Question: How representative the solid tumor sample is to that entire tumor lesion in terms of somatic mutation profile
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gravatar for CY
13 months ago by
CY290
United States
CY290 wrote:

I know this is not a very valid question.

Although the allele frequency of somatic mutation from tumor WES data can't reflect the overall fraction of that mutation in entire tumor lesion. I guess many factors can affect such representativeness ( sample extraction process, the tumor volume or the tumor heterogeneity ).

Is there any studies (publications) or tool investigating this and trying make some kind of estimation?

somatic mutation tumor • 377 views
ADD COMMENTlink modified 13 months ago • written 13 months ago by CY290

It's going to vary by tumor type. Fast growers will be homogeneous due to "clonality" but there's no measure of "the entire lesion".

ADD REPLYlink written 13 months ago by karl.stamm3.4k

You mean fast grower does not have enough time to diverge, right?

ADD REPLYlink written 13 months ago by CY290

No, somatic mutations happen in individual cells, so you'll start with one cell with an arbitrary background, who suddenly evolves the ability to multiply quickly. It can become the majority of tumor mass. Its offspring may continue to mutate, or may stably reproduce the original.
I think the first time any bit of the tumor develops the ability to multiply quickly it will reproduce uncontrollably. That's what cancer is. The "entire tumor lesion" can be poorly defined masses, and every cell is an individual.

ADD REPLYlink written 13 months ago by karl.stamm3.4k

I got what you are saying. I got a picture like this:

At the beginning, some immature tumor cells battle with immune system and able to form a fair amount of small subclones through a long period of time. Once a subclone fully developed into mature tumor cells, it expand quickly and become dominant.

If this is the most case, I would imagine the tumor heterogeneity be kept at minimum level since the most of the tumor cells are from the same subclone and only subject to short period of diverge.

How do you think of this?

ADD REPLYlink written 13 months ago by CY290

What is it that you want to estimate, exactly?

ADD REPLYlink written 13 months ago by Sean Davis25k

I am not sure if I understand teh question correctly. But, you should look at one of those multi region WXS/WGS studies. Somatic mutation profile varies a lot within the bulk tumor based on biopsy site. So its pretty heterogeneous.

ADD REPLYlink written 13 months ago by poisonAlien2.7k
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