AlphaGenome predictions

AlphaGenome reads a megabase of DNA and predicts where it is transcribed, where the chromatin is open, how it splices, and how it folds. We ask it about TAL1 in two cell lines, stack the answers that share units on one axis, and then score an oncogenic insertion against the reference to see the enhancer it creates.

Prerequisites#

• the AlphaGenome plugin, which contributes the adapters these tracks use, the query panel, and the variant right-click item
• nothing installed locally, and no AlphaGenome API key: the page reads two stored predictions, each recorded once, so following it spends no quota

Where the data comes from#

We made two predictions over the TAL1 locus once against AlphaGenome and froze them under stable tokens, and the list below also carries the hg38 annotation they are read against. The locus and the variant follow the AlphaGenome team's worked example.

• the reference prediction over chr1:46,700,048..47,748,623, all eleven output types, K562 and GM12878, as the manifest a browser reads it through: https://0t0e9nn6bj.execute-api.us-east-2.amazonaws.com/Prod/api/predict/demo-tal1-interval
• the variant prediction, the same window scored twice for the Jurkat MuTE insertion, in CD34+ common myeloid progenitors: https://0t0e9nn6bj.execute-api.us-east-2.amazonaws.com/Prod/api/predict/demo-tal1-variant-cd34
• the oncogenic TAL1 variants as a variant track, the insertion among them: https://jbrowse.org/demos/alphagenome_test.bed
• hg38's NCBI RefSeq annotation: https://jbrowse.org/genomes/GRCh38/ncbi_refseq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz
• the hg38 sequence: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit

Predicted assays from sequence#

AlphaGenome is given a window of reference sequence and returns what an RNA-seq, DNase, ATAC, CAGE, PRO-cap or ChIP-seq experiment in a named cell type would have produced over it, plus splice junctions and a contact map. One request carries all of them, per biosample, so asking about K562 and GM12878 together gives two cell types to read against each other.

The model takes sequence, so it answers just as readily for sequence that does not exist: change one base, ask again, and the difference between the two answers is the variant's predicted effect.

The window is a megabase centered on TAL1 on chr1, a transcription factor whose misexpression drives T-cell acute lymphoblastic leukemia. It is on in K562, an erythroleukemia line, and off in GM12878, a lymphoblastoid line, the control in the locus figures below.

The AlphaGenome plugin#

The plugin is beta and not in the plugin store yet, so it loads by URL from the plugins array in config.json (see configuring plugins):

{
  "plugins": [
    {
      "name": "AlphaGenome",
      "umdUrl": "https://jbrowse.org/demos/alphagenome-plugin/jbrowse-plugin-alphagenome.umd.js"
    }
  ]
}

On JBrowse Desktop, install it once from the start screen at Global plugins... → Add custom plugin, with that URL as the plugin URL and the name AlphaGenome.

The plugin holds no API key. It talks to a small service that runs the prediction, stores the arrays, and hands the browser a manifest of byte ranges. The public instance is the default; setApiRoot points it at your own.

The plugin is Apache-2.0, but AlphaGenome's API is offered as a free service for non-commercial use, so the public instance, and any instance run with your own key, carries that restriction.

Ask for a prediction#

Open the session below and the locus is already in view, with RefSeq genes and the oncogenic TAL1 variants above it and no predictions yet.

{
  "defaultSession": {
    "name": "TAL1",
    "views": [
      {
        "id": "alphagenome_lgv",
        "type": "LinearGenomeView",
        "assembly": "hg38",
        "loc": "chr1:47,189,833..47,259,832",
        "tracks": ["genes", "tal1_variants"]
      }
    ]
  }
}

jbrowse set-default-session --session - << 'EOF'
{
  "name": "TAL1",
  "views": [
    {
      "id": "alphagenome_lgv",
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr1:47,189,833..47,259,832",
      "tracks": ["genes", "tal1_variants"]
    }
  ]
}
EOF

AlphaGenome predictions… in the view menu opens the query panel. Four things go into a request:

• what to predict. Eleven output types; asking for all of them is one call, and the presets pick the usual groups
• which cell types and tissues. The box searches the catalog of predictable tracks by biosample, and marks a biosample that has none of the output types asked for. This page uses K562 and GM12878 for the locus, and CD34+ progenitors for the variant
• how wide a window. 16 kb, 100 kb, 500 kb or 1 Mb, centered on the view. The panel prints the interval it will ask about
• a variant, or none. Left empty, the locus is predicted as it is

A wide request takes minutes, so it is registered and the browser polls for it. Requests are keyed by content with the window rounded to 4 kb, so asking again for what this page already asked returns at once, which is why the prediction behind the figures below is instant. The rounding matters because a view's region comes from an integer pixel offset, and two browser windows of different widths ask about the same locus in coordinates tens of bases apart. A hit can therefore return a window up to about 2 kb off the one asked for, and the track list names the interval that came back.

Two cell lines on one axis#

A finished prediction is a list of tracks, often thousands. None cost anything to add, because the service stores the arrays and a track is only an HTTP range request into one. Filter the list to polyA plus, tick K562 and GM12878, and Add selected puts both in a single multi-wiggle track.

