Collaboration Phenotypes

Contact authors listed below are open to engaging others in the development of their phenotypes. Unless the status of the phenotype is marked as final, these phenotypes cannot be viewed in-depth until the author has shared access with you and you have logged into PheKB. Click on an author's name to send an email to him or her expressing your interest in collaborating.

Title Institution Phenotype Attributes Description Status Contact Author Type of Phenotype
(Arrhythmias) EKG Intervals, Phenotype/Genotype correlations VUMC CPT Codes, ICD 10 Codes, ICD 9 Codes, Laboratories, Medications, Natural Language Processing, Vital Signs Genetic testing for rare variants associated with inherited arrhythmia syndromes (i.e. Long QT Syndrome, Brugada Syndrome, etc.) is becoming increasingly common in clinical practice, as is the incidental detection of these variants during research or commercial sequencing. Testing Davogustto, Giovanni Ernesto Disease or Syndrome, Other Trait
Acute kidney injury (AKI) Columbia University CPT Codes, ICD 10 Codes, ICD 9 Codes, Laboratories Final Ning Sunny Shang Disease or Syndrome
Asparaginase-induced acute pancreatitis Vanderbilt University Medical Center This algorithm selects patients in the Synthetic Derivative, Vanderbilt's de-identified electronic health record database, who have had pegaspargase-induced or L-asparaginase-induced acute pancreatitis. In development Lincoln Shade Disease or Syndrome, Drug Response - adverse effect or efficacy
Aspirin-Exacerbated Respiratory Disease Brigham and Women's Hospital CPT Codes, ICD 10 Codes, ICD 9 Codes, Medications BACKGROUND: Aspirin-exacerbated respiratory disease (AERD) is characterized by 3 clinical features: asthma, nasal polyposis, and respiratory reactions to cyclooxygenase-1 inhibitors (nonsteroidal anti-inflammatory drugs). Electronic health records (EHRs) contain information on each feature of this triad. In development Katherine Cahill Disease or Syndrome
Bactrim-induced Stevens-Johnson syndrome/toxic epidermal necrolysis (BI-SJS/TEN) Vanderbilt University Medical Center CPT Codes, ICD 10 Codes, ICD 9 Codes, Medications, Natural Language Processing This algorithm selects patients in the Synthetic Derivative, Vanderbilt's de-identified electronic health record database, who have had Bactrim-induced Stevens-Johnson syndrome/toxic epidermal necrolysis. In development Lincoln Shade Disease or Syndrome, Drug Response - adverse effect or efficacy
Benign Prostatic Hyperplasia (BPH) Vanderbilt University Medical Center CPT Codes, ICD 9 Codes, Laboratories, Medications, Natural Language Processing Validated Sarah Stallings Disease or Syndrome
Bipolar (BD) MGB Biobank Mass General Brigham ICD 10 Codes, ICD 9 Codes, Medications Algorithm to identify bipolar disorder developed at MGB and tested at VUMC and Geisinger.    Testing Vivian Gainer Disease or Syndrome
Body Mass Index (BMI) CHOP CPT Codes, ICD 10 Codes, ICD 9 Codes, Medications 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. Final John Connolly
bone scan utilization Stanford University School of Medicine CPT Codes, ICD 10 Codes, ICD 9 Codes, Natural Language Processing Objective Final Tina Hernandez-Boussard Other Trait
Breast Cancer CPT Codes, ICD 10 Codes, ICD 9 Codes, Laboratories, Medications, Natural Language Processing 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. Final Ning Sunny Shang Disease or Syndrome
Chronic Kidney Disease Columbia University, Mayo Clinic, VUMC CPT Codes, ICD 9 Codes, Laboratories 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. Final Ning Sunny Shang Disease or Syndrome
Chronic pain cohort ICD 9 Codes, Medications Primary care patients who have a diagnostic indication of chronic non-malignant pain for which they are on long-term opioid therapy Validated Reesa Laws Disease or Syndrome
Colorectal Cancer (CRC) Group Health/UW CPT Codes, ICD 9 Codes, Laboratories, Medications, Natural Language Processing, Vital Signs 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. Final David Carrell Disease or Syndrome
Consistent Care Harvard University CPT Codes, ICD 10 Codes, ICD 9 Codes Final Elizabeth Wood Karlson Other Trait
Depression KPWA/UW CPT Codes, ICD 10 Codes, ICD 9 Codes, Medications 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. Final David Carrell Disease or Syndrome
Diverticular Disease Severity, Left Colonic Vanderbilt University Medical Center CPT Codes, ICD 10 Codes, ICD 9 Codes This algorithm builds off prior phenotyping work from Pacheco & Thompson available in the PheKB phenotype "Diverticulosis and Diverticulitis" as well as the manuscripts from Joo et al (2023)(1) and De Roo et al (2023) (2) . Final Thomas Ueland Disease or Syndrome
