Both FOR with parapharyngeal & rectopharyngeal extension T3N1Mx 28 CR Undifferentiated carcinoma; loc adv T4N1Mx. check details Tumour involv PNS, clivus, paratracheal & prevertebral muscles, ant nasal cavity and ext to both middle cranial fossa (extradural mass) T4N1Mx As evaluated with computed tomography scans taken at the last visit, 15 cases were classified as complete response to treatment (CR), that is, no evidence of disease was present, and 13 were classified as partial response
to treatment (PR), that is, residual disease or metastasis was present. Gene profiles were analysed to identify a suite of biomarker genes capable of predicting a patient’s response to treatment. (Analysis is described in the Additional file 1.) Pathway analysis Pathway analysis was performed using GeneSpring GX (version 10). BioPAX format pathways were imported into GeneSpring GX via http://biopax.org. The “Find Similar Pathway Tool” was used to identify pathways with considerable enrichment of the genes from our study. P-values were calculated using hypergeometric distribution or the Fisher’s exact test; the cut-off was set at < 0·05. Results Of the SC79 66 patients with NPC, there were more males
than females (49 males, 17 females; see Table 1), a finding consistent with previous studies indicating that the incidence of NPC is higher in men than in women (male: Fossariinae female ratio = 3:1). We selected 66 samples for this study (36 newly diagnosed NPC (pre-treatment) and 30 post-treatment samples). Patient age, gender and other variables are shown in Table 1. To obtain genome-wide expression data for the samples, 66 hybridizations using Temsirolimus Affymetrix GeneChip were performed. NPC gene signature identification Microarray hybridizations were carried out to generate gene expression profiles for 66 blood samples from NPC patients, irrespective of treatment stage, and 33 control samples from Mount Miriam Cancer Hospital. Data analysis flow of the microarray data is shown in Figure 1 and in the Additional file 1. Using
multivariate logistic regression analysis, we first selected 121 combinations of six probe sets with an AUC greater than 0·90 that separate NPC samples from unaffected controls and from patients with other diseases. The 121 combinations of six probe sets comprised 234 unique probe sets. Figure 1 Data Analysis Outline. (a) Microarray gene profiling raw data were pre-processed for quality control before analysis. First, all samples were normalized using MAS5 algorithm and only probes flagged as “present” were retained. The “present” probes were then compared with the list generated in MAQC studies for Affymetrix Human U133 plus 2; non-overlapped probes were deemed unreliable and, therefore, excluded.