Interpretation for lowfrevariant
0
0
Entering edit mode
6.4 years ago
Tania ▴ 180

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 • 1.7k views
ADD COMMENT
1
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
1
Entering edit mode

You can have look with the genomic position and the chromosome

ADD REPLY
1
Entering edit mode

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 REPLY
1
Entering edit mode

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 REPLY
0
Entering edit mode

Thanks WouterDeCoster and Titus so much.

ADD REPLY
1
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 2052 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6