Scatterplot showing all 99 samples matched for <i>FCGR3B</i> CNV with PRT-REDVR, Sequenom and qPCR.

<p><b>A.</b> qPCR vs Sequenom. qPCR values represent raw copy number, Sequenom values represent absolute copy numbers, <b>B.</b> Sequenom vs qPCR. Both Sequenom and qPCR raw copy number values are presented, showing a low concordance rate between the two platforms, <b>C.</b> qPCR vs PRT-REDVR. qPCR values represent raw unrounded copy number, PRT-REDVR values represent absolute copy number; and <b>D.</b> Sequenom vs PRT-REDVR. Sequenom values represent raw unrounded copy numbers, PRT-REDVR values represent absolute copy number. The broader scater plots of qPCR signal intensity show wider variability of copy number calls, suggesting more copy number calls from qPCR were discordant with the Sequenom and PRT-REDVR. D exhibits a more clustered plot indicating higher agreement of CN calls between Sequenom and PRT.</p

Primer sequences and single nucleotide variation (SNV) identified for <i>FCGR3A/B</i> in Sequenom MassARRAY.

<p>Primer sequences and single nucleotide variation (SNV) identified for <i>FCGR3A/B</i> in Sequenom MassARRAY.</p

Positive control total <i>FCGR3</i> copy number estimates from repeat tests.

<p>The nine positive control DNA samples shown were repeated in every experiment and total <i>FCGR3</i> copy number calculated. Each point represents an individual copy number measurement (as indicated by the colour and number), plotted on the y-axis representing the quality score as a log probability of the copy number being an alternative to the copy number shown. The dotted line shows the quality score threshold of 0.05, with samples below this threshold being accepted. The lower the point on the y-axis, the more confident we are of the copy number. 190 tests are shown, with 183 being below the quality threshold. Of these 183, 2 show the incorrect copy number, both in C0081 calling a 6 instead of a 4.</p

Analysis of raw quantification data (logEC50) for Sequenom MassARRAY.

<p>Correlation between raw individual copy number calls from the probes designed at 5′-, 3’-, and centre regions of the genes <i>FCGR3A</i> (A, B, and C) and <i>FCGR3B</i> (D, E, and F). Note that there is a clear seperation of 2 cluster plots indicating batch effects, as circled, due to different experimental batches. <b>A</b>, <b>3’ vs 5′; B, 3’ vs centre;</b> and <b>C, 5′ vs centre</b>; <b>D</b>, <b>5′ vs 3’; E, 3’ vs centre;</b> and <b>F, 5′ vs centre.</b> A and D, correlation between the 5- and 3- prime probes were slightly affected, probably due to the probes distance.</p

Percentage of concordant results of <i>FCGR3B</i> CN calls between the three different assays.

<p>Percentage of concordant results of <i>FCGR3B</i> CN calls between the three different assays.</p

Analysis of raw copy number quantification data for PRT.

<p>Correlation between individual duplicated PRT copy number. Individual results from FAM-labelled (Y-axis) versus Hex-labelled (X-axis) representing internal replication of the assay, are plotted for 99 samples. Colour coded according to the integer copy number of each samples as estimated in REDVR.</p

Copy Number Data from Population genetics of immune-related multilocus copy number variation in Native Americans

Individual copy number dat

Tables S11 and S13 from Population genetics of immune-related multilocus copy number variation in Native Americans

Genotyping of 53 trios and Reference samples with known copy numbers from the European Collection of Cell Cultures

Distribution of raw unrounded copy number estimates of <i>FCGR3A</i>.

<p>A, Analysis was carried out using 160 samples genotyped with Sequenom. Unrounded copy number estimates are in bins of 0.1, with the count of each bin displayed on the y-axis. Blue indicates samples that were called as duplications, and red samples that were called as deletions. The red bars indicate copy number loss (CN<2); black bars indicate copy number normal (CN = 2); blue bars indicate copy number gain (CN>3). <b>B</b>, Distribution frequency of absolute copy number call for the samples genotyped with Sequenom MassARRAY and PRT-REDVR shows a higher rate of copy number normal (CN = 2) being called by Sequenom.</p

Supplementary Material from Population genetics of immune-related multilocus copy number variation in Native Americans

Supplementary material, including text, figures and tables