Technology

Hi-C Proximity-Guided Assembly

Regain ultra-long-range genomic contiguity with Phase Genomics’ patent-pending Proximo™ Hi-C and ProxiMeta™ Hi-C technology.

ProxiMeta™ metagenome deconvolution method

Explore the depths of the microbial world


The ProxiMeta Hi-C metagenomic deconvolution method reveals which DNA sequences originated in the same cell, enabling assembly of whole genomes from mixed samples in their natural state — no culturing or high-molecular-weight DNA extraction required. Like Proximo Hi-C, ProxiMeta Hi-C is based on capturing physical DNA proximity with in vivo Hi-C. This powerful new source of information allows sequences from the same species and/or strain to be grouped, yielding dozens or even hundreds of genomes for rare, unculturable, and novel microbes easily and affordably.



ProxiMeta Hi-C uses in vivo cross-linking to fix DNA sequences which were present inside the same intact cell. Cross-linking generates linkage information between all DNA sequences inside the same cell, so it also generates data about which chromosomes were present inside the same cell (e.g., for eukaryotic metagenomics) and which plasmids were associated with which host genomes (e.g., for identification of anti-microbial resistance plasmids in strains).



The cross-linked chromatin is fragmented and proximity ligated, creating chimeric junctions between sequences originating from the same cell. Illumina paired-end sequencing these junctions measures which pairs of sequences were in close physical proximity in vivo, which can then be used to group sequences by cellular origin.



The chromatin structure information generated by ProxiMeta Hi-C is used deconvolute metagenomes by identifying which groups of contigs were present inside the same cell, creating individual genome assemblies for the species and strains which were originally present in the sample, including estimating cellular abundance. Because no culturing is required, novel genomes can be detected and characterized as they were in nature, and mutations, plasmids, and multiple chromosomes can be placed into a specific species or strain. Available reference data is then used to add context to the genomes extracted from a sample. Because reference data is not used as an input to the deconvolution process, the biases and limitations of known reference data do not affect the results for a sample: the pure chromatin structural data drives deconvolution, with reference data applied to layer in known scientific information after the fact.


Proximo™ scaffolding method

Get chromosome-scale scaffolds for virtually any genome


Proximo uses Hi-C to measure the structure of DNA in vivo and scaffold contigs into entire chromosomes. This powerful scaffolding approach requires only a biological sample in its natural, intact state—no need to isolate high-molecular-weight DNA. Chromosome-scale scaffolds generated with Proximo empower you to answer biological questions you never could have before and make important new discoveries.


Inside the cell, chromosomes are typically organized into a hairball-like chromatin structure. DNA sequences found on the same chromosome tend to be closer in physical space. Sequences located closer together on a chromosome are also more likely to be in close physical proximity than sequences farther apart on the chromosome. Hi-C measures genomic proximity, providing structural information of the genome to complement more commonly available sequence information.



In Proximo Hi-C, chromatin is cross-linked with formaldehyde to fix DNA sequences in close physical proximity. The cross-linked chromatin is fragmented, and the resulting junctions are extracted and proximity ligated. These junctions capture chromatin structure information. Illumina paired-end sequencing is then used to read both ends of the ligated fragments, identifying the sequences that were originally in close proximity in vivo.


Proximo Hi-C reads are mapped to a set of contigs from a draft assembly. The number of Hi-C read pairs mapped to a given ligation site reflects the physical proximity between those two loci.


This structural information is used first to place contigs into chromosome groups...


...and then used to order and orient the contigs into whole chromosome-scale scaffolds.


Complete chromosome-scale scaffolds and deconvoluted metagenomes, along with a commitment to personalized service without hidden costs.