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Exon capture and bulk segregant analysis: rapid discovery of causative mutations using high-throughput sequencing

Florencia del Viso1, Dipankan Bhattacharya1, Yong Kong2, Michael J Gilchrist3 and Mustafa K Khokha1*

Author Affiliations

1 Department of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520, USA

2 Department of Molecular Biophysics and Biochemistry and W. M. Keck Foundation Biotechnology Resource Laboratory, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520, USA

3 Division of Systems Biology, MRC-National Institute for Medical Research, Mill Hill, London, NW7 1AA, UK

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BMC Genomics 2012, 13:649  doi:10.1186/1471-2164-13-649

Published: 21 November 2012



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.


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.


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.

Exon capture sequencing; Forward genetics; Xenopus tropicalis; Bulk segregant analysis; Cilia; Kidney development; SNP discovery; Genome assembly; ccdc40; pax8