Proximo Hi-C Platform

The Proximo Hi-C Platform, developed by Phase Genomics, is a proximity ligation-based genomics solution designed to convert draft contig assemblies into chromosome-scale, reference-quality genome assemblies. It is intended for researchers working across a broad range of organisms, including human, animal, plant, fungi, and microbe sample types, with applications in agriculture, medicine, and functional genomics.

Proximo Hi-C kits use in vivo proximity ligation technology to trap short-, long-, and ultra-long-range intracellular DNA contacts. Chimeric junctions originating from the same cell are recovered, converted into a short-read sequencing library, and subjected to paired-end sequencing. The resulting data can be used to scaffold genomes, phase haplotypes, model 3D genome conformation, and detect structural genomic variation.

Kit Features and Specifications

• Five sample-type-specific kits available: human, animal, plant, fungi, and microbe
• Produces high-quality, long-range sequencing data
• Does not require high-molecular-weight (HMW) DNA extraction
• Compatible with Illumina and Element sequencers; yields dual-indexed proximity ligation libraries
• Available as user-friendly 2-pack kits

Library Preparation Workflow

• The full workflow, from tissue sample to FASTA files and figures, is typically completed within one month
• The library prep protocol consists of 8 steps and can be completed in one to two working days
• Requires approximately 3 hours of hands-on time
• Includes several stopping points for flexibility during the protocol
• Sequencing requires approximately 50 to 100 million paired-end reads
• If a draft assembly is not yet available, Phase Genomics can help facilitate traditional sequencing projects prior to Hi-C scaffolding
• Consultation on data analysis and interpretation services is available

Key Applications

• Genome scaffolding: Transforms draft assemblies into end-to-end chromosome-scale assemblies across diverse species and sample types; can be integrated with other computational approaches to produce high-quality eukaryotic genomes
• 3D genomics: Constructs high-resolution maps of chromatin interactions to identify promoter-enhancer connections, associate non-coding variants with target promoters in disease contexts, and assess the impact of structural variations on gene regulation
• Haplotype phasing and structural variant detection: Uses Hi-C signal to phase genomes and detect complex rearrangements including balanced translocations, chromothripsis, and copy number changes; supports collection of SNV, CNV, SV, and phase data from a single library preparation

Proximo is supported by dedicated computational analysis tools, published protocols, and an FAQ and video library. For cytogenomic genome characterization, Phase Genomics also offers the CytoTerra Platform. Downloadable library prep protocols are available by kit and sample type, and the platform has been used to generate or improve reference genomes across a documented list of metazoans and microbes.