Pharmacogenetic testing affects choice of therapy among women considering tamoxifen treatment

Abstract Background Pharmacogenetic testing holds major promise in allowing physicians to tailor therapy to patients based on genotype. However, there is little data on the impact of pharmacogenetic test results on patient and clinician choice of therapy. CYP2D6 testing among tamoxifen users offers a potential test case of the use of pharmacogenetic testing in the clinic. We evaluated the effect of CYP2D6 testing in clinical practice to determine whether genotype results affected choice of hormone therapy in a prospective cohort study. Methods Women planning to take or currently taking tamoxifen were considered eligible. Participants were enrolled in an informational session that reviewed the results of studies of CYP2D6 genotype on breast cancer recurrence. CYP2D6 genotyping was offered to participants using the AmpliChip CYP450 Test. Women were classified as either poor, intermediate, extensive or ultra-rapid metabolizers. Results were provided to clinicians without specific treatment recommendations. Follow-up was performed with a structured phone interview 3 to 6 months after testing to evaluate changes in medication. Results A total of 245 women were tested and 235 completed the follow-up survey. Six of 13 (46%) women classified as poor metabolizers reported changing treatment compared with 11 of 218 (5%) classified as intermediate, extensive or ultra-rapid metabolizers (P < 0.001). There was no difference in treatment choices between women classified as intermediate and extensive metabolizers. In multi-variate models that adjusted for age, race/ethnicity, educational status, method of referral into the study, prior knowledge of CYP2D6 testing, the patients' CYP2D6 genotype was the only significant factor that predicted a change in therapy (odds ratio 22.8; 95% confidence interval 5.2 to 98.8). Genetic testing did not affect use of co-medications that interact with CYP2D6. Conclusions CYP2D6 genotype testing led to changes in therapy among poor metabolizers, even in the absence of definitive data that an alternative medicine improved outcomes. Pharmacogenetic testing can affect choice of therapy, even in the absence of definitive data on clinical impact

Analytical Validation of AmpliChip p53 Research Test for Archival Human Ovarian FFPE Sections

<div><p>The p53 tumor suppressor gene (<i>TP53</i>) is reported to be mutated in nearly half of all tumors and plays a central role in genome integrity. Detection of mutations in p53 can be accomplished by many assays, including the AmpliChip p53 Research Test. The AmpliChip p53 Research Test has been successfully used to determine p53 status in hematologic malignancies and fresh frozen solid tissues but there are few reports of using the assay with formalin fixed, paraffin-embedded (FFPE) tissue. The objective of this study was to describe analytical performance characterization of the AmpliChip p53 Research Test to detect p53 mutations in genomic DNA isolated from archival FFPE human ovarian tumor tissues. Method correlation with sequencing showed 96% mutation-wise agreement and 99% chip-wise agreement. We furthermore observed 100% agreement (113/113) of the most prevalent TP53 mutations. Workflow reproducibility was 96.8% across 8 samples, with 2 operators, 2 reagent lots and 2 instruments. Section-to-section reproducibility was 100% for each sample across a 60 μm region of the FFPE block from ovarian tumors. These data indicate that the AmpliChip p53 Research Test is an accurate and reproducible method for detecting mutations in <i>TP53</i> from archival FFPE human ovarian specimens.</p></div

The 32 mutations called by both Sanger and the AmpliChip p53 Research Test (Cohort 2).

<p>The 32 mutations called by both Sanger and the AmpliChip p53 Research Test (Cohort 2).</p

Samples obtained and tested in the prevalent mutation study.

<p>Samples obtained and tested in the prevalent mutation study.</p

Summary of section-to-section reproducibility

<p>Summary of section-to-section reproducibility</p

Accuracy of detection of the top six prevalent mutations by the AmpliChip p53 Research Test.

<p>Samples are those from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0131497#pone.0131497.t009" target="_blank">Table 9</a>, tested in triplicate.</p

Discrepant resolution of mutations called by Sanger only (Cohort 2).

<p>Discrepant resolution of mutations called by Sanger only (Cohort 2).</p

Analytical reproducibility of AmpliChip p53 Research Test mutation calls.

<p>Analytical reproducibility of AmpliChip p53 Research Test mutation calls.</p

Discrepant resolution of the 4 mutations called only by the AmpliChip p53 Research Test (Cohort 1)

<p>Discrepant resolution of the 4 mutations called only by the AmpliChip p53 Research Test (Cohort 1)</p

Cohort 2 samples and exon failures for the AmpliChip p53 Research Test and Sanger sequencing.

<p>Cohort 2 samples and exon failures for the AmpliChip p53 Research Test and Sanger sequencing.</p