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Gene fusion calls and the DNA behind them

TL;DR: a fusion caller hands you a table of gene pairs and a junction coordinate, and nothing about the DNA event underneath. Load STAR-Fusion's table beside the long RNA reads it was called from, count the molecules that cross each junction, then find where the chromosome actually broke: for K562's BCR-ABL1 that is 122 kb away from the junction the caller reports, inside ABL1's first intron.

Prerequisites

  • nothing to read along. Everything below is for rebuilding the data
  • a JBrowse to open them in: Desktop takes a local file by path, Web through Add track
  • Command line tools (JBrowse CLI)
  • samtools, to sort and merge the four Iso-Seq runs
  • bedGraphToBigWig and liftOver, both from the UCSC utilities
  • python3, for depmap_to_jbrowse.py and lift_bnd_vcf.py

The two python helpers are one file each:

curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/depmap_to_jbrowse.py
curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/lift_bnd_vcf.py

Where the data comes from

Four PacBio Iso-Seq runs from ENCODE, two tables out of DepMap's 24Q4 release, and the DNA breakpoints on hg19:

K562

K562 is a chronic myeloid leukemia line carrying the Philadelphia chromosome, the t(9;22) that fuses BCR to ABL1. Its transcripts here are long RNA reads, its fusion calls come from DepMap's short-read pipeline, and its DNA breakpoints from a linked-read run.

Both DepMap tables cover every line in the release. depmap_to_jbrowse.py filters to one line and writes a STAR-Fusion TSV from the fusion table and a bedGraph from the copy-number segments. K562 is model ACH-000551, and its WGS copy-number profile is PR-aheaZL:

python3 depmap_to_jbrowse.py fusions OmicsFusionFiltered.csv ACH-000551 K562.star-fusion.tsv
python3 depmap_to_jbrowse.py segments OmicsCNSegmentsProfile.csv PR-aheaZL K562_cn.bedGraph
sort -k1,1 -k2,2n K562_cn.bedGraph |
  awk 'NR==FNR{ok[$1];next} ($1 in ok)' hg38.chrom.sizes - > K562_cn.sorted.bedGraph
bedGraphToBigWig K562_cn.sorted.bedGraph hg38.chrom.sizes K562_cn.bw

The DNA breakpoints arrive on hg19. A breakend record carries a second coordinate inside its ALT string, so a plain liftOver of the POS column produces a valid VCF whose partner coordinates still point at hg19. lift_bnd_vcf.py moves both:

python3 lift_bnd_vcf.py calls.hg19.vcf.gz hg19ToHg38.over.chain.gz \
  ./liftOver calls.hg38.vcf liftwork
bgzip calls.hg38.vcf && tabix -p vcf calls.hg38.vcf.gz

The script's five arguments are the input VCF, the chain, the liftOver binary, the output VCF and a scratch directory.

Triaging the calls

The SV inspector opens the STAR-Fusion table beside a circular view of it, one chord per row. Add → SV inspector, then a File Type of STAR-Fusion, which the wizard cannot infer from a .tsv extension.

Searching the table narrows both halves. chr9 leaves BCR--ABL1 and NUP214--XKR3, one junction seen from both sides, with more junction reads than anything else in the file.

Each row's caret menu has Open in linear genome view, which goes to its breakpoint. Type the partner's window into the location box after it to hold both side by side, then turn on Read connections → View as pairs to merge each molecule's two alignments onto one row. Flip the chr22 region ([rev]), since XKR3 is on the minus strand.

NUP214--XKR3 as two regions of one view with reads linked, opened from its row in the SV inspector. The breakpoints are banded green and each line is one Iso-Seq molecule running from NUP214 into XKR3. Open in JBrowse: Import form ↗ · All 44 calls ↗ · Searched for chr9 ↗ · Linked reads ↗ (large dataset — this session takes a while to load)

The steps behind the figure above, run against your own data.

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses hg38.
  2. Click the view's title in its header and enter "Add → SV inspector, File Type → STAR-Fusion"
  3. Import form → File Type → STAR-FusionOnly needed when the filename does not end in the type, which is why a STAR-Fusion `.tsv` has to be named and a `.vcf.gz` does not.
  4. Drag the bar at the bottom edge of the view to resize it (620px here).

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session — swap in your own files afterwards.

