Question: Sample contamination level over 30%
0
gravatar for haiying.kong
17 months ago by
haiying.kong230
Germany
haiying.kong230 wrote:

I have a pair of samples (normal and blood) that are whole exome sequenced. I checked contamination level of the samples. Tumor is contaminated at level of 30%. If I do validation experiment for any findings from this pair of samples, can I get my work published?

next-gen • 672 views
ADD COMMENTlink written 17 months ago by haiying.kong230

Tumor is contaminated with what?

ADD REPLYlink written 17 months ago by genomax63k

cross-individual contamination.

ADD REPLYlink written 17 months ago by haiying.kong230

How did you determine that?

ADD REPLYlink written 17 months ago by andrew.j.skelton735.5k

run ContEst in GATK tools

ADD REPLYlink written 17 months ago by haiying.kong230
1

It might be an idea to add this into your OP along with commands ran, and your experimental context.

ADD REPLYlink written 17 months ago by andrew.j.skelton735.5k

No, that is not the point!

My point is not how to find contamination level. Assuming the computation is correct!

Then if a tumor sample has such high level of contamination, can I still use any findings from the sample? The sample is WES, and if I validate with extra experiment on other samples for any findings from this highly contaminated tumor sample, can I still publish?

ADD REPLYlink written 17 months ago by haiying.kong230
2

What do you think? If you were reviewing such a paper would you consider this acceptable? How did the contamination occur in first place?

ADD REPLYlink written 17 months ago by genomax63k

I am asking for someone else. Because I saw it published on IF 5+ journal. They did not mention contamination level,.

ADD REPLYlink written 17 months ago by haiying.kong230
1

I don't think we can answer this question without full context as @andrew said above. In general, if something was contaminated then your conclusions are always going to have a cloud hanging over them (unless there is a clear experimental case/explanation for presence of that contamination).

ADD REPLYlink written 17 months ago by genomax63k

The point is:

whatever they find from the contaminated sample is just suggestion for possible finding. All suggested findings are validated on other samples.

Does this make the work qualified for publication?

ADD REPLYlink written 17 months ago by haiying.kong230
1

If there is independent experimental validation across many samples then it may be acceptable but you would still have to explain why contamination exists at that high level.

That said, consider this quote from ContEst paper

a typical cancer project might expect >10% of the samples to have 1.5% contamination, causing ~0.2 errors/Mb per sample, which is a significant fraction of the typical somatic mutation rate of 1/Mb per sample.

If you had 30% contamination then ...

ADD REPLYlink modified 17 months ago • written 17 months ago by genomax63k

If I were a reviewer, I would consider data with 30% cross-contamination to be completely useless and evidence of a lack of concern for accuracy, so I'd reject it.

That said, just because some tool reported 30% cross-contamination does not mean you actually have 30% cross-contamination.

ADD REPLYlink written 17 months ago by Brian Bushnell16k

in fact i used ContEST and verifyBamID to estimate contamination. both gave abot 30%. i used same software tested other samples. none are bad at this level.

ADD REPLYlink written 17 months ago by haiying.kong230

If you have a good number of samples, you can then discard the problematic sample and proceed with downstream analyses.

The question whether a sample with 30% contamination is still publishable is not a bioinformatics question, but if there is one thing we learned from the last few years is anything is publishable, you just have to find the "appropriate" venue.

ADD REPLYlink modified 17 months ago • written 17 months ago by h.mon24k

The thing is that there is only one pair of samples, normal and tumor, for this study whole exome sequenced. After identifying interesting mutations, these mutations are validated on larger number of samples with sanger sequencing which is much cheaper than WES. You are right about "appropriate" venue. This is exactly what I saw. Some people do research to make living, I think.

ADD REPLYlink written 17 months ago by haiying.kong230
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