Results of EQA for PCR.

<p><a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002011#pntd-0002011-t005" target="_blank">Table 5</a> shows results of external quality assurance for PCR. During the initial phase (phase I) PCR samples were analyzed at DITM by IS<i>2404</i> standard PCR and IS<i>2404</i> quantitative real-time PCR (qPCR). During the transitional phase (phase II) diagnostic sample pairs where analyzed in parallel at INH (IS<i>2404</i> dry-reagent-based [DRB] PCR) and DITM as described for phase I. Positivity rates and case confirmation rates are provided for IS<i>2404</i> DRB- and standard PCR, and additional diagnostic yields were calculated for IS<i>2404</i> qPCR. N/A, not applicable.</p>a<p>Swab samples, DNA extract were prepared from swab samples.</p>b<p>FNA samples, DNA extract were prepared from fine-needle aspirate samples.</p>c<p>Punch samples, DNA extract were prepared from 3-mm punch biopsy samples.</p>d<p>Total per phase and laboratory.</p>e<p>INH applied IS<i>2404</i>-DRB-PCR. <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002011#pntd.0002011-Siegmund1" target="_blank">[21]</a></p>f<p>DITM applied standard, gel-based, IS<i>2404</i> PCR <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002011#pntd.0002011-Stinear1" target="_blank">[17]</a> and IS<i>2404</i> qPCR <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002011#pntd.0002011-Fyfe1" target="_blank">[27]</a>, <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002011#pntd.0002011-World7" target="_blank">[42]</a> on all DNA extracts tested negative with standard PCR. For qPCR the additional diagnostic yield (i.e. the deviation of total final result from total result of standard PCR) were 5.7% (phase I) and 6.1% (phase II).</p>g<p>Final result of standard PCR and qPCR.</p>h<p>Phase I, initial phase of implementation of the national reference laboratory at INH from September through December 2010.</p>i<p>Positivity rate, number of positive samples divided by the total number of samples tested.</p>j<p>Case confirmation rate, number of laboratory confirmed BUD patients divided by the total number of suspected BUD cases.</p>k<p>Rate of false negative results at INH as determined by re-testing of DNA extracts at DITM by standard PCR.</p>l<p>Rate of concordant results from sample pairs at INH and DITM.</p>m<p>Phase II, transitional phase of implementation of the national reference laboratory at INH from January 2011 through April 2012.</p>n<p>Total results of the initial and the transitional phase.