Question: Interpretation for lowfrevariant
0
gravatar for Tania
6 months ago by
Tania120
Tania120 wrote:

Hi every one

If we have this variant:

GT:GQ:DP:VF:GQX:PL:AD ==> 0/1:99:910:0.095:99:549,0,17114:824,86

And it did not pass, it is reported as LowVariantFreq

I understand that this is because AD =824,86. which means we have 824 reads support the ref and 86 only support the alt.

But it is a stop gain variant, so I wanna double check before throwing it. Is it artefact? Should be ignored or still of interest? Does it mean the patient is mosaic for example?

Thanks

vcf • 339 views
ADD COMMENTlink written 6 months ago by Tania120
1

Hi , What is your variant (del ins snv ) ? what is the context of this base ? low complexity region or not ? this 2 points should help you to decide the reality of your variant.

Best

ADD REPLYlink written 6 months ago by Titus610

I don't know about the region, how do we know? it is: G -> A AC=42;AF=0.5;AN=80;DP=27355;EXON;FC=Missense_V425I;GI=SUCLG2;QD=17.62;SF=2,3,9,13,16,17,19,24,26,27,28,30,33,43,44,49,75,86,89,91,93,96,100,101,102,104,105,113,114,117,123,124,127,129,131,132,133,134,135,137;TI=NM_001177599

and 0/1:99:910:0.095:99:549,0,17114:824,86

ADD REPLYlink written 6 months ago by Tania120
1

You can have look with the genomic position and the chromosome

ADD REPLYlink written 6 months ago by Titus610
1

Makes complete sense that the variant gets discarded since it has such a low frequency, but there are still 86 reads supporting the alternative allele there. Best you can do is validate with another sequencing technology.

ADD REPLYlink written 6 months ago by WouterDeCoster30k
1

Agreed WouterDeCoster , but for example with SANGER she got low chance to confirmed, it's the eternal question i think we have to wait more precise and low cost technologies like one cells target to my mind ...

ADD REPLYlink modified 6 months ago • written 6 months ago by Titus610

Thanks WouterDeCoster and Titus so much.

ADD REPLYlink written 6 months ago by Tania120
1

Nobody asked if this is a tumour or germline sample? If tumour, then low frequency is expected; if germline, then variants should ideally be called at a 50:50 split between ref and alt reads. The frequency of this region is a bit worrying if it's a germline sample and you should look at the alignments in the BAM file over the region in which the variant is called - use IGV to view the alignments.

ADD REPLYlink written 6 months ago by Kevin Blighe24k

Nobody asked if this is a tumour or germline sample?

Valid question, but I consider information like that up to the OP to provide.

ADD REPLYlink written 6 months ago by WouterDeCoster30k

By the way mosaic problematic (low fraction) and tumour are quite close in bioinfomatique analysis...

ADD REPLYlink written 6 months ago by Titus610

Yes, but it was neither specifically stated if this sample was expected to show mosaicism or not. On the contrary, it was just posed as a question if the low frequency meant that mosaicism could be present. No-one's to know other than the OP, who should be well versed on the source of the sample and the history of the individual from which it was taken.

ADD REPLYlink written 6 months ago by Kevin Blighe24k

What mean OP (English is not my maternal language and to me acronym are not easy sorry) ? original post ? If i understand your the problem concerned details not enough in the original post is that you mean ?

ADD REPLYlink written 6 months ago by Titus610

Hi Titus! Yes, 'OP' means 'original poster', i.e., Tania. The problem is that there was not enough information in the question (a common problem on Biostars); so, the result of that is that we either speculate (guess) or ask for more information.

Thanks!

ADD REPLYlink written 6 months ago by Kevin Blighe24k

Hi Kevin, How can I know if it mosaicism or not? We have an individual with a very rare phenotype, what else we can check to decide? I don't have any more information about him, but could ask. But what information I should relate to this?

ADD REPLYlink written 6 months ago by Tania120

You haven't told us anything about the source of the sample. Blood? Transformed lymphocytes? Tissue biopt? Hereditary or acquired phenotype?

ADD REPLYlink written 6 months ago by WouterDeCoster30k
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