GenotypeDataReplicate18Chrom21

R rda file containing the genotype matrix for 201 individuals and 21204 SNPs on chromosome 2

Illustration of marker-level testing.

<p><i>Top:</i> Marker-level tests at three markers for the gemcitabine study. The phenotype (IC50, a continuous outcome described in “Gemcitabine pharmacogenomic study”) is plotted as a function of LRR, along with the regression line. The -values for the three -tests are, respectively, from left to right. 0.25, 0.0008, and 0.0008, respectively, from left to right. <i>Bottom:</i> Plot of from the marker-level tests as a function of position along the chromosome. The three tests from the top part of the figure are plotted in red.</p

Power as a function of method and CNV size.

<p>The CNV-level testing approach uses a false positive CNV call rate of 0.01; the marker-level approach uses the probit transformation. The lower dashed line represents the type I error rate, while the upper dashed line represents the “oracle” power that would be possible if the true CNV status were known, with no measurement error.</p

Plot of from Gemcitabine marker-level tests as a function of position along the chromosome.

<p>The shaded region denotes a region of significant elevation, as detected by the methods described in “Marker-level testing”. The top of the plot contains annotations describing the results of the CNV-level analysis in three distinct regions. is the mean adjusted IC50 for cell lines with a called CNV in that region; is the mean adjusted IC50 for cell lines without a called CNV in that region.</p

Effect of CNV-calling threshold () on the power to detect a CNV.

<p>Continuous outcome, 10,000 replications per cell, CNV size = 30 markers).</p

Example of LRR data for a simulated CNV.

<p><i>Left:</i> The noise, randomly drawn from among the observed measurement errors for a single subject. <i>Middle:</i> The spiked-in signal. <i>Right:</i> The resulting simulated data, which looks qualitatively similar to the real CNV in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0034262#pone-0034262-g001" target="_blank">Figure 1</a>.</p

Example of LRR data for a putative CNV on Chromosome 3 for a cell line in the gemcitabine study.

<p>The gray region denotes the estimated boundary of the CNV. The points in the gray region have a mean LRR of −0.98; the surrounding points have a mean of −0.11.</p

Pathway results for Danish sister pairs (n = 93); showing only genes related to the Discovery findings.

<p>Pathway results for Danish sister pairs (n = 93); showing only genes related to the Discovery findings.</p

Most significant pathway results for Finnish mothers with recurrent SPTB (n = 10).

<p>Most significant pathway results for Finnish mothers with recurrent SPTB (n = 10).</p

HSPA1L and GR protein levels in decidualized human endometrial stromal fibroblasts.

<p>Cultured ESFs were transfected with WT or Ala268Thr <i>HSPA1L</i>-pcDNA3.1 constructs or with empty pcDNA3.1 vector (control). Cells were treated with decidualization media supplemented with 100nM dexamethasone (glucocorticoids) for 72h. Both cytosolic and nuclear protein were extracted, and HSPA1L and GR protein levels were measured by Western blot. Band intensity of HSPA1L or GR was normalized to band intensity of the corresponding β-actin. Cytosolic (A) and nuclear (B) HSPA1L levels as well as cytosolic (C) and nuclear (D) GR levels are shown for control (empty vector), WT and Ala268Thr sample groups. Each experiment was performed as triplicates in three different passages (n = 9 each group, except n = 8 for nuclear control group) and bars represent mean + SEM. Significant p-value <0.05 is presented with an asterisk. Cytosolic GR levels were significantly higher (p = 0.04) in the WT compared to the Ala268Thr group as well as in the WT compared to the control group (p = 0.04).</p