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<h2>Registered Report: Melanoma genome sequencing reveals frequent <em>PREX2</em> mutations</h2> <p><br> <strong>Abstract:</strong></p> <p>The <a href="https://osf.io/e81xl/wiki/home/" rel="nofollow">Reproducibility Project: Cancer Biology</a> seeks to address growing concerns about reproducibility in scientific research by conducting replications of 50 papers in the field of cancer biology published between 2010 and 2012. This Registered Report describes the proposed replication plan of key experiments from ‘Melanoma genome sequencing reveals frequent <em>PREX2</em> mutations’ by Berger and colleagues, published in <em>Nature</em> in 2012 (<a href="http://www.nature.com/nature/journal/v485/n7399/full/nature11071.html" rel="nofollow">Berger et al., 2012</a>). The key experiments that will be replicated are those reported in Figure 3B and Supplementary Figure S6. In these experiments, Berger and colleagues show that somatic <em>PREX2</em> mutations identified through whole-genome sequencing of human melanoma can contribute to enhanced lethality of tumor xenografts in nude mice (Figure 3B, S6B, and S6C; <a href="http://www.nature.com/nature/journal/v485/n7399/full/nature11071.html" rel="nofollow">Berger et al., 2012</a>). The Reproducibility Project: Cancer Biology is a collaboration between the <a href="https://cos.io/" rel="nofollow">Center for Open Science</a> and <a href="https://www.scienceexchange.com/" rel="nofollow">Science Exchange</a>, and the results of the replications will be published by <a href="https://elifesciences.org/" rel="nofollow"><em>eLife</em></a>.</p> <hr> <h3>Contents</h3> <p>This component contains additional materials relating to the Registered Report for Study 44: Berger et al., 2012 (<em>Nature</em>).</p> <p>The published Registered Report can be found <a href="https://elifesciences.org/content/3/e04180" rel="nofollow">here</a>. </p> <p><strong>Registered Report Initial Draft</strong>:</p> <ul> <li>This document represents the first draft of the selected experimental protocols. It contains the information that the Core team, with help from scientist volunteers, was able to glean from the original publication and its supplemental materials before the original authors were contacted for their input.<ul> <li><a href="https://osf.io/57ug6/" rel="nofollow">Study 44 Registered Report initial draft</a></li> </ul> </li> </ul> <p><strong>Data Estimation</strong>:</p> <ul> <li>When original data was unable to be obtained, or original qualitative data was quantified (for example, Western blots), the estimated data is contained here. Examples include densitometric quantification of Western blot bands, or estimations of means and variances from published graphs.<ul> <li><a href="https://osf.io/yjsed/" rel="nofollow">Study 44 Figure 3B survival analysis.pzfx</a></li> </ul> </li> </ul> <p><strong>Power Calculations</strong>:</p> <ul> <li> <ul> <li>These documents contain details about how power calculations were performed, and include spreadsheets documenting statistical tests as well as any PRISM files, R scripts or additional materials used.</li> <li><a href="https://osf.io/cp5yq/" rel="nofollow">Study 44 Power Calculations</a></li> </ul> </li> </ul>
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