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Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
Published on: October 18, 2013
Exon capture and bulk segregant analysis: rapid discovery of causative mutations using high-throughput sequencing
Florencia del Viso1, Dipankan Bhattacharya, Yong Kong
1Department of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.
BMC Genomics
|November 23, 2012
Summary
This study introduces a novel method combining bulk segregant analysis and exon capture sequencing for rapid identification of mutations in vertebrate models like Xenopus tropicalis. This approach efficiently clones mutants and generates valuable genomic resources.
Area of Science:
- Genomics
- Developmental Biology
- Comparative Genomics
Background:
- Exome sequencing is a powerful tool for human genetic analysis but faces challenges in model organisms.
- Identifying causative mutations in vertebrate models is hindered by large variant numbers and incomplete genome assemblies.
- Xenopus tropicalis presents unique challenges due to its genome assembly quality.
Purpose of the Study:
- To develop a streamlined method for identifying mutations in Xenopus tropicalis mutants.
- To combine bulk segregant analysis (BSA) with exome sequencing for efficient mutant cloning.
- To address challenges posed by incomplete and incorrect genome assemblies.
Main Methods:
- Utilized exon capture sequencing in conjunction with BSA.
- Applied the combined method to Xenopus tropicalis mutants from forward genetic screens.
- Leveraged sequence data to generate linkage information and assemble genomic scaffolds.
Main Results:
- Demonstrated the first use of exon capture sequencing for mutation identification in a non-mammalian vertebrate.
- Successfully identified causative mutations and generated linkage information.
- Facilitated genome assembly, identified misassembles, and discovered thousands of SNPs for fine mapping.
Conclusions:
- Exon capture sequencing combined with BSA offers a rapid and cost-effective method for cloning mutants.
- The approach is generalizable to any model system with a genome assembly, regardless of its quality.
- The method provides critical genomic resources, particularly for unpolished assemblies.