Nothing happens? Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fdemos%2Fcancer_sv%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22SvInspectorView%22%2C%22displayName%22%3A%22Add+%E2%86%92+SV+inspector%2C+File+Type+%E2%86%92+STAR-Fusion%22%2C%22assembly%22%3A%22hg38%22%2C%22fileType%22%3A%22STAR-Fusion%22%2C%22height%22%3A620%7D%5D%7D&sessionName=JBrowse+docs%3A+cancer_sv%2Fk562_fusion_inspector_form

This session spec pastes after &session=spec- on any JBrowse Web instance.

{
  "views": [
    {
      "type": "SvInspectorView",
      "displayName": "Add → SV inspector, File Type → STAR-Fusion",
      "assembly": "hg38",
      "fileType": "STAR-Fusion",
      "height": 620
    }
  ]
}

Loaded against config: https://jbrowse.org/demos/cancer_sv/config.json

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "SvInspectorView",
      "displayName": "Add → SV inspector, File Type → STAR-Fusion",
      "assembly": "hg38",
      "fileType": "STAR-Fusion",
      "height": 620
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/cancer_sv/config.json \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

The steps behind the figure above, run against your own data.

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses hg38.
  2. Click the view's title in its header and enter "All 44 STAR-Fusion calls"
  3. Import form → Open file from URL or local computer → URL → Enter URL → OpenOpen the form with Add → SV inspector (or Add → Spreadsheet view); set File Type and Assembly in the same form before clicking Open.
  4. Import form → File Type → STAR-FusionOnly needed when the filename does not end in the type, which is why a STAR-Fusion `.tsv` has to be named and a `.vcf.gz` does not.
  5. Drag the bar at the bottom edge of the view to resize it (620px here).

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session — swap in your own files afterwards.

Nothing happens? Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fdemos%2Fcancer_sv%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22SvInspectorView%22%2C%22displayName%22%3A%22All+44+STAR-Fusion+calls%22%2C%22assembly%22%3A%22hg38%22%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fcancer_sv%2FK562.star-fusion.tsv%22%2C%22fileType%22%3A%22STAR-Fusion%22%2C%22height%22%3A620%7D%5D%7D&sessionName=JBrowse+docs%3A+cancer_sv%2Fk562_fusion_inspector_all

This session spec pastes after &session=spec- on any JBrowse Web instance.

{
  "views": [
    {
      "type": "SvInspectorView",
      "displayName": "All 44 STAR-Fusion calls",
      "assembly": "hg38",
      "uri": "https://jbrowse.org/demos/cancer_sv/K562.star-fusion.tsv",
      "fileType": "STAR-Fusion",
      "height": 620
    }
  ]
}

Loaded against config: https://jbrowse.org/demos/cancer_sv/config.json

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "SvInspectorView",
      "displayName": "All 44 STAR-Fusion calls",
      "assembly": "hg38",
      "uri": "https://jbrowse.org/demos/cancer_sv/K562.star-fusion.tsv",
      "fileType": "STAR-Fusion",
      "height": 620
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/cancer_sv/config.json \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

The steps behind the figure above, run against your own data.

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses hg38.
  2. Click the view's title in its header and enter "Search "chr9": the reciprocal pair"
  3. Import form → Open file from URL or local computer → URL → Enter URL → OpenOpen the form with Add → SV inspector (or Add → Spreadsheet view); set File Type and Assembly in the same form before clicking Open.
  4. Import form → File Type → STAR-FusionOnly needed when the filename does not end in the type, which is why a STAR-Fusion `.tsv` has to be named and a `.vcf.gz` does not.
  5. Type "chr9" into the table's search box (the magnifier above the grid)In the SV inspector the circular view draws only the rows the search leaves, so this narrows the chords too — it does not change which regions the circle shows, which is the 'show only regions with data' checkbox beside it.
  6. Drag the bar at the bottom edge of the view to resize it (620px here).

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session — swap in your own files afterwards.

Nothing happens? Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fdemos%2Fcancer_sv%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22SvInspectorView%22%2C%22displayName%22%3A%22Search+%5C%22chr9%5C%22%3A+the+reciprocal+pair%22%2C%22assembly%22%3A%22hg38%22%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fdemos%2Fcancer_sv%2FK562.star-fusion.tsv%22%2C%22fileType%22%3A%22STAR-Fusion%22%2C%22filterText%22%3A%22chr9%22%2C%22height%22%3A620%7D%5D%7D&sessionName=JBrowse+docs%3A+cancer_sv%2Fk562_fusion_inspector_pair

This session spec pastes after &session=spec- on any JBrowse Web instance.

