A) CNV map for OR loci based on high-resolution oligonucleotide tiling arrays. 851 ORs are ordered according to their location along the chromosomes, as indicated on the left; rows represent genes, columns are individuals; gains are shown in red, losses in blue and un-changed dosage in green (calls were made relative to the male reference individual NA19154). Note that the non-uniform genomic distribution of ORs results in an unbalanced representation of chromosomes in panel A. Also, note that ‘gains’ on chromosome X do not represent CNVs but refer to the expected male/female dosage difference. CNV calls are given for all 25 individuals (i.e. a self-vs.-self-replicate of NA19154 was included as a control; see Methods). Due to the resolution of the figure single CNVs may not be visible (all events are given in Table S2). Samples appear in the following order (1–25); NA10851, NA11997, NA12003, NA12004, NA12005, NA12006, NA12246, NA12248, NA12865, NA15510, NA18501, NA18502, NA18504, NA18505, NA18506, NA18508, NA18611, NA18856, NA18945, NA18946, NA18972, NA19103, NA19128, NA19141, NA19154. B) qPCR and microarray measurements of 122 OR loci for 13 individuals. The right panel represents qPCR results, and the left panel the corresponding microarray measurements (i.e. the measure R; see Methods). Sixty of the 122 ORs were tested in 13 individuals, thus only data for these samples is shown (for the full dataset, see Table S1). OR loci were sorted based on copy-number variability as assessed with our microarrays; the top 40 rows represent genes categorized as CNVs by microarrays; the lower part refers to loci not scored as a CNVs with the arrays, but scored as CNVs by qPCR (see Table 2). qPCR data was normalized relative to NA19154, and inverted (values multiplied with −1) to fit to the microarray scale. OR2BH1P and OR9G1 showed homozygous deletion in the reference individual, thus the qPCR values of these ORs were not normalized. Relative intensities are color coded, as indicated by the color scales. Homozygously deleted OR alleles are shown in the right panel in black. Samples appear in the following order; NA12003, NA12004, NA12005, NA12006, NA12246, NA12248, NA12865, NA18504, NA18508, NA18856, NA19103, NA19141, NA19154. C) qPCR-measurements and array (R) measures for the 56 most variable OR loci. The most variable OR loci were selected based on variance in qPCR results. Representation and sample order is as in panel B.

Variance in array measurements is indicated along OR loci, with loci arranged according to genomic coordinates. The variance of individual array measurements for each OR is plotted in grey. Array variance of ORs that were assayed by qPCR is color-coded; green: OR genes; red: OR pseudogenes. Black squares indicate ORs listed in Table 3; representative ORs from each cluster are indicated by red doted lines.

Red and blue dots indicate copy-number variable and non-variable ORs, respectively (copy-number variability is expressed in terms of the measure R, see Methods, which we found to correlate well with gene dosage). Percentage DNA sequence identity (“% identity”) to the closest paralog in the human genome is plotted versus the array-based (i.e., R-measure-based) variance. Correlation for ORs affected by CNVs is C = 0.26 (P_value = 10⁻⁵), whereas for non-variable ORs it is C = 0.15 (P_value = 10⁻⁴). Linear regression fits for each dataset are indicated with red and blue dashed lines, respectively.

A) Gains and losses of OR loci were called using our microarrays (see Methods). Gains are shown in blue; losses in orange; n is the number of total calls considered (24 samples multiplied by the number of genes in each category). OR loci with a one-to-one (“1-2-1”) ortholog in the chimpanzee genome are significantly (P_value<0.001; Mann-Whitney U test) less often affected by CNVs than loci lacking a 1-2-1 ortholog. B) Frequencies of CNV loci are given separately for intact OR genes and pseudogenes in each of the evolutionary classes. “Frequency”: relative frequency of being called a CNV for a set.

Plot depicting median normalized log₂-ratios of microarray intensities for OR loci affected by deletion I (chr11: 55127497–55238834), a bi-allelic CNV. Each individual is color-coded as indicated in the legend shown to the right. Black arrows indicate samples that consistently failed to produce results in the qPCR and standard PCR assays, indicating a potential homozygous deletion.