RNA and DNA variant difference
i have 1 patient samples ( normal, tumor), and find out the fusion gene throughout RNA-seq(eg. CPM--CCT2 gene is fusion transcription).
next, i ran the DNA sequence(whole genome sequence). However, fusion gene(CPM--CCT2) do not appear in DNA sequence.
About 95% of fusion gene ( by RNA sequence) do not appear in DNA sequence as fusion gene.
why????
1 answer
RNA-seq is a false-positive or DNA-seq is a false-negative given that all pipelines were ran properly and sample selection for RNA-seq and DNA-seq was appropriate and comparable. You will probably need to validate by experiment, e.g. Sanger sequencing on the cDNA spanning the fusion break points.
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