Histograms of raw unrounded copy number estimates.

<p>The raw unrounded copy number estimates for all 576 samples analysed. Unrounded copy number estimates are in bins of 0.1, with the count of each bin displayed on the y-axis: a) from QPCR assay, b) from PPRT assay, and c) from triplex PRT assay.</p

Scatterplots showing reproducibility of positive controls between different experiments.

<p>These figures plot known copy number from control samples against actual raw copy number values, for each experiment. Note that all five populations are not represented: several experiments tested samples from more than one population, which was an additional control against systematic bias. The legend on the graphs indicates the population from which the majority of samples in that particular experiment derived. a) QPCR assay, b) PPRT assay, c) Triplex PRT assay.</p

Beta-defensin copy number distributions in different populations.

<p>Beta-defensin copy number, as determined by triplex PRT, are shown for the five populations studied, as counts and as a percentage.</p

Percentage of discordant results between the three different methods.

<p>Pairwise discordance rates are shown, for a first-pass test of all 576 samples.</p

Illustration of the PPRT assay.

<p><b>A.</b> Primer design and sequence of region test and reference regions. The sequence shows several differences between chromosome 8 (test) and chromosome 21 (reference). The red arrow show the variable position used to distinguish test from reference amplicon sequences, and quantified by PPRT. F: forward primer, R: reverse primer, and S: sequencing primer. <b>B.</b> Pyrograms from PPRT testing of samples with 3 and 4 beta-defensin copies. Two variable sites are highlighted in yellow. The second variable site (corresponding to the site highlighted with the red arrow in Figure 1a), with the percentage of each allele shown, gave reproducible values and used for quantification. For the top pyrogram, the ratio of the C variant (representing the test amplicon) to the T variant (representing the reference amplicon) is 1.5∶1, indicating a diploid copy number of three for the test sequence. For the bottom pyrogram, the ratio is 2∶1, indicating a diploid copy number of four.</p

Populations analysed and DNA source information.

<p>Populations analysed and DNA source information.</p

Histograms of raw unrounded copy number estimates comparing results from poor and good quality DNA.

<p>The raw unrounded copy number estimates for all 576 samples analysed. Unrounded copy number estimates are in bins of 0.1, with the count of each bin displayed on the y-axis. Results from the good quality DNA cohorts (UK, Danish, Czech) are shown in grey, results from the poor quality DNA cohorts (Portuguese, Ghanaian) are shown in black. a) From QPCR assay, b) from PPRT assay, c) from triplex PRT assay.</p

Bland-Altman plots showing differences in copy number estimation between methods.

<p>a) Triplex PRT minus QPCR, b) Triplex PRT minus PPRT, c) Triplex PRT minus QPCR, good quality DNA only.</p

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

Individual copy number dat

Tables S8 and S9 from Population genetics of immune-related multilocus copy number variation in Native Americans

Diploid copy number distributions of DEFB and FCGR3B loci for worldwide populations (Human Genome Diversity Project panel) and allele frequencies and fCNV inferred using CoNVEM (A) and CNVice (B)