In my talk I am going to overview current trends in implementation of genome data in personalized medicine approaches in Japan. Several ambitious projects, including Tohoku Medical MegaBank providing data for Integrative Japanese Genome variation database are supported by government and the first results illustrate importance of in-deep geographically-oriented genome projects. Remarkably, Russia and Japan face similar issues, suffering from lack of “national” genomes knowledge in gene diagnostics. Limited data on nation-specific features of genomes reflect on daily medical assistance, for example in the field of onco-diagnostics. Since 2015, in the frame of collaboration among RIKEN, Tatarstan Cancer Center and several Russian institutions we have initiated pilot “Pharmaco-FANTOM” project. Based on the next-generation sequencing data, we analyze the primary sequence of key genes with clinical diagnostics importance both in somatic and germline polymorphism. The first data have revealed several critical clinical cases where European and USA standards and targets in cancer diagnostics have only limited applicability in Russia.