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TCGA / GDC germline somatic wildtype mutations

I am using open access GDC Data Portal (TCGA) - Analysis Center - Correlation Plot. Primary variable is Mutation/SNV. Variable to correlate is Gene Expression. Box plot legend for the two boxes says: Mutated VS Wildtype. Considering that germline mutations are not exposed in open access - What does Mutated actually mean: Only Somatic or Somatic + Germline ? and what does Wildtype actually mean: Not mutated or Not Somatic ?

correlation mutation germline tcga
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updated by Zhenyu Zhang Zhenyu Zhang • written by jomo018 jomo018

1 answer

"mutated" means somatic mutation only. GDC does not perform germline variant calling.

wildtype in the GDC context simply means no somatic mutations called at this locus.

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written by Zhenyu Zhang Zhenyu Zhang

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