Harmonized Data

TOPMed Harmonized Clinical Variables

The TOPMed Data Coordinating Center curation team has produced forty-four (44) harmonized phenotype variables from seventeen (17) NHLBI studies. The 17 studies whence the 44 clinical variables have been identified, in alphabetic order, are:

  • Atherosclerosis Risk in Communities Study (ARIC)

  • Cardiovascular Health Study (CHS)

  • Cleveland Family Study (CFS)

  • Coronary Artery Risk Development in Young Adults Study (CARDIA)

  • Epidemiology of Asthma in Costa Rica Study (CRA)

  • Framingham Heart Study (FHS)

  • Genetic Epidemiology Network of Arteriopathy (GENOA)

  • Genetic Epidemiology of COPD (COPDGene)

  • Genetics of Cardiometabolic Health in Amish (Amish)

  • Genetics of Lipid Lowering Drugs and Diet Network Study (GOLDN)

  • Genome-Wide Association Study of Venous Thrombosis Study (VTE)

  • Heart and Vascular Health Study (HVH)

  • Hispanic Community Health Study - Study of Latinos (HCHS_SOL)

  • Jackson Heart Study (JHS)

  • Multi-Ethnic Study of Atherosclerosis (MESA)

  • Study of Adiposity in Samoans (SAS)

  • Women’s Health Initiative (WHI)

List of harmonized variables:

Variable Name

Variable Description

TYPE

UNITS

VARIABLE_SOURCE

VALUES

cac_volume_1

Coronary artery calcium volume using CT scan(s) of coronary arteries

decimal

cubic millimeters

UMLS

cac_score_1

Coronary artery calcification (CAC) score using Agatston scoring of CT scan(s) of coronary arteries

decimal

UMLS

cimt_1

Common carotid intima-media thickness, calculated as the mean of two values: mean of multiple thickness estimates from the left far wall and from the right far wall.

decimal

mm

UMLS

cimt_2

Common carotid intima-media thickness, calculated as the mean of four values: maximum of multiple thickness estimates from the left far wall, left near wall, right far wall, and right near wall.

decimal

mm

UMLS

carotid_stenosis_1

Extent of narrowing of the carotid artery.

encoded

UMLS

0=None||1=1%-24%||2=25%-49%||3=50%-74%||4=75%-99%||5=100%

carotid_plaque_1

Presence or absence of carotid plaque.

encoded

UMLS

0=Plaque not present||1=Plaque present

height_baseline_1

Body height at baseline.

decimal

cm

UMLS

current_smoker_baseline_1

Indicates whether subject currently smokes cigarettes.

encoded

UMLS

0=Does not currently smoke cigarettes||1=Currently smokes cigarettes

weight_baseline_1

Body weight at baseline.

decimal

kg

UMLS

ever_smoker_baseline_1

Indicates whether subject ever regularly smoked cigarettes.

encoded

UMLS

0=Never a cigarette smoker||1=Current or former cigarette smoker

bmi_baseline_1

Body mass index calculated at baseline.

decimal

kg/m^2

UMLS

hemoglobin_mcnc_bld_1

Measurement of mass per volume, or mass concentration (mcnc), of hemoglobin in the blood (bld).

decimal

g / dL = grams per deciliter

UMLS

hematocrit_vfr_bld_1

Measurement of hematocrit, the fraction of volume (vfr) of blood (bld) that is composed of red blood cells.

decimal

% = percentage

UMLS

rbc_ncnc_bld_1

Count by volume, or number concentration (ncnc), of red blood cells in the blood (bld).

decimal

millions / microliter

UMLS

wbc_ncnc_bld_1

Count by volume, or number concentration (ncnc), of white blood cells in the blood (bld).

decimal

thousands / microliter

UMLS

basophil_ncnc_bld_1

Count by volume, or number concentration (ncnc), of basophils in the blood (bld).

decimal

thousands / microliter

UMLS

eosinophil_ncnc_bld_1

Count by volume, or number concentration (ncnc), of eosinophils in the blood (bld).

decimal

thousands / microliter

UMLS

neutrophil_ncnc_bld_1

Count by volume, or number concentration (ncnc), of neutrophils in the blood (bld).

decimal

thousands / microliter

UMLS

lymphocyte_ncnc_bld_1

Count by volume, or number concentration (ncnc), of lymphocytes in the blood (bld).

decimal

thousands / microliter

UMLS

monocyte_ncnc_bld_1

Count by volume, or number concentration (ncnc), of monocytes in the blood (bld).

