Large-scale genotyping of polymorphic inversions in human populations. S. Villatoro1, C. Aguado1, D. Vicente1, D. Izquierdo1, M. Puig1, M. Cáceres1,2 1) Institut de Biotecnologia i de Biomedicina, Universitat Autonòma de Barcelona, Barcelona, Spain; 2) Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
In the last years, different types of structural variants (SVs) have been discovered in the human genome and their importance in human diseases, complex traits and evolution has become increasingly clear. Among the different types of SVs, inversions are the less known due to the difficulty to analyze them and with few exceptions, their frequency and distribution in human populations has not been widely studied. As part of a larger project towards the complete characterization of inversions in humans (INVFEST), we have set up a custom assay based on hybridization of probes that allows us to interrogate inversions with simple breakpoints, as well as inversions flanked by long repetitive sequences. Using this new technique, we have developed a high-throughput protocol to genotype 41 inversions in a large number of samples. In this study, first, inversions were genotyped in 90 individuals of European origin (CEU) and compared with previous results obtained by PCR in order to calculate the accuracy of our method, which was established in a 99%. Then, we analyzed additional samples up to a total of 550 individuals from different populations included within the 1000 Genomes Project: CEU, Toscani (TSI), Yoruba (YRI), Luhya (LWK), Chinese (CHB), Japanese (JPT) ,and Gujarati Indians (GIH), with an European, African and Asian origin, respectively. Using the data obtained, the genotyping-success rate of this method was estimated in a 98%. Besides, in all cases the genetic transmission in 60 mother-father-child European and Yoruba trios was correct. Next, we estimated the global inverted allele frequencies on the unrelated samples, which ranged between 0.5-98.8% and all inversions were in Hardy-Weinberg equilibrium in each population. Finally, significant differences among populations were found for some of the inversions, with Fst statistic values between 0.01-0.49. In conclusion, this assay provides a powerful, reliable and fast high-throughput method to genotype a wide range of inversions, which has allowed us to create the largest map of the frequency and distribution of these SVs in human populations. In addition, this information has opened the possibility to explore the association of inversions with nucleotide variation, gene expression, and phenotypic features. Support: European Research Council (ERC) Starting Grant (INVFEST) under the European Union Seventh Research Framework Programme (FP7).