Read count-based method for high-throughput allelic genotyping of transposable elements and structural variants

BMC Genomics

William F. Burkholder¹  Stephen R. Quake²  Yao Min Ong¹  Alexandre Kuhn¹ 

[1] Microfluidics Systems Biology Lab, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Proteos Building, Room #03-04, 61 Biopolis Drive, Singapore 138673, Singapore;Visiting Investigator, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore

关键词: Alu;    LINE-1;    Next-generation sequencing;    Structural variation;    Transposable element;    Genotyping;   

Others  :  1219103
DOI  :  10.1186/s12864-015-1700-4

 received in 2015-05-20, accepted in 2015-06-15,  发布年份 2015

【 摘 要 】

Background

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.

Results

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.

Conclusions

This method can benefit a wide range of applications from the routine genotyping of animal and plant populations to the functional study of structural variants in humans.

【 授权许可】

   
2015 Kuhn et al.

【 图 表 】

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