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High-resolution copy-number variation map reflects human olfactory receptor diversity and evolution.

Hasin Y, Olender T, Khen M, Gonzaga-Jauregui C, Kim PM, Urban AE, Snyder M, Gerstein MB, Lancet D, Korbel JO - PLoS Genet. (2008)

Bottom Line: Furthermore, our results show an enrichment of CNVs among ORs with a close human paralog or lacking a one-to-one ortholog in chimpanzee.Quantitative PCR experiments performed for 122 sampled ORs agreed well with the microarray results and uncovered 23 additional CNVs.Comparison to the chimpanzee reference genome revealed that all of the deletion alleles are human derived, therefore indicating a profound effect of human-specific deletions on the individual OR gene content.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.

ABSTRACT
Olfactory receptors (ORs), which are involved in odorant recognition, form the largest mammalian protein superfamily. The genomic content of OR genes is considerably reduced in humans, as reflected by the relatively small repertoire size and the high fraction ( approximately 55%) of human pseudogenes. Since several recent low-resolution surveys suggested that OR genomic loci are frequently affected by copy-number variants (CNVs), we hypothesized that CNVs may play an important role in the evolution of the human olfactory repertoire. We used high-resolution oligonucleotide tiling microarrays to detect CNVs across 851 OR gene and pseudogene loci. Examining genomic DNA from 25 individuals with ancestry from three populations, we identified 93 OR gene loci and 151 pseudogene loci affected by CNVs, generating a mosaic of OR dosages across persons. Our data suggest that approximately 50% of the CNVs involve more than one OR, with the largest CNV spanning 11 loci. In contrast to earlier reports, we observe that CNVs are more frequent among OR pseudogenes than among intact genes, presumably due to both selective constraints and CNV formation biases. Furthermore, our results show an enrichment of CNVs among ORs with a close human paralog or lacking a one-to-one ortholog in chimpanzee. Interestingly, among the latter we observed an enrichment in CNV losses over gains, a finding potentially related to the known diminution of the human OR repertoire. Quantitative PCR experiments performed for 122 sampled ORs agreed well with the microarray results and uncovered 23 additional CNVs. Importantly, these experiments allowed us to uncover nine common deletion alleles that affect 15 OR genes and five pseudogenes. Comparison to the chimpanzee reference genome revealed that all of the deletion alleles are human derived, therefore indicating a profound effect of human-specific deletions on the individual OR gene content. Furthermore, these deletion alleles may be used in future genetic association studies of olfactory inter-individual differences.

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Related in: MedlinePlus

Copy-number variability expressed as variance of experimental measures.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.
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pgen-1000249-g002: Copy-number variability expressed as variance of experimental measures.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.

Mentions: Subsequently, we validated CNVs by performing qPCR on 122 OR loci (104 ORgenes and 18 pseudogenes), which were selected to represent both high and low variability loci (Figure 2, S2) and which included similar amounts of novel and already known CNVs. Sixty validation experiments were carried out with a panel of only 13 samples, while the other 62 experiments were performed in 23 samples. We initially compared individual microarray intensities (normalized log2-intensity ratios) to qPCR outcomes (normalized Cp-values). In general, qPCR results revealed an acceptable correlation to the normalized microarray values (Figure S3A, S3B), with the exception of a small group of 23 OR loci that displayed considerable qPCR inter-subject variability despite low-variability microarray values (Figure S3A, S3B ). We added these 23 cases to our list of copy-number variable OR loci (Table 2; Figure S4).


High-resolution copy-number variation map reflects human olfactory receptor diversity and evolution.

Hasin Y, Olender T, Khen M, Gonzaga-Jauregui C, Kim PM, Urban AE, Snyder M, Gerstein MB, Lancet D, Korbel JO - PLoS Genet. (2008)

Copy-number variability expressed as variance of experimental measures.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.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2570968&req=5

pgen-1000249-g002: Copy-number variability expressed as variance of experimental measures.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.
Mentions: Subsequently, we validated CNVs by performing qPCR on 122 OR loci (104 ORgenes and 18 pseudogenes), which were selected to represent both high and low variability loci (Figure 2, S2) and which included similar amounts of novel and already known CNVs. Sixty validation experiments were carried out with a panel of only 13 samples, while the other 62 experiments were performed in 23 samples. We initially compared individual microarray intensities (normalized log2-intensity ratios) to qPCR outcomes (normalized Cp-values). In general, qPCR results revealed an acceptable correlation to the normalized microarray values (Figure S3A, S3B), with the exception of a small group of 23 OR loci that displayed considerable qPCR inter-subject variability despite low-variability microarray values (Figure S3A, S3B ). We added these 23 cases to our list of copy-number variable OR loci (Table 2; Figure S4).

Bottom Line: Furthermore, our results show an enrichment of CNVs among ORs with a close human paralog or lacking a one-to-one ortholog in chimpanzee.Quantitative PCR experiments performed for 122 sampled ORs agreed well with the microarray results and uncovered 23 additional CNVs.Comparison to the chimpanzee reference genome revealed that all of the deletion alleles are human derived, therefore indicating a profound effect of human-specific deletions on the individual OR gene content.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.

ABSTRACT
Olfactory receptors (ORs), which are involved in odorant recognition, form the largest mammalian protein superfamily. The genomic content of OR genes is considerably reduced in humans, as reflected by the relatively small repertoire size and the high fraction ( approximately 55%) of human pseudogenes. Since several recent low-resolution surveys suggested that OR genomic loci are frequently affected by copy-number variants (CNVs), we hypothesized that CNVs may play an important role in the evolution of the human olfactory repertoire. We used high-resolution oligonucleotide tiling microarrays to detect CNVs across 851 OR gene and pseudogene loci. Examining genomic DNA from 25 individuals with ancestry from three populations, we identified 93 OR gene loci and 151 pseudogene loci affected by CNVs, generating a mosaic of OR dosages across persons. Our data suggest that approximately 50% of the CNVs involve more than one OR, with the largest CNV spanning 11 loci. In contrast to earlier reports, we observe that CNVs are more frequent among OR pseudogenes than among intact genes, presumably due to both selective constraints and CNV formation biases. Furthermore, our results show an enrichment of CNVs among ORs with a close human paralog or lacking a one-to-one ortholog in chimpanzee. Interestingly, among the latter we observed an enrichment in CNV losses over gains, a finding potentially related to the known diminution of the human OR repertoire. Quantitative PCR experiments performed for 122 sampled ORs agreed well with the microarray results and uncovered 23 additional CNVs. Importantly, these experiments allowed us to uncover nine common deletion alleles that affect 15 OR genes and five pseudogenes. Comparison to the chimpanzee reference genome revealed that all of the deletion alleles are human derived, therefore indicating a profound effect of human-specific deletions on the individual OR gene content. Furthermore, these deletion alleles may be used in future genetic association studies of olfactory inter-individual differences.

Show MeSH
Related in: MedlinePlus