Phenotype Discovery and Geographic Disparities of Late-Stage Breast Cancer Diagnosis across U.S. Counties: A Machine Learning Approach

Cancer Epidemiol Biomarkers Prev. 2022 Jan;31(1):66-76. doi: 10.1158/1055-9965.EPI-21-0838. Epub 2021 Oct 25.


Background: Disparities in the stage at diagnosis for breast cancer have been independently associated with various contextual characteristics. Understanding which combinations of these characteristics indicate highest risk, and where they are located, is critical to targeting interventions and improving outcomes for patients with breast cancer.

Methods: The study included women diagnosed with invasive breast cancer between 2009 and 2018 from 680 U.S. counties participating in the Surveillance, Epidemiology, and End Results program. We used a machine learning approach called Classification and Regression Tree (CART) to identify county "phenotypes," combinations of characteristics that predict the percentage of patients with breast cancer presenting with late-stage disease. We then mapped the phenotypes and compared their geographic distributions. These findings were further validated using an alternate machine learning approach called random forest.

Results: We discovered seven phenotypes of late-stage breast cancer. Common to most phenotypes associated with high risk of late-stage diagnosis were high uninsured rate, low mammography use, high area deprivation, rurality, and high poverty. Geographically, these phenotypes were most prevalent in southern and western states, while phenotypes associated with lower percentages of late-stage diagnosis were most prevalent in the northeastern states and select metropolitan areas.

Conclusions: The use of machine learning methods of CART and random forest together with geographic methods offers a promising avenue for future disparities research.

Impact: Local interventions to reduce late-stage breast cancer diagnosis, such as community education and outreach programs, can use machine learning and geographic modeling approaches to tailor strategies for early detection and resource allocation.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • Breast Neoplasms / epidemiology*
  • Female
  • Humans
  • Machine Learning*
  • Mammography / statistics & numerical data
  • Medically Uninsured / statistics & numerical data
  • Middle Aged
  • Neoplasm Invasiveness
  • Phenotype
  • Poverty Areas
  • Residence Characteristics*
  • Rural Population
  • SEER Program
  • United States / epidemiology