Med) segment average was obtained as the mean the log2-transformed

Med) segment average was obtained as the mean the log2-transformed copy number values for the probes in the segment.Assessing the genomic instabilityThe degree of genomic instability in a tumour was quantified by the total aberration level, using a similar method as described previously [38]. Let K fS1 ,:::,SR g denote the segmentation obtained with PCF for a particular sample, where Si is the indices of the probes belonging to the i’th segment. Let d1 ,:::,dR designate the segment length (in nucleotides) and 1 ,:::,R the corresponding y y segment averages. The Total Aberration Index (TAI) is then defined as PR TAI y di :DSi D diPRiiThus, TAI is basically a MedChemExpress Tubastatin A weighted sum of the segment averages and represents the absolute deviation from the normal copy number state, averaged over all genomic locations (for illustration see Figure S1 and for examples see Figure 1).Genomic Instability in Ovarian CancerFigure 4. Survival analysis in relation to genomic instability. Kaplan-Meier survival curves illustrating progression-free survival (PFS) and overall survival (OS) time (in months) for serous ovarian cancers patients with Total Aberration Index (TAI) above and below the median in the Norwegian cohort (above) and the Australian cohort (below). Test results are based on log-rank tests. Note that high TAI implies a significant survival advantage, both with regard to progression-free survival and to overall survival in the Norwegian cohort, as well as for overall survival in the Australian cohort. doi:10.1371/journal.pone.0054356.gSurvival analysisThe Kaplan-Meier estimator and the log-rank test were used to obtain survival curves and to compare survival rates in patients with TAI below and above the median. To investigate the relationship between survival and TAI as a continuous variable, Cox proportional hazard models were fitted with TAI as the predictor. Analyses were performed separately on the Norwegian and Australian cohort. All computations were performed using the statistical system R (v 2.12.2).Table 2. Survival analysis of the Norwegian and Australian SOC patients.Progression-free survival Origin of data Norway Log-rank P = 0.024 Cox HR = 0.77 [0.62, 0.96] p = 0.Overall survival Log-rank p,0.001 Cox HR = 0.70 [0.56, 0.88] p = 0.001 p = 0.030 HR = 0.69 [0.51, 0.95] p = 0.Mutation testingComprehensive germ-line testing for the Australian cohort was completed in a certified diagnostic pathology laboratory using sequencing and multiplex ligation-dependent probe amplification [39].AustraliaP = 0.HR = 0.91 [0.70, 1.20] p = 0.Log-rank: Log-rank tests comparing groups with above and below median TAI. Cox: Cox proportional hazard regression with TAI as continuous variable. HR: Hazard ratio with 95 confidence interval for an increase in TAI of 1SD. doi:10.1371/journal.pone.0054356.tGenomic Instability in Ovarian CancerResults Frequency of aberrationsThe analysis of copy number data in serous ovarian cancers revealed that the aberrations in the Norwegian and Australian cohorts were broadly concordant (Figure 2 and Figure 3), with the most frequent gains occurring on chromosome arms 1q, 3q, 8q, and 20q, and the most frequent losses occurring on chromosome arms 4q, 5q, 6 p, 8 p, 13, 16q, 18q, and the whole of the X chromosome (Figure 2). In the Australian cohort, 115103-85-0 supplier additional copy number gains were observed on 1 p and losses on 17 p and 22q (Figure 2b). The aberration patterns are also conform to those with high resolution arrays or sequencing data.Med) segment average was obtained as the mean the log2-transformed copy number values for the probes in the segment.Assessing the genomic instabilityThe degree of genomic instability in a tumour was quantified by the total aberration level, using a similar method as described previously [38]. Let K fS1 ,:::,SR g denote the segmentation obtained with PCF for a particular sample, where Si is the indices of the probes belonging to the i’th segment. Let d1 ,:::,dR designate the segment length (in nucleotides) and 1 ,:::,R the corresponding y y segment averages. The Total Aberration Index (TAI) is then defined as PR TAI y di :DSi D diPRiiThus, TAI is basically a weighted sum of the segment averages and represents the absolute deviation from the normal copy number state, averaged over all genomic locations (for illustration see Figure S1 and for examples see Figure 1).Genomic Instability in Ovarian CancerFigure 4. Survival analysis in relation to genomic instability. Kaplan-Meier survival curves illustrating progression-free survival (PFS) and overall survival (OS) time (in months) for serous ovarian cancers patients with Total Aberration Index (TAI) above and below the median in the Norwegian cohort (above) and the Australian cohort (below). Test results are based on log-rank tests. Note that high TAI implies a significant survival advantage, both with regard to progression-free survival and to overall survival in the Norwegian cohort, as well as for overall survival in the Australian cohort. doi:10.1371/journal.pone.0054356.gSurvival analysisThe Kaplan-Meier estimator and the log-rank test were used to obtain survival curves and to compare survival rates in patients with TAI below and above the median. To investigate the relationship between survival and TAI as a continuous variable, Cox proportional hazard models were fitted with TAI as the predictor. Analyses were performed separately on the Norwegian and Australian cohort. All computations were performed using the statistical system R (v 2.12.2).Table 2. Survival analysis of the Norwegian and Australian SOC patients.Progression-free survival Origin of data Norway Log-rank P = 0.024 Cox HR = 0.77 [0.62, 0.96] p = 0.Overall survival Log-rank p,0.001 Cox HR = 0.70 [0.56, 0.88] p = 0.001 p = 0.030 HR = 0.69 [0.51, 0.95] p = 0.Mutation testingComprehensive germ-line testing for the Australian cohort was completed in a certified diagnostic pathology laboratory using sequencing and multiplex ligation-dependent probe amplification [39].AustraliaP = 0.HR = 0.91 [0.70, 1.20] p = 0.Log-rank: Log-rank tests comparing groups with above and below median TAI. Cox: Cox proportional hazard regression with TAI as continuous variable. HR: Hazard ratio with 95 confidence interval for an increase in TAI of 1SD. doi:10.1371/journal.pone.0054356.tGenomic Instability in Ovarian CancerResults Frequency of aberrationsThe analysis of copy number data in serous ovarian cancers revealed that the aberrations in the Norwegian and Australian cohorts were broadly concordant (Figure 2 and Figure 3), with the most frequent gains occurring on chromosome arms 1q, 3q, 8q, and 20q, and the most frequent losses occurring on chromosome arms 4q, 5q, 6 p, 8 p, 13, 16q, 18q, and the whole of the X chromosome (Figure 2). In the Australian cohort, additional copy number gains were observed on 1 p and losses on 17 p and 22q (Figure 2b). The aberration patterns are also conform to those with high resolution arrays or sequencing data.