Istency between the two study cohorts. doi:10.1371/journal.pone.0054356.gPatient population and clinicopathological dataThe Norwegian cohort, diagnosed and treated at the Department of Gynecological Oncology at the Oslo University Hospital The Norwegian Radiumhospital during the period May 1992 to February 2003, consisted of 74 patients diagnosed with SOC on routine pathology reports. All patients underwent primary surgery, followed by adjuvant platinum-based chemotherapy. A summary of the clinicopathological characteristics is shown in Table 1 and detailed information is provided in Table S1 (see also [32]). Progression-free survival (PFS) was defined as the time interval that DLS 10 site elapsed between diagnosis and progression, based on the first confirmed sign of disease recurrence according to Gynecologic Cancer InterGroup (GCIG) definitions. Overall survival was defined as the time interval that elapsed between diagnosis and death of any cause [32]. Sensitivity to platinum-based chemotherapy was defined as no relapse within six months after the completion of the treatment. The second cohort, originally analysed in MedChemExpress DBeQ Australia [33], consisted of 70 patients diagnosed with SOC from 1988 to 2005, including 56 cases from Australia (from the Australian Ovarian Cancer Study (AOCS) and the Gynaecological Oncology Biobank at Westmead) and 14 cases from Japan. All patients received first-line platinum-based chemotherapy. A summary of the clinicopathological characteristics is shown in Table 1 and additional information is provided in Table S2 (further genetic information can be provided from AOCS Group on request). For this cohort, PFS was defined as the time interval between the date of diagnosis and the first confirmed sign of disease progression based on GCIG definitions. Overall survival was defined as the time interval between the date of histological diagnosis and the date of death from any cause [34]. Chemotherapy response was stratified based on progression-free interval; less than six months to disease progression was chosen as an end point to define resistantSegmentation and estimation of copy number dataTo segment the 1655472 copy number data the Piecewise Constant Fitting (PCF) algorithm [35?7] was applied to log2-transformed copy number values for each sample. For a given number of breakpoints, PCF identifies the least-squares optimal segmentation of the data. The number of breakpoints, and thus the bias-variance trade-off, is controlled by a penalty parameter cw0 (c 12 in this study). The least number of probes in a segment was set to 3. For each segment a corresponding (log2-transformed) 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).Gen.Istency between the two study cohorts. doi:10.1371/journal.pone.0054356.gPatient population and clinicopathological dataThe Norwegian cohort, diagnosed and treated at the Department of Gynecological Oncology at the Oslo University Hospital The Norwegian Radiumhospital during the period May 1992 to February 2003, consisted of 74 patients diagnosed with SOC on routine pathology reports. All patients underwent primary surgery, followed by adjuvant platinum-based chemotherapy. A summary of the clinicopathological characteristics is shown in Table 1 and detailed information is provided in Table S1 (see also [32]). Progression-free survival (PFS) was defined as the time interval that elapsed between diagnosis and progression, based on the first confirmed sign of disease recurrence according to Gynecologic Cancer InterGroup (GCIG) definitions. Overall survival was defined as the time interval that elapsed between diagnosis and death of any cause [32]. Sensitivity to platinum-based chemotherapy was defined as no relapse within six months after the completion of the treatment. The second cohort, originally analysed in Australia [33], consisted of 70 patients diagnosed with SOC from 1988 to 2005, including 56 cases from Australia (from the Australian Ovarian Cancer Study (AOCS) and the Gynaecological Oncology Biobank at Westmead) and 14 cases from Japan. All patients received first-line platinum-based chemotherapy. A summary of the clinicopathological characteristics is shown in Table 1 and additional information is provided in Table S2 (further genetic information can be provided from AOCS Group on request). For this cohort, PFS was defined as the time interval between the date of diagnosis and the first confirmed sign of disease progression based on GCIG definitions. Overall survival was defined as the time interval between the date of histological diagnosis and the date of death from any cause [34]. Chemotherapy response was stratified based on progression-free interval; less than six months to disease progression was chosen as an end point to define resistantSegmentation and estimation of copy number dataTo segment the 1655472 copy number data the Piecewise Constant Fitting (PCF) algorithm [35?7] was applied to log2-transformed copy number values for each sample. For a given number of breakpoints, PCF identifies the least-squares optimal segmentation of the data. The number of breakpoints, and thus the bias-variance trade-off, is controlled by a penalty parameter cw0 (c 12 in this study). The least number of probes in a segment was set to 3. For each segment a corresponding (log2-transformed) 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).Gen.
