The $100 Genome Meets the FDA Rulebook: DNA Sequencing’s Next Act Isn’t Just About Speed or Cost

A sub‑$100 human genome has arrived in practice, not just on conference slides. MGI/Complete Genomics’ T20×2 platform promises roughly 50,000 whole genomes a year at under one hundred dollars apiece, and Ultima Genomics has been dangling three trillion free reads—about nine thousand genomes—to lure academics onto its wafer-based system. The headline writes itself: price is no longer the bottleneck. Yet the balance sheets of the companies selling those genomes tell a more complicated story. Illumina, still the volume leader and de facto landlord of the short‑read ecosystem, reported around $1.04 billion in “core” revenue in the first quarter of 2025, essentially flat year over year. Oxford Nanopore Technologies, the long‑read insurgent, guided investors to roughly £105 million for the first half, up smartly after a bruising 2024. Cheaper data has not automatically translated into faster top‑line growth.

The broader market has reflected that tension. Estimates put DNA sequencing revenues at roughly twelve to fifteen billion dollars in 2024, a figure that has crawled rather than sprinted since the COVID surge faded. Forecasts still imagine a tripling by the mid‑2030s, but only if clinical reimbursement, regulatory clarity and multi‑omics integration show up on schedule. Until then, the industry is in a curious limbo: awash in technological innovation, constrained by economics and policy.

Sticker Shock in Reverse: When $100 Genomes Don’t Grow a Market

The years after the pandemic produced an odd hangover. Public‑health surveillance and emergency diagnostics evaporated almost overnight, and routine clinical genomics was not yet ready to fill the hole. At the same time, capital grew expensive. Higher interest rates, a shut IPO window and skittish venture investors forced many start‑ups—and even mid‑size biotechs—to freeze or shrink sequencing‑heavy programs. Core facilities and hospital labs paused big capital purchases while they waited for the next generation of hardware: Illumina’s NovaSeq X, PacBio's Revio, Element’s AVITI and others. When those boxes finally arrived, they demanded twelve to eighteen months of validation work before labs felt comfortable scaling again.

Vendors cut prices faster than volume could grow. The relentless fall in dollars per gigabase—sub‑$100 genomes in high‑throughput environments, $200 consumable costs from Illumina on its largest flow cells—meant that unit counts rose while revenue per run shrank. Add in regulatory fog. In the United States, the Food and Drug Administration moved to bring laboratory‑developed tests—thousands of which rely on sequencing—under medical‑device oversight. Europe’s IVDR regime added its own paperwork drag. Hospital labs hesitated to scale assays that might need expensive revalidation. Reimbursement remained patchy: whole‑genome sequencing is still not broadly covered outside rare disease programs or certain oncology niches. And geopolitics complicated everything from procurement to data governance, as export controls and U.S.–China tensions made global rollouts harder.

Despite that, the next decade still looks larger, not smaller. A reasonable base‑case view has the market climbing from roughly fifteen billion dollars in 2024 to the mid‑forties by 2035, an annual growth rate a touch above ten percent. A bullish scenario—broad reimbursement for whole genomes, fast regulatory clarity, <$50 consumables at scale, and seamless multi‑omics workflows—pushes the figure north of sixty billion. The bear case is equally clear: prolonged regulatory fights, slow hospital adoption, capital scarcity and another round of price compression could keep growth closer to six percent a year. In all versions, the sources of demand are similar: clinical genomics for oncology, rare disease, non‑invasive prenatal testing and pharmacogenomics; structural and long‑read applications moving from R&D curiosities to routine tools; spatial and proteomic add‑ons that turn sequencing into one node in a richer assay; and national population programs that keep high‑throughput lines humming.

Short Reads Lose Their Monopoly; Long Reads Lose Their Excuse

For a decade, short‑read sequencing was synonymous with Illumina. That era is over. PacBio, long known for its high‑accuracy long reads, built Onso, a benchtop short‑read machine based on “sequencing by binding,” and markets it on a simple promise: more than ninety percent of bases at Q40 accuracy, far above what most sequencing‑by‑synthesis boxes routinely claim. Element Biosciences entered with AVITI, a system that uses “avidity” chemistry to slash reagent volumes while maintaining accuracy through the homopolymer stretches that often trip competitors. MGI/Complete Genomics, still effectively blocked from much of the U.S. market, is pushing its DNBSEQ family into Europe, the Middle East and Latin America, positioning the hulking T20×2 for national biobanks and offering smaller instruments to core labs. Singular Genomics, after layoffs in 2024, is trying to carve out a spatial‑biology‑infused niche for its G4 series. Ultima Genomics, meanwhile, is betting that a radically different flow architecture—200‑millimeter wafers run like semiconductor fabs—plus aggressive pricing can pry open the highest‑throughput customers.

