Question: gene expression for cancer identification
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gravatar for maryak
11 months ago by
maryak10
maryak10 wrote:

As we know that RNA-seq is a relatively expensive method but we use gene expression for cancer detection or identification of cancer related genes why cannot we rely on bio marker tests for cancer diagnosis.I am new to bioinformatics i excuse in advance if my question is insane. Any help in this regard will be appreciated

rna-seq gene • 349 views
ADD COMMENTlink modified 10 months ago by Biostar ♦♦ 20 • written 11 months ago by maryak10
2

why cannot we rely on bio marker tests for cancer diagnosis

You absolutely can. But to get there one needs to gather evidence about which biomarkers would be reliable to do the testing with. That is what people spend years/money identifying. Finally a regulatory body (e.g. FDA in US) needs to approve that test, since we are dealing with human healthcare (if the test is for human cancers).

ADD REPLYlink modified 11 months ago • written 11 months ago by genomax71k

It's quite common to use non-RNA-Seq methods for expression-based biomarkers. For example from qPCR. however, RNA-Seq or microarrays are commonly used at the early stages when you are trying to identify a set of biomarkers that might be of future value.

ADD REPLYlink written 11 months ago by russhh4.7k

As we know that RNAseq is a relatively expensive method

[citation needed]

why cannot we rely on bio marker tests for cancer diagnosis

Can you please give a few example of these tests and also explain what you mean by "cancer diagnosis". Plus, it would help if you mentioned why you think biomarkers are not already being used in cancer diagnoses.

ADD REPLYlink written 11 months ago by RamRS24k

Examples of tumor markers include prostate-specific antigen (PSA) for prostate cancer, cancer antigen 125 (CA 125) for ovarian cancer, calcitonin for medullary thyroid cancer, alpha-fetoprotein (AFP) for liver cancer and human chorionic gonadotropin (HCG) for germ cell tumors, such as testicular cancer and ovarian cancer. I just asked if we compare these two methods(diagnosis of cancer using biomarkers and RNA gene expression) which will more be reliable in detecting cancer

ADD REPLYlink modified 11 months ago • written 11 months ago by maryak10

Both should be reliable where you have a validated biomarker (like the examples you provide above). Until you have a validated (set of) biomarker(s) you can't use RNAseq per se for cancer diagnosis.

ADD REPLYlink modified 11 months ago • written 11 months ago by genomax71k

Actually no bio markers are diagnostic of cancer by themselves, the whole idea behind a marker molecule is to raise a suspicion (or not) about a disease being present in a patient without invasive procedures, typically taking a quantitative value as reference. If the suspicion exists, diagnosis algorithms present a subsequent step(s) to take after the bio marker measurement to actually make a diagnosis. The only 100% accepted way by good practices of confirming cancer would be pathology, even the most famous markers such as the prostate antigen requiere a biopsy and pathology study to diagnose cancer in spite of a very high initial antigen measurement. You can see an example of what I said here https://www.esmo.org/Guidelines/Genitourinary-Cancers/Cancer-of-the-Prostate/eUpdate-Treatment-Algorithms

Who knows maybe one day RNA-seq will be as reliable as a pathologist or even more!

ADD REPLYlink written 11 months ago by mike-zx140
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