Case study 3: Ovarian tumors treated with platinum-based chemotherapy.

<p>Biasograms represent 119 tumors, with <i>Y</i> indicating the outcome vector (tumor response), and <i>B</i> indicating the bias vector defined as a binary indicator of microarray batch, as A) 2002-09-20 vs. all other dates, or B) 2002-10-23 vs. all other dates.</p

Case study 2: Breast tumors treated with neoadjuvant paclitaxel, fluorouracil, doxorubicin, and cyclophosphamide.

<p>A) Biasogram representing the training cohort of 133 tumors. B) Biasogram representing the independent validation cohort of 100 tumors. In both biasograms, <i>Y</i> indicates the outcome vector (tumor response), <i>B</i> indicates the bias vector (fraction of present calls), and the colorgram indicates a bivariate histogram of 22,283 expression values. The green open or filled circles indicate probe sets in the DLDA30 signature, with the filled circles indicating probes that, when omitted, improved the predictor's performance. C) Chart indicating area under the curve (AUC) in the validation cohort for predictors derived with the indicated number of bias-correlated probe sets omitted.</p

Case study 1: 26 breast tumors treated with neoadjuvant docetaxel.

<p>A) Tumor response is correlated with the fraction of present calls. B) Biasogram with a heatmap representing all 12,625 probe sets, and the 92 putatively discriminatory genes indicated in green. C) Biasogram displaying only the 1191 probe sets with variance above 2. In the biasograms, <i>Y</i> indicates the outcome vector (tumor response), <i>B</i> indicates the bias vector (fraction of present calls), the colorgram indicates a bivariate histogram of expression values, and the green circles indicate probe sets identified in the original study. The arrow indicates CYBA, the only gene that was validated in a second patient cohort.</p

Interpretation of the “biasogram”.

<p>The biasogram is an orthogonal projection of a gene expression matrix onto a plane defined by previously defined vectors quantifying an outcome <i>Y</i> and bias <i>B</i> for each patient. Each point represents a gene, or probe set. <i>Y</i> and <i>B</i> define axes for a skew coordinate system in which the position of each point indicates its Pearson correlation coefficient with <i>Y</i> and <i>B</i>, respectively. The angle between <i>Y</i> and <i>B</i> represents the correlation between <i>Y</i> and <i>B</i>. For the sake of explanation, only a single gene is represented in this figure. In general, a biasogram for many thousands of genes can be represented by a heatmap rather than by individual points. PCC, Pearson correlation coefficient.</p

Additional file 1: Figure S1A. of A robust prognostic gene expression signature for early stage lung adenocarcinoma

TCGA LUAD RNAseq − stage I and II ESLA − 7, DFS. Figure S1B: TCGA LUAD RNAseq − stage I and II ESLA − 7, DFS − no treatment. Figure S1C: TCGA LUAD RNAseq − stage I and II CIN25, DFS. Figure S1D: TCGA LUAD RNAseq − stage I and II CIN25, DFS − no treatment. Figure S1E: TCGA LUAD RNAseq − stage I and II CCP, DFS. Figure S1F: TCGA LUAD RNAseq − stage I and II CCP, DFS − no treatment. (PDF 20 kb

Additional file 3: of A robust prognostic gene expression signature for early stage lung adenocarcinoma

TCGA LUSC clinical data. (TXT 124 kb

Additional file 3: of TumorTracer: a method to identify the tissue of origin from the somatic mutations of a tumor specimen

Table comparing TumorTracer to ICOMS. (DOCX 14 kb

Additional file 1: of TumorTracer: a method to identify the tissue of origin from the somatic mutations of a tumor specimen

Contains Supplementary Figs. 1–3. (PDF 547 kb