title: Differences in gene and protein expression and the effects of race/ethnicity on breast cancer subtypes.
abstract: BACKGROUND
  Differences in gene or protein expression patterns between breast cancers according to race/ethnicity and cancer subtype.
  
  
  METHODS
  Transcriptional profiling was performed using Affymetrix HG-U133A platform in 376 patients and reverse phase protein array analysis (RPPA) was done for 177 proteins in 255 patients from a separate cohort. Unsupervised clustering was conducted, as well as supervised comparison by race and tumor subtype. Standard statistical methods, BRB-Array tools, and Ingenuity Pathways software packages were used to analyze the data.
  
  
  RESULTS
  Median age was 50 years in both the cohorts. In the RPPA cohort, 54.5% of the tumors were hormone receptor-positive (HR-positive), 20.7% HER2-positive, and 24.71% triple-negative (TNBC). One hundred and forty-seven (57.6%), 47 (18.43%), and 46 (18.1%) of the patients were White, Hispanic, and Black, respectively. Unsupervised hierarchical clustering of the protein expression data showed no distinct clusters by race (P values were 0.492, 0.489, and 0.494 for the HR-positive, HER2-positive, and TNBC tumors respectively). In the gene expression cohort, 54.2% of the tumors were HR-positive, 16.5% HER2-positive, and 29.3% TNBC. Two hundred and sixteen (57.5%), 111 (29.52%), and 32 (8.52%) patients were White, Hispanic, and Black, respectively. No probe set with a false discovery rate (FDR) of <0.05 showed an association with race by breast cancer subtype; similar results were obtained using pathway and gene set enrichment analysis methods.
  
  
  CONCLUSIONS
  We did not detect a significant variation in RNA or protein expression comparing different race/ethnicity groups of women with breast cancer.
  
  
  CONCLUSIONS
  More research on the complex network of factors that result in outcomes differences among race/ethnicities is needed.
authors.affiliation: Authors' Affiliations: Departments of Breast Medical Oncology, Biostatistics, Pathology, Systems Biology, and Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas; and Division of Hematology-Oncology, Yale University, New Haven, Connecticut.
authors.forename: Mariana
authors.initials: M
authors.lastname: Chavez-Macgregor
authors.forename: Shuying
authors.initials: S
authors.lastname: Liu
authors.forename: Debora
authors.initials: D
authors.lastname: De Melo-Gagliato
authors.forename: Huiqin
authors.initials: H
authors.lastname: Chen
authors.forename: Kim-Anh
authors.initials: KA
authors.lastname: Do
authors.forename: Lajos
authors.initials: L
authors.lastname: Pusztai
authors.forename: W
authors.initials: W
authors.lastname: Fraser Symmans
authors.forename: Lakshmy
authors.initials: L
authors.lastname: Nair
authors.forename: Gabriel N
authors.initials: GN
authors.lastname: Hortobagyi
authors.forename: Gordon B
authors.initials: GB
authors.lastname: Mills
authors.forename: Funda
authors.initials: F
authors.lastname: Meric-Bernstam
authors.forename: Ana M
authors.initials: AM
authors.lastname: Gonzalez-Angulo
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D014408:Biomarkers, Tumor / Q000096:biosynthesis / Q000235:genetics; D044383:Black People / Q000706:statistics & numerical data; D001943:Breast Neoplasms / Q000145:classification* / Q000208:ethnology* / Q000235:genetics / Q000473:pathology; D016000:Cluster Analysis; D015331:Cohort Studies; D005260:Female; D015870:Gene Expression; D006630:Hispanic or Latino / Q000706:statistics & numerical data; D006801:Humans; D008875:Middle Aged; D018719:Erb-b2 Receptor Tyrosine Kinases / Q000096:biosynthesis / Q000235:genetics; D044465:White People / Q000706:statistics & numerical data; D055815:Young Adult
chemical_list: D014408:Biomarkers, Tumor; D018719:Erb-b2 Receptor Tyrosine Kinases; C508053:ERBB2 protein, human