Determining the impact of uncharacterized inversions in the human genome by droplet digital PCR
- Marta Puig1,
- Jon Lerga-Jaso1,
- Carla Giner-Delgado1,
- Sarai Pacheco1,
- David Izquierdo1,
- Alejandra Delprat1,
- Magdalena Gayà-Vidal2,
- Jack F. Regan3,
- George Karlin-Neumann3 and
- Mario Cáceres1,4
- 1Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain;
- 2CIBIO/InBIO Research Center in Biodiversity and Genetic Resources, University of Porto, 4485-661 Vairão, Portugal;
- 3Digital Biology Center, Bio-Rad Laboratories, Pleasanton, California 94588, USA;
- 4ICREA, 08010 Barcelona, Spain
Abstract
Despite the interest in characterizing genomic variation, the presence of large repeats at the breakpoints hinders the analysis of many structural variants. This is especially problematic for inversions, since there is typically no gain or loss of DNA. Here, we tested novel linkage-based droplet digital PCR (ddPCR) assays to study 20 inversions ranging from 3.1 to 742 kb flanked by inverted repeats (IRs) up to 134 kb long. Of those, we validated 13 inversions predicted by different genome-wide techniques. In addition, we obtained new experimental human population information across 95 African, European, and East Asian individuals for 16 inversions, including four already validated variants without high-throughput genotyping methods. Through comparison with previous data, independent replicates and both inversion breakpoints, we demonstrate that the technique is highly accurate and reproducible. Most studied inversions are widespread across continents, and their frequency is negatively correlated with genetic length. Moreover, all except two show clear signs of being recurrent, and we could better define the factors affecting recurrence levels and estimate the inversion rate across the genome. Finally, the generated genotypes have allowed us to check inversion functional effects, validating gene expression differences reported before for two inversions and finding new candidate associations. Therefore, the developed methodology makes it possible to screen these and other complex genomic variants quickly in a large number of samples for the first time, highlighting the importance of direct genotyping to assess their potential consequences and clinical implications.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.255273.119.
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Freely available online through the Genome Research Open Access option.
- Received September 11, 2019.
- Accepted April 17, 2020.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