{
  "views": [
    {
      "type": "SvInspectorView",
      "displayName": "Search \"chr9\": the reciprocal pair",
      "assembly": "hg38",
      "uri": "https://jbrowse.org/demos/cancer_sv/K562.star-fusion.tsv",
      "fileType": "STAR-Fusion",
      "filterText": "chr9",
      "height": 620
    }
  ]
}

Loaded against config: https://jbrowse.org/demos/cancer_sv/config.json

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "SvInspectorView",
      "displayName": "Search \"chr9\": the reciprocal pair",
      "assembly": "hg38",
      "uri": "https://jbrowse.org/demos/cancer_sv/K562.star-fusion.tsv",
      "fileType": "STAR-Fusion",
      "filterText": "chr9",
      "height": 620
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/cancer_sv/config.json \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

The steps behind the figure above, run against your own data.

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses hg38.
  2. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses the “ncbi_refseq_hg38” track.
  3. Track menu → Gene glyph → Representative transcript“ncbi_refseq_hg38”.
  4. Drag the bar at the bottom edge of the track to resize it.“ncbi_refseq_hg38”.
  5. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses the “K562_star_fusion” track.
  6. Track menu → Set feature height → Collapsed“K562_star_fusion”.
  7. Drag the bar at the bottom edge of the track to resize it.“K562_star_fusion”.
  8. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses the “K562_isoseq” track.
  9. Drag the bar at the bottom edge of the track to resize it.“K562_isoseq”.
  10. Drag the bottom edge of the coverage band to resize it.“K562_isoseq”.
  11. Track menu → Filter by... → Split alignments → Only split alignmentsA read filter drops reads in the worker before layout, so it thins the coverage histogram along with the pileup.“K562_isoseq”.
  12. Track menu → Read connections → View as pairs / link supplementary alignments (checked)“K562_isoseq”.
  13. Track menu → Show... → Show legend (checked)“K562_isoseq”.
  14. Track menu → Read connections → Use curved connectors (checked)Draws a read's alignments joined by a curve rather than a straight line. Worth it when the two ends sit in different displayed regions, where the curve reads as one read crossing the gap.“K562_isoseq”.
  15. Track menu → Read connections → Show read arcs“K562_isoseq”.
  16. Drag the handle at the edge of the arc band to resize it (90px here).Its tooltip reads "Drag to resize arcs area"; there is no menu entry for the height.“K562_isoseq”.
  17. Track menu → Read height → Custom... → 4px“K562_isoseq”.
  18. Type your region of interest into the location box and press Enter.This figure is at chr9:131,186,500-131,199,515 chr22:16,795,568-16,808,583[rev].
  19. View menu → Zoom to region / use the location box, then add a highlightThis figure highlights 2 regions; highlights can also be set with the &highlight= URL parameter.

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session — swap in your own files afterwards.

Nothing happens? Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fdemos%2Fcancer_sv%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22hg38%22%2C%22loc%22%3A%22chr9%3A131%2C186%2C500-131%2C199%2C515+chr22%3A16%2C795%2C568-16%2C808%2C583%5Brev%5D%22%2C%22highlight%22%3A%5B%7B%22refName%22%3A%22chr9%22%2C%22start%22%3A131198915%2C%22end%22%3A131199115%7D%2C%7B%22refName%22%3A%22chr22%22%2C%22start%22%3A16807983%2C%22end%22%3A16808183%7D%5D%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22ncbi_refseq_hg38%22%2C%22geneGlyphMode%22%3A%22longestCoding%22%2C%22height%22%3A60%7D%2C%7B%22trackId%22%3A%22K562_star_fusion%22%2C%22type%22%3A%22LinearVariantDisplay%22%2C%22displayMode%22%3A%22collapsed%22%2C%22height%22%3A30%7D%2C%7B%22trackId%22%3A%22K562_isoseq%22%2C%22type%22%3A%22LinearAlignmentsDisplay%22%2C%22height%22%3A600%2C%22coverageHeight%22%3A150%2C%22filterBy%22%3A%7B%22split%22%3A%22only%22%7D%2C%22linkedReads%22%3A%22normal%22%2C%22showLegend%22%3Atrue%2C%22showBezierConnections%22%3Atrue%2C%22readConnections%22%3A%22arc%22%2C%22readConnectionsHeight%22%3A90%2C%22featureHeight%22%3A4%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+cancer_sv%2Fk562_fusion_inspector_reads

This session spec pastes after &session=spec- on any JBrowse Web instance.

