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A set with 100 artificial patients was built using randomly sampled copy number values from the GBM data.
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Four hundred randomly sampled hard copy surveys were selected by CMS staff from all mailed surveys coded as being completed surveys.
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This cohort contains mutation data for 507 samples, copy number data for 778 samples, expression data for 526 samples and methylation data for 311 samples.
cnvHap updates the positions of these cluster positions within a generalized expectation maximization framework and then reports the per-sample copy number genotypes (Fig. 3).
For the remainder of the samples, copy number calling was done jointly on KIR3DL1 and KIR3DS1 using unsupervised clustering with a finite mixture model.
The sample copy number was estimated by interpolation from the standard curve, calculated as an average of the 3 dilutions and expressed as the proportion of PBMCs infected.
In cell culture samples, copy numbers ranged between 5.3 × 10 and 1.4 × 10 copies/μL (median 7.0 × 10) of DNA extract (Table 4).
After amplification, data files containing the sample replicate CT values for each reporter dye were imported into the CopyCaller software analysis tool (Life Technologies) to calculate sample copy number values by relative quantification, using the comparative CT (ΔΔCT) method.
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