التفاصيل البيبلوغرافية
| العنوان: |
Expression profiling of formalin-fixed paraffin-embedded primary breast tumors using cancer-specific and whole genome gene panels on the DASL® platform. |
| المؤلفون: |
Reinholz, Monica M., Eckel-Passow, Jeanette E., Anderson, S. Keith, Asmann, Yan W., Zschunke, Michael A., Oberg, Ann L., McCullough, Ann E., Dueck, Amylou C., Beiyun Chen, April, Craig S., Wickham-Garcia, Eliza, Jenkins, Robert B., Cunningham, Julie M., Jin Jen, Perez, Edith A., Jian-Bing Fan, Lingle, Wilma L. |
| المصدر: |
BMC Medical Genomics; 2010, Vol. 3, p60-75, 16p |
| مصطلحات موضوعية: |
GENETIC research, ONCOLOGY, NUCLEIC acids, GENETIC regulation, CELL division, OSTEOSARCOMA, TUMOR proteins, TUMOR markers, EPIDERMAL growth factor, DNA topoisomerase II |
| مستخلص: |
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 Panelv1 (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. [ABSTRACT FROM AUTHOR] |
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| قاعدة البيانات: |
Complementary Index |
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