Question: SNPs based on cDNA sequence could be artifacts of RNA editing
0
gravatar for salvatore.digiorgio
12 days ago by
ITALIA-FIRENZE-
salvatore.digiorgio10 wrote:

Hello,

I'm using (dbSNP Build 151) and I would to discard all variants SNPs derived from cDNA. I read from the website there should be a flag indicating which SNPs were obtained from cDNA, but I could not identify it. Is flag present in vcf file? Or I should download some other file?

Best regards, Salvatore

snp rna • 117 views
ADD COMMENTlink modified 12 days ago by Kevin Blighe21k • written 12 days ago by salvatore.digiorgio10
1

Dear Salvatore. I have edited my answer. The Molecule Type is actually a greater indicator of these events, and not the weight.

ADD REPLYlink written 11 days ago by Kevin Blighe21k
2
gravatar for Kevin Blighe
12 days ago by
Kevin Blighe21k
University College London Cancer Institute
Kevin Blighe21k wrote:

dbSNP / NCBI does not explicitly report these. From the FAQ (Frequently Asked Questions):

I'm concerned that submitted SNPs based on cDNA sequence could be artifacts of RNA editing. Does dbSNP track potential RNA-edited artifacts?

We do not directly track SNPs that could be potential RNA-edited artifacts. However, we do flag SNPs derived from cDNA that DO NOT map to the genome contigs but DO map to RefSeq transcripts.

[source: https://www.ncbi.nlm.nih.gov/books/NBK44446/#Content.im_concerned_that_submitted_snps]

-----------------------

They appear to be flagged by the 'Molecule Type' in the dbSNP records, with them being marked as 'cDNA'. Looking at some of the published studies on this topic, namely:

Of the variants at which I have looked from these studies, all do indeed have a Molecule Type of 'cDNA'. For example:

hh

...look to the left, at Molecule Type.

Keep in mind, that this is not absolute proof that these are RNA editing events. These are just variants that do not map to the genome references but that do appear in cDNA.

Kevin

ADD COMMENTlink modified 11 days ago • written 12 days ago by Kevin Blighe21k
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