eMERGE GHC/University of Washington Group

Autoimmune Disease Phenotype

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

Owner Phenotyping Groups: 
eMERGE Columbia Group
View Phenotyping Groups: 
001
American-Swiss Allergy Phenotyping Group
BioVU Phenotyping
Clostridium Difficile Colitis Phenotype Group
Data Science to Patient Value Initiative (D2V) - Colorado
Denny’s Group at Vandy
eMERGE CCHMC Group
eMERGE CCHMC/BCH Group
eMERGE CHOP Group
eMERGE Columbia Group
eMERGE Geisinger Group
eMERGE GHC/University of Washington Group
eMERGE Harvard Group
eMERGE Marshfield Group
eMERGE Mayo Group
eMERGE Meharry Group
eMERGE Mount Sinai Group
eMERGE Northwestern Group
eMERGE Phenotype WG
eMERGE Vanderbilt Group
Farr Institute Kidney Working Group
GPC
NIH Collaboratory Group
PCORI CDRN/PPRN
PCORI MidSouth CDRN
PCORI MidSouth CDRN/Duke Group
PCORI MidSouth CDRN/Greenway Group
PCORI MidSouth CDRN/HSSC Group
PCORI MidSouth CDRN/Meharry Group
PCORI MidSouth CDRN/UNC Group
PCORI MidSouth CDRN/VUMC Group
PGPop WG
PGx model group
PGx Workgroup
PheMA Test Group
Precision Medicine and Health Disparities Collaborative
Resistant hypertension WG
Vanderbilt - Music Cognition Lab
Vanderbilt - SD/RD Group
VESPA - Vanderbilt Electronic Systems for Pharmacogenomic Assessment
Final

Breast Cancer

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.

Owner Phenotyping Groups: 
eMERGE Columbia Group
View Phenotyping Groups: 
001
American-Swiss Allergy Phenotyping Group
BioVU Phenotyping
Clostridium Difficile Colitis Phenotype Group
Data Science to Patient Value Initiative (D2V) - Colorado
Denny’s Group at Vandy
eMERGE CCHMC Group
eMERGE CCHMC/BCH Group
eMERGE CHOP Group
eMERGE Columbia Group
eMERGE Geisinger Group
eMERGE GHC/University of Washington Group
eMERGE Harvard Group
eMERGE Marshfield Group
eMERGE Mayo Group
eMERGE Meharry Group
eMERGE Mount Sinai Group
eMERGE Northwestern Group
eMERGE Phenotype WG
eMERGE Vanderbilt Group
Farr Institute Kidney Working Group
GPC
NIH Collaboratory Group
PCORI CDRN/PPRN
PCORI MidSouth CDRN
PCORI MidSouth CDRN/Duke Group
PCORI MidSouth CDRN/Greenway Group
PCORI MidSouth CDRN/HSSC Group
PCORI MidSouth CDRN/Meharry Group
PCORI MidSouth CDRN/UNC Group
PCORI MidSouth CDRN/VUMC Group
PGPop WG
PGx model group
PGx Workgroup
PheMA Test Group
Precision Medicine and Health Disparities Collaborative
Resistant hypertension WG
Vanderbilt - Music Cognition Lab
Vanderbilt - SD/RD Group
VESPA - Vanderbilt Electronic Systems for Pharmacogenomic Assessment
VICTR Phenotyping
Final

CAAD (Carotid Artery Atherosclerosis Disease)

Carotid artert atherosclerosis disease (CAAD) is measured in cases and controls by both structured data, including ICD diagnosis codes, and quantitative measurements of carotid stenosis based on doppler and other imaging technologies.

The phenotype algorithm includes typical eMERGE pseudo code for implementing the structured data components of the algorithm, as well as a portable natural language processing (NLP) system used to extract percent stenosis measurements from imaging reports.

Owner Phenotyping Groups: 
eMERGE GHC/University of Washington Group
View Phenotyping Groups: 
eMERGE Phenotype WG
Final

Chronic Kidney 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.

