Joint Open Genome and Omics Platform (JoGo)

JoGo catalogs 4.7 million haplotypes across 19,194 MANE-standardized protein-coding human genes using a novel ACTG hierarchical nomenclature and enables functional variant mapping and cross-assembly haplotype comparison.

Key Features:

• ACTG Hierarchical Nomenclature: Assigns numeric identifiers in descending order of global frequency at four levels: A (amino acid), C (coding), T (transcript), and G (gene body).
• Cross-Assembly Haplotype Integration: Assigns haplotype IDs globally across all sequences including those from GRCh38 and CHM13v2 reference assemblies, embedding reference haplotypes within the same frequency-ranked space.
• Functional Variant Mapping: Maps variants from ClinVar, GWAS Catalog, and GTEx onto corresponding ACTG-haplotypes.
• Expression Quantitative Trait Locus Analysis: Provides haplotype-expression QTL results from 1280 HapMap RNA-seq samples across three independent studies.
• Multi-Modal Search: Enables search by gene name, variant ID, or ACTG code.
• Privacy-Preserving Local Viewer: Supports secure local integration with user data.

Scientific Applications:

• Haplotype Diversity Exploration: Facilitates high-resolution exploration of haplotype diversity for identifying functional variants relevant to gene regulation.
• Disease Association Research: Supports identification of haplotypes and functional variants associated with disease through integrated ClinVar and GWAS data.
• Precision Medicine: Enables interpretation of genetic results across studies, populations, and clinical settings through standardized haplotype nomenclature.
• Gene Regulation Studies: Links haplotype structure to expression variation through haplotype-eQTL analysis.

Methodology:

High-fidelity long-read sequencing was used to assemble haplotype-resolved contigs for 258 globally sampled genomes, including 108 sequenced in-house.