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GenomePaint Allelic imbalance Example

Zhou Lab

Sep 28, 2021

3.7K

Whole Genome Sequencing

St. Jude's own Dr.Xiaotu Ma coined the term "AI Check" after designing this visualization. Compare the allelic imbalance of heterozygous SNP markers in a tumor genome against a patient's germline genome, as a targeted method for evaluating loss-of-heterozygosity.

Learn more about the AICheck track.

Loading Visualization

runproteinpaint({
  host: "https://proteinpaint.stjude.org",
  holder: visualizationContainer[0],
  parseurl: true,
  block: true,
  nobox: 1,
  noheader: 1,
  genome: "hg19",
  position: "chr8:126890266-132795076",
  nativetracks: "RefGene",
  tracks: [
    {
      "type": "aicheck",
      "file": "proteinpaint_demo/hg19/aicheck/file.gz",
      "name": "Demo sample tumor allelic imbalance",
    },
  ]
});

Visualization Code

runproteinpaint({
  host: "https://proteinpaint.stjude.org",
  holder: visualizationContainer[0],
  parseurl: true,
  block: true,
  nobox: 1,
  noheader: 1,
  genome: "hg19",
  position: "chr8:126890266-132795076",
  nativetracks: "RefGene",
  tracks: [
    {
      "type": "aicheck",
      "file": "proteinpaint_demo/hg19/aicheck/file.gz",
      "name": "Demo sample tumor allelic imbalance",
    },
  ]
});

GenomePaint Allelic imbalance Example

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Loading Visualization

Visualization Code