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr9:131,186,500-131,199,515 chr22:16,795,568-16,808,583[rev]",
      "highlight": [
        {
          "refName": "chr9",
          "start": 131198915,
          "end": 131199115
        },
        {
          "refName": "chr22",
          "start": 16807983,
          "end": 16808183
        }
      ],
      "tracks": [
        {
          "trackId": "ncbi_refseq_hg38",
          "geneGlyphMode": "longestCoding",
          "height": 60
        },
        {
          "trackId": "K562_star_fusion",
          "type": "LinearVariantDisplay",
          "displayMode": "collapsed",
          "height": 30
        },
        {
          "trackId": "K562_isoseq",
          "type": "LinearAlignmentsDisplay",
          "height": 600,
          "coverageHeight": 150,
          "filterBy": {
            "split": "only"
          },
          "linkedReads": "normal",
          "showLegend": true,
          "showBezierConnections": true,
          "readConnections": "arc",
          "readConnectionsHeight": 90,
          "featureHeight": 4
        }
      ]
    }
  ]
}

Loaded against config: https://jbrowse.org/demos/cancer_sv/config.json

The same view with jbrowse-anywidget. Point the adapter at your own file.

from jbrowse_anywidget import LinearGenomeView, fetch_hub

view = LinearGenomeView(
    assembly=fetch_hub("hg38"),
    location="chr9:131,186,500-131,199,515 chr22:16,795,568-16,808,583[rev]",
)

view.add_track({
    "type": "FeatureTrack",
    "trackId": "my_track_1",
    "name": "My track 1",
    "assemblyNames": ["hg38"],
    "adapter": {"type": "BamAdapter", "uri": "https://your-server/your-file"},
})
view.add_track({
    "type": "FeatureTrack",
    "trackId": "my_track_2",
    "name": "My track 2",
    "assemblyNames": ["hg38"],
    "adapter": {"type": "BamAdapter", "uri": "https://your-server/your-file"},
})
view.add_track({
    "type": "FeatureTrack",
    "trackId": "my_track_3",
    "name": "My track 3",
    "assemblyNames": ["hg38"],
    "adapter": {"type": "BamAdapter", "uri": "https://your-server/your-file"},
})

view  # display the widget

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr9:131,186,500-131,199,515 chr22:16,795,568-16,808,583[rev]",
      "highlight": [
        {
          "refName": "chr9",
          "start": 131198915,
          "end": 131199115
        },
        {
          "refName": "chr22",
          "start": 16807983,
          "end": 16808183
        }
      ],
      "tracks": [
        {
          "trackId": "ncbi_refseq_hg38",
          "geneGlyphMode": "longestCoding",
          "height": 60
        },
        {
          "trackId": "K562_star_fusion",
          "type": "LinearVariantDisplay",
          "displayMode": "collapsed",
          "height": 30
        },
        {
          "trackId": "K562_isoseq",
          "type": "LinearAlignmentsDisplay",
          "height": 600,
          "coverageHeight": 150,
          "filterBy": {
            "split": "only"
          },
          "linkedReads": "normal",
          "showLegend": true,
          "showBezierConnections": true,
          "readConnections": "arc",
          "readConnectionsHeight": 90,
          "featureHeight": 4
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/cancer_sv/config.json \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

BCR--ABL1 takes the rest of this page in the same layout. The build script adds the STAR-Fusion calls as this track:

{
  "type": "VariantTrack",
  "trackId": "K562_star_fusion",
  "name": "K562 STAR-Fusion calls (DepMap 24Q4)",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "StarFusionAdapter",
    "starFusionLocation": { "uri": "K562.star-fusion.tsv" }
  }
}
jbrowse add-track-json '{
  "type": "VariantTrack",
  "trackId": "K562_star_fusion",
  "name": "K562 STAR-Fusion calls (DepMap 24Q4)",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "StarFusionAdapter",
    "starFusionLocation": { "uri": "K562.star-fusion.tsv" }
  }
}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "VariantTrack",
  "trackId": "K562_star_fusion",
  "name": "K562 STAR-Fusion calls (DepMap 24Q4)",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "StarFusionAdapter",
    "starFusionLocation": { "uri": "K562.star-fusion.tsv" }
  }
}

BCR-ABL1 across three regions

Right-click a read that crosses the junction and choose Split current view to show split alignments, or type the locations into the location box separated by spaces. The transcript reaches ABL1 at more than one place, so this view uses three regions, the BCR donor and two acceptor windows.

