How To Calculate Non-Transcribed Strand Mutation In Sequencing

Question

[Liyf]

Some researchers found mutations were significantly enriched in the non-transcribed DNA strand when doing next-generation sequencing, Is there any database for transcribed direction of every gene?

[Chris Evelo]

Huh? Can you explain how a mutation could be present in the non-transcribed strand only? Maybe you could add a reference for the "Some researchers found..." part of your question.

[Liyf]

The paper is "Integrated analysis of somatic mutations and focal copy-number changes identifies key genes and pathways in hepatocellular carcinoma", in it they say G>T transversions were significantly enriched in the non-transcribed DNA strand. Thank you for your advice.

[Damian Kao]

Do you mean there are more transcription errors in the anti-sense transcribed mRNA? There can't be more mutations in the anti-sense DNA compared to sense DNA since they are complementary.

[Liyf]

Yes, I think so. But the paper "Integrated analysis of somatic mutations and focal copy-number changes identifies key genes and pathways in hepatocellular carcinoma", in it they say G>T transversions were significantly enriched in the non-transcribed DNA strand.

Answer 1

[Ido Tamir]

Every sane database of transcripts/genes includes the location of the transcripts together with the direction.

http://central.biomart.org/

http://genome.ucsc.edu/cgi-bin/hgTables?command=start