decimal

thousands / microliter

UMLS

platelet_ncnc_bld_1

Count by volume, or number concentration (ncnc), of platelets in the blood (bld).

integer

thousands / microliter

UMLS

mch_entmass_rbc_1

Measurement of the average mass (entmass) of hemoglobin per red blood cell(rbc), known as mean corpuscular hemoglobin (MCH).

decimal

pg = picogram

UMLS

mchc_mcnc_rbc_1

Measurement of the mass concentration (mcnc) of hemoglobin in a given volume of packed red blood cells (rbc), known as mean corpuscular hemoglobin concentration (MCHC).

decimal

g /dL = grams per deciliter

UMLS

mcv_entvol_rbc_1

Measurement of the average volume (entvol) of red blood cells (rbc), known as mean corpuscular volume (MCV).

decimal

fL = femtoliter

UMLS

pmv_entvol_bld_1

Measurement of the mean volume (entvol) of platelets in the blood (bld), known as mean platelet volume (MPV or PMV).

decimal

fL = femtoliter

UMLS

rdw_ratio_rbc_1

Measurement of the ratio of variation in width to the mean width of the red blood cell (rbc) volume distribution curve taken at +/- 1 CV, known as red cell distribution width (RDW).

decimal

% = percentage

UMLS

bp_systolic_1

Resting systolic blood pressure from the upper arm in a clinical setting.

decimal

mmHg

UMLS

bp_diastolic_1

Resting diastolic blood pressure from the upper arm in a clinical setting.

decimal

mmHg

UMLS

antihypertensive_meds_1

Indicator for use of antihypertensive medication at the time of blood pressure measurement.

encoded

UMLS

0=Not taking antihypertensive medication||1=Taking antihypertensive medication

race_1

Harmonized race category of participant.

encoded

UMLS

AI_AN=American Indian_Alaskan Native or Native American||Asian=Asian||Black=Black or African American||HI_PI=Native Hawaiian or other Pacific Islander||Multiple=More than one race||Other=Other race||White=White or Caucasian

ethnicity_1

Indicator of Hispanic or Latino ethnicity.

encoded

UMLS

both=ethnicity component dbGaP variable values for a subject were inconsistent/contradictory (e.g. over multiple visits)||HL=Hispanic or Latino||notHL=not Hispanic or Latino

hispanic_subgroup_1

classification of Hispanic/Latino background for Hispanic/Latino subjects where country or region of origin information is available

encoded

UMLS

CentralAmerican=Central American||CostaRican=from Costa Rica||Cuban=Cuban||Dominican=Dominican||Mexican=Mexican||PuertoRican=Puerto Rican||SouthAmerican=South American

annotated_sex_1

Subject sex, as recorded by the study.

encoded

UMLS

female=Female||male=Male

geographic_site_1

Recruitment/field center, baseline clinic, or geographic region.

encoded

UMLS

subcohort_1

A distinct subgroup within a study, generally indicating subjects who share similar characteristics due to study design. Subjects may belong to only one subcohort.

encoded

UMLS

lipid_lowering_medication_1

Indicates whether participant was taking any lipid-lowering medication at blood draw to measure lipids phenotypes

encoded

UMLS

0=Participant was not taking lipid-lowering medication||1=Participant was taking lipid-lowering medication.

fasting_lipids_1

Indicates whether participant fasted for at least eight hours prior to blood draw to measure lipids phenotypes.

encoded

UMLS

0=Participant did not fast_or fasted for fewer than eight hours prior to measurement of lipids phenotypes.||1=Participant fasted for at least eight hours prior to measurement of lipids phenotypes.

total_cholesterol_1

Blood mass concentration of total cholesterol

decimal

mg/dL

UMLS

triglycerides_1

Blood mass concentration of triglycerides

decimal

mg/dL

UMLS

hdl_1

Blood mass concentration of high-density lipoprotein cholesterol

decimal

mg/dL

UMLS

ldl_1

Blood mass concentration of low-density lipoprotein cholesterol

decimal

mg/dL

UMLS

vte_prior_history_1

An indicator of whether a subject had a venous thromboembolism (VTE) event prior to the start of the medical review process (including self-reported events).

encoded

UMLS

0=did not have prior VTE event||1=had prior VTE event

vte_case_status_1

An indicator of whether a subject experienced a venous thromboembolism event (VTE) that was verified by adjudication or by medical professionals.

encoded

UMLS

0=Not known to ever have a VTE event_either self-reported or from medical records||1=Experienced a VTE event as verified by adjudication or by medical professionals

age

age at measurement

decimal

years