DO NOT USE - Eating Disorders Vanderbilt University Medical Center CPT Codes, ICD 10 Codes, ICD 9 Codes This entry should be deleted Testing Lea Davis Disease or Syndrome
Eating disorders Vanderbilt University Medical Center ICD 10 Codes, ICD 9 Codes, Vital Signs Algorithm to identify Anorexia Nervosa, Bullimia Nervosa, and Eating Disorders NOS. Developed at VUMC and tested at MGH. Testing Lea Davis Disease or Syndrome
ECG Traits Extracted from Electrocardiograms using Natural Language Processing VUMC CPT Codes, ICD 10 Codes, ICD 9 Codes, Medications, Natural Language Processing Common genetic variants can be associated with electrocardiographic abnormalities, i.e. arrhythmias and conduction system disease. This algorithm provides a NLP tool to extract ECG traits from the interpretative text  generated in the ECG read. This includes: 1) Tachycardia and ectopy cases: Validated Davogustto, Giovanni Ernesto Disease or Syndrome, Other Trait
Electronic Health Record-based Phenotyping Algorithm for Familial Hypercholesterolemia Mayo Clinic CPT Codes, ICD 9 Codes, Laboratories, Medications, Natural Language Processing Familial hypercholesterolemia (FH) is a relatively common Mendelian genetic disorder that is associated with elevated plasma low-density lipoprotein cholesterol (LDL-C) levels and dramatically increased lifetime risk for premature atherosclerotic cardiovascular disease (ASCVD). Final Maya Safarova Disease or Syndrome
Functional seizures Vanderbilt University Medical Center CPT Codes, ICD 10 Codes, ICD 9 Codes, Natural Language Processing Algorithm to detect functional seizures, also known as: Psychogenic nonepileptic seizures Nonepileptic attack disorder Pseudoseizures Hystero-epilepsy Conversion disorder with seizures Dissociative Seizures Final Slavina Goleva Disease or Syndrome
Genotyping of Surgical Patients (NT460) Data This PheKB page is for uploading data that supports manuscript concept sheet NT460 Genotyping of surgical patients: A machine-learning tool for a future precision medicine approach for prevention of postoperative complications. Testing Mathias Aagaard Christensen
Heparin-induced thrombocytopenia (HIT) Vanderbilt University ICD 9 Codes, Laboratories, Medications, Natural Language Processing In development Jason Hansen Karnes Disease or Syndrome, Drug Response - adverse effect or efficacy
Laboratory based definition for Acute Kidney Injury PCCI ICD 10 Codes, Laboratories Developed as a supplement to ICD Pieces trial –UH3DK104655   In development George Oliver Disease or Syndrome
Major Adverse Cardiac Events while on Clopidogrel Vanderbilt University CPT Codes, ICD 9 Codes, Medications Patients with Major Adverse Cardiac Events (MACE) while on Clopidogrel. A MACE event can be either a revascularization event (bypass surgery or angioplasty/intracardiac stenting) or an acute myocardial infarction (AMI). A revascularization event is defined by the presence of a bypass, an angioplasty or a stent CPT code. An AMI event has been illustrated in our previous algorithm. Testing Wei-Qi Wei Drug Response - adverse effect or efficacy
Multimodal Analgesia Stanford University School of Medicine CPT Codes, ICD 10 Codes, ICD 9 Codes, Medications Described in this document are the Stanford University algorithms for extracting both cases and controls of Multimodal analgesia from electronic health records (EHR) for surgical patients. Final Tina Hernandez-Boussard Other Trait
Obsessive-compulsive disorder Vanderbilt University Medical Center ICD 10 Codes, ICD 9 Codes, Medications, Natural Language Processing This algorithm for obsessive-compulsive disorder was developed from March 2016 to September 2017 at VUMC in collaboration with the OCD Psychiatric Genomcis Consortium workgroup and clinicans at VUMC. It has been internally valdiated and is now ready for validation at another PsycheMERGE site.  Testing Lea Davis Disease or Syndrome
Ovarian/Uterine Cancer (OvUtCa) KPWA/UW CPT Codes, ICD 10 Codes, ICD 9 Codes, Laboratories, Medications, Vital Signs The KPWA/UW-led ovarian/uterine cancer phenotype has been validated at Mayo Clinic, the secondary phenotype development site.  Validation results at both the primary and secondary sites were strong and the phenotype is ready for network wide implementation.  The pseudo code document posted 11/30/2017 is correct as is and should be used by network sites for phenotype implementation.  A validated Final David Carrell Disease or Syndrome
Peanut Allergy Vanderbilt University, Vanderbilt University Medical Center CPT Codes, Laboratories Food allergy is defined as an immune response that occurs reproducibly to a given food, typically an immunoglobulin E (IgE)-mediated clinical reaction to specific protein epitopes.  Over the last 20-30 years, food allergy has grown into a major public health problem. Final Jonathan Hemler Disease or Syndrome
