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There seem to be a lot of "genetic consulting" services that focus on things like cancer, with a modus operandi of:

  1. Do targeted gene sequencing (usually on a few tumor suppressor genes related to cancer the customer is at-risk of)
  2. Analyse the respective data and compile a genetic report outlining risks

The few analyses that I've seen around WGS compared to targeted sequencing claim fairly high accuracy of WGS, including on tumor suppressor genes, sufficient that I wouldn't worry about it, given that TGS will also have some degree of error. So it seems to me like there's little point in using a targeted approach compared to WGS nowadays, given that I can buy a 100x WGS for 1k and some of the targeted tests cost upwards of that.

The other question would be whether the clinics have any "specific" data. I doubt this? I've not heard of a lot of closed-source genetic data, besides maybe that of pharma research companies on a few niche topics. So it seems like a Promethease report could match whatever a specialist would be doing here... or even just searching the variants of concern on clinvar.

Is there any reasons I'm missing why these services still exist? Is it just consumers being misinformed? Or am I glancing over some big problems or benefits?


I guess this might be a bit of a silly question, but hopefully the answers to this will help me elucidate some underlying questions about applied genetics.

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  • $\begingroup$ Leading question that may help you self-answer: you mention the depth of WGS, but what depth does targeted sequencing (such as these genetic counseling services provide) usually have? With what frequency would you expect to see mutations implicated in cancer risk? $\endgroup$ Commented Jun 12, 2022 at 20:44
  • $\begingroup$ The frequency itself depends since we're not talking single base mutations, the depth for most targeted sequencing offers I could find is unspecified. $\endgroup$
    – George
    Commented Jun 13, 2022 at 22:11

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First of all: one thing is the cost for research, one is the cost for diagnostic. Diagnostic tests undergo a series of validation procedures (of which I am not expert) that inevitably lead to an increase in price.

So, the cost of a research WGS can be as low as 1K; the cost of a WGS test validated by FDA would be much higher. The same is true for targeted. You can sequence an amplicon for 4$. But if you want to use a test that is approved by FDA the price would probably increase. Also, interpreting variants you get from WGS is not an easy task. There may be false positives, false negatives, difficult situations. It's not that you can do it yourself, unless you are REALLY an expert. In addition, targeted test are designed to screen for genes responsible of the majority of cases, so in a large majority of cases you would spend more money and still get the same result you would get with amplicon sequencing.

This said, I am sure that the direction we will see in the near future (if personalized medicine stops being a buzzword and starts being reality) is a shift towards more comprehensive screenings such as WGS.

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