Intrinsic subtypes from PAM50 gene expression assay in a population-based breast cancer cohort: differences by age, race, and tumor characteristics

Cancer Epidemiol Biomarkers Prev. 2014 May;23(5):714-24. doi: 10.1158/1055-9965.EPI-13-1023. Epub 2014 Feb 12.

Abstract

Background: Data are lacking to describe gene expression-based breast cancer intrinsic subtype patterns for population-based patient groups.

Methods: We studied a diverse cohort of women with breast cancer from the Life After Cancer Epidemiology and Pathways studies. RNA was extracted from 1 mm punches from fixed tumor tissue. Quantitative reverse-transcriptase PCR was conducted for the 50 genes that comprise the PAM50 intrinsic subtype classifier.

Results: In a subcohort of 1,319 women, the overall subtype distribution based on PAM50 was 53.1% luminal A, 20.5% luminal B, 13.0% HER2-enriched, 9.8% basal-like, and 3.6% normal-like. Among low-risk endocrine-positive tumors (i.e., estrogen and progesterone receptor positive by immunohistochemistry, HER2 negative, and low histologic grade), only 76.5% were categorized as luminal A by PAM50. Continuous-scale luminal A, luminal B, HER2-enriched, and normal-like scores from PAM50 were mutually positively correlated. Basal-like score was inversely correlated with other subtypes. The proportion with non-luminal A subtype decreased with older age at diagnosis, P Trend < 0.0001. Compared with non-Hispanic Whites, African American women were more likely to have basal-like tumors, age-adjusted OR = 4.4 [95% confidence intervals (CI), 2.3-8.4], whereas Asian and Pacific Islander women had reduced odds of basal-like subtype, OR = 0.5 (95% CI, 0.3-0.9).

Conclusions: Our data indicate that over 50% of breast cancers treated in the community have luminal A subtype. Gene expression-based classification shifted some tumors categorized as low risk by surrogate clinicopathologic criteria to higher-risk subtypes.

Impact: Subtyping in a population-based cohort revealed distinct profiles by age and race.

Publication types

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

MeSH terms

  • Adolescent
  • Adult
  • Age Factors
  • Aged
  • Aged, 80 and over
  • Biomarkers, Tumor / genetics*
  • Breast Neoplasms / classification*
  • Breast Neoplasms / genetics*
  • Breast Neoplasms / pathology
  • Carcinoma, Basal Cell / genetics*
  • Carcinoma, Basal Cell / pathology
  • Cohort Studies
  • Continental Population Groups
  • Estrogen Receptor alpha / metabolism
  • Female
  • Follow-Up Studies
  • Gene Expression Regulation, Neoplastic*
  • Humans
  • Immunoenzyme Techniques
  • Middle Aged
  • Neoplasm Staging
  • Prognosis
  • RNA, Messenger / genetics
  • Receptor, ErbB-2 / metabolism
  • Receptors, Progesterone / metabolism
  • Reverse Transcriptase Polymerase Chain Reaction
  • Young Adult

Substances

  • Biomarkers, Tumor
  • Estrogen Receptor alpha
  • RNA, Messenger
  • Receptors, Progesterone
  • estrogen receptor alpha, human
  • ERBB2 protein, human
  • Receptor, ErbB-2