JoGo 1.0: the ACTG hierarchical nomenclature and database covering 4.7 million haplotypes across 19,194 human genes
The Joint Open Genome and Omics Platform 1.0 (JoGo) is a global, long-read-based human haplotype database covering 19 194 MANE-standardized protein-coding genes. JoGo introduces a novel ACTG hierarchical nomenclature-A (amino acid), C (coding), T (transcript), and G (gene body)-that assigns numeric identifiers in descending order of global frequency. Using high-fidelity long-read sequencing, we assembled haplotype-resolved contigs for 258 globally sampled genomes, including 108 sequenced in-house. We cataloged 174 376 A-, 300 610 C-, 486 288 T-, and 3 695 204 G-level haplotypes (4 656 478 in total). Haplotype IDs are assigned once globally across all sequences, including those originating from GRCh38 and CHM13v2 reference assemblies, embedding reference haplotypes within the same frequency-ranked space and enabling direct cross-assembly comparison. JoGo maps functional variants from ClinVar, GWAS Catalog, and GTEx onto their corresponding ACTG-haplotypes and provides haplotype-expression QTL results from 1280 HapMap RNA-seq samples across three independent studies. The web portal provides flexible search by gene name, variant ID, or ACTG code. It offers both an interactive online viewer and a privacy-preserving local viewer for secure integration with user data. JoGo enables high-resolution exploration of haplotype diversity, facilitating the identification of functional variants relevant to gene regulation, disease associations, and precision medicine. JoGo 1.0 is freely accessible at https://jogo.csml.org.
Authors
- Toyoyuki Takada (ORCID: https://orcid.org/0000-0001-6796-2085)
- Patrícia Severino (ORCID: https://orcid.org/0000-0002-6682-9343)
- Ryo Teraoka (ORCID: https://orcid.org/0000-0003-0837-4552)
- Yosuke Kawai (ORCID: https://orcid.org/0000-0003-0666-1224)
- Masahiro Ohira (ORCID: https://orcid.org/0000-0002-5433-5303)
- N Mitsuhashi (ORCID: https://orcid.org/0000-0003-3300-7308)
- Daisuke Satoh (ORCID: https://orcid.org/0000-0002-9866-1346)
- Masao Nagasaki
- Toshiaki Katayama (ORCID: https://orcid.org/0000-0003-2391-0384)
- Yuki Moriya (ORCID: https://orcid.org/0000-0001-8195-5893)
- Shuichi Kawashima (ORCID: https://orcid.org/0000-0001-7883-3756)
- Hiroki Hashimoto (ORCID: https://orcid.org/0000-0002-4672-1490)
- Tsuyoshi Hachiya (ORCID: https://orcid.org/0000-0002-5274-3266)
- S. Machida
- Takatomo Fujisawa (ORCID: https://orcid.org/0000-0001-8978-3344)
- Yayoi Sekiya
- Toshiaki Katayama
- Yifan Huangfu (ORCID: https://orcid.org/0000-0003-3494-9858)
- Yasuyuki Ohkawa (ORCID: https://orcid.org/0000-0001-6440-9954)
- Akihiro Asakura
- Mayumi Kamada (ORCID: https://orcid.org/0000-0002-2555-7345)
- Minae Kawashima
- Yoko Kuroki
- Taichi Matsubara
- Atsushi Doi
- Katsushi Tokunaga
- Yuichiro Hara
- Samuel Papa Kwesi Owusu
Institutions
- National Institute of Genetics (JP)
- Kyushu University (JP)
- Kajima Corporation (Japan) (JP)
- Kyoto University (JP)
- National Center for Global Health and Medicine (JP)
- RIKEN BioResource Research Center (JP)
- National Cancer Center Hospital East (JP)
- Research Organization of Information and Systems (JP)
- Kitasato University (JP)
- The University of Tokyo (JP)
Publication Details
- Journal
- Nucleic Acids Research
- Published
- 2025-10-23
- DOI
- https://doi.org/10.1093/nar/gkaf1232
- Citations
- 1
- Primary Topic
- Genomics and Rare Diseases
- Type
- article
- Field-Weighted Citation Impact
- 1.82