16 research outputs found

    Mutational spectrum from SA and MSA-Cap libraries, prepared from PCL-tumour or PCL-buccal swab samples.

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    <p>Non-filtered variants were identified in each sample using Broad Institute Best Practice pipeline version 1.0.5273 upon comparison to human hg19 reference sequence and categorized according to putative gene effect. The cumulative number of variants for each library type is shown on the x axis and the sample and library type on the y axis. Variant categories, as assigned by the Ensembl database, are on the right side of the figure.</p

    Genotype concordance for SNP calls in a PCL-tumour sample and a HapMap (NA12813) sample.

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    <p>For the PCL-tumour sample, the variants called by deep sequencing were compared to data from Affymetrix SNP 6.0 DNA array while for the HapMap sample published data were used for the comparison.</p

    Copy number profiles estimated by deep sequencing of PCL-tumour samples, prepared using the SA- or MSA-Cap methods.

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    <p>Chromosomes 1 to 22 plus X and Y are shown on the x axis. The log<sub>2</sub> ratio of the normalized by the normal depth values for the PCL-tumour libraries is represented on the y axis. Arrows point towards the detected by deep sequencing and previously identified by SNP6 array copy number changes: gain (6p), del (6q), del (12p), del (13q) and del (17p).</p

    The poor diagnostic accuracy illustrated by ROC curves.

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    <p>The diagnostic accuracy of the RI to predict the PFS and OS was evaluated by ROC curves. The true positive rate (sensitivity) was plotted as a function of the false positive rate (1- specificity) for a series of time dependent cut-off points illustrating the level of discrimination is quantified by area under curve (AUC) for OS and PFS being poor between 60–70%.</p

    Melphalan resistance gene index validation by clinical outcome.

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    <p>The individual RIs were assigned from gene expression data of the HOVON 65/GMMG-HD4 trial dividing tumor samples into groups of sensitive patients with low 0–25% RI, intermediate RI from 25–75% and resistant patients with the highest 75–100% RI. The impact of this assignment was subsequently evaluated with respect to PFS and overall OS as illustrated by log relative hazard for PFS (1A) and OS (1B) as a function of the individual RI levels. The P-values are the maximum likelihood tests for no RCS-association between log Relative Hazard and the RI and the dashed lines represent 95% confidence intervals. A landmark Kaplan-Meier analysis was performed from the time of HDM and we found that resistant, intermediate and sensitive patient groups had a median PFS of 18, 32 and 28 months, respectively (1C). The OS for the resistant group had a median of 45 months but not reached for the intermediate and resistant groups (1D) following a median observation time of 38 months. The P-values are the log-rank-test results for no difference between the estimated survival curves.</p

    Univariate and multivariate Cox proportional hazard models.

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    <p>The sensitive and intermediate RI groups were merged into a common non-resistant group of patients. The redefined non-resistant (RI 0–75%) and resistant (RI 75–100%) groups were analysed by univariate (P-value  = 0.003 for PFS and P-value  = 0.00089 for OS) as well as a multivariate Cox proportional hazard models documenting an association with PFS and OS (P-value of 0.0063 and 0.0025), independent of age, sex and ISS staging. The appropriateness of the Cox proportional hazard models using the dichotomized resistance index was checked using cumulative martingale residuals.</p