Please refer to attached documents.
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.
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. Electronic health record (EHR) data linked to large, multi-site biobanks facilitate exploration of the genetic component of depression.
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.
Described in this document are the Stanford University algorithms for extracting both cases and controls of digital rectal examination (DRE) from electronic health records (EHR) of prostate cancer patients. DRE is a clinical procedure, part of a set of quality metrics used to determine quality care for these patients. In this regard, DRE is defined as quality care when it is performed within a time period of up to six months before first treatment for prostate cancer. For the purposes of this algorithm a case is defined as DRE documented, whereas a control is DRE not documented.
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.