Choice is good for buyers, but it also raises switching costs. Everything from library prep and automation to alignment pipelines, quality systems and staff training has been optimized for Illumina’s SBS chemistry. Moving even a fraction of work to a rival box means re‑validating assays, rewriting scripts and negotiating new service contracts. That friction is one reason the short‑read market feels crowded but not yet commoditized.

Long reads tell a parallel story. They began as the expensive, error‑prone way to glimpse genome regions short reads simply could not resolve. PacBio’s Revio changed the math, multiplying HiFi output roughly fifteen‑fold over the Sequel IIe and delivering day‑scale runs with per‑base accuracy that rivals short reads while preserving the ability to phase haplotypes and call structural variants. Oxford Nanopore’s Kit 14 pushed its simplex accuracy above Q20 and, by reading both strands of a molecule, reached around Q30 in duplex mode. ONT never ceded its defining advantages: ultra‑long reads that can span megabases, portable devices that fit in a pocket, and native methylation calling baked into the electrical signal itself. Together, those advances moved long reads out of the “nice to have” column. Population projects, clinical genetics labs dealing with repeat expansions or balanced translocations, and gene therapy manufacturers verifying vector integrity are now building long‑read capacity on purpose.

Structural variation remains a pain point where neither short nor long reads always deliver fast answers. Here, mapping technologies have found room to grow. Bionano Genomics' Stratys system offers roughly four times the throughput of its Saphyr predecessor, letting cytogenetics and rare‑disease labs detect large rearrangements in days rather than weeks. Nabsys is taking a different tack with electronic, rather than optical, mapping, pitching high‑resolution "HD" maps to oncology and cytogenetics customers and backing the push with fresh capital. These tools are supplements, not substitutes, but they plug clinically meaningful gaps and justify their own line items in lab budgets.

China’s Low‑Cost Offensive and the Politics of DNA

China is no longer just a vast customer base; it is a price setter. Companies such as MGI/Complete Genomics, the broader BGI Group, GeneMind and Novogene are exporting high‑throughput machines and bargain consumables into markets that are more open to them—Europe, the Middle East, parts of Latin America—while remaining largely fenced out of U.S. federal and many hospital contracts. Their advantage is structural. National population programs keep their factories busy, allowing them to quote sub‑$100 genomes at healthy margins. Alternative chemistries like DNBSEQ avoid some of Illumina’s intellectual‑property tripwires, and domestic component supply chains reduce dependence on U.S. vendors. Many of these firms also sell “full‑stack” packages: sequencing, informatics and clinical reporting bundled at prices Western contract research organizations struggle to match.

Constraints are just as real. Regulatory and political barriers—from procurement bans to CFIUS‑style reviews and data‑privacy regimes—limit access to sensitive markets. Patent battles with Illumina have whipsawed product availability. And trust is not trivial; some health systems balk at shipping germline data to servers they do not control or across borders they do not fully trust. Still, even laboratories that never touch a Chinese flow cell feel the ripple: Illumina and its Western rivals now set prices against an aggressive floor defined in Shenzhen or Wuhan, not San Diego.

The Road to 2035

If the past few years were defined by technology outpacing business models, the next decade will hinge on policy, integration and proof of value. Clinical reimbursement remains the single most powerful lever. When insurers routinely pay for whole‑genome sequencing in oncology and rare disease, volume jumps and price sensitivity softens. Regulatory clarity matters almost as much; laboratories cannot invest confidently in assays that may be relabeled medical devices overnight. Integration will separate winners from commodity players. Sequencing is becoming one layer in a stack that includes full‑length RNA profiling, spatial transcriptomics, single‑cell multi‑omics and even single‑molecule protein sequencing. Platforms that make those transitions seamless—chemistry to software to clinical report—will capture more of the margin.

Buyers have grown more sophisticated. They now model total cost per answer, not just per gigabase. Staff time, compute, storage, quality control and validation can dwarf consumables when throughput is moderate. Ecosystem fit is paramount: a box that does not play nicely with 10x Genomics, an existing LIMS, or a validated pipeline imposes hidden taxes. Vendor durability is also under quiet scrutiny. A gleaming instrument is worthless if the company behind it cannot service the hardware or ship reagents in three years.

Geopolitics remains the wild card. Export controls could reshuffle supply chains again. Data‑localization laws may force global research consortia to rethink how they share raw reads. Conversely, national genome programs—from the Gulf states to Scandinavia to Southeast Asia—could provide the steady work that amortizes the biggest machines and funds the next chemistry overhaul.

For now, the industry’s headline act—the relentless march to cheaper, better genomes—continues. But the subtext has changed. In 2025, the winners will be the ones who navigate regulators, integrate workflows and persuade cautious lab directors that switching horses midstream will not drown them in validation paperwork. That is a story even Wall Street can read.