How to interpret the eQTLs in cancer
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4.1 years ago
darklings ▴ 480

According to the paper PancanQTL: systematic identification of cis-eQTLs and trans-eQTLs in 33 cancer types, they conducted the eQTL mapping using RNA-seq and genotype data from TCGA.

I am a bit confused about the meaning of cancer eQTL. I know that an eQTL is a locus that explains a fraction of the genetic variance of a gene expression phenotype, so the eQTLs identified from cancer (and normal?) samples are the loci that may lead to gene expression disturbance during tumor transformation and development?

RNA-Seq SNP eqtl TCGA • 1.4k views
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i think you are right. The paper used the tumor and matched normal data to identify somatic mutation and evaluated the effects on the tumor sample gene expression.

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Oh wow thanks, now I am a bit confused about why I asked this question at that time...

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