What % of colon cancer patients does a general colon PCR array detect - (Jan/29/2015 )

Dear Forum,

I have a pretty simple question - if we were to take biopsies of 100 stage 1 or 2 colon cancer patients, and then dPCR them using a standard Colon Cancer Mutation PCR array that covers 86 of the most prevalent mutations (like this one, for example: http://www.sabiosciences.com/qbiomarker_product/HTML/SMH-021A.html),

in how many would we find colon cancer?

I am asking because after looking through a lot of literature, it seems very difficult to answer this end-to-end question. It seems to be easy to identify which genes and mutation spots are most common, but I am totally unclear how many different types of mutations per spot occur, and how many of these mutations per spot would be covered by the standard assay that covers that spot.

So I am looking for a more general, maybe experience-based answer: If one applies a standard, commercial general cancer PCR array to a biopsy that is guaranteed to have that cancer, what's the hit rate. A rough number is enough - is it 90%? 50%? 10%?

Thanks so much!

-JohnBhakdi-

You can't say that. Colon cancers have a specific genetic pathway that is implied in majority of the cases, many other cancers have not. Also a presence of hotspot mutations or regions makes the molecular analysis easier That is, CML patients have BCR/ABL in some 90%, PV patients have JAK2 V617F in 95% and other JAK2 region deletions in another 3-5%.. but when I was trying to select 7 most frequent sites of mutations in one type of lymphoma, in 96 samples I only got like 2-3 posiitive on ANY of the mutations. You see, in genome-wide study, the MLL gene was responsible for around 30 % of mutations, but the gene itself is huge and the mutations were not clusterer, so the most often single mutations had only percentage frequency.

As for different mutations within the same base, they happen, but that is also very specific. The kit uses ARMS technology, so it detects both wild-type or mutant, if you don't have a product from either one, the sequence is different from both variants. Sometimes the single assay has some information what additional mutations it may cover.

So you need to look on your cancer specific data. And, there are never any guarantees..

-Trof-