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bio_med_guy t1_is2lo6e wrote

Well in clinical practice, for example in hematological malignancies, they usually do different type of sequencing called targeted Sequencing for specific genes which they know would be of interest for that class of blood disease. Same with other types of solid cancers looking for biomarkers to classify the patients, in order to know which treatment protocol would be most suitable.

In clinical trial however, this is still learning process. So they would want to collect as much data as possible from the patients to categorize them into which patient group had the most robust effect when using the drug and what kind of side effect you would expect with these category of people. That's why the whole transcriptomic analysis and possibly other highthrouput data as well. Saying so, before admission to clinical trials and based on previous pre-clinical data, some companies might place requirement for certain biomarker in the group of patient to be admitted to the clinical trial.

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Cheddarific OP t1_is4buvh wrote

Transcriptome is undoubtedly fascinating in oncology, but the real question is how that translates into actual proteins, right? Like measuring the amount of time each student studies each textbook page for a test rather than capturing the actual results of the test; you get more data one way, but the data you really want is the smaller set, right?

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bio_med_guy t1_is4tp5k wrote

Yeah okay, didn't understand your question. The problem with proteomics is you need alot of starting material in order to get data, specially when talking about discovery highthrouput data which sometimes is not available in case of patients in clinial trials. In cases of clinical practice you do not need that much, as different techniques are being used such as flow cytometry, which works for few biomarkers but not for highthrouput discovery data. However that limitation is being approached now from several directions including spatial proteomics.

On the other hand, transcriptomic analysis can be done with very small amount of starting material, and with much cheaper price. Simply as this amount will be amplified during the procedure, which cannot be achieved for proteomics.

Did that answer your question??

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