Additional file 2: of INDELseek: detection of complex insertions and deletions from next-generation sequencing data

Figures S1-S14. Complex indels detected in samples 1–14 and orthogonal validation. (PDF 1637 kb

Additional file 1: Table S1. of A three-miRNA signature as promising non-invasive diagnostic marker for gastric cancer

Downregulated miRNAs associated with gastric cancer at a cut-off value of 2-fold difference. (DOCX 16 kb

Extracted from MDA231 breast cancer cells, breast tumor sample with nuclear staining of hRad9 (A) and a control tumor sample with no nuclear staining (B)

The relative position for molecular weights (in KDa) are indicated on the right. Protein extracts were treated with λ phosphatase (100 and 500 units respectively).<p><b>Copyright information:</b></p><p>Taken from "Localization of hRad9 in breast cancer"</p><p>http://www.biomedcentral.com/1471-2407/8/196</p><p>BMC Cancer 2008;8():196-196.</p><p>Published online 11 Jul 2008</p><p>PMCID:PMC2483722.</p><p></p

SLC19A3 is frequently down-regulated through promoter hypermethylation in breast cancer.

<p>(A) Fold change relationship between SLC19A3 mRNA expression and methylation percentage in those 15 breast cancer patients (mean ± SD). (B) Correlation analysis of the fold changes between SLC19A3 mRNA expression and methylation percentage (Spearman rank correlation, R² = −0.77, <i>P</i><0.0005).</p

Increased percentage of SLC19A3 DNA methylation in primary breast cancer tissues.

<p>Percentage of SLC19A3 promoter methylation between tumor tissues and their paired adjacent non-tumor breast tissues from the 15 breast cancer patients by MS-qPCR. Percentage of methylation in tissue samples was calculated by the following equation: % meth = 100/[1+2^{ΔCt(meth-unmeth)}]%. ΔCt_{(meth-unmeth)} was calculated by subtracting the Ct values of methylated SLC19A3 signal from the Ct values of umnethylated SLC19A3 signal. Statistical difference was analyzed by Wilcoxon test, <i>P</i><0.005.</p

Patient characteristics.

<p>*DCIS, Ductal carcinoma in situ.</p

Down-regulated SLC19A3 gene expression in primary breast cancer tissues.

<p>Relative SLC19A3 mRNA expression between tumor tissues and their paired adjacent non-tumor breast from breast cancer patients (n = 15) by real-time qPCR. Expression of SLC19A3 mRNA (Log₁₀ scale at Y-axis) was normalized to GAPDH. The lines inside the boxes denote the medians. The boxes mark the interval between the 25^th and 75^th percentiles. The whiskers denote the interval between the 10^th and 90^th percentiles. Statistical difference was analyzed by Wilcoxon test, <i>P</i><0.005.</p

Plasma methylated SLC19A3 DNA levels across tumor stages from both Phase I and II validation.

<p>(A) Box plot of plasma methylated SLC19A3 DNA level in 80 NC, 27 ductal carcinoma in situ (DCIS) plus 71 BC patients across various TNM stages. (B) Box plot of plasma methylated SLC19A3 DNA level in 80 NC and 65 GC patients across various TNM stages. The box represents the interquartile range and the line across the box indicates the median value. Relative plasma level of methylated SLC19A3 DNA is expressed as 2^{−ΔCt(Dig-Undig)}. ΔCt_(Dig-Undig) is calculated by subtracting the Ct values of digested plasma DNA from the Ct values of undigested plasma DNA. Statistically significant differences were determined using Mann-Whitney tests.</p

The receiver operating characteristics (ROC) curve for plasma methylated SLC19A3 DNA in the Phase II blinded validation (n = 78).

<p>(A) Area under curve (AUC) value was 89%. At cutoff value of 0.41, sensitivity was 87% and specificity was 85% in discriminating 39 breast cancer patients from 20 control subjects. (B) Area under curve (AUC) value was 82%. At cutoff value of 0.41, sensitivity was 85% and specificity was 85% in discriminating 20 gastric cancer patients from 20 control subjects.</p

Quantitative analysis of plasma methylated SLC19A3 DNA on a group (n = 165) of plasma samples by MSRED-qPCR.

<p>Scatter plots of plasma levels of methylated SLC19A3 DNA in 60 healthy normal subjects, 45 gastric cancer (GC) and 60 breast cancer (BC) patients. Plasma level of methylated SLC19A3 DNA is expressed as 2^{ΔCt(undigest-digest)}. ΔCt_{(undigest-digest)} is calculated by subtracting the Ct values of digested plasma DNA from the Ct values of undigested plasma DNA. Since Ct of undigest should be ≤Ct of digest, the expression level is ranging from 1 to 0. The horizontal black lines denote the means. The blue errors bars denote the ± standard deviations (SD). Statistically significant differences were determined using Mann-Whitney <i>U</i> tests, <i>P</i><0.0001.</p