Caucasian (European)

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

Cardiorespiratory Fitness Algorithm (eMERGE Mayo Network Phenotype)

Please refer to attached documents.

Owner Phenotyping Groups:

eMERGE Columbia Group

eMERGE Mayo 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

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

Final

Consistent Care

Owner Phenotyping Groups:

eMERGE Harvard Group

View Phenotyping Groups:

eMERGE Phenotype WG

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

Developmental Language Disorder

APT-DLD
Version 1.0, July 2020

Automated Phenotyping Tool for identifying DLD cases in health-systems data (APT-DLD) is an algorithm for classifying/identifying developmental language disorder cases in electronic health records system data. APT-DLD can be used to:
1. Identify pediatric DLD cases from electronic health record systems using ICD9 and ICD10 codes
2. Study epidemiology and population-level charateristics of DLD from EHRs

The How-To guide for using APT-DLD is provided in the files listed below.

Owner Phenotyping Groups:

Vanderbilt - Music Cognition Lab

Final

Diverticulosis and Diverticulitis

An algorithm for finding patients with diverticulosis, and of those, patients who also have diverticulitis, and to also find control patients. Control patients will have had a colonoscopy but have no evidence of diverticula.

Simple NLP (a portable program is posted here, with instructions, and support is availabe from NU as needed) of colonoscopy reports is the gold standard algorithm, but if the text of colonoscopy reports is not available, an alternate algorithm using CPT & ICD-9 codes can be used, which is also posted.

Owner Phenotyping Groups:

eMERGE Phenotype WG

View Phenotyping Groups:

eMERGE Phenotype WG

Final