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PATHJF CASC15/SOX4::HOXA13 Translocation

Mullighan Lab

27 4

Oct 5, 2023

< 1k

Whole Genome Sequencing

RNA Sequencing

ATAC Sequencing

HiChIP

Depiction of H3K27ac HiChIP, H3K27ac coverage, diagnostic/germline sample WGS and WTS coverage in a T-ALL patient, showcasing enhancer hijacking of the CASC15/SOX4 enhancers by HOXA13. The heatmap represent interactions between genomic loci, with color coding denoting interaction strength.

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{
  "host": "https://proteinpaint.stjude.org/",
  "parseurl": true,
  "block": true,
  "nobox": true,
  "noheader": true,
  "genome": "hg38",
  "position": "chr7:27096538-27307355",
  "nativetracks": "RefGene",
	"width": 400,
  "subpanels": [
    {
      "chr": "chr6",
      "start": 21535417,
      "stop": 22264643,
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      "leftborder": "rgba(200,0,0,.1)"
    }
  ],
  "tracks": [
    {
      "type": "hicstraw",
      "file": "ppolonen/hg38/HICHIP/H3K27ac_HiChIP_PATHJF.hic",
      "name": "HiChIP",
      "percentile_max": 95,
      "mincutoff": 0,
      "pyramidup": 1,
      "enzyme": ""
    },
    {
      "type": "bigwig",
      "file": "ppolonen/hg38/HICHIP/H3K27ac_HiChIP_PATHJF.coverage.bw",
      "name": "H3K27ac HiChIP",
      "scale": {
        "min": 0,
        "max": 100
      },
      "pcolor": "#FF2600"
    },
    {
      "type": "bigwig",
      "file": "ppolonen/hg38/ATAC/MERGED-SJTALL022648_D1-PATHJF.nuc.bw",
      "name": "ATAC-nuc",
      "scale": {
        "min": 0,
        "max": 15
      },
      "pcolor": "#40A5EE"
    },
    {
      "type": "bigwig",
      "file": "ppolonen/hg38/ATAC/MERGED-SJTALL022648_D1-PATHJF.free.bw",
      "name": "ATAC-free",
      "scale": {
        "min": 0,
        "max": 15
      },
      "pcolor": "#40A5EE"
    },
    {
      "type": "bigwig",
      "file": "ppolonen/hg38/WGS/SJTALL002072_D2-PATHJF_D.bw",
      "name": "WGS-D",
      "scale": {
        "min": 0,
        "max": 150
      },
      "pcolor": "#113F91"
    },
    {
      "type": "bigwig",
      "file": "ppolonen/hg38/WGS/SJTALL002072_G2-PATHJF_G.bw",
      "name": "WGS-G",
      "scale": {
        "min": 0,
        "max": 150
      },
      "pcolor": "#113F91"
    },
    {
      "type": "bigwig",
      "file": "ppolonen/hg38/RNA/SJTALL002072_D1.STAR.Signal.UniqueMultiple.str1.out.bw",
      "name": "RNA-D-str1",
      "pcolor": "#195C37"
    },
    {
      "type": "bigwig",
      "file": "ppolonen/hg38/RNA/SJTALL002072_D1.STAR.Signal.UniqueMultiple.str2.out.bw",
      "name": "RNA-D-str2",
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    }
  ]
}

Visualization Code

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  "host": "https://proteinpaint.stjude.org/",
  "parseurl": true,
  "block": true,
  "nobox": true,
  "noheader": true,
  "genome": "hg38",
  "position": "chr7:27096538-27307355",
  "nativetracks": "RefGene",
	"width": 400,
  "subpanels": [
    {
      "chr": "chr6",
      "start": 21535417,
      "stop": 22264643,
      "width": 400,
      "leftborder": "rgba(200,0,0,.1)"
    }
  ],
  "tracks": [
    {
      "type": "hicstraw",
      "file": "ppolonen/hg38/HICHIP/H3K27ac_HiChIP_PATHJF.hic",
      "name": "HiChIP",
      "percentile_max": 95,
      "mincutoff": 0,
      "pyramidup": 1,
      "enzyme": ""
    },
    {
      "type": "bigwig",
      "file": "ppolonen/hg38/HICHIP/H3K27ac_HiChIP_PATHJF.coverage.bw",
      "name": "H3K27ac HiChIP",
      "scale": {
        "min": 0,
        "max": 100
      },
      "pcolor": "#FF2600"
    },
    {
      "type": "bigwig",
      "file": "ppolonen/hg38/ATAC/MERGED-SJTALL022648_D1-PATHJF.nuc.bw",
      "name": "ATAC-nuc",
      "scale": {
        "min": 0,
        "max": 15
      },
      "pcolor": "#40A5EE"
    },
    {
      "type": "bigwig",
      "file": "ppolonen/hg38/ATAC/MERGED-SJTALL022648_D1-PATHJF.free.bw",
      "name": "ATAC-free",
      "scale": {
        "min": 0,
        "max": 15
      },
      "pcolor": "#40A5EE"
    },
    {
      "type": "bigwig",
      "file": "ppolonen/hg38/WGS/SJTALL002072_D2-PATHJF_D.bw",
      "name": "WGS-D",
      "scale": {
        "min": 0,
        "max": 150
      },
      "pcolor": "#113F91"
    },
    {
      "type": "bigwig",
      "file": "ppolonen/hg38/WGS/SJTALL002072_G2-PATHJF_G.bw",
      "name": "WGS-G",
      "scale": {
        "min": 0,
        "max": 150
      },
      "pcolor": "#113F91"
    },
    {
      "type": "bigwig",
      "file": "ppolonen/hg38/RNA/SJTALL002072_D1.STAR.Signal.UniqueMultiple.str1.out.bw",
      "name": "RNA-D-str1",
      "pcolor": "#195C37"
    },
    {
      "type": "bigwig",
      "file": "ppolonen/hg38/RNA/SJTALL002072_D1.STAR.Signal.UniqueMultiple.str2.out.bw",
      "name": "RNA-D-str2",
      "pcolor": "#195C37"
    }
  ]
}

PATHJF CASC15/SOX4::HOXA13 Translocation

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Visualization Code