title: Copy number and gene expression differences between African American and Caucasian American prostate cancer.
abstract: BACKGROUND
  The goal of our study was to investigate the molecular underpinnings associated with the relatively aggressive clinical behavior of prostate cancer (PCa) in African American (AA) compared to Caucasian American (CA) patients using a genome-wide approach.
  
  
  METHODS
  AA and CA patients treated with radical prostatectomy (RP) were frequency matched for age at RP, Gleason grade, and tumor stage. Array-CGH (BAC SpectralChip2600) was used to identify genomic regions with significantly different DNA copy number between the groups. Gene expression profiling of the same set of tumors was also evaluated using Affymetrix HG-U133 Plus 2.0 arrays. Concordance between copy number alteration and gene expression was examined. A second aCGH analysis was performed in a larger validation cohort using an oligo-based platform (Agilent 244K).
  
  
  RESULTS
  BAC-based array identified 27 chromosomal regions with significantly different copy number changes between the AA and CA tumors in the first cohort (Fisher's exact test, P < 0.05). Copy number alterations in these 27 regions were also significantly associated with gene expression changes. aCGH performed in a larger, independent cohort of AA and CA tumors validated 4 of the 27 (15%) most significantly altered regions from the initial analysis (3q26, 5p15-p14, 14q32, and 16p11). Functional annotation of overlapping genes within the 4 validated regions of AA/CA DNA copy number changes revealed significant enrichment of genes related to immune response.
  
  
  CONCLUSIONS
  Our data reveal molecular alterations at the level of gene expression and DNA copy number that are specific to African American and Caucasian prostate cancer and may be related to underlying differences in immune response.
authors.affiliation: Department of Urology, New York University School of Medicine, New York, New York 10016, USA.
authors.forename: Amy E
authors.initials: AE
authors.lastname: Rose
authors.forename: Jaya M
authors.initials: JM
authors.lastname: Satagopan
authors.forename: Carole
authors.initials: C
authors.lastname: Oddoux
authors.forename: Qin
authors.initials: Q
authors.lastname: Zhou
authors.forename: Ruliang
authors.initials: R
authors.lastname: Xu
authors.forename: Adam B
authors.initials: AB
authors.lastname: Olshen
authors.forename: Jessie Z
authors.initials: JZ
authors.lastname: Yu
authors.forename: Atreya
authors.initials: A
authors.lastname: Dash
authors.forename: Jerome
authors.initials: J
authors.lastname: Jean-Gilles
authors.forename: Victor
authors.initials: V
authors.lastname: Reuter
authors.forename: William L
authors.initials: WL
authors.lastname: Gerald
authors.forename: Peng
authors.initials: P
authors.lastname: Lee
authors.forename: Iman
authors.initials: I
authors.lastname: Osman
mesh_terms: D001741:Black or African American / Q000235:genetics*; D000368:Aged; D002869:Chromosome Aberrations; D002877:Chromosomes, Human / Q000235:genetics; D016000:Cluster Analysis; D055028:Comparative Genomic Hybridization; D056915:DNA Copy Number Variations / Q000235:genetics*; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D052138:Genes, Neoplasm / Q000235:genetics; D006801:Humans; D007109:Immunity / Q000235:genetics; D008297:Male; D008875:Middle Aged; D011471:Prostatic Neoplasms / Q000235:genetics*; D044465:White People / Q000235:genetics*