To similarity in signature construction and chose the best performing one (CINGECS) for further analysis. Multivariate Cox analyses were subsequently performed with remaining worsening GEP signatures from univariate Title Loaded From File Analysis (HR .1 and p,0.05) and CINGECS. Stepwise refinements were applied at the end. For data processing and analyses including survival analysis, we used R system [32] and its standard library `survival’. [33].Enrichment pGamma p-valueEnrichment p- value Gamma p-value(corrected) value (corrected)5.6.1.8361028 1.2.5.6.2.5.9.1.1.9.5.1.1.45610 11.4 3.13.27.26.Table 1. List of statistically significant KEGG pathways from IF analysis using CINGECS genes.6.3.3.7.5.5.2.2.Results CINGEC and SurvivalWe first estimated CINGEC scores of two MM aCGH datasets, 60 patient samples of the Mayo clinic and 100 patient samples of the UAMS collection, and compared them with the genome instability index (GII) that measures the fraction of aberrant genomic regions in a genome [34] (Figure S1). In both cases, CINGEC and GII were significantly correlated; correlation 0.62 (Figure S1(c); p = 4.66861028) for Mayo patient sample data and 0.43 (Figure S1(d); p = 9.19461026) for UAMS patient aCGH data. However, the data distribution suggests that aberration events covering whole chromosomes or arms make big impact on GII but little on 16985061 CINGEC, whereas highly complicated copy number profiles with numerous small scale interstitial abnormalities clearly dominate samples with high CINGEC score (Figures S1 (c) and (d)). Since CIN is known to cause adverse effects on patient survival in cancer, we tested if this was also the case in myeloma. Analysis using aCGH data from Mayo clinic clearly indicated that patients grouped according to their CINGEC score had significantly different OS (Figure 2(a); HR = 1.70 with 95 confidence interval (CI) = 1.16?.49 and p-value = 0.00671). In contrast, the survival difference was not that significant when GII was used (Figure 2(b); HR = 1.60, CI = 1.09?.33, p = 0.0158). In particular, the survival difference between the top quartile of CINGEC score and the rest quartiles combined (HR = 4.38, CI = 1.72?1.16, p = 0.00197) were substantially greater 23148522 than in GII (HR = 2.74, CI = 1.12?.74, p = 0.0281). We next validated if this effect of CINGEC on prognosis was reproducible in an independent MM aCGH dataset. In the UAMS aCGH dataset where patients were treated on the total therapy II protocol, patients grouped according to their CINGEC score also had significantly different OS (Figure 2(c); HR = 1.73,43 5 11.355Genes in pathway (number)Impact factor29.28.18.9.802 doi:10.1371/journal.pone.0066361.t001 Hsa04115: p53 signaling pathwayHsa04110: Cell cycleHsa03420: Nucleotide excision repairHsa03430: Mismatch repairHsa03030: DNA replicationPathway nameChromosome Instability and Prognosis in MMFigure 3. OS difference among different risk groups by CINGECS. (a) UAMS, (b) APEX, (c) HOVON dataset. doi:10.1371/journal.pone.0066361.gCI = 1.11?.72, p = 0.0164) while GII-based patient groups were not (Figure 2(d); HR = 1.56, CI = 0.96?.54, p = 0.0758).CINGECS Genes and PathwaysTo further understand the Title Loaded From File molecular difference between MM patients with high and low degrees of CIN, we analyzed the MMRC reference collection using data from 246 samples where both aCGH and GEP data were available. 214 probesets (160 genes; Table S1) were differentially expressed between samples in top 25 and bottom 25 CINGEC. 189 probesets (144 genes) were up-re.To similarity in signature construction and chose the best performing one (CINGECS) for further analysis. Multivariate Cox analyses were subsequently performed with remaining worsening GEP signatures from univariate analysis (HR .1 and p,0.05) and CINGECS. Stepwise refinements were applied at the end. For data processing and analyses including survival analysis, we used R system [32] and its standard library `survival’. [33].Enrichment pGamma p-valueEnrichment p- value Gamma p-value(corrected) value (corrected)5.6.1.8361028 1.2.5.6.2.5.9.1.1.9.5.1.1.45610 11.4 3.13.27.26.Table 1. List of statistically significant KEGG pathways from IF analysis using CINGECS genes.6.3.3.7.5.5.2.2.Results CINGEC and SurvivalWe first estimated CINGEC scores of two MM aCGH datasets, 60 patient samples of the Mayo clinic and 100 patient samples of the UAMS collection, and compared them with the genome instability index (GII) that measures the fraction of aberrant genomic regions in a genome [34] (Figure S1). In both cases, CINGEC and GII were significantly correlated; correlation 0.62 (Figure S1(c); p = 4.66861028) for Mayo patient sample data and 0.43 (Figure S1(d); p = 9.19461026) for UAMS patient aCGH data. However, the data distribution suggests that aberration events covering whole chromosomes or arms make big impact on GII but little on 16985061 CINGEC, whereas highly complicated copy number profiles with numerous small scale interstitial abnormalities clearly dominate samples with high CINGEC score (Figures S1 (c) and (d)). Since CIN is known to cause adverse effects on patient survival in cancer, we tested if this was also the case in myeloma. Analysis using aCGH data from Mayo clinic clearly indicated that patients grouped according to their CINGEC score had significantly different OS (Figure 2(a); HR = 1.70 with 95 confidence interval (CI) = 1.16?.49 and p-value = 0.00671). In contrast, the survival difference was not that significant when GII was used (Figure 2(b); HR = 1.60, CI = 1.09?.33, p = 0.0158). In particular, the survival difference between the top quartile of CINGEC score and the rest quartiles combined (HR = 4.38, CI = 1.72?1.16, p = 0.00197) were substantially greater 23148522 than in GII (HR = 2.74, CI = 1.12?.74, p = 0.0281). We next validated if this effect of CINGEC on prognosis was reproducible in an independent MM aCGH dataset. In the UAMS aCGH dataset where patients were treated on the total therapy II protocol, patients grouped according to their CINGEC score also had significantly different OS (Figure 2(c); HR = 1.73,43 5 11.355Genes in pathway (number)Impact factor29.28.18.9.802 doi:10.1371/journal.pone.0066361.t001 Hsa04115: p53 signaling pathwayHsa04110: Cell cycleHsa03420: Nucleotide excision repairHsa03430: Mismatch repairHsa03030: DNA replicationPathway nameChromosome Instability and Prognosis in MMFigure 3. OS difference among different risk groups by CINGECS. (a) UAMS, (b) APEX, (c) HOVON dataset. doi:10.1371/journal.pone.0066361.gCI = 1.11?.72, p = 0.0164) while GII-based patient groups were not (Figure 2(d); HR = 1.56, CI = 0.96?.54, p = 0.0758).CINGECS Genes and PathwaysTo further understand the molecular difference between MM patients with high and low degrees of CIN, we analyzed the MMRC reference collection using data from 246 samples where both aCGH and GEP data were available. 214 probesets (160 genes; Table S1) were differentially expressed between samples in top 25 and bottom 25 CINGEC. 189 probesets (144 genes) were up-re.
