Disease or Syndrome

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

caMRSA

This algorithm is for community associated MRSA (Methicillin-resistant Staphylococcus aureus, read more at http://en.wikipedia.org/wiki/MRSA). Note this algorithm will use lab results and not ICD-9 codes, as ICD-9 codes are not specific enough for this algorithm and/or are not used consistently for this phenotype.  Thus, we expect the actual number of cases to be higher than what the eMERGE RC (Record Counter) estimated, and, as we will be studying patients aged 0 to 89, we would like for all sites to participate, please...

Owner Phenotyping Groups: 
eMERGE Northwestern Group
View Phenotyping Groups: 
eMERGE Phenotype WG
Final

Cataracts

We used a multi-modal strategy consisting of structured database querying, natural language processing on free-text documents, and optical character recognition on scanned clinical images to identify cataract subjects and related cataract attributes.

Owner Phenotyping Groups: 
eMERGE Marshfield 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

Crohn's Disease - Demonstration Project

Crohn's Disease phenotype algorithm for the DNA DataBank Demonstration Project.  Case records are required to have more than 2 occurrences of ICD 9 codes and medications.  Control records are required to not have ICD 9 codes or keyword mention of crohn* or Regional enteritis and excludes additional phenotypes as defined by ICD 9 codes and keywords.

Data source summary:

 

Diagnostic Codes?

Owner Phenotyping Groups: 
Vanderbilt - SD/RD Group
View Phenotyping Groups: 
Vanderbilt - SD/RD Group
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

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