CNICS cohort data are harmonized across eight contributing sites in nine domains as detailed below:
a.     Demographic
b.     Diagnosis
c.     Laboratory
d.     Medication
e.     Health Care Utilization
f.      Vital Status
g.     Patient Reported measures and Outcomes (PROs)
h.     Antiretroviral Resistance
i.      Biologic Specimens

a.     Demographic Data
CNICS Ages at First and Last Visit July 2015Age distribution of the CNICS cohort at patients’ initial visit and most recent visit, at which time over 30% of the cohort was >50 years old
  • Demographic information in CNICS is collected using standard categories at the time a patient initiates care and includes: sex, birth year, race and Hispanic data as classified by the Health Resources and Services Administration standard coding, and risk factors for HIV acquisition coded according to the 1993 Centers for Disease Control and Prevention classification system (1993 Revised Classification System for HIV Infection and Expanded Surveillance Case Definition for AIDS Among Adolescents and Adults. MMWR Recomm Rep 1992;41(RR-17):1-19). The distribution of demographic characteristics in the CNICS cohort is provided in the table below:
Demographic characteristicsof the CNICS Cohort
(N= 32,247 as of Nov 2015)
Age at first visit
<20 208 1%
20-29 5,595 17%
30-39 11,095 34%
40-49 10,230 32%
50-59 4,207 13%
>59 912 3%
Male 26,412 82%
Female 5,834 18%
Transgendered 291 1%
White 16,419 51%
Black 12,384 38%
Asian/Pacific Islander 677 2%
Multiracial 182 <1%
Other/unspecified 2,585 8%
No 20,763 64%
Yes 3,679 11%
Unspecified 7,805 24%
Risk factors for HIV acquisition
MSM* 17,035 53%
Injection drug users (IDU) 3,467 11%
MSM and IDU 2,201 7%
Heterosexual contact 7,770 24%
Other 833 3%
Unspecified 941 3%
*Men who have sex with men

b.     Diagnosis Data
  • Diagnoses are prospectively recorded in the Electronic Medical Record (EMR) by the treating clinician
  • Historical diagnoses are collected at the patient’s initial visit to a CNICS site and coded as ‘patient reported’ with or without outside documentation
  • Diagnosis data are mapped to a standardized set of diagnosis codes and harmonized across CNICS sites
  • Diagnoses collected in CNICS are 1) verified via medical record review and/or adjudication, 2) confirmed via laboratory test results and/or medications, and 3) unconfirmed as listed below:
Verified diagnoses
AIDS-Defining Illnesses* ADIs are verified in accordance with the 1993 revised classification system for HIV infection and expanded surveillance case definition for AIDS among adolescents and adults(1)
Malignancies* Incident invasive cancers (AIDS-defining, non-AIDS defining) have been verified through 2014
Myocardial infarctions** MIs have been centrally ascertained and adjudicated through 2013
Other Central ascertainment and adjudication of cerebrovascular accidents is underway
*Medical record verified Diagnoses are verified through review of medical records using standard criteria
**Adjudicated diagnoses Diagnoses are centrally ascertained and adjudicated by a panel of physician experts
Confirmed diagnoses
Anemia Hematocrit or hemoglobin values can be used to classify individuals with anemia
Chronic Kidney disease Creatinine values can be used to classify individuals with CKD; recommend using CKD-EPI equation to compute GFR, but other equations can be applied if appropriate
Diabetes Diabetes-related medication, laboratory, and diagnosis data can be used to classify individuals with diabetes
Dyslipidemia Lipid-related medication and laboratory data can be used to classify individuals with dyslipidemia
Hepatitis B HBV serology and DNA data can be used to classify individuals with HBV infection
Hepatitis C HCV serology and RNA data can be used to classify individuals with HCV infection
Hypertension Hypertension-related medication, vital sign, and diagnosis data can be used to classify individuals with hypertension and whether treated and controlled
Unconfirmed diagnoses
Cerebrovascular disease Includes only CVAs and TIAs
Coronary artery disease  Includes only CAD and MI diagnoses
Kidney disease Includes acute and chronic renal insufficiency
Liver disease Includes ascites, cirrhosis, hepatic encephalopathy, etc.
Psychiatric Includes anxiety, cognitive, mood and personality disorders, psychosis
Substance use Includes alcohol, tobacco, and other substances; Patient Reported Outcome (PRO) substance use data, when available, can be used in combination with substance use diagnoses
Pulmonary disease Includes COPD, asthma
Venous thromboembolism Includes deep vein thrombosis, pulmonary embolism

