About JCGA web database

The next-generation sequencing (NGS)-based cancer gene panel tests have been used in clinical practice, in Japan, since June 2019. A cancer genome database of Japanese patients, with mutational profiles unaffected by racial differences, has been extremely important in improving the interpretation of the detected gene alterations. Thus, we constructed the Japanese version of the Cancer Genome Atlas (JCGA) based on the whole-exome sequencing data of 4,907 surgically resected primary tumor samples obtained from 4,753 Japanese patients with cancer who were enrolled in Project HOPE. Project HOPE is a prospective molecular profiling study for multiple tumor types using multi-omics technology utilizing NGS. It was launched at the Shizuoka Cancer Center, in January 2014. The cohort consisted of 134 tumor types classified based on the criteria set by Oncotree and/or The Cancer Genome Atlas. The JCGA graphically provides genome information on 460 cancer-associated genes. The JCGA has been used by the molecular tumor boards that are the so-called expert panel of our institute to interpret the gene alterations detected in the NGS-based cancer gene panel tests and to prepare the reports that explain putative biological causes that drive tumor progression.

Overview of the English version of the JCGA

On the homepage of the JCGA, users can search by entering the official gene symbol, trivial gene symbol, or official gene ID (Entrez ID) in the search window or gene grid function. The resulting display page of each gene provides following five contents: 1) Basic information, such as links to relevant bioinformatic resources and gene maps showing chromosomal location, exon-intron organization, and coding region; 2) Pathway map, which shows the association between cancer signaling pathways and the selected gene; 3) Graphs indicating Frequency of somatic alterations, which indicate the frequency of somatic gene alterations in 30 principal tumor types; 4) Distribution of the tumor mutational burden (TMB) in 30 principle tumor types sorted in ascending order of the median value of TMB in each tumor type; and 5) list of driver somatic variants.

The frequency of somatic gene alterations are useful in estimating the primary tumor types in patient with unknown primary tumors. The TMB distribution can be used to assess its relative ranking of TMB of patients, and is useful in predicting the therapeutic effect of immune checkpoint inhibitors.