Read count-based method for high-throughput allelic genotyping of transposable elements and structural variants
Alexandre Kuhn, Yao Min Ong, Stephen R. Quake, William F. Burkholder
TL;DR
This paper introduces a cost-effective and accurate method for genotyping transposable elements and structural variants using read count-based analysis of PCR products.
Contribution
A novel high-throughput genotyping method for transposable elements and structural variants using next-generation sequencing and read counts.
Findings
The method is flexible, efficient, and does not require rounds of optimization.
It is cost-effective and highly accurate for genotyping structural variants.
Applicable to genotyping in animal, plant, and human populations.
Abstract
Like other structural variants, transposable element insertions can be highly polymorphic across individuals. Their functional impact, however, remains poorly understood. Current genome-wide approaches for genotyping insertion-site polymorphisms based on targeted or whole-genome sequencing remain very expensive and can lack accuracy, hence new large-scale genotyping methods are needed. We describe a high-throughput method for genotyping transposable element insertions and other types of structural variants that can be assayed by breakpoint PCR. The method relies on next-generation sequencing of multiplex, site-specific PCR amplification products and read count-based genotype calls. We show that this method is flexible, efficient (it does not require rounds of optimization), cost-effective and highly accurate. This method can benefit a wide range of applications from the routine…
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Taxonomy
TopicsChromosomal and Genetic Variations · Genomic variations and chromosomal abnormalities · Genomics and Phylogenetic Studies