Dataset DOI: 10.5061/dryad.4qrfj6qq1

Description of the data and file structure

The data were collected for a study examining the rate at which cancer types present in families were documented in family history records in the EHR.

Files and variables

File: assessing_cancer_fhx.rds

Description: 

An R data file containing information on socio-demographics and healthcare utilization for 903 patients from 721 families. Each observation/row in the data is a unique opportunity to document a cancer type that occurred in the family. For example, a patient with both lung cancer and breast cancer occurring among their relatives would appear twice. Other data included are data pertaining to the relatives and data about the type of cancer.  

Important note: Because the EHR data used by this study was updated between the time of initial submission and and the time of publication, race and ethnicity values changed for a handful of patients. Thus, the number of patients with White race or Hispanic ethnicity have changed slightly from the published article. However, these changes had a minimal effect on the results.

Variables

• family_id: randomly-assigned unique identifier for each family
• patient_id: randomly-assigned unique identifier for each patient (each patient belongs to only one family)
• successful_fhx_documentation: Binary indicator, with a value of 1 indicating that the cancer type was successfully documented in the patient's family history record, and a value of 0 indicating that the cancer type was not documented. Cancer type is indicated by the variable cancer_type_grouping_1.
• patient_sex: recorded sex of patient
• patient_agecat: age category for each patient. Values are as follows:
  • under30: < 30 years
  • x30.49: 30-49 years
  • x50.69: 50-69 years
  • over69: > 69 years
• patient_white_race: recorded race of patient. A value of 'white' indicates White race, while a value of 'non.white' indicates a non-White race, that race is unknown, or that multiple races were recorded for the patient.
• patient_ethnicity: recorded ethnicity of patient. Values are as follows: Hispanic, non-Hispanic, or unknown ethnicity. 
• patient_mhhinc_of_census_tract: categorical variable indicating the median household income of patient's census tract of residence. Values are as follows:
  • inc50k: < $50,000/year (low)
  • inc50.100k: $50,000-$100,000/year
  • inc100k: > $100,000/year (high)
• patient_number_of_encounters: categorical variable indicating the number of encounters for each patient. Values are as follows:
  • x1: 1 encounter
  • x2.4: 2-4 encounters
  • x5.9: 5-9 encounters
  • x10.19: 10-19 encounters
  • over19: > 19 encounters
• nearest_affected_relative: categorical variable indicating the closest relative to the patient who has the cancer type indicated in the variables cancer_type_grouping_1 and cancer_type_grouping_by_sex. Values are as follows:
  • twin.x1st: nearest relative is a monozygotic twin or first degree relative (monozygotic twins were grouped with first degree relatives because of low numbers of twins)
  • x2nd: nearest relative is a second degree relative
• yrs_since_relative_diagnosis: time in years between the first family member diagnosis of the cancer type specified in cancer_type_grouping_1 and the patient's last office visit encounter. Provides an indication of how much time was available for the cancer to be documented in the patient's family history record.
• cancer_type_grouping_1: the cancer type occurring in the patient's family, for which successful documentation (indicated by variable successful_fhx_documentation) is being assessed. This variable determines the grouping used to produce Figure 2 in the published paper.
• cancer_type_grouping_by_sex: categorical variable indicating whether a cancer type is specific to one sex or another. Values are: "female-specific", "male-specific", and "non-sex-specific". This variable determines the grouping used to produce Figure 3 in the published paper.

File: assessing_cancer_fhx.R

Description: This file contains the R code used to produce Table 2 and Figures 2 and 3 found in the published paper.

Code/software

The R script assessing_cancer_fhx.R was run in R version 4.4.2. Required packages are gee, emmeans, dplyr, htmlTable, flextable, and ggplot2. 

The R command install.packages() can be used to install the required packages if they are not already installed.

To run assessing_cancer_fhx.R, set the working directory to match the location of assessing_cancer_fhx.rds by using the R command setwd().

Human subjects data

The Healthy Nevada Project study was reviewed and approved by the University of Nevada, Reno Institutional Review Board (project 956068-12). All participants gave their informed consent before participation. All data used for research were deidentified, and the data included in this submission were limited to data necessary for study replication.