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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
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Blood Pressure
These are the algorithms for the PRIMED Harmonized systolic and diastolic blood pressures (SBP and DBP). The overall procedure of gathering single BP values per individual consists of:
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Body Mass Index (BMI)
These are the PRIMED Harmonization instructions for body mass index (BMI).
Overall procedure
1. Extract trait measurements using measurement codes and calculations
2. Convert measurement units to expected units, if necessary
3. Apply measurement exclusion criteria, other than statistical outliers
4. Remove statistical outliers
5. Compute a single value per individual for inclusion in analysis
6. Calculate counts of flagged individuals
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Body Mass Index (BMI)
eMERGE-IV BMI Algorithm adapted from Geisinger Extreme Obesity Algorithm (2013). BMI is being implemented as a quantitative trait. PheKB maintains a catalog of the Geisinger Extreme Obesity algorithm, on which this is based (Phenotpe 121). This algorithm is for analysis. Sites only contributing covariates can simply compile the designated data.
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bone scan utilization
Objective
Clinical care guidelines recommend that newly diagnosed prostate cancer patients at high risk for metastatic spread receive a bone scan prior to treatment and that low risk patients not receive it. The objective was to develop an automated pipeline to interrogate heterogeneous data to evaluate the use of bone scans using a two different Natural Language Processing (NLP) approaches.
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Breast Cancer
These are the PRIMED Harmonization instructions for breast cancer (BC). We are using the breast cancer definition used by the eMERGE program, with some slight modifications. Follow this document for implementation.
Modifications:
We will only include cis females in the analyses
The standard definition requires controls be age 18+. If the age distribution of cases within a study is much older (e.g. 30+), then studies may filter controls based on age >= the minimum age of identified cases
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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.
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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.
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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...
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