Predicted RNA-seq in two cell types is a comparison only if the rows share a y-axis. Everything measured in the same units goes onto one axis: several biosamples of one assay, and DNase beside ATAC, splice sites beside splice site usage, CAGE beside PRO-cap, histone ChIP beside TF ChIP. Untick Stack on a shared scale for one track per pick instead.

On that shared axis, TAL1 carries predicted transcription in K562 and essentially none in GM12878, on the annotated exons. The lane to the right is STIL, predicted in both lines, which shows the flat GM12878 row is a prediction rather than a track that failed to load.

Where the chromatin is open#

Add the DNase and ATAC tracks for both biosamples the same way. All four land in one track, because accessibility is one scale, and a DNase peak in K562 should also be an ATAC peak in K562.

On the shared axis, predicted ATAC in K562 sits well above everything else across the window, while the same cell line's DNase resolves into peaks. On a per-row scale the two would look alike. The GM12878 rows are not empty either; chromatin is open at plenty of places that are not transcribed.

Splicing and folding#

The other two output types are not quantitative rows and never join a stacked track.

Splice junctions come back as arcs, a sashimi plot. AlphaGenome returns tens of thousands for a megabase, so the adapter ships them whole and thresholds them in the browser. Add the K562 and GM12878 polyA junctions and zoom in to TAL1. The adapter's own threshold is low, which over one gene leaves dozens of faint arcs around a few strong ones; raise the Min score slider in the K562 track's menu and the strong ones remain, landing on the exon boundaries the RefSeq track draws. The track colors arcs by strand, one color here because every junction over TAL1 is on the gene's strand, and the GM12878 lane is empty because TAL1 is off there.

Contact maps come back as a triangle at 2 kb bins, and only for about a dozen cell lines, GM12878 among them. Predicted maps are much less skewed than sequenced ones, so the display saturates at the 95th percentile rather than at a fraction of the maximum.

At the 70 kb this page has been sitting at, a 2 kb map is thirty-five bins across; zoom out to the whole predicted megabase and the domain structure appears. Navigating after the prediction is free, since the adapter reads whatever range the view asks for from the stored arrays.

Scoring a variant#

TAL1 is off in GM12878 and on in K562, and in T-ALL patients it is switched on in a lineage where it should be silent. One way that happens is a small insertion upstream of the gene that creates a binding site, and one of those is in the variant track on screen.

Right-click it and the last row of the menu reads Predict variant effect with AlphaGenome. It opens the query panel with the variant loaded: the chip names the position and the two alleles, and the Predict button renames itself to match. Run it, and the same window comes back twice, once for the reference sequence and once with the insertion in place.

The recorded prediction this page reads is for the Jurkat insertion, chr1:47239296 C>CCGTTTCCTAACC, scored in CD34+ common myeloid progenitors: the cell type the worked example uses, and the closest match AlphaGenome has to the CD34+ hematopoietic cells Mansour et al. studied. To reach it, remove K562 from the biosample box, add "common myeloid progenitor, CD34-positive", and type the insertion into the variant box. Any other variant or biosample is a real API call rather than a stored answer.

Before running one yourself:

• the variant has to be inside the window. The panel warns when it is not, and offers to navigate there
• splice junctions go sparse in variant mode. AlphaGenome reports only junctions the variant could plausibly affect, which for a variant nowhere near a splice site is none. Clear the variant to get the whole locus back

Reading the difference#

Adding a track from a variant prediction gives two tracks: the reference and alternate curves together, and a third row for their difference, where positive is a gain from the insertion and negative a loss. Add the CD34+ DNase, polyA plus RNA-seq and H3K27ac tracks, and zoom to TAL1 and the insertion. The figure below closes the reference and alternate tracks and keeps the three difference rows.

On the three difference rows, accessibility rises sharply at the insertion itself, H3K27ac, the mark of an active enhancer, rises across the locus, and predicted transcription rises over the TAL1 exons. The DNase difference row is set to Score → Autoscale type → Local in its track menu: the default clips the outermost percent of each sign, which on a row this sparse flattens the gain at the insertion.

AlphaGenome returns the alternate prediction laid out along the alternate sequence, 12 bases longer than the reference here. The plugin maps it back onto reference coordinates before subtracting, the way AlphaGenome's own variant scorers do, collapsing the inserted bases onto the base they follow, so every difference compares one reference base with itself.

What a prediction is, as configuration#

The tracks the panel adds are session tracks, and their adapters address a stored array through a presigned URL that expires within the hour, so a track config copied out of one session does not load in the next. Re-open the panel and rebuild the same query instead; requests are keyed by content, so the same query lands back on the same arrays for free.

See also#

• RNA-seq visualization
• ChromHMM chromatin states
• Structural variants from Hi-C
• Plugins

References#

Avsec Ž, et al. AlphaGenome: advancing regulatory variant effect prediction with a unified DNA sequence model. bioRxiv (2025). https://doi.org/10.1101/2025.06.25.661532

Mansour MR, et al. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element. Science 346:1373-1377 (2014). https://doi.org/10.1126/science.1259037

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