title: Exon capture and bulk segregant analysis:  rapid discovery of causative mutations using high-throughput sequencing.
abstract: BACKGROUND
  Exome sequencing has transformed human genetic analysis and may do the same for other vertebrate model systems. However, a major challenge is sifting through the large number of sequence variants to identify the causative mutation for a given phenotype. In models like Xenopus tropicalis, an incomplete and occasionally incorrect genome assembly compounds this problem. To facilitate cloning of X. tropicalis mutants identified in forward genetic screens, we sought to combine bulk segregant analysis and exome sequencing into a single step.
  
  
  RESULTS
  Here we report the first use of exon capture sequencing to identify mutations in a non-mammalian, vertebrate model. We demonstrate that bulk segregant analysis coupled with exon capture sequencing is not only able to identify causative mutations but can also generate linkage information, facilitate the assembly of scaffolds, identify misassembles, and discover thousands of SNPs for fine mapping.
  
  
  CONCLUSIONS
  Exon capture sequencing and bulk segregant analysis is a rapid, inexpensive method to clone mutants identified in forward genetic screens. With sufficient meioses, this method can be generalized to any model system with a genome assembly, polished or unpolished, and in the latter case, it also provides many critical genomic resources.
authors.affiliation: Department of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.
authors.forename: Florencia
authors.initials: F
authors.lastname: del Viso
authors.forename: Dipankan
authors.initials: D
authors.lastname: Bhattacharya
authors.forename: Yong
authors.initials: Y
authors.lastname: Kong
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Gilchrist
authors.forename: Mustafa K
authors.initials: MK
authors.lastname: Khokha
mesh_terms: D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping; D002999:Clone Cells; D059472:Exome; D005091:Exons; D008040:Genetic Linkage; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D008540:Meiosis / Q000235:genetics; D008969:Molecular Sequence Data; D009154:Mutation; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D014981:Xenopus / Q000235:genetics*; D029867:Xenopus Proteins / Q000235:genetics*
chemical_list: D029867:Xenopus Proteins