c.     Laboratory and Vital Signs Data
  • Laboratory test results are uploaded directly from clinical laboratory medicine systems and harmonized across CNICS sites implementing standardized units and clinical interpretations. In addition, CNICS captures vital signs including blood pressure, height and weight as follows: 
CNICS Laboratory Data
Cardiac enzymes
Chemistries (BUN, Cr, electrolytes)
Chlamydia (PCR, culture, DFA)
Coagulation panel
Cryptococcal antigen
EBV (serology, PCR)*
Gonorrhea (PCR, DFA, culture)
Hemoglobin A1c
Hepatitis A serology
Hepatitis B (serology, DNA)
Hepatitis C (serology, RNA, genotype)
Herpes simplex (serology, DFA, culture)
HIV-1 (serology, viral load, RNA, resistance)
Liver Function Tests (LFTs)
Lipids (total cholesterol, LDL, HDL, triglycerides)
Quantiferon gold
T cell subsets
Toxoplasmosis serology
Vitamin D*
Vital signs
Blood pressure (SBP, DBP)

d.     Medication Data
  • Medications prescribed (including start/stop dates) are entered into the EMR by clinicians, pharmacy prescription fill/refill data are available at some sites, which are used to compute courses of therapy
  • Antiretroviral medications are verified through medical record review. Historical antiretroviral treatment collected at the patient’s initial visit to a CNICS site is coded as to completeness and level of date precision
  • The addition of new classes of medications in CNICS is guided by the expanding research agenda. Medication data captured in CNICS include:
CNICS Medication Data
Anticoagulants (includes Warfarin, LMWH)
Antiretrovirals (includes NRTI, NNRTI, PI, EI, INSTI)
Diabetes medications (includes oral and injectable insulin)
Lipid lowering medications
Psychiatric medications (includes antidepressants, antianxiety, antipsychotics, mood stabilizers)

e.     Health Care Utilization Data
  • Outpatient encounter/appointment systems, and inpatient systems, are the sources of health care utilization data in CNICS, which include:
Health Care Utilization Data
Patient enrollment date (initial visit)
Primary care visits and appointment status
Specialty care visits*

f.     Vital Status
  • CNICS sites use local procedures to track deaths and maintain death registries
  • CNICS subscribes to National Death Indexes which CNICS sites query semiannually to ensure complete ascertainment of death dates
  • Sites collect cause of death data from State Death Certificates, the National Death Index (NDI)+ as ICD-10 codes, and through medical record review. The completeness of cause of death data varies by CNICS site with cause of death unknown for approximately 35% of the CNICS cohort overall

Patient Reported measures and Outcomes (PROs)

  • PROs are collected at CNICS sites during routine clinical encounters using validated survey instruments that patients complete using touch-screen tablets or PCs connected to a wireless network with SSL/TLS encryption
  • Patients complete PRO assessments every four to six months and results are available at the time of the encounter for use in clinical care. Over 73,000 PRO assessments completed by over 14,000 patients are available for research in the following domains: 
CNICS PRO Domain Instrument
Depression and anxiety Patient Health Questionnaire (PHQ-9, PHQ-5)
Adherence Adult AIDS Clinical Trials Group (AACTG) Visual Analog Scale (VAS), and a self-rating system
Smoking, alcohol
and drug use
Alcohol Use Disorders Identification Test (AUDIT-C), full AUDIT, Mini International Neuropsychiatric Interview (MINI), The Alcohol, Smoking and Substance Involvement Screening Test (ASSIST)
Sexual risk behaviors HIV Risk Assessment for Positives (HRAP)
Symptom burden HIV Symptom Index
Physical activity level Lipid Research Clinical Questionnaire (LRCQ)
Body morphology Fat Redistribution and Metabolism (FRAM)
Quality of life EuroQol, EQ-5D

h.     Antiretroviral Resistance Data
  • CNICS has addressed the proprietary and technical challenges of collecting resistance data from commercial laboratories for each site
  • CNICS captures viral resistance data including full nucleotide genotype, phenotype, and tropism assays with the capability for expansion to include new drug targets

Biologic Specimens
  • CNICS provides access to biologic speciments linked to patient's comprehensive clinical data in the CNICS Research Platform. Information about the CNICS specimen repository is available here