Correlation matrix and variability of the methylation levels measured at 1,320 CpG sites across the 63 samples included in the study.

<p>(A) Each individual sample is indicated by a black line on the axes. The methylation levels in the samples taken at remission during induction therapy at day 29 and during consolidation therapy at days 50 and 106 are highly correlated with the methylation levels in the non-leukemic samples (median Pearson's correlation coefficient (<i>R</i>) = 0.96), while the diagnostic ALL samples are less similar both to each other and to the samples taken after treatment, and to the non-leukemic samples (median <i>R</i> = 0.83). The scale for the correlation coefficients is shown to the right of the matrix. The red color indicates higher correlation (greater similarity), while the light yellow indicates less correlation (less similarity). (B) Histograms of the standard deviations (SD) for the methylation levels measured for 1,320 CpG sites across 20 ALL samples (blue) and across the combined 33 remission samples and 13 non-leukemic controls (red). SD bins are shown on the horizontal axis. The vertical bars show the proportion of observations in each SD bin. The CpG sites show greater variability in the ALL samples than in the remission samples and non-leukemic controls (Wilcoxon Rank-Sum P<0.001).</p

Clinical information for the 20 patients with acute lymphoblastic leukemia and 13 controls included in the study.

<p>BCP indicates B-cell precursor ALL; T-ALL, T-cell ALL; HeH, high hyperdiploidy; amp(21), amplification of chr 21; HR, high risk; SR, standard risk; IR, intermediate risk; NA, not available.</p>a<p>White blood cell count at diagnosis (10⁹/L).</p>b<p>The NOPHO ALL 2000 protocol was used.</p>c<p>DNA from was available from bone marrow taken from the patients on day 29,50, and/or 106 after the initiation of therapy, all patients were in morphological remission with less than 5% leukemic blasts.</p

Differential methylation in ALL cells.

<p>(A) Heatmap of the methylation profiles of the 28 CpG sites that are differentially methylated between the diagnostic ALL samples, bone marrow cells at remission and non-leukemic bone marrow cells. The ALL samples (orange) and bone marrow cells during remission (blue) form two distinct groups. Thirteen bone marrow cell samples from non-leukemic controls (purple) cluster among the samples collected during remission. The scale for the methylation β-values is shown below the heatmap. The elongated heights of the dendrogram branches between the ALL samples compared to the normal samples illustrate the increased variability in the ALL samples for the 28 CpG sites. Graphs showing the differences in methylation level between CpG sites in the (B) <i>WDR35</i> and (C) <i>FXYD2</i> genes at the time of diagnosis (left vertical axis) and during remission (right vertical axis). The data points for each paired sample are connected with a red line for B-cell precursor (BCP) samples and with a blue line for T-ALL samples. The corresponding CpG methylation levels in 13 non-leukemic control samples are shown as black horizontal lines to the right of the graphs. The CpG site at chr2:20,052,748 in the <i>WDR35</i> gene (B) was hypermethylated in diagnostic ALL samples and hypomethylated at remission and in non-leukemic controls, while the CpG site at chr11:7,203,745 in the <i>FXYD2</i> gene (C) displayed the opposite pattern. The BCP and T-ALL samples display the same pattern of methylation difference in these two genes.</p

Correlation between the methylation levels (β-values) of two CpG sites located in the <i>COL6A2</i>, <i>EYA4</i>, <i>FXYD2</i> and <i>MYO3A</i> genes.

<p>The Pearson's correlation coefficients (<i>R</i>) across the 20 acute lymphoblastic leukemia (ALL) samples taken at ALL diagnosis (green) and the 20 matched bone marrow samples taken at remission (blue) for the four genes are shown in panels A–D. The positions of the CpG sites for which the β-values are plotted are indicated on the axes in each panel (Human Genome Build 36). The inter-individual variation between the pairs of CpG sites in the remission cells is consistently lower than between the ALL cells, which speaks against the variation in ALL cells arising because of methodological factors.</p

Volcano plot of the AI data from 105 heterozygous cSNPs in 13 cell lines

<p><b>Copyright information:</b></p><p>Taken from "Allelic imbalance in gene expression as a guide to -acting regulatory single nucleotide polymorphisms in cancer cells"</p><p></p><p>Nucleic Acids Research 2007;35(5):e34-e34.</p><p>Published online 31 Jan 2007</p><p>PMCID:PMC1865061.</p><p>© 2007 The Author(s).</p> AI for each SNP was determined by calculating the fluorescence signal ratio between the two alleles (/) in RNA (cDNA) and genomic DNA for each heterozygous SNP. The level of AI obtained by dividing the signal ratio in RNA by the corresponding ratio in DNA is plotted on the horizontal axis. The -value for the difference between allelic ratios in RNA and DNA based on five replicate assays is plotted on the vertical axis. Spots above the horizontal dashed line represent the SNPs showing AI at a -value < 0.0001 that were selected for further analysis

Electrophoretic mobility shift assay images for the SNP alleles of the and genes

<p><b>Copyright information:</b></p><p>Taken from "Allelic imbalance in gene expression as a guide to -acting regulatory single nucleotide polymorphisms in cancer cells"</p><p></p><p>Nucleic Acids Research 2007;35(5):e34-e34.</p><p>Published online 31 Jan 2007</p><p>PMCID:PMC1865061.</p><p>© 2007 The Author(s).</p> Three lanes are shown for each SNP allele. From left to right these are: a control reaction with labeled probe only, a reaction containing both labeled probe and nuclear extract and a reaction where an unlabeled probe is added in excess as a competitor, in addition to the labeled probe and nuclear extract. For the and genes, the two lanes are shown: a reaction with labeled probe and nuclear extract and a reaction where the unlabeled competitor probe is added. The sequences of the allele-specific EMSA probes are given in

Recovery of genes and SNPs at the different stages of our process for screening for allelic imbalance

<p><b>Copyright information:</b></p><p>Taken from "Allelic imbalance in gene expression as a guide to -acting regulatory single nucleotide polymorphisms in cancer cells"</p><p></p><p>Nucleic Acids Research 2007;35(5):e34-e34.</p><p>Published online 31 Jan 2007</p><p>PMCID:PMC1865061.</p><p>© 2007 The Author(s).</p

CpGs’ distance from TSS.

<p>We measured CpGs’ distance from the transcription start site (TSS). a) Distance from TSS of all the CpGs on the methylation array. b) Distance from TSS of hypermethylated CpGs (dotted line) and distance from TSS of hypomethylated CpGs (continuous line). On the x-axis, the distance from TSS is measured in bp-s, and on the y-axis N represents the number of CpGs.</p

Survival curves of 10 differentially methylated CpG sites.

<p>We performed a survival test on each of the CpG sites. The methylation values are divided into 3 groups: low (0–0.25), medium (0.25–0.75) and high (0.75–1). As a result we found 10 CpG sites whose methylation level differs in different survival groups. The x-axis shows survival in years and the y-axis shows overall survival.</p

The concordance between microarray and qRT-PCR measurements.

<p>On the y-axis is shown average log2fold-change determined by Illumina array and qRT-PCR (8 sample pairs). Error bars indicate standard error of the mean (SEM).</p