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. 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.

journal_name

BMC Genomics

journal_title

BMC genomics

authors

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

doi

10.1186/1471-2164-13-649

subject

Has Abstract

pub_date

2012-11-21 00:00:00

pages

649

issn

1471-2164

pii

1471-2164-13-649

journal_volume

13

pub_type

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