title: Expression profiling of formalin-fixed paraffin-embedded primary breast tumors using cancer-specific and whole genome gene panels on the DASL® platform.
abstract: BACKGROUND
  The cDNA-mediated Annealing, extension, Selection and Ligation (DASL) assay has become a suitable gene expression profiling system for degraded RNA from paraffin-embedded tissue. We examined assay characteristics and the performance of the DASL 502-gene Cancer Panel v1 (1.5K) and 24,526-gene panel (24K) platforms at differentiating nine human epidermal growth factor receptor 2- positive (HER2+) and 11 HER2-negative (HER2-) paraffin-embedded breast tumors.
  
  
  METHODS
  Bland-Altman plots and Spearman correlations evaluated intra/inter-panel agreement of normalized expression values. Unequal-variance t-statistics tested for differences in expression levels between HER2 + and HER2 - tumors. Regulatory network analysis was performed using Metacore (GeneGo Inc., St. Joseph, MI).
  
  
  RESULTS
  Technical replicate correlations ranged between 0.815-0.956 and 0.986-0.997 for the 1.5K and 24K panels, respectively. Inter-panel correlations of expression values for the common 498 genes across the two panels ranged between 0.485-0.573. Inter-panel correlations of expression values of 17 probes with base-pair sequence matches between the 1.5K and 24K panels ranged between 0.652-0.899. In both panels, erythroblastic leukemia viral oncogene homolog 2 (ERBB2) was the most differentially expressed gene between the HER2 + and HER2 - tumors and seven additional genes had p-values < 0.05 and log2 -fold changes > |0.5| in expression between HER2 + and HER2 - tumors: topoisomerase II alpha (TOP2A), cyclin a2 (CCNA2), v-fos fbj murine osteosarcoma viral oncogene homolog (FOS), wingless-type mmtv integration site family, member 5a (WNT5A), growth factor receptor-bound protein 7 (GRB7), cell division cycle 2 (CDC2), and baculoviral iap repeat-containing protein 5 (BIRC5). The top 52 discriminating probes from the 24K panel are enriched with genes belonging to the regulatory networks centered around v-myc avian myelocytomatosis viral oncogene homolog (MYC), tumor protein p53 (TP53), and estrogen receptor α (ESR1). Network analysis with a two-step extension also showed that the eight discriminating genes common to the 1.5K and 24K panels are functionally linked together through MYC, TP53, and ESR1.
  
  
  CONCLUSIONS
  The relative RNA abundance obtained from two highly differing density gene panels are correlated with eight common genes differentiating HER2 + and HER2 - breast tumors. Network analyses demonstrated biological consistency between the 1.5K and 24K gene panels.
authors.affiliation: Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First St SW, Rochester, Minnesota 55905, USA. reinholz.monica@mayo.edu
authors.forename: Monica M
authors.initials: MM
authors.lastname: Reinholz
authors.forename: Jeanette E
authors.initials: JE
authors.lastname: Eckel-Passow
authors.forename: S Keith
authors.initials: SK
authors.lastname: Anderson
authors.forename: Yan W
authors.initials: YW
authors.lastname: Asmann
authors.forename: Michael A
authors.initials: MA
authors.lastname: Zschunke
authors.forename: Ann L
authors.initials: AL
authors.lastname: Oberg
authors.forename: Ann E
authors.initials: AE
authors.lastname: McCullough
authors.forename: Amylou C
authors.initials: AC
authors.lastname: Dueck
authors.forename: Beiyun
authors.initials: B
authors.lastname: Chen
authors.forename: Craig S
authors.initials: CS
authors.lastname: April
authors.forename: Eliza
authors.initials: E
authors.lastname: Wickham-Garcia
authors.forename: Robert B
authors.initials: RB
authors.lastname: Jenkins
authors.forename: Julie M
authors.initials: JM
authors.lastname: Cunningham
authors.forename: Jin
authors.initials: J
authors.lastname: Jen
authors.forename: Edith A
authors.initials: EA
authors.lastname: Perez
authors.forename: Jian-Bing
authors.initials: JB
authors.lastname: Fan
authors.forename: Wilma L
authors.initials: WL
authors.lastname: Lingle
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology*; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008928:Mitochondria / Q000235:genetics; D016612:Paraffin Embedding; D018719:Erb-b2 Receptor Tyrosine Kinases / Q000235:genetics
chemical_list: D018719:Erb-b2 Receptor Tyrosine Kinases; C508053:ERBB2 protein, human