The CNICS repository maintains data on the CNICS Cohort from 8 contributing sites in the following domains: (a) demographics, (b) diagnoses, (c) laboratory test data, (d) medication data, (e) health care utilization, (f) vital status, (g) patient reported outcomes (PROs),(h) antiretroviral resistance, and (i) biologic specimens. The details of each domain are provided below.

a. Demographic Data include sex, race/Hispanic, birth year, and risk factor for HIV acquisition collected at the time the patient initiates care using standard categories. Race and Hispanic data are classified by HRSA standard coding, and risk factors for HIV acquisition coded according to the 1993 CDC classification system. The accompanying figure shows the age distribution of the CNICS cohort at patients’ initial and most recent visit at which time 30% of the cohort was >50 years old. The demographic distribution of the CNICS cohort as of March 2014 can be viewed here  082014.Age Distribution

b. Diagnosis Data are harmonized across CNICS sites and mapped to a standardized set of diagnosis codes. Diagnoses are prospectively recorded in the Electronic Health Record (EHR) 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. CNICS captures three types of diagnosis data: 1) diagnoses verified via medical record review/adjudication; 2) diagnoses confirmed via laboratory values and/or medications; and 3) unconfirmed diagnoses. Diagnoses available in CNICS are listed here. ·      

  • Malignancy data are a key focus for diagnosis verification including collection of detailed information on tumor site, histopathology, stage and grade. Currently, 1,978 invasive cancer diagnoses have been verified and include: Kaposi sarcoma 752 (38%), non-Hodgkin lymphoma 368 (19%), anal 121 (6%), lung 80 (4%), Hodgkin lymphoma 78 (4%), liver 35 (2%), melanoma 47 (2%) colorectal 31 (1.5%), testicular 22 (1%), and oral cavity/pharynx 13 (0.6%).


c. Laboratory Data collected and maintained in CNICS include plasma HIV-1 RNA levels, CD4+ T cell counts, chemistries, lipids, hematology, coagulation, liver function, and serology tests. Laboratory data are uploaded directly from clinical site laboratory medicine systems and are harmonized across CNICS sites using standard units and clinical interpretations. Laboratory data available in CNICS are listed here.

d. Medication Data collected and maintained in CNICS include antiretroviral, antihypertensive, lipid lowering, psychiatric, and diabetes medications. Clinicians enter medication data (including start/stop dates) into the EHR or pharmacy prescription fill/refill data are available at some sites and used to compute courses of therapy. Antiretroviral medication data are verified through medical record review, and 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 submitted to CNICS is guided by the expanding research agenda such as those used in the treatment of a condition under investigation. Medications available in CNICS are listed here.

e. Utilization Data include patient enrollment date (initial visit), primary care visits, and hospitalizations; limited data are available on appointments and specialty encounters. These data are captured through outpatient encounter and appointment systems, as well as hospital systems at CNICS sites.

f. Vital Status Data: CNICS sites use local procedures to track deaths and maintain death registries. CNICS subscribes to the Social Security Death Index (SSDI), which is used to verify death dates. CNICS sites query the SSDI semiannually to ensure complete ascertainment of death data. Sites collect cause of death data from State Death Certificates and 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, and cause of death is unknown for approximately 25% of the CNICS cohort overall.

g. Patient Reported Outcomes (PROs) data are collected at CNICS sites during routine clinical encounters using touch-screen tablets or PCs connected to a wireless network using SSL/TLS encryption. Patients complete a clinical assessment every 4-6 months that includes the following domains: depression and anxiety (PHQ); adherence (AACTG, VAS, and self-rating item); smoking, alcohol, and drug use (AUDIT-C with full AUDIT and MINI once a year if at-risk and ASSIST); sexual risk behaviors; symptom burden (HIV Symptom index); physical activity level (LRCQ); body morphology (FRAM); and Quality of Life (EuroQual; EQ-5D). As of March 2014, over 47,000 assessments were completed by over 10,800 patients and used in clinical care at the time of the encounter and for research.

h. Antiretroviral Resistance Data are complex in format and heterogeneous in availability. CNICS has made considerable progress in overcoming the proprietary and technical challenges of collecting resistance data from commercial laboratories for each site. CNICS captures diverse viral resistance data including full nucleotide genotype, phenotype, and tropism assays with the capability for expansion to include new drug targets (i.e., integrase).

i. Specimen Data are also managed centrally in CNICS. Specimen repositories at all CNICS sites collect specimens on both targeted populations of interest (e.g., treatment naïve individuals initiating therapy, “elite” controllers and/or long-term non-progressors, etc.) and, at specified sites, specimens are collected on all consenting patients, thereby creating a broad set of potential controls and facilitating capture of specimens surrounding rare events (e.g. MIs, death, etc.). Sites collect a range of specimen types, including plasma, serum, viably frozen PBMCs, and snap frozen PBMCs. Patients at each site have been consented to allow their specimens to be used for genetic studies. Each of the CNICS sites has experience with sample preparation and quality assurance through the ACTG/AVEU/HVTN networks.