Student attitudes toward personal genome testing.

a<p>For yes/no questions, the number (and percentage) of subjects responding yes is reported. For Likert items, the number (and percentage) of subjects who agreed or strongly agreed with the statement is reported.</p>b<p>McNemar's test for binary response questions and Wilcoxon signed-rank test for Likert-scale items comparing pre- to post-course responses.</p>c<p>Fisher's exact test for binary response questions and Mann-Whitney <i>U</i>-test for Likert-scale items comparing post-course responses between genotyped and non-genotyped groups.</p

Student scores assessing knowledge of genomics.

<p>Knowledge scores of non-genotyped students on the post-course survey compared to the pre-course survey improved by an average of 1% (46% to 47%), while genotyped students demonstrated an average 31% improvement (38% to 69%). Bar graphs show mean (±S.D.) percentage score on knowledge questions.</p

Student perceptions of knowledge about genetics and personal genome testing.

a<p>The number (and percentage) of subjects who agreed or strongly agreed with each statement is reported.</p>b<p>Wilcoxon signed-rank test comparing pre- to post-course responses.</p>c<p>Mann-Whitney <i>U</i>-test comparing post-course responses between genotyped and non-genotyped groups.</p

Student reflection on genotyping offer and experience.

a<p>The number (and percentage) of subjects who agreed or strongly agreed with each statement is reported.</p>b<p>Mann-Whitney <i>U</i>-test comparing post-course responses between genotyped and non-genotyped groups.</p

Analysis of PSA recurrence-free survival.

a<p>Log rank test (univariate analysis) or Wald test (multivariate analysis).</p>b<p>Analyzed as a continuous variable.</p>c<p>Stratification based on limited representation of Gleason 6 and 4+4 cases.</p>d<p>Stratifies pathologic stage based on organ confinement.</p

Incorporation of proliferation index improves prognostic value.

<p>(<b>A</b>) Kaplan-Meier analysis comparing multivariate models based on clinicopathologic data (<i>left</i>) and clinicopathologic data plus the tri-marker proliferation index (<i>right</i>). Cases are grouped by tertile. Log-rank test <i>P</i>-values are indicated. (<b>B</b>) ROC curve analysis comparing multivariate models based on clinicopathologic data (<i>left</i>) and clinicopathologic data plus the tri-marker proliferation index (<i>right</i>). Analysis done at 8 years follow-up (the median follow-up time for the cohort). Areas under the curve (AUC) are indicated.</p

Clinicopathological characteristics of tissue microarray cases.

a<p>Determined from pathology report (not tissue microarray core).</p

Immunostaining of Ki-67, TOP2A and E2F1 are prognostic.

<p>(<b>A</b>) Immunostaining of proliferation markers Ki-67, TOP2A and E2F1; representative positive and negative cases shown. (<b>B</b>) Pairwise comparison of immunostain scores across cases. Pearson correlation (R) values shown. (<b>C</b>) Kaplan-Meier analysis of Ki-67 (<5% <i>vs.</i> ≥5% tumor nuclei), TOP2A (<5% <i>vs.</i> ≥5% tumor nuclei) and E2F1 (<50% <i>vs.</i> ≥50% tumor nuclei) immunostaining. <i>P</i>-values (log-rank test) shown. (<b>D</b>) Kaplan-Meier analysis of combined marker staining (see keys). <i>P</i>-values (log-rank test) shown.</p

Receiver-operating characteristic (ROC) curve analysis.

a<p>Evaluated at 8 years follow-up (the median follow-up time).</p>b<p>Analyzed as a continuous variable.</p>c<p>Stratification based on limited representation of Gleason 6 and 4+4 cases.</p>d<p>Stratifies pathologic stage based on organ confinement.</p

A proliferation signature cluster in prostate cancer.

<p>(<b>A</b>) Unsupervised cluster analysis of prostate cancers (data set from ref. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020293#pone.0020293-Lapointe1" target="_blank">[19]</a>) reveals molecular subtypes of prostate cancer (1, 2 and 3, labeled), and gene-expression features reflecting underlying biological processes. <i>Left</i>, thumbnail heatmap of the cluster analysis. <i>Right</i>, enlarged view of the “proliferation cluster”, with selected genes shown (<i>MKI67</i>, <i>TOP2A</i> and <i>E2F1</i> in red text, marked by arrow). Red and green expression levels reflect high and low values, respectively (see key). Red filled circles (<i>below</i>) identify lymph node metastases. (<b>B</b>) Overlap matrix of proliferation cluster genes (N = 94) with canonical pathway (CP) gene sets identifies top gene set matches (all significant, <i>P</i><0.001) all relating to cell-cycle/proliferation. Solid blue fill indicates overlapping membership between proliferation cluster and queried gene sets.</p