Designing a brand-new antisense oligonucleotide drug for a single patient's unique mutation — from sequencing to bedside
For most ultra-rare disease patients, the path to a diagnosis is itself a years-long odyssey. Whole-genome sequencing (WGS) or whole-exome sequencing (WES) of the patient — often paired with parental "trio" sequencing — is used to identify a single causal variant. When that variant is private to one family, or even unique to one individual, no approved drug exists that was designed with this patient in mind. That gap is precisely what an individualized therapy program is built to close.
A patient with an unexplained, progressive, often neurological syndrome is enrolled for genomic sequencing after other diagnostic avenues fail. The typical pipeline:
• Whole-genome or whole-exome sequencing of the patient, ideally alongside unaffected parents (trio analysis) to identify de novo variants • Variant filtering: remove common polymorphisms (population allele frequency >0.1% in gnomAD), retain rare, predicted-damaging variants • Functional annotation: splice-site disruption, nonsense mutation, frameshift, or deep-intronic variant creating a cryptic splice site • Segregation and phenotype matching: does the variant location and predicted mechanism plausibly explain the patient's specific clinical presentation? • Confirmation: Sanger sequencing validates the candidate variant; RNA sequencing from patient fibroblasts or blood can directly show the aberrant splicing or transcript effect
The defining feature of the "N-of-1" scenario is that the variant is private — found in this one patient (or one family) and essentially nowhere else in the literature or population databases — meaning no existing clinical trial, and often no existing drug candidate, was ever built to address it.
Conventional drug development targets a mechanism shared across thousands of patients, which is what justifies the enormous fixed cost of a development program. When a causal mutation is unique to a single patient, that economic logic breaks down entirely — there is no market-sized population to amortize a traditional 10–15 year, billion-dollar development pathway against.
Antisense oligonucleotide (ASO) chemistry is unusually well suited to this problem because the same well-characterized chemical backbone and delivery approach can be re-used across many different patients — only the ~18–22 nucleotide sequence itself changes to match each patient's specific mutation. This turns "designing a new drug" into something closer to "writing a new short sequence into an already-validated chemical platform," which is what makes an individualized therapy feasible on a clinically meaningful timescale at all.
The precedent case is milasen, an individualized ASO created in 2018 for a single patient, Mila Makovec, with a unique intronic mutation causing Batten disease. From mutation identification to first dose took roughly one year — versus a decade or more for a conventional new drug.
Once the causal mutation and its molecular mechanism are understood, a custom antisense oligonucleotide is designed to bind — through simple Watson-Crick base pairing — the patient's specific mutant RNA sequence. Because the chemistry, backbone, and general design rules are already well established from prior approved ASO drugs, this step can move from sequence to synthesized, purified drug substance in a matter of weeks.
Depending on the mutation's molecular consequence, the ASO is designed for one of several mechanisms:
• Splice modulation: for mutations that create a cryptic splice site (as in milasen), the ASO is designed to bind that new splice site and steer the spliceosome back toward correct, near-normal exon inclusion • Steric-block knockdown: for a toxic gain-of-function mutant transcript, the ASO can be designed to sterically block translation or promote RNase H-mediated degradation of the mutant transcript specifically • Allele-selective targeting: where possible, the sequence is designed to discriminate the mutant allele from the healthy allele by even a single nucleotide, preserving normal gene function
Design proceeds computationally: candidate sequences are generated tiling across the mutation site, each scored for predicted binding affinity (melting temperature), secondary-structure accessibility of the target RNA, and specificity.
Before synthesis, every candidate sequence is checked computationally against the entire reference transcriptome for unintended complementary binding sites elsewhere in the genome — an off-target hybridization event could silence or disrupt an unrelated, essential gene. Candidates with problematic off-target matches are discarded.
The surviving lead sequence is synthesized using solid-phase chemistry on a well-established chemical backbone (e.g., 2'-O-methoxyethyl phosphorothioate, or phosphorodiamidate morpholino) — the same platform chemistry used in already-approved ASO drugs. Because the backbone chemistry itself does not need to be re-invented, manufacturing and purification can draw directly on existing GMP-compatible processes, compressing a step that would otherwise take years down to weeks.
This is the central efficiency of the N-of-1 ASO approach: only the ~20-nucleotide sequence is truly novel per patient. Everything else — delivery route, chemical backbone, manufacturing process, general safety profile of the platform — is inherited from prior experience, dramatically shortening the path from mutation to drug substance.
A conventional new drug undergoes years of preclinical testing across multiple animal species, dose ranges, and toxicology endpoints before ever reaching a human. For a single patient facing a rapidly progressive, otherwise untreatable disease, that timeline is not available. Preclinical safety testing is instead conducted at a deliberately minimal — but not absent — scale: enough evidence to support a reasonable judgment that the risk of proceeding is justified.
Even under extreme time pressure, a defensible minimal preclinical package typically still includes:
• In-vitro tolerability in the patient's own cells (fibroblasts, induced pluripotent stem cell-derived neurons, or other relevant patient-derived cell type) to confirm the ASO engages the intended target without obvious cytotoxicity • A small in-vivo tolerability study, often in a single rodent species, at doses spanning the anticipated clinical range, focused on acute tolerability rather than a full chronic toxicology program • Manufacturing quality release testing: identity, purity, and sterility of the synthesized drug substance, which is non-negotiable regardless of program size • Where feasible, comparison to the established safety profile of the platform chemistry (backbone) from prior approved or investigational ASOs sharing the same chemical class
What is knowingly not done, by necessity: chronic multi-species toxicology, full carcinogenicity or reproductive toxicity studies, and large-cohort dose-ranging — the kind of program that would normally take years and hundreds of animals.
The ethical and scientific justification for this compressed program rests on a few converging factors: the disease is rapidly progressive and otherwise fatal or severely disabling; the platform chemistry itself (independent of the specific sequence) has an established safety track record from prior ASO programs; and the alternative — waiting years for a conventional program — is not a genuinely available option for this particular patient.
This is a real, not merely formal, trade-off: minimal-scale testing provides meaningfully less certainty than a conventional program would. Clinicians and regulators reviewing an individualized program are explicitly accepting a higher level of residual uncertainty about rare or delayed adverse effects, in exchange for the only realistic chance of intervening on the patient's timeline.
Milasen underwent toxicology testing in a single non-human primate and a rodent tolerability study — far short of a conventional multi-year, multi-species program — a scale considered reasonable given the chemistry's prior track record and the patient's rapidly progressive disease course.
Regulators have increasingly recognized that a rigid, one-size-fits-all approval pathway cannot serve patients whose disease is caused by a mutation found in no one else on record. Individualized-treatment pathways — such as single-patient Investigational New Drug (IND) applications in the United States — allow a physician-sponsor to seek authorization to treat one named patient, under expedited but not absent oversight.
A standard new drug approval requires evidence from controlled trials across many patients, establishing statistical evidence of safety and efficacy for a defined population. An individualized-treatment pathway instead evaluates a much narrower, and different, question: given everything currently known about this specific patient, this specific mutation, and this specific molecule's design and manufacturing quality, is it reasonable to proceed with treating this one person?
Key regulatory mechanisms enabling this include:
• Single-patient (or "compassionate use") IND applications, submitted by the treating physician rather than a commercial sponsor • Expedited review timelines — sometimes days for a patient in medical crisis — reflecting the urgency, while still requiring a manufacturing quality dossier and available safety data • Close regulator-sponsor dialogue in place of the arms-length review typical of a standard application, given the compressed timeline and small evidentiary base
"Expedited" does not mean "unreviewed." Even under a single-patient pathway, regulators still require: a chemistry, manufacturing, and controls (CMC) package confirming the drug substance is what it is claimed to be and is free of contamination; a summary of the (necessarily limited) preclinical safety data generated; documented informed consent reflecting the elevated uncertainty; and a plan for monitoring the patient and reporting any adverse events after dosing.
The balance being struck is explicit rather than hidden: regulators are accepting a smaller, faster evidentiary package than they would for a conventional drug, in direct exchange for enabling treatment on a timeline that matches this particular patient's disease trajectory — while still insisting on the baseline safeguards that even an expedited pathway should not skip.
Milasen was authorized under an FDA single-patient IND in 2018, illustrating how existing regulatory mechanisms — originally designed for compassionate use of already-developed drugs — were adapted to authorize an entirely new, purpose-built molecule for one patient.
Once cleared, the individualized drug is finally administered to the single patient whose mutation defined its design from the outset. Because the preceding testing was necessarily limited in scale, this moment carries a different weight than a conventional drug launch: the patient's own response is, in a very real sense, the first and only dataset this molecule will ever generate at this dose in this person.
Dosing typically occurs in a controlled clinical setting (often intrathecal injection for central nervous system-directed ASOs, mirroring the route used by approved ASOs treating similar tissues) with baseline clinical, laboratory, and — where relevant — imaging or electrophysiological assessments captured immediately beforehand, so that any subsequent change has a clear reference point.
Because the preclinical safety base is thin by design, the clinical team typically front-loads intensive short-term monitoring: vital signs, neurological exams, laboratory safety panels, and any disease-specific biomarkers are tracked far more frequently in the hours and days immediately following the first dose than would be typical even for a new therapy with a conventional safety record.
For an individualized therapy, "monitoring" is not merely a safety formality — it is effectively the only evidence-generation mechanism available. There is no larger trial cohort to draw statistical conclusions from; each subsequent dose, each follow-up assessment, and each observed change in the patient's disease trajectory directly informs whether treatment continues, whether the dose is adjusted, and how the risk-benefit judgment for this patient evolves over time.
This creates a distinctive clinical posture: closer and more frequent follow-up than almost any approved therapy would warrant, sustained for as long as treatment continues, precisely because the limited pre-treatment data means every observation carries outsized informational weight.
Mila Makovec received her first dose of milasen in January 2018 and continued periodic re-dosing with close clinical monitoring; her case became a widely cited proof-of-concept that a genuinely new drug, designed for and administered to a single patient, could move from an identified mutation to bedside treatment within about a year.