Cross-reactivity matrix for the newly added assays in <i>HRAS</i> and <i>PIK3CA</i>.

<p>Cross-reactivity matrix for the newly added assays in <i>HRAS</i> and <i>PIK3CA</i>.</p

Correlation Between Mutation Calls in Cell Lines and Those Reported in the Literature.

<p>MND, mutation not detected.</p

Figure 1

<p>(<b>A</b>) Schematic diagram for the process of generating the positive control for MUT-MAP. (<b>B</b>) The positive control is a mixture of mutant plasmids and wild-type human genomic DNA. The positive control was created such that the resulting C_Ts range from 9–16 across all wild-type and mutant assays. Pk_H1047X covers multiple hotspot mutations resulting in a lower overall C_T as it is detecting more than one plasmid in the positive control.</p

Mutation Coverage Breakdown by Gene.

<p>Mutation Coverage Breakdown by Gene.</p

Evaluation of assay sensitivity.

<p>Linearized plasmids containing the mutant sequence were mixed and diluted into a background of wild-type genomic DNA from 50-0.1% mutant (blue diamonds). A sample containing 5% of the corresponding mutant plasmid with a wild-type genomic DNA background was diluted in nuclease-free water (red squares). Samples were run on the panel and assay sensitivity was determined. The C_T of wild-type genomic DNA alone is indicated by the green triangles.</p

Prevalence of oncogenic mutations detected by MUT-MAP in (A) breast and (B) colorectal tumors compared to COSMIC database and literature citations.

<p>Prevalence of oncogenic mutations detected by MUT-MAP in (A) breast and (B) colorectal tumors compared to COSMIC database and literature citations.</p

Quality control process for panel validation: Intra- and inter-chip reproducibility.

<p>MUT-MAP panel qPCR assays were run in duplicate and C_T outputs were plotted to determine both intra- and inter-chip reproducibility. Data for a typical mutation panel run are shown, with r² values of 0.995 and 0.990 for inter- and intra-chip reproducibility, respectively.</p

Comparison of the sensitivity of MUT-MAP and a next generation sequencing platform.

<p>(<b>A and B</b>) Nine FFPE samples with known mutation status were mixed together in varying concentrations following a Latin Square design to generate a seven-member Latin Square panel. The percentage of the mutant allele in each mix was calculated based on the mutant fraction of the parental samples as determined by analysis with the SuraSeq500 panel. For those mutations not detected by the NGS panel, 50% mutation in the parental sample was assumed. (<b>C</b>) The seven Latin Square samples were analyzed on MUT-MAP as well as by the SuraSeq500 panel on Ion Torrent in order to compare mutation calls and sensitivity levels of both platforms.</p

Cross-reactivity matrix for the newly added assays in <i>HRAS</i> and <i>PIK3CA</i>.

<p>Cross-reactivity matrix for the newly added assays in <i>HRAS</i> and <i>PIK3CA</i>.</p

Gene expression correlations between matched primary and metastatic ER+ breast cancer tumor samples.

<p>(A) Gene expression correlations between 61 matched primary and metastatic tumor samples for 90 genes from the breast cancer gene expression assay. Each dot represents the mean fold change between primary and metastatic samples for a single gene. (B) Correlation plots of genes that showed a greater than 1.5 fold difference in expression between matched primary and metastatic samples (FDR-adjusted P<0.05). Each dot represents the fold change between primary and metastatic samples for a single patient. The solid diagonal line (y = x) and the dashed lines (y = x±1) are shown to highlight the magnitude of the absolute differences between x and y axes.</p