Owner Phenotyping Groups: 
eMERGE Columbia Group
View Phenotyping Groups: 
001
American-Swiss Allergy Phenotyping Group
BioVU Phenotyping
Clostridium Difficile Colitis Phenotype Group
Data Science to Patient Value Initiative (D2V) - Colorado
Denny’s Group at Vandy
eMERGE CCHMC Group
eMERGE CCHMC/BCH Group
eMERGE CHOP Group
eMERGE Columbia Group
eMERGE Geisinger Group
eMERGE GHC/University of Washington Group
eMERGE Harvard Group
eMERGE Marshfield Group
eMERGE Mayo Group
eMERGE Meharry Group
eMERGE Mount Sinai Group
eMERGE Northwestern Group
eMERGE Phenotype WG
eMERGE Vanderbilt Group
Farr Institute Kidney Working Group
GPC
NIH Collaboratory Group
PCORI CDRN/PPRN
PCORI MidSouth CDRN
PCORI MidSouth CDRN/Duke Group
PCORI MidSouth CDRN/Greenway Group
PCORI MidSouth CDRN/HSSC Group
PCORI MidSouth CDRN/Meharry Group
PCORI MidSouth CDRN/UNC Group
PCORI MidSouth CDRN/VUMC Group
PGPop WG
PGx model group
PGx Workgroup
PheMA Test Group
Precision Medicine and Health Disparities Collaborative
Resistant hypertension WG
Vanderbilt - Music Cognition Lab
Vanderbilt - SD/RD Group
VESPA - Vanderbilt Electronic Systems for Pharmacogenomic Assessment
Final

Clostridium Difficile Colitis

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.

Validation:

Owner Phenotyping Groups: 
Clostridium Difficile Colitis Phenotype Group
eMERGE GHC/University of Washington Group
eMERGE Vanderbilt Group
View Phenotyping Groups: 
Clostridium Difficile Colitis Phenotype Group
Denny’s Group at Vandy
eMERGE Phenotype WG
Final

Colorectal Cancer (CRC)

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.

Owner Phenotyping Groups: 
eMERGE GHC/University of Washington Group
View Phenotyping Groups: 
Clostridium Difficile Colitis Phenotype Group
Denny’s Group at Vandy
eMERGE CCHMC/BCH Group
eMERGE CHOP Group
eMERGE Columbia Group
eMERGE Geisinger Group
eMERGE GHC/University of Washington Group
eMERGE Harvard Group
eMERGE Marshfield Group
eMERGE Mayo Group
eMERGE Mount Sinai Group
eMERGE Northwestern Group
eMERGE Phenotype WG
eMERGE Vanderbilt Group
GPC
NIH Collaboratory Group
PCORI CDRN/PPRN
PCORI MidSouth CDRN
PGPop WG
PGx model group
PGx Workgroup
PheMA Test Group
Resistant hypertension WG
Vanderbilt - SD/RD Group
VESPA - Vanderbilt Electronic Systems for Pharmacogenomic Assessment
Final

Depression

Depression accounts for substantial morbidity and mortality worldwide and risk of experiencing it may have a genetic component.  Depressive disorders manifest along a gradient from mild to severe.[1]  Electronic health record (EHR) data linked to large, multi-site biobanks[2] facilitate exploration of the genetic component of depression.

Owner Phenotyping Groups: 
eMERGE GHC/University of Washington Group
View Phenotyping Groups: 
eMERGE Phenotype WG
Final

Hearing Loss

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 wei-qi.wei@vanderbilt.edu or Joshua Denny at josh.denny@vanderbilt.edu

Owner Phenotyping Groups: 
Denny’s Group at Vandy
eMERGE Phenotype WG
eMERGE Vanderbilt Group
View Phenotyping Groups: 
Denny’s Group at Vandy
eMERGE CCHMC Group
eMERGE CCHMC/BCH Group
eMERGE CHOP Group
eMERGE Columbia Group
eMERGE Geisinger Group
eMERGE GHC/University of Washington Group
eMERGE Harvard Group
eMERGE Marshfield Group
eMERGE Mayo Group
eMERGE Meharry Group
eMERGE Mount Sinai Group
eMERGE Northwestern Group
eMERGE Phenotype WG
eMERGE Vanderbilt Group
Vanderbilt - SD/RD Group
Final

Herpes Zoster

Herpes zoster, also known as zoster or shingles, is caused by a virus called varicella zoster virus (VZV). Initial infection with the virus causes chickenpox. After chickenpox resolves the virus continues to resides in certain nerve cells. It may remain latent for many years. It may also re-activate, many years later, and cause shingles which is a painful skin rash. How the virus remains latent in the body is not well understood.

Owner Phenotyping Groups: 
eMERGE GHC/University of Washington Group
View Phenotyping Groups: 
eMERGE Phenotype WG
Final

Pages