On June 2018, we released our genome reference panel, 3.5KJPNv2 for a Japanese population of 3,552 individuals, which includes the allele frequencies of the population including X chromosome and mitochondria genome. The data on X chromosome and mitochondria for a large Japanese population is the first case. Previousely, we used iJGVD for data distribution, but it was now integrated into “jMorp” (Japanese Multi Omics Reference Panel). In jMorp, the genome data is provided by aiming to easy comparison with the other international data.
In contrast to the last version of the panel, 3.5KJPN, which is released in September 2017 in iJGVD, we employed the GATK pipeline, which is now considered as an internationally standard method, for reanalysis for the sequencing data.
The SNVs information over1% frequency is freely accessed without any data transfer agreement, while the rare variant information (lower than 1% in frequency) is accessible with the registration of ORCID ID and an agreement of data transfer.
The details of the released data are described below:
The positions, allele frequencies, allele counts of all SNVs, mitochondria and X chromosome in the Japanese whole-genome reference panel from Tohoku Medical Megabank Project.
The dataset is used the GRCh37/hg19 human reference genome for analysis of autosomes and X chromosome including some decoy sequences, which is the equivalent with those used in international 1000 genome project, and revised Cambridge Reference Sequence (rCRS) for analysis of mitochondria.
Users can immediately download the data upon agreement to follow our user guidelines which include: 1) allowed to use only for non-profit (academic) purposes; 2) prohibition of identification of the cohort participants; 3) prohibition of contact with the cohort participants; etc.
You can go through the website called jMorp (Japanese Multi Omics Reference Panel) ,click “Genome”, then search your interest. Please see the blow link for more details.
・How to use jMorp
You can access the data through