ArticleBMC genomics2013
A systematic evaluation of hybridization-based mouse exome capture system.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Mammalian splicing divergence is shaped by drift, buffering inLife science alliance · 2022Article
- Pervasive allele-specific regulation on RNA decay in hybrid mice.Life science alliance · 2018Article
- Global analysis of regulatory divergence in the evolution of mouse alternative polyadenylation.Molecular systems biology · 2016Article
- Extensive allele-specific translational regulation in hybrid mice.Molecular systems biology · 2015Article
- Predominant contribution of cis-regulatory divergence in the evolution of mouse alternative splicing.Molecular systems biology · 2015Article
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Authors and funding
5 authors.
Funding
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Abstract
backgroundExome sequencing is increasingly used to search for phenotypically-relevant sequence variants in the mouse genome. All of the current hybridization-based mouse exome capture systems are designed based on the genome reference sequences of the C57BL/6 J strain. Given that the substantial sequence divergence exists between C57BL/6 J and other distantly-related strains, the impact of sequence divergence on the efficiency of such capture systems needs to be systematically evaluated before they can be widely applied to the study of those strains.
resultsUsing the Agilent SureSelect mouse exome capture system, we performed exome sequencing on F1 generation hybrid mice that were derived by crossing two divergent strains, C57BL/6 J and SPRET/EiJ. Our results showed that the C57BL/6 J-based probes captured the sequences derived from C57BL/6 J alleles more efficiently and that the bias was higher for the target regions with greater sequence divergence. At low sequencing depths, the bias also affected the efficiency of variant detection. However, the effects became negligible when sufficient sequencing depth was achieved.
conclusionSufficient sequence depth needs to be planned to match the sequence divergence between C57BL/6 J and the strain to be studied, when the C57BL/6 J-based Agilent SureSelect exome capture system is to be used.
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