Summary of gene methylation and GC prognosis in the component studies.

1<p>The prognostic outcome was based on disease-free survival (DFS). The brackets displayed the p-value for studies that showed significance. NS: Not significant.</p

Genes differentially methylated in case-control studies of normal tissue, serum and plasma from gastric cancer and non-cancer subjects.

1<p>Odds ratio (OR) describes the likelihood of gene methylation observed in samples from gastric cancer compared to non-cancer subjects. Only genes in which there were significant differences in methylation between the two groups are displayed (<i>p</i><0.05). Genes for which there was no significant difference are displayed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036275#pone.0036275.s004" target="_blank">Table S2</a>.</p

Genes differentially methylated in case-control studies of tumour and normal gastric tissue from GC subjects.

1<p>Odds ratio (OR) describes the likelihood of gene methylation observed in tumour compared to normal gastric tissue. Only the genes for which there was a significant difference in methylation frequency between the two groups are displayed (p<0.05). Genes for which there was no significant difference are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036275#pone.0036275.s003" target="_blank">Table S1</a>.</p

Association of pre- and post-chemotherapy mutation patterns with clinicopathological features.

<p>^a Mutant→Mutant, Mutant→Wildtype, Wildtype→Mutant cases</p><p>^b Fisher’s exact test, two-sided <i>P</i> value</p><p>^c Two-sample t-test, two-sided <i>P</i> value</p><p>^d One WT→WT was not evaluable for overall response</p><p>^e<i>P</i> value from analysis of CR/PR vs SD</p><p>Association of pre- and post-chemotherapy mutation patterns with clinicopathological features.</p

Study cases according to mutation status in pre- and post-chemotherapy samples and their clinicopathological and tumor response characteristics (n = 40 pairs).

<p><b>Abbreviations:</b> C1, + = tumor response ≥25% after cycle 1 chemotherapy, C1,— = tumour response <25% after cycle 1 chemotherapy; CR, complete response; ER, estrogen receptor status; Met, Presence of metastasis; MT, mutant; NE, non evaluable (patient had already started on another line of treatment); ORR, overall response rate; PgR, progesterone receptor; PR, partial response; SD, stable disease; T3, >50mm in greatest dimension; T4, tumor of any size with direct extension to the chest wall and/or to the skin (ulceration or skin nodules); WT, wildtype; -, negative/no; +, positive/yes</p><p>^a Status of respective mutation in pre-chemotherapy sample</p><p>^b Status of respective mutation in post-chemotherapy sample</p><p>^c Arm A, randomized to receive doxorubicin in first cycle; Arm B, randomized to receive docetaxel in first cycle</p><p>^d Age in years</p><p>Study cases according to mutation status in pre- and post-chemotherapy samples and their clinicopathological and tumor response characteristics (n = 40 pairs).</p

Oncogenic mutations detected pre- and post-chemotherapy.

<p>Representative chromatograms of (A) <i>PIK3CA E542K</i> in a MT→MT case HOB045, (B) <i>EGFR S768I</i> in a MT→WT case HOB035, and (C) <i>MET Y1230C</i> detected in a WT→MT case HOB090. The expected positions for the unextended primer (UEP) and the nucleotide and mutation status (mutant [MT] or wildtype [WT]) based on the size of the extension products are indicated above the gray vertical dashed lines.</p