An allele frequency panel based on short-read whole-genome sequencing analysis of 61,000 Japanese individuals, produced by the Tohoku Medical Megabank Organization (ToMMo) at Tohoku University. The project includes other datatypes such as STRs, long-read SVs and short-read CNVs.
The data can be explored interactively with the Table Browser or the Data Integrator. For programmatic access, our REST API can be used; the track name is tommo60kjpn. For bulk download, the VCF file can be obtained from our download server.
The original data can also be downloaded from the jMorp website, specifically the Downloads section.
Genomic DNA was obtained from peripheral blood, saliva, or cord blood samples. Sequencing was performed on Illumina HiSeq 2500, HiSeq X Five, NovaSeq 6000, and MGI DNBSeq G400/T7 instruments. Reads were aligned to the GRCh38 reference using BWA 0.7.15 or BWA-mem2 2.1. Alignments underwent base quality score recalibration (BQSR) with the GATK BaseRecalibrator tool. SNV/indel calling was performed using GATK HaplotypeCaller, followed by multisample joint genotyping with Sentieon Genomics tools and variant quality score recalibration (VQSR) filtering. Related samples were identified and removed using KING 2.3.1, resulting in the final allele frequency panel.
We provide documentation that indicates how all source files of the varFreqs track were converted in the makeDoc file of the track. For some tracks, python scripts were necessary and are also available from GitHub.
Tadaka S, Kawashima J, Hishinuma E, Saito S, Okamura Y, Otsuki A, Kojima K, Komaki S, Aoki Y, Kanno T et al. jMorp: Japanese Multi-Omics Reference Panel update report 2023. Nucleic Acids Res. 2024 Jan 5;52(D1):D622-D632. PMID: 37930845; PMC: PMC10767895