A read crossing the junction is one alignment on chr22 and a supplementary alignment on chr9. Read connections → Use curved connectors draws a curve between the two across the region divider. Filter by... → Split alignments → Only split alignments drops every read that stays on one chromosome.

Near-identical curves stack into one line. Read connections → Show read arcs adds a band under the coverage where each junction is drawn once, thickened by the reads behind it. An arc needs both ends in view, and each acceptor window receives one. The vertical at the BCR donor stands for the molecules whose ABL1 alignment lands in neither window.

BCR on chr22 beside two ABL1 windows on chr9 as three regions of one view, showing only split reads with supplementary alignments linked. The arc band draws one counted arc from the BCR donor into each ABL1 window, and only the right-hand window carries a STAR-Fusion band. Open this view in JBrowse ↗

The steps behind the figure above, run against your own data.

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses hg38.
  2. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses the “ncbi_refseq_hg38” track.
  3. Track menu → Gene glyph → Representative transcript“ncbi_refseq_hg38”.
  4. Drag the bar at the bottom edge of the track to resize it.“ncbi_refseq_hg38”.
  5. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses the “K562_isoseq” track.
  6. Track menu → Read height → Track sizing → Fixed read height + autogrow track height“K562_isoseq”.
  7. Drag the bottom edge of the coverage band to resize it.“K562_isoseq”.
  8. Track menu → Filter by... → Split alignments → Only split alignmentsA read filter drops reads in the worker before layout, so it thins the coverage histogram along with the pileup.“K562_isoseq”.
  9. Track menu → Read connections → View as pairs / link supplementary alignments (checked)“K562_isoseq”.
  10. Track menu → Read connections → Use curved connectors (checked)Draws a read's alignments joined by a curve rather than a straight line. Worth it when the two ends sit in different displayed regions, where the curve reads as one read crossing the gap.“K562_isoseq”.
  11. Track menu → Read connections → Show read arcs“K562_isoseq”.
  12. Drag the handle at the edge of the arc band to resize it (90px here).Its tooltip reads "Drag to resize arcs area"; there is no menu entry for the height.“K562_isoseq”.
  13. Track menu → Show... → Show legend (checked)“K562_isoseq”.
  14. Track menu → Read height → Custom... → 4px“K562_isoseq”.
  15. Type your region of interest into the location box and press Enter.This figure is at chr22:23,286,000-23,293,000 chr9:130,778,000-130,785,000 chr9:130,851,000-130,858,000.
  16. View menu → Zoom to region / use the location box, then add a highlightThis figure highlights 2 regions; highlights can also be set with the &highlight= URL parameter.

Some settings have no written step yet — see the Session spec tab.

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session — swap in your own files afterwards.

Nothing happens? Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fdemos%2Fcancer_sv%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22hg38%22%2C%22loc%22%3A%22chr22%3A23%2C286%2C000-23%2C293%2C000+chr9%3A130%2C778%2C000-130%2C785%2C000+chr9%3A130%2C851%2C000-130%2C858%2C000%22%2C%22highlight%22%3A%5B%7B%22refName%22%3A%22chr22%22%2C%22start%22%3A23290313%2C%22end%22%3A23290513%7D%2C%7B%22refName%22%3A%22chr9%22%2C%22start%22%3A130853964%2C%22end%22%3A130854164%7D%5D%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22ncbi_refseq_hg38%22%2C%22geneGlyphMode%22%3A%22longestCoding%22%2C%22height%22%3A90%7D%2C%7B%22trackId%22%3A%22K562_isoseq%22%2C%22type%22%3A%22LinearAlignmentsDisplay%22%2C%22heightMode%22%3A%22grow%22%2C%22growMaxHeight%22%3A2400%2C%22coverageHeight%22%3A190%2C%22filterBy%22%3A%7B%22split%22%3A%22only%22%7D%2C%22linkedReads%22%3A%22normal%22%2C%22showBezierConnections%22%3Atrue%2C%22readConnections%22%3A%22arc%22%2C%22readConnectionsHeight%22%3A90%2C%22showLegend%22%3Atrue%2C%22featureHeight%22%3A4%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+cancer_sv%2Fk562_bcr_abl_split

This session spec pastes after &session=spec- on any JBrowse Web instance.

