The leave-one-out cross-validation results for each model in the qpure method.

<p>In the second column the number in the brackets is the pre-defined number of components. The smaller prediction error is related a better prediction model.</p

Design of mixing experiments.

<p>Design of mixing experiments.</p

Overview of the qpure method.

<p>Circos plots of the SNP array data for a paired normal (ND) and tumor (TD) sample showing regions of LOH in the tumor sample (A). The chromosome ideograms are shown on the outer wheel, the logR and BAF values are plotted in the middle and inner wheel respectively. The density plot of the probes in LOH regions (B) is used to calculate the d-score (C). The d-score is compared to the density plots of probes within regions of LOH for the cell line: normal DNA mixtures which represent different cellularity (D). The d-score and cellularity are highly correlated (E). Three plots from the left to the right are the scatter plot only, with fitting the simple linear model and with fitting the spline regression model respectively.</p

Somatic Point Mutation Calling in Low Cellularity Tumors

<div><p>Somatic mutation calling from next-generation sequencing data remains a challenge due to the difficulties of distinguishing true somatic events from artifacts arising from PCR, sequencing errors or mis-mapping. Tumor cellularity or purity, sub-clonality and copy number changes also confound the identification of true somatic events against a background of germline variants. We have developed a heuristic strategy and software (<a href="http://www.qcmg.org/bioinformatics/qsnp/" target="_blank">http://www.qcmg.org/bioinformatics/qsnp/</a>) for somatic mutation calling in samples with low tumor content and we show the superior sensitivity and precision of our approach using a previously sequenced cell line, a series of tumor/normal admixtures, and 3,253 putative somatic SNVs verified on an orthogonal platform.</p></div

Details of verification using amplicon-based sequencing on the Ion Torrent.

<p>Details of verification using amplicon-based sequencing on the Ion Torrent.</p

ELF5 specifies breast cancer subtype.

<p>(A) Sub network of breast cancer subtype gene sets derived from forced ELF5 expression in MCF7 luminal breast cancer cells (inner node color) and knockdown of ELF5 expression in HCC1937 basal breast cancer cells. Node size is proportional to gene set size; thicker green lines indicate greater gene set overlap. Nodes are positioned according to similarity in gene sets. Labels in bold type indicate the functional significance of the four clusters generated, label is plain type is the gene set name. The full network is shown in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001461#pbio.1001461.s016" target="_blank">Figure S16</a>. (B–D) expression signature analysis of the ELF5-induced changes in molecular subtype produced by ELF5 knockdown in HCC1937 cells (B), or forced ELF5 expression in MCF7 cells (C), or T47D cells (D). Bars show the indicated comparisons that produce the associated <i>p</i>-values. BS, borderline significance; NS, not significant.</p

ELF5 suppresses the estrogen-sensitive phenotype.

<p>(A) Western blot showing reduced expression of key genes involved in the response to estrogens following induction of ELF5 expression. (B) Reduced transcriptional activity of reporters of <i>ER</i> and <i>FOXA1</i> (<i>UGT2B17</i> promoter) transcriptional activity following induction of ELF5 in MCF7 cells. Black bars, -DOX, grey bars +DOX 72 h for <i>ERE</i> and 24 h and 48 h for <i>FOXA1</i>. (C) Cell accumulation in MCF7-V5 cell cultures with (+E) or without (−E) 10 nM estrogen treatment, or following expression of ER (+ER) and 10 nM E in the context of induced ELF5. Black bars, -DOX; grey bars +DOX, 72 h and 144 h, respectively. (D) interaction of ELF5-regulated gene sets with estrogen-regulated gene sets. <i>p</i>-Values and odds ratios derived from hypergeometric tests. Number of genes in brackets. (E) Enrichment of gene sets in ELF5 ChIP targets either down (Dn) or Up in response to forced ELF5-V5 expression in T47D cells with DOX. P-Values for hypergeometric tests from GSEA (upper case) or Oncomine (lower case).</p

Overlap in somatic mutation calls.

<p>Verified somatic mutation calls were compared across three callers in 5 different tumor purity mixtures. Values are number of calls in 100%, 80%, 60%, 40% and 20% tumor content mixture, from top to bottom.</p

Elf5 modulates the adhesion of breast cancer cells.

<p>(A) Quantification of detached cells in cultures treated with DOX (+D) compared to no induction (−D). (B) Ability of DOX-treated cells to replate 4 h after trypsin destruction of attachment proteins, compared to untreated cells. Data are expressed as a percentage of replated untreated cells. (C) Proportion of apoptotic cells in DOX treated (grey bars) compared to untreated (black bars) T47D-ELF5-V5 cells, measured by flow cytometry using the M30 antibody. (D) Expression and activation of key cell adhesion proteins following DOX induction of ELF5-V5 expression.</p

Variant calling software tools.

<p>Variant calling software tools.</p