Pediatric Lipid Distribution for Development of Pediatric Familial Hypercholesterolemia Geisinger ICD 10 Codes, ICD 9 Codes, Laboratories, Medications Primary aims of the peds FH phenotyping are: In development Ken Borthwick Other Trait
Post-operative Complications from Major General Surgeries Algorithm Vanderbilt CPT Codes, ICD 9 Codes Post-operative Complications as defined by the American College of Surgeon's National Surgical Quality Improvement Program (NSQIP) are a set of 21 clinical conditions that occur 30 days from the date of operation. Testing Tom Mou Disease or Syndrome
Prostate Cancer Northwestern University Feinberg School of Medicine CPT Codes, ICD 10 Codes, ICD 9 Codes In development Luke Rasmussen Disease or Syndrome
Prostate Cancer Staging Stanford University School of Medicine CPT Codes, ICD 10 Codes, ICD 9 Codes, Laboratories, Natural Language Processing In development Tina Hernandez-Boussard Other Trait
Rheumatology Auto-Immune characteristics Harvard Medical School Laboratories, Medications Dear, To identify cases with auto-immune rheumatologic phenotye (for  NT198) we request information about auto-antibody (whether it was tested and what the restults were) and drug information (whether it was prescribed) for each patients that is enrolled in eMERGE. We are requesting every mention of any of the expanded generic drugs. Final Rachel Knevel Other Trait
RxNorm RxCUI codes for Cancer Therapies University of Iowa Medications This phenotype includes RxNorm RxCUI codes for cancer therapies. These codes map to drug records in the PCORnet Common Data Model and other data sources. The phenotype was developed in 2019. Please see the associated files for additional information.  Final Ryan Carnahan Other Trait
Sexual assault disclosures in clinical notes Vanderbilt University Medical Center Natural Language Processing Please refer to the attached publication for the algorithm definition and performance metrics. Validated Allison Lake Other Trait
Sexual assault disclosures in clinical notes (v2) Vanderbilt University Medical Center Natural Language Processing Updates to the original algorithm listed under PheKB phenotype #1710 and published here. Additional inclusion and exclusion terms have been added. Testing Allison Lake Other Trait
Sickle Cell Disease Medical College of Wisconsin ICD 9 Codes Final Daniel Michalik Disease or Syndrome
Statins and MACE Vanderbilt University CPT Codes, ICD 9 Codes, Laboratories, Natural Language Processing Phenotype Description:  Patients on statins for primary prevention who develop an AMI or 1st AMI.  Below are algorithms used to identify AMI and 1st AMI cohort 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 Final Wei-Qi Wei Drug Response - adverse effect or efficacy
STOP CRC Cohort Group Health Cooperative CPT Codes, ICD 9 Codes This is a cohort identification phenotype for the STOP CRC trial, which is testing a culturally tailored, health care system–based program to improve CRC screening rates in OCHIN, a community-based collaborative network of more than 200 Federally Qualified Healthcare Centers. Validated Michelle Smerek Disease or Syndrome
Systemic lupus erythematosus (SLE) Vanderbilt University Medical Center ICD 9 Codes, Laboratories, Medications, Natural Language Processing We used Vanderbilt’s Synthetic Derivative (SD), a de-identified version of the EHR, with 2.5 million subjects. We selected all individuals with at least one SLE ICD-9 code (710.0) yielding 5959 individuals. To create a training set, 200 were randomly selected for chart review. A subject was defined as a case if diagnosed with SLE by a rheumatologist, nephrologist, or dermatologist. Final April Barnado Disease or Syndrome
Tourette Syndrome Vanderbilt University Medical Center ICD 10 Codes, ICD 9 Codes, Natural Language Processing Testing Lea Davis Disease or Syndrome
Type1 or Type 2 Diabetes Mellitus Mayo Clinic ICD 9 Codes, Laboratories, Medications, Natural Language Processing Phenotyping algorithm for the identification of patients with type 1 or type 2 diabetes mellitus (DM) preoperatively using routinely available clinical data from electronic health records. Final Sudhi Upadhyaya
Urinary Incontinence Stanford University CPT Codes, ICD 10 Codes, ICD 9 Codes, Natural Language Processing Description of a weakly supervised machine learning approach for extracting treatment-related side effects (Urinary Incontinence) following prostate cancer therapy from multiple types of free-text clinical narratives, including progress notes, discharge summaries, history and physical notes. Prostatectomy surgery and radiation therapy are our treatments of interest for prostate cancer. Final Tina Hernandez-Boussard Disease or Syndrome