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr22:23,286,000-23,293,000 chr9:130,778,000-130,785,000 chr9:130,851,000-130,858,000",
      "highlight": [
        {
          "refName": "chr22",
          "start": 23290313,
          "end": 23290513
        },
        {
          "refName": "chr9",
          "start": 130853964,
          "end": 130854164
        }
      ],
      "tracks": [
        {
          "trackId": "ncbi_refseq_hg38",
          "geneGlyphMode": "longestCoding",
          "height": 90
        },
        {
          "trackId": "K562_isoseq",
          "type": "LinearAlignmentsDisplay",
          "heightMode": "grow",
          "growMaxHeight": 2400,
          "coverageHeight": 190,
          "filterBy": {
            "split": "only"
          },
          "linkedReads": "normal",
          "showBezierConnections": true,
          "readConnections": "arc",
          "readConnectionsHeight": 90,
          "showLegend": true,
          "featureHeight": 4
        }
      ]
    }
  ]
}

Loaded against config: https://jbrowse.org/demos/cancer_sv/config.json

The same view with jbrowse-anywidget. Point the adapter at your own file.

from jbrowse_anywidget import LinearGenomeView, fetch_hub

view = LinearGenomeView(
    assembly=fetch_hub("hg38"),
    location="chr22:23,286,000-23,293,000 chr9:130,778,000-130,785,000 chr9:130,851,000-130,858,000",
)

view.add_track({
    "type": "FeatureTrack",
    "trackId": "my_track_1",
    "name": "My track 1",
    "assemblyNames": ["hg38"],
    "adapter": {"type": "BamAdapter", "uri": "https://your-server/your-file"},
})
view.add_track({
    "type": "FeatureTrack",
    "trackId": "my_track_2",
    "name": "My track 2",
    "assemblyNames": ["hg38"],
    "adapter": {"type": "BamAdapter", "uri": "https://your-server/your-file"},
})

view  # display the widget

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr22:23,286,000-23,293,000 chr9:130,778,000-130,785,000 chr9:130,851,000-130,858,000",
      "highlight": [
        {
          "refName": "chr22",
          "start": 23290313,
          "end": 23290513
        },
        {
          "refName": "chr9",
          "start": 130853964,
          "end": 130854164
        }
      ],
      "tracks": [
        {
          "trackId": "ncbi_refseq_hg38",
          "geneGlyphMode": "longestCoding",
          "height": 90
        },
        {
          "trackId": "K562_isoseq",
          "type": "LinearAlignmentsDisplay",
          "heightMode": "grow",
          "growMaxHeight": 2400,
          "coverageHeight": 190,
          "filterBy": {
            "split": "only"
          },
          "linkedReads": "normal",
          "showBezierConnections": true,
          "readConnections": "arc",
          "readConnectionsHeight": 90,
          "showLegend": true,
          "featureHeight": 4
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/cancer_sv/config.json \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

Where the DNA broke

BCR-ABL1 is amplified as well as expressed. Both chr9 breakpoints fall inside a segment at roughly seven copies while the chr22 partners sit at one. DepMap's segmentation covers no interval over BCR itself, so that window has an arc but no copy-number step.

A fusion caller only reports transcribed junctions, so its arcs land on exon boundaries and cannot say where the amplified block begins. ENCODE's 10X Chromium linked-read run on K562 (ENCSR053AXS) puts the chr9 DNA breakpoint at 130,731,760, and DepMap's copy-number segmentation steps up at 130,731,326. The transcript junction is 122 kb to the right of both, inside ABL1's first intron: the amplicon boundary is a DNA break, and the transcript is spliced from it to the nearest exon.

SplitThreader applied the same reasoning to the ERBB2 amplicon in SK-BR-3 (Nattestad et al. 2018): copy-number steps and breakpoints describing the same interval are evidence of one event.

Reproduce it end to end

scripts/build_cancer_sv_demo.sh builds everything above from public sources:

curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/build_cancer_sv_demo.sh
bash build_cancer_sv_demo.sh    # builds ./cancer_sv_build/jbrowse2
npx --yes serve cancer_sv_build/jbrowse2

It merges the four ENCODE Iso-Seq alignments, converts the DepMap release into a STAR-Fusion TSV and a copy-number bigWig, and lifts the ENCODE linked-read breakpoints onto hg38. The same run builds the COLO829 half of the demo, which Complex rearrangements and derivative alleles walks through.

See also

References

  • Nattestad M, et al. Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line. Genome Research (2018). https://doi.org/10.1101/gr.231100.117