Abstract: Introduction and Objectives There has been recent interest in the elevated risk of prostate cancer in men with Lynch syndrome, where a DNA mismatch repair gene mutation such as in MSH2 is inherited. These cancers may possess more than 10-fold the usual number of mutations and their study may present clues as to how cancers evolve, metastasise and respond to therapy. Here we present results from genome sequencing of paired prostate cancer metastasis and primary tumour samples from a patient with a mutator phenotype implicating a mismatch repair defect. We aimed to determine the clonality of the metastasis in relation to the primary cancer and to characterise the underlying molecular cause of the mutator phenotype. Methods Our patient was a 64 year-old man with Gleason 9 prostate cancer who developed metastatic disease at 22 months post-radical prostatectomy. Fresh frozen tumour samples were taken from his original prostatectomy specimen and at percutaneous biopsy of a bone metastasis at 35 post-operative months. Tissue samples were cryosectioned and tumour content confirmed by a pathologist prior to mechanical homogenisation and simultaneous DNA and RNA extraction (Allprep Micro Kit, Qiagen). Whole genome sequencing was performed to 40x coverage and transcriptome sequencing to 120 million reads per sample both on the Illumina HiSeq2000 platform. Genome Analysis ToolKit was used for WGS read alignment and single nucleotide variants called using MuTect. Results Subclonal analysis revealed that the metastasis derived from a subclone of the primary tumour accounting for just 30% of the cells, rather than the dominant subclone accounting for 70%. Transcriptome sequencing revealed a novel MSH2-NRXN1 fusion transcript present in both primary and metastasis. WGS data confirmed an intrachromosomal translocation event resulting in a truncated MSH2 gene product and inactivation. A high number of mutations with overrepresentation of C{$>$}T and T{$>$}C mutations and indels consistent with a mutator phenotype from DNA mismatch repair was seen (35,515 mutations in primary, 64,716 in metastasis). Allele-specific copy number analysis revealed loss of heterozygosity at 2p21, consistent with loss of the other MSH2 allele. Conclusions The subclonal origin of metastasis suggests that different selection pressures may exist between primary and metastatic sites and optimal therapy and response to that therapy may also differ. We have shown also how the mismatch repair gene MSH2 may be inactivated in sporadic prostate cancer.