The combination of tumor genome sequence data and mutant identification with genetic interaction networks and insights into relative mutability should continue to present novel therapeutic opportunities in the future.
WGS has been applied to mutant identification in C. elegans and shown to be suitable for detecting a variety of DNA lesions (Chu et al. 2012; Flibotte et al. 2010; Hillier et al. 2008; Hobert 2010; Sarin et al. 2008; Shen et al. 2008), although methods to reliably identify small insertion/deletions (indels) and duplications are still being refined (Smith 2011).
Whole-genome sequencing for mutant identification was conducted on Illumina GAIIx and HiSeq2000 instruments according to the manufacturer's instructions.
It is obvious that if the crossing step could be omitted, the overall time and effort needed for mutant identification would be considerably reduced.
For example, calculations show that only 56 families have to be screened to identify a missense mutation in a 1 Kb exon target and only 650 families need to be screened to identify a codon stop mutation, thereby reducing the overall time and costs spent on mutant identification.
We have successfully applied a SNP- and WGS-based cloning strategy for mutant identification in C.elegans.
Moreover, it reduces the costs of mutant identification, since it employs a single whole-genome sequencing run for both mutant mapping as well as mutant identification.
In addition, this technology may be applicable to genetic screens, including genome-wide RNAi or feeding-defective mutant identification.
As pointed out before [9], the combined SNP/WGS strategy that we describe here for C. elegans, can of course be applied for mutant identification in many other model system species in which positional cloning has traditionally been tedious.
In our specific example of mutant identification in the C. elegans genome, the experimental system allows narrowing down the region of interest to a fraction of the genome by traditional mapping and the system allows the following-up of dozens of variants by various experimental strategies (including sequencing multiple alleles, rescue analysis, RNAi analysis etc.; [1]).
