Background: Localisation of the breakpoints of chromosomal translocations has aided the discovery of several disease genes but has traditionally required laborious investigation of chromosomes by fluorescent-in-situ-hybridisation approaches. Here we report a strategy that utilises genome-wide paired-end massively parallel DNA sequencing to rapidly map translocation breakpoints. We used this method to fine map a de novo t(5;6)(q21;q21) translocation in a child with bilateral, young-onset Wilms tumor.
Methods and Results: We undertook genome-wide paired-end sequencing of approximately six million randomly generated ~3 kb fragments from constitutional DNA containing the translocation and identified six fragments in which one end mapped to chromosome 5 and the other to chromosome 6. This mapped the translocation breakpoints to within 1.7kb. We designed PCR assays that amplified across the rearrangement junction to characterise the breakpoints at sequence level resolution. The 6q21 breakpoint transects and truncates HACE1, an E3 ubiquitin-protein ligase that has been implicated as a somatically inactivated target in Wilms tumorigenesis. To evaluate the contribution of HACE1 to Wilms tumor predisposition we mutationally screened the gene in 450 individuals with Wilms tumor. We identified one child with unilateral Wilms tumor and a truncating HACE1 mutation.
Conclusions: These data indicate that constitutional disruption of HACE1 likely predisposes to Wilms tumor. However, HACE1 mutations are rare and therefore can only make a small contribution to Wilms tumor incidence. More broadly, this study demonstrates the utility of genome-wide paired-end sequencing in the delineation of apparently balanced chromosomal translocations, for which it is likely to become the method of choice.