Additional file 3: of An evaluation of processing methods for HumanMethylation450 BeadChip data

Multidimensional scaling plot of distances between samples in COAD, scaling dimensions 1 vs 2, samples colored by plates. Euclidean distances between sample pairs are computed for a common set of 5000 features having the largest standard deviations across all samples. Features containing SNPs or mapping to the sex chromosomes were excluded. (PDF 7 kb

Additional file 4: of An evaluation of processing methods for HumanMethylation450 BeadChip data

Density distributions of Beta values for the Type I (solid lines) and Type II (dashed lines) probes for six PBLs replicates under different processing methods. (PDF 50 kb

Additional file 1: of At least two well-spaced samples are needed to genotype a solid tumor

SOM: LOH can confound mutation classification. (DOCX 423 kb

Additional file 2: Figure S1. of At least two well-spaced samples are needed to genotype a solid tumor

Data from the 8 tumors not in Fig. 2. (PDF 223 kb

Posterior distributions of mutation rate for tumor U.

<p>(A) mutation rate before gland formation. (B) mutation rate after gland formation. The dashed line indicates the mean of the posterior distribution.</p

Posterior distribution of asymmetric division rate (x-axis) for tumor U.

<p>Dashed line indicates the mean of the posterior distribution.</p

Parameters in our model.

<p>Parameters in our model.</p

Summary of posterior distributions for different sequencing depths.

<p>The first column and second column show the mean and standard deviation of each parameter’s posterior distribution for the 300 simulated tumors respectively. The top row is the summary of for mutation rate before gland formation. The middle row is for the mutation rate after gland formation while the third row shows the results for the asymmetric division rate. The black dots, red dots and green dots represent the results when the mean sequencing depths are 20, 40, and 80 respectively, per single gland. We see little improvement of parameter estimation with even higher sequencing depths. The other generating parameter values used were: NCSC = 32, T3 = 100, and <i>v</i> = 1.1<i>m</i> for the negative binomial distribution used to generate sequencing depth.</p

Schematic of tumor growth and the two types of CSC division.

<p>(A) The three stages of the growth model: formation of the first gland, exponential growth of gland number, and constant size phase (the length of which is 100 generations). (B). Schematic of cell differentiation process during Constant Size phase. Each yellow oval represents a CSC, while each white oval represents a non-CSC (cells which have limited differentiation capability).</p

Summary of posterior distributions for different sequencing depths.

<p>The first column and second column show the mean and standard deviation of each parameter’s posterior distribution for the 300 simulated tumors respectively. The top row is the summary of for mutation rate before gland formation. The middle row is for the mutation rate after gland formation while the third row shows the results for the asymmetric division rate. The black dots, red dots and green dots represent the results when the mean sequencing depths are 20, 40, and 80 respectively, per single gland. We see little improvement of parameter estimation with even higher sequencing depths. The other generating parameter values used were: NCSC = 32, T3 = 100, and <i>v</i> = 1.1<i>m</i> for the negative binomial distribution used to generate sequencing depth.</p