Genome-wide analysis of chemically induced mutations in mouse in phenotype-driven screens

Background: N-ethyl-N-nitrosourea (ENU) mutagen has become the method of choice for inducing random mutations for forward genetics applications. However, distinguishing induced mutations from sequencing errors or sporadic mutations is difficult, which has hampered surveys of potential biases in the methodology in the past. Addressing this issue, we created a large cohort of mice with biological replicates enabling the confident calling of induced mutations, which in turn allowed us to conduct a comprehensive analysis of potential biases in mutation properties and genomic location. Results: In the exome sequencing data we observe the known preference of ENU to cause A : T ⇒ G : C $A:T\Rightarrow G:C$ transitions in longer genes. Mutations were frequently clustered and inherited in blocks hampering attempts to pinpoint individual causative mutations by genome analysis only. Furthermore, ENU mutations were biased towards areas in the genome that are accessible in testis, potentially limiting the scope of forward genetic approaches to only 1-10 % of the genome. Conclusion: ENU provides a powerful tool for exploring the genome-phenome relationship, however forward genetic applications that require the mutation to be passed on through the germ line may be limited to explore only genes that are accessible in testis.