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FAQ on DNA PCR
Apr 12, 1999

Dear Dr. Holodniy:

I have a question on "Qualitative DNA PCR", but before I ask that I thought I would attempt to summarize your previous comments on the topic of PCR, so as to reduce repetitive questions and leave you more time to answer the new ones :-))

1. RNA PCR measures HIV RNA in cell free blood plasma

2. DNA PCR measures HIV DNA inside blood cells.

3. Chiron bDNA assay measure viral load but is not a PCR based test.

4. DNA PCR (Roche) is the only FDA test approved for measuring HIV viral load. However, the RNA PCR is presumed to be equally valid.

5. PCR tests are not FDