SynapseX Genome

AI and quantum
for the human genome.

A laboratory for variant interpretation. The agent gathers the public evidence, writes and runs the analysis in your workspace, escalates a subproblem to quantum only where that is honest — and seals every run into a record someone else can re-run.

Lab live in chatFree simulators liveSubstitution Atlas in developmentReal QPU early access
$0simulators and public evidence, every plan
24 qexact statevector simulation, 0 credits
SHA-256sealed, reproducible run records
Localprofile a file without uploading it
$0simulators and public evidence, every plan
24 qexact statevector simulation, 0 credits
SHA-256sealed, reproducible run records
Localprofile a file without uploading it
$0simulators and public evidence, every plan
24 qexact statevector simulation, 0 credits
SHA-256sealed, reproducible run records
Localprofile a file without uploading it
Why this is hard

Two genomes in one.
We read one of them well.

THE ~2%

The blueprint.

A small fraction of the sequence spells out proteins directly. We read it comparatively well: change a codon and you can often reason from the amino acid to the protein to the phenotype.

THE OTHER ~98%

The control panel.

The rest decides when, where and how much of each protein gets made — millions of switches and dials, most of them cell-type specific. It is where the majority of trait-associated variants land, and where interpretation is still hard.

A single substitution can change a protein, weaken a splice site, create or destroy a transcription-factor motif, or do nothing at all — and which of those it does usually depends on the cell type you ask about.

The search space

Nine billion
single-letter questions.

9 billion
possible single-letter changes across one human genome — three alternatives at every position
3,100 Mb
base pairs in one copy of that genome (GRCh38)
~20,000
protein-coding genes, spanning roughly 2% of the sequence
>90%
of trait-associated variants found by genome-wide association studies fall outside protein-coding sequence (Maurano et al., Science, 2012)

Sources: GRCh38 assembly statistics; GENCODE/Ensembl gene counts; Maurano et al., Science 2012 (10.1126/science.1222794). Rounded down to the figure each source supports.

The interpretation loop

From a coordinate
to a record.

I
step 1 / 5running

Bring the locus

A coordinate, an rsID, or a shortlist exported from your own pipeline as CSV or TSV. Nothing has to be uploaded to start: on the desktop the agent can profile a local file in place and return only the profile.

What you can run today

Work that produces evidence, not adjectives.

Everything in this section runs today. None of it depends on the Substitution Atlas, which is still in development.

Inside the quantum lab

Variant evidence dossiers

Point at a locus and get the public record assembled and cited: classification, population frequency, the published mechanism, and an explicit line between what is established and what is not.

Cohort prioritisation

Rank a shortlist exported from your own pipeline by criteria you can read and change — no black box, and the ranking code stays in your workspace.

Hybrid escalation

Combinatorial and electronic-structure subproblems get a quantum path when that is honest: you bring the encoding, the free simulator runs first, hardware only on approval, classical baseline always reported.

Reproducible figures

Plots and tables come back with the manifest that produced them, ready to attach to a paper or a review.

Scripted, if you prefer

The same lab from Python or the CLI, and from your own agent over MCP where that access is open — same backends, same balance, same sealed records.

Start exploring

Six loci, six mechanisms.
Open any one in the lab.

Each card is a real, publicly documented variant with its GRCh38 coordinate verified against Ensembl. Clicking one opens the lab with a question the agent can answer today from public sources — and it will cite them.

Variantcoding
chr11:5227002:T>A
rs334

Sickle cell disease

The founding molecular disease. A single substitution changes the sixth amino acid of β-globin from glutamate to valine, and the mutant haemoglobin polymerises when deoxygenated.

Gene
HBB
Biosample
Erythroid
free · agent + public evidenceOpen in chat
Variantsplice
chr11:5226925:C>T
rs33915217

β-thalassaemia

A change five bases into intron 1 (HBB c.92+5G>A) weakens the splice donor, so a fraction of transcripts are mis-spliced and β-globin output falls. The phenotype tracks how much correct splicing survives.

Gene
HBB
Biosample
Erythroid
free · agent + public evidenceOpen in chat
Variantnon-coding
chr1:109274968:G>T
rs12740374

LDL cholesterol

A non-coding change that creates a C/EBP transcription-factor binding site in a liver enhancer, altering SORT1 expression in hepatocytes. One of the first regulatory variants mapped from a genome-wide association signal to a mechanism.

Gene
CELSR2 · PSRC1 · SORT1
Biosample
Liver
free · agent + public evidenceOpen in chat
Variantnon-coding
chr16:53767042:T>C
rs1421085

Obesity risk

Inside an FTO intron, this change disrupts a conserved ARID5B repressor motif. The published mechanism runs through de-repression of IRX3 and IRX5 in adipocyte precursors, not through FTO itself.

Gene
FTO → IRX3 · IRX5
Biosample
Adipocyte
free · agent + public evidenceOpen in chat
Variantnon-coding
chr5:1295113:G>A
rs1242535815

TERT promoter (C228T)

A promoter change that creates a new ETS-family binding motif upstream of TERT, recruiting GABP and reactivating telomerase. Among the most recurrent non-coding somatic changes in human cancer.

Gene
TERT
Biosample
Melanoma · glioma
free · agent + public evidenceOpen in chat
Variantcoding
chrX:153905816:C>T
rs104894760

Nephrogenic diabetes insipidus

An X-linked coding change in the vasopressin V2 receptor. Published work groups AVPR2 variants by whether the receptor misfolds and is retained in the cell, or reaches the surface and fails to signal — two mechanisms with different therapeutic logic.

Gene
AVPR2
Biosample
Kidney
free · agent + public evidenceOpen in chat

These descriptions state the published mechanism for each variant. They are not predictions produced by SynapseX, and nothing here is medical advice or a diagnostic result.

Quantum, honestly

Where a quantum step
earns its place.

No one has demonstrated a quantum advantage for genomics, and we will not be the first to claim one in marketing copy. What exists is a set of subproblems where a quantum method is a legitimate thing to try — and the discipline to run the classical baseline next to it, on the free simulator, before anyone spends a credit.

0 cr
simulator probes
1
balance across models and compute
Both
quantum and classical, side by side
See the backend catalog
maturity of the published recordOperational
Quantum kernels for classificationEARLY ACCESS
parity with classical models on reduced omics data; no advantage shown at scale
hardware, toy scale
Combinatorial solves (assembly, phasing)EARLY ACCESS
annealer and gate demonstrations on small instances inside hybrid solvers
hardware, toy scale
Electronic structure for binding energeticsEARLY ACCESS
few-orbital fragments with the protein as point charges; not variant-specific yet
hardware, fragment scale
Free simulation to try any of themLIVE
bring the circuit or the Hamiltonian; exact statevector to 24 qubits, at 0 credits
0 credits
Substitution AtlasWAITLIST
a precomputed map of variant effects and our own sequence model — in development
request access
Custody and provenance

Your data.
Your machine.

Genomic data is not a spreadsheet you can re-download. The defaults here assume that: the cheapest way to analyse a file is often without moving it, and anything that does move is versioned, hashed and checked on arrival.

local profilingversioned datasetssha256 on arrivalapproval before spend

Profile without uploading

On the desktop, the schema, column ranges, missing-value counts and a SHA-256 of a tabular file are computed on your machine. Only the profile travels.

Append-only versions

Re-uploading a dataset creates a new version instead of overwriting one. An old run still points at the bytes it actually used.

Verified at the far end

The runner re-checks the bytes against the sealed hash before executing. A mismatch fails the run rather than quietly analysing the wrong file.

Nothing spends silently

Paid hardware shows an estimate and waits for your approval, reserves against it, then settles for actual usage.

Four ways in

Same lab.
Four front doors.

LIVE

The lab, in chat

No install, no code required.

A persistent workspace with Python and notebooks behind a conversation. Ask for the evidence on a locus and watch the analysis get written, run and explained.

  • Free simulators at 0 credits
  • Charts rendered in the thread
  • Every run recorded
Open the lab
BETA

Desktop & CLI

For data that should not move.

The agent runs on your machine and can profile a local tabular file in place — schema, column ranges, missing-value counts and a SHA-256 — returning the profile without the file.

  • Local-first file access
  • Scoped, confirm-class permissions
  • macOS, Linux, Windows
Download
LIVE

API & Python SDKs

For pipelines that already exist.

Scoped keys and a prepaid wallet over the same backends: list what is available, get an estimate, submit the job, pull the sealed record back.

  • Scoped, rotatable API keys
  • Reserve then settle, per job
  • Queryable usage ledger
See the API platform
EARLY ACCESS

MCP for your own agent

Bring your own intelligence.

The lab is built to be driven over the Model Context Protocol, so an agent you already run can list backends, estimate, submit and fetch evidence without our models in the loop. Credentials are opening with early partners.

  • Backend catalog and estimates
  • Job submission and results
  • Sealed evidence retrieval
Request access
FAQ

What people ask
before they trust it with a genome.

The lab. You get a persistent workspace with Python and notebooks, an agent that reads and writes the code with you, a versioned dataset store, free quantum simulators at 0 credits, and a sealed, reproducible record of every run. Point it at a locus and it gathers the public evidence, writes the analysis, runs it and shows its work. What is not live is the Substitution Atlas, a precomputed map of predicted variant effects across the genome — that is in development, and this page never pretends otherwise.

Not yet, and we will not say we do. Today the agent reasons over public records, published literature and open models, and runs the analysis you approve. A sequence-to-function model of our own is in development, and access to it opens with the Substitution Atlas. Everything on this page that is live is labelled live.

In small, hard subproblems inside a classical pipeline — a combinatorial solve, a kernel evaluation, a few-orbital electronic-structure calculation. The published record is proof-of-concept scale: toy assembly instances on annealers, quantum kernels reaching parity with classical models on reduced datasets, lattice-model folding of short chains. No result shows a quantum advantage for genomics at any realistic scale. We put a quantum step in front of you when it is the honest tool for that subproblem, we run it on the free simulator first, and we tell you what it cost against the classical baseline.

Only if you send it. On the desktop app the agent can profile a tabular file in place — schema, column ranges, missing-value counts, a SHA-256 of the bytes — and only that profile comes back. When you do upload, the dataset is versioned and sealed: re-uploading creates a new version rather than overwriting, the runner verifies the bytes against the sealed hash on arrival, and a run whose data does not match refuses to execute. Note that this is a data-custody design, not a regulatory certification: we make no HIPAA or GDPR compliance claim for your use of it.

Each run freezes a content-hashed manifest of its code, its declared dependencies, its inputs and the backend, so the same inputs always produce the same fingerprint. Paid runs come back with an execution receipt sealed by the executing service under a SHA-256 Merkle root. Either way this proves integrity and reproducibility, not origin, and we describe it that way.

Nothing. Quantum simulation runs at 0 credits on every plan and free compute runs are included each month. Paid hardware — real QPUs and GPU workers — asks for an estimate and your approval before a credit moves, then settles for what was actually used. You cannot be surprised by a bill you did not approve.

No. Nothing here is a diagnostic device and no output is medical advice. It is a research instrument: it helps you gather evidence, model a hypothesis and keep a reproducible record. Clinical interpretation stays with qualified people and validated assays.

Through the API platform and the Python SDKs: the same backends, the same balance and the same sealed records the chat uses, with scoped keys and a queryable ledger. Driving the lab from your own agent over the Model Context Protocol is built and opening with early partners rather than self-serve today — ask and we will tell you where it stands.

Open a locus.
Keep the receipt.

Start free: the lab, the public evidence and the simulators cost nothing. The Substitution Atlas and our own sequence model are in development — ask for early access and we will tell you honestly where they are.

Research use only. Not a diagnostic device and not medical advice.

SynapseX Genome is a research instrument. It does not diagnose, treat or make clinical recommendations, and no output should be relied on for medical decisions. Variant mechanisms described on this page are drawn from published literature and public records; genome coordinates are GRCh38.Runs are hash-sealed, and paid runs carry a Merkle-sealed receipt from the executing service: that proves integrity and reproducibility, not origin.