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.
Highlights
Exome sequencing is increasingly used to search for phenotypically-relevant sequence variants in the mouse genome
Exome capture To evaluate whether sequence divergence could affect exome capture, especially in a mixed genetic background, we performed exome sequencing on a F1 hybrid mouse derived from crossing C57BL/6 J and SPRET/EiJ mice using an Agilent SureSelect XT Mouse All Exon Kit (Methods)
With a design based on the genome sequences of C57BL/6 J strain (UCSC genome browser mm9), the kit contains 565,918 probes of length 120 nucleotides that are targeted at the exonic regions of 24,306 genes
Summary
Exome 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. The current design of mouse exome capture probes is based on the genome reference sequences of the C57BL/6 J strain and the robustness of applying such systems in other strains has been shown in a study that mapped putative N-ethylN-nitrosourea (ENU)-induced mutations in four different inbred Mus musculus strains [12]. The marginal differences between the genomes of C57BL/6 J and the other strains used in that study do not allow for a systematic evaluation of the effects of sequence divergence on the efficiency of sequence capture and variant detection. The effect of sequence divergence could be even greater in a mixed genetic background
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