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Open Access Highly Accessed Research article

Personal receptor repertoires: olfaction as a model

Tsviya Olender1*, Sebastian M Waszak2, Maya Viavant1, Miriam Khen1, Edna Ben-Asher1, Alejandro Reyes3, Noam Nativ1, Charles J Wysocki4, Dongliang Ge5 and Doron Lancet1*

Author affiliations

1 Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel

2 Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland

3 Genome Biology Unit. European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany

4 Monell Chemical Senses Center, 3500 Market Street, Philadelphia, PA, 19104, USA

5 Center for Human Genome Variation, Duke University School of Medicine, Durham, NC, United States of America

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Citation and License

BMC Genomics 2012, 13:414  doi:10.1186/1471-2164-13-414

Published: 21 August 2012

Abstract

Background

Information on nucleotide diversity along completely sequenced human genomes has increased tremendously over the last few years. This makes it possible to reassess the diversity status of distinct receptor proteins in different human individuals. To this end, we focused on the complete inventory of human olfactory receptor coding regions as a model for personal receptor repertoires.

Results

By performing data-mining from public and private sources we scored genetic variations in 413 intact OR loci, for which one or more individuals had an intact open reading frame. Using 1000 Genomes Project haplotypes, we identified a total of 4069 full-length polypeptide variants encoded by these OR loci, average of ~10 per locus, constituting a lower limit for the effective human OR repertoire. Each individual is found to harbor as many as 600 OR allelic variants, ~50% higher than the locus count. Because OR neuronal expression is allelically excluded, this has direct effect on smell perception diversity of the species. We further identified 244 OR segregating pseudogenes (SPGs), loci showing both intact and pseudogene forms in the population, twenty-six of which are annotatively “resurrected” from a pseudogene status in the reference genome. Using a custom SNP microarray we validated 150 SPGs in a cohort of 468 individuals, with every individual genome averaging 36 disrupted sequence variations, 15 in homozygote form. Finally, we generated a multi-source compendium of 63 OR loci harboring deletion Copy Number Variations (CNVs). Our combined data suggest that 271 of the 413 intact OR loci (66%) are affected by nonfunctional SNPs/indels and/or CNVs.

Conclusions

These results portray a case of unusually high genetic diversity, and suggest that individual humans have a highly personalized inventory of functional olfactory receptors, a conclusion that might apply to other receptor multigene families.

Keywords:
Olfactory receptor; Genetic polymorphism; Haplotypes; Single nucleotide polymorphism; Copy number variation; Olfaction; Gene family