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BMC Genomics 2012 Nov 21;13:649. doi: 10.1186/1471-2164-13-649.
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Exon capture and bulk segregant analysis: rapid discovery of causative mutations using high-throughput sequencing.

del Viso F , Bhattacharya D , Kong Y , Gilchrist MJ , Khokha MK .

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. CONCLUSION: 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.

PubMed ID: 23171430
PMC ID: PMC3526394
Article link: BMC Genomics
Grant support: [+]

Species referenced: Xenopus tropicalis
Genes referenced: atp1a1 c3h2orf68 ccdc40 cdh16 hnf1a hnf1b il1b maf pax2 pax8 psd4 rgn sftpb slc5a9 slc7a8 tmem150a usp39
GO keywords: ciliary basal body organization [+]
Morpholinos: pax8 MO3

Disease Ontology terms: primary ciliary dyskinesia

Article Images: [+] show captions
References [+] :
Abu-Daya, Absence of heartbeat in the Xenopus tropicalis mutation muzak is caused by a nonsense mutation in cardiac myosin myh6. 2009, Pubmed, Xenbase