Schematic diagram of genomic and transcriptional analyses.

<p>(<b>A</b>) Genomic analyses. (<b>B</b>) Transcriptional analyses. Individual cohorts are portrayed.</p

Copy number alterations and tumor ploidy in EGFR/KRAS mutation groups.

<p>(<b>A</b>) Pattern of gross copy number alterations measured as fraction of the genome altered by copy number gain or loss in adenocarcinoma tumors stratified by <i>EGFR</i> and <i>KRAS</i> mutation status (EGFR:red, KRAS:light blue, EGFRwt/KRASwt:gray), stage, gender and patient smoking status. Copy number alterations were called using log₂ratio ± 0.12 as thresholds for identification of copy number gain and loss. P-values were calculated using ANOVA for indicated groups, ***: P< 0.001, **: P< 0.01, *: P< 0.05. Top axis indicates number of cases per group. (<b>B</b>) mGISTIC regions discriminating between <i>EGFR</i>-mutated (red), <i>KRAS</i>-mutated (light blue) and EGFRwt/KRASwt (gray) adenocarcinoma tumors. mGISTIC regions identified by Fisher’s exact test (Bonferroni adjusted p-value < 0.05) with an additional requirement of > 20% frequency difference between the lowest and highest groups. The y-axis describes the frequency of copy number gain or loss in respective group. (<b>C</b>) Distribution of GAP-ploidy across the adenocarcinoma EGFR/KRAS mutation groups for 141 tumors analyzed by GAP. A GAP-ploidy of two equals a diploid, three a triploid genome and four a tetraploid genome. Curves were generated by an Epanechnikov smoothing kernel with 0.1 smoothing bandwidth. </p

Patient characteristics.

<p>Patient characteristics.</p

Frequency of positive tumor markers and median and IQR for each tumor marker.

<p>Frequency of positive tumor markers and median and IQR for each tumor marker.</p

Multivariable cox regression for disease-free survival.

<p>Multivariable cox regression for disease-free survival.</p

Disease-free survival for cases with none or one positive tumor marker vs cases with two or more positive tumor markers at time of diagnosis.

<p>(A) All tumor markers included. Log rank test p< 0.001. (B) NSE excluded. Log rank test p<0.001.</p

Disease-free survival according to number of elevated tumor markers.

<p>(A) All tumor markers included. Log rank trend test p = 0.003 (B) NSE excluded. Log rank trend test p = 0.001.</p

Frequency of patients with 0–5 elevated tumor markers and 0–4 elevated tumor markers (NSE excluded).

<p>Frequency of patients with 0–5 elevated tumor markers and 0–4 elevated tumor markers (NSE excluded).</p

Additional file 1: of Epigenetic modifications in KDM lysine demethylases associate with survival of early-stage NSCLC

Figure S1. Quality control processes for DNA methylation chip data. Quality control measures and exclusion criteria as applied to Harvard, Spain, Norway, Sweden, and The Cancer Genome Atlas (TCGA) sample cohorts. (PDF 642 kb

Additional file 2: of Epigenetic modifications in KDM lysine demethylases associate with survival of early-stage NSCLC

Table S1. Annotation of CpG sites in KDM gene family. (PDF 677 kb