Dispatch / Carlsbad, California
Arima
Arima
Genomics
The biotech that stopped reading DNA as a line and started reading it as origami - and turned that re-reading into cancer tests.
The biotech that stopped reading DNA as a line and started reading it as origami - and turned that re-reading into cancer tests.
Somewhere in Florida, in a CLIA-certified lab, a paraffin block pulled off a hospital shelf is about to give up a secret it has been holding for years. The tumor sample is small. It is fixed. By the standards of modern sequencing, it should be a frustrating sample - the kind that yields shrugs and equivocal reports. Instead, a six-hour wet-lab protocol developed by a 46-person company in Carlsbad will crosslink the DNA inside its nuclei, snip it, biotinylate it, ligate the pieces that were touching, and feed the result to an Illumina sequencer. The output will not be a list of variants. It will be a contact map - a picture of which parts of the genome were neighbors, in three dimensions, at the moment the cell was preserved. Inside that picture is a gene fusion that other panels missed. Arima Genomics built the chemistry that found it.
That is the company today: a small, deeply technical outfit selling research kits to the world's largest sequencing centers while quietly walking its core chemistry into oncology clinics. Its research brand is its name. Its clinical brand is Aventa. The connective tissue between them is Hi-C - a proximity-ligation method that captures how chromatin folds.
Most sequencing tools read the genome like a book. Arima reads it like a knot. The distinction sounds academic until you remember that cancer is often a knotting problem: genes that should never speak to each other start sharing enhancers; chromosomes break and rejoin in ways a linear read can describe only as "weird coverage." Three-dimensional context is where structural variants live. Arima built a way to see them.
The company was spun out of UC San Diego in 2015 by Siddarth Selvaraj and William Alaynick. For a decade it has been the unflashy supplier of chromatin conformation - kits, protocols, services - to genome projects everywhere. The Wellcome Sanger Institute picked it as a Hi-C partner in 2020. Active Motif resells its service. Vertebrate Genomes, Earth BioGenome, Darwin Tree of Life - if a chromosome-scale assembly came out of a public sequencing center in the last five years, there is a reasonable chance Arima's reads are in the scaffold.
Then, in June 2025, two things happened on the same day. Illumina Ventures led a $22 million Series C. And Tom Willis - veteran of ParAllele and Sequenta, both acquired - replaced Selvaraj as CEO. Selvaraj stayed on as President and COO. The signal was unmistakable. Arima had a chemistry the research market loved. Now it wanted the clinical market too.
More of the genome. More of what matters.
The recipe sounds dramatic and is not. Crosslink the DNA inside intact nuclei so pieces that are physically close stay close. Cut the DNA with restriction enzymes. Mark the new ends with biotin. Ligate. Sequence the resulting pairs. Wherever you see two distant parts of the genome stitched together in a read, you have evidence they were in contact in three dimensions.
That basic idea has been around since 2009. Several companies have tried to commercialize it. What Arima did - and what kept buyers coming back - was unglamorous engineering. They moved from one restriction enzyme to a mix that produces more uniform coverage. They compressed the protocol from roughly two days to six hours. They made it work on FFPE blocks, the embalmed, formalin-soaked tissue samples that pathology labs have been hoarding for decades. None of these are press-release achievements on their own. Together, they make a research curiosity into something a clinical lab can run on a Tuesday.
Today's Arima catalogue reflects that long, patient sanding. There is a genome-wide kit for labs that want unbiased chromatin maps. There is a Capture HiC product for groups who want higher resolution at specific loci - promoters, regulatory hotspots, the usual suspects. There is a genome-assembly workflow that uses long-range Hi-C signal to scaffold contigs into full chromosomes. And there is Aventa, the clinical face: FusionPlus for solid tumors, Lymphoma for B-cell malignancies, both designed around the FFPE samples a pathologist actually has on hand.
The pitch to oncologists is uncomfortably simple: your current panel sees about 60 percent of what is rearranged in this tumor. Run Aventa, and you see the rest - including the cryptic fusions and the enhancer-hijacking events that move drug eligibility around. It is a pitch made easier by the fact that the chemistry has been proven, over and over, on the research side.
Six-hour proximity-ligation prep for genome-wide chromatin contact maps. The flagship reagent.
Targeted enrichment - promoter capture and custom panels - for higher-resolution interaction mapping.
Long-range Hi-C reads stitched into chromosome-scale scaffolds. The reason Sanger picked them.
FFPE-friendly solid-tumor test for gene fusions and structural rearrangements other panels miss.
3D-genome signal applied to lymphoma classification and diagnosis. CLIA-run.
Custom Hi-C and structural-variant work for translational R&D groups.
Arima is roughly the size of a startup that just exited stealth. Its customer list is the size of a multinational. That asymmetry - small team, large reach - is what kits-as-a-business model is supposed to look like when it works.
Source: Crunchbase, GenomeWeb, company disclosures.
Selvaraj and Alaynick incorporate Arima Genomics out of UC San Diego, betting that 3D genome structure has commercial legs.
$7M round (Co-Win Ventures, Berkeley Catalyst). The research-kit business takes shape.
Wellcome Sanger Institute names Arima its Hi-C technology partner; high-coverage HiC early access launches.
Joint venture with Protean BioDiagnostics produces a CLIA-certified clinical lab in Florida. Hi-C goes from instrument-room curiosity to clinical product.
$22M led by Illumina Ventures. Tom Willis becomes CEO; Selvaraj stays on as President and COO. The mandate: scale the clinical pipeline.
Bring sequence and structure together to find more of what drives disease.
Hi-C and proximity-ligation is a quiet corner of genomics with a few persistent residents: Dovetail Genomics (now Cantata Bio) and Phase Genomics on the chromatin side; Bionano Genomics on optical mapping; Illumina, PacBio, and Oxford Nanopore on the broader sequencing and structural-variant front. Arima's edge is less about the underlying chemistry - the patents and protocols overlap - and more about the protocol's clinical-readiness: FFPE compatibility, six-hour turnaround, and a clinical partner already running tests under CLIA. The Illumina Ventures lead is, among other things, a vote on which corner of that field is closest to the bedside.
The TeamUCSD-trained genomicist who built the original Hi-C chemistry into a product. Handed off the CEO seat in 2025 to focus on operations.
Co-founded Arima in 2015 alongside Selvaraj; longtime collaborator on the proximity-ligation work that became the kit business.
Twenty-plus years building genomics companies - founder/CEO of ParAllele BioScience (acquired by Affymetrix) and Sequenta. Joined June 2025.
Return to the Florida lab. The contact map has come back from the sequencer. Where a standard fusion panel saw a flat readout, the Hi-C signal shows two distant parts of the patient's genome were, in fact, neighbors at the moment of fixation - and that the neighborhood matches a known oncogenic rearrangement. The pathologist updates the report. The oncologist updates the plan. The patient becomes eligible for a targeted therapy they were not eligible for an hour ago. None of that involves new biology. It involves an old block, a six-hour kit, and a company in Carlsbad that spent a decade making the third dimension of DNA something a Tuesday lab tech can run without thinking about it. The block goes back on the shelf. It is, suddenly, more interesting than it has been in years.