer risk factors include age, race/ethnicity, reproductive factors, and benign breast disease. Family history of breast cancer and hereditary cancer syndromes, such as BRCA1/BRCA2 mutations, confer the strongest risk for this disease.
Chronic kidney disease (CKD) is defined as an abnormality of kidney structure or function present for longer than 3 months. CKD can occur as a result of heterogeneous disorders affecting the kidney. In the United States, an estimated 13.6% of adults have CKD. Notably, adjusted mortality rates are higher for patients with CKD than those without, and rates increase with CKD stage. The purpose of this algorithm is to enable accurate CKD diagnosis and staging based on EHR data.
Note: Attached documents contain full case definition and two different control definitions. One is for controls with 2 years of follow up, the other for controls with 1 year of follow up. All available controls with 2 years of follow up were used in Vanderbilt's study. The control population was supplemented by controls with only 1 year of follow up. At the time of study, many of the available controls had experienced their qualifying events somewhat recently and 2 years had not yet passed for full follow up.
Clostridium difficile, also known as "C. diff," is a species of bacteria that causes severe diarrhea and other intestinal disease when competing bacteria in the gut have been wiped out by antibiotics (see Wikipedia entry). In rare cases a C. diff infection can progress to toxic megacolon which can be life-threatening. In a very small percentage of the adult population C. difficile bacteria naturally reside in the gut. Other people accidentally ingest spores of the bacteria while patients in a hospital or nursing home.
A pheontype defining patients with strong evidence of having been diagnosed with colorectal cancer (cases) and patients who clearly do not have such diagnoses (controls). This phenotype is being used for sequencing studies. The only NLP involved in this phenotype is a very simple string search applied to pathology reports.
Phenotype Description: individuals with sensorineural hearing loss (SNHL)
Below are algorithms used to identify individuals with SNHL at BioVU. If you have questions regarding any of the information presented on this page, you may contact either:
Wei-Qi Wei at email@example.com or Joshua Denny at firstname.lastname@example.org
Fibromyalgia has been estimated to affect 12-17% of rheumatoid arthritis patients (1, 2).
This algorithm was created to identify fibromyalgia patients in a population of rheumatoid arthritis patients. The gold standard used for diagnosis of fibromyalgia was that the treating rheumatologist made a clinical diagnosis of fibromyalgia. Rheumatoid arthritis patients were identified by using a previously validated algorithm (3).
Algorithm included the following conditions:
Non-alcoholic fatty liver disease (NAFLD)
This algorithm predicts those who are going to be exposed to warfarin, simvastatin, or clopidogrel as three medications that have known pharmacogenomic influences. This algorithm was used to select individuals for the Vanderbilt PREDICT (Pharmacogenomic Resource for Enhanced Decisions in Care & Treatment) program, which prospectively tests individuals at risk of needing medications whose efficacy is effected by genetic variants.
For more information on PREDICT, see http://mydruggenome.org.