title: Read count-based method for high-throughput allelic genotyping of transposable elements and structural variants.
abstract: 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.
authors.affiliation: 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. alexandre.m.kuhn@gmail.com.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Kuhn
authors.affiliation: 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. yaomin81@gmail.com.
authors.forename: Yao Min
authors.initials: YM
authors.lastname: Ong
authors.affiliation: Depts. of Bioengineering and Applied Physics and Howard Hughes Medical Institute, Stanford University, Clark Center, Room E300, 318 Campus Drive, Stanford, CA, 94305, USA. quake@stanford.edu.|Visiting Investigator, Institute of Molecular and Cell Biology, A*STAR, Singapore, 138673, Singapore. quake@stanford.edu.
authors.forename: Stephen R
authors.initials: SR
authors.lastname: Quake
authors.affiliation: 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. wfburkholder@gmail.com.
authors.forename: William F
authors.initials: WF
authors.lastname: Burkholder
mesh_terms: D000483:Alleles; D004251:DNA Transposable Elements / Q000235:genetics*; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D011110:Polymorphism, Genetic / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D004251:DNA Transposable Elements