DOI: 10.5061/dryad.4qrfj6qq1
title: Data from: Assessing completeness of cancer family history in EHRs using genetically-defined kinships: a cross-sectional study

description: The data in this submission is intended to allow others to replicate the
 results reported in our study article “Assessing completeness of cancer
 family history in EHRs using genetically-defined kinships: a
 cross-sectional study,” published in Genetics in Medicine Open in 2025. In
 this study, we leveraged genetic data from the Healthy Nevada Project to
 identify patients at Renown Health (a large regional hospital in Reno,
 Nevada) who were related by blood. We then examined the electronic health
 records of patients with cancer-affected blood-relatives to see whether
 their relatives’ cancer type was successfully documented in the patient’s
 family history record. Across all cancer types, 45.2% (95% confidence
 interval: 42.0-48.4%) of cancers were successfully documented. Here we
 provide the data and R code used to fit the generalized estimating
 equations used to produce the key results in our study. If additional data
 is desired, please see the data availability statement included with our
 study article for details on access criteria.
description: # Data from: Assessing completeness of cancer family history in EHRs using
 genetically-defined kinships: a cross-sectional study Dataset DOI:
 [10.5061/dryad.4qrfj6qq1](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: &lt; 30 years * x30.49: 30-49 years * x50.69: 50-69 years *
 over69: &gt; 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:
 &lt; $50,000/year (low) * inc50.100k: $50,000-$100,000/year * inc100k:
 &gt; $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: &gt; 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.