To this effect, we applied RNA-Seq to nine JPA samples in combination with 10x Genomics’ linked-reads in six of these samples to assess its performance in the discovery and detailed characterization of low frequency BRAF fusions including two with novel fusion partners PTPRZ1 and TOP2B. We also generated in situ Hi-C libraries from primary JPA tumor samples in order to gain more insight into the association between fusion-partner genes and nuclear topology. Here, BRAF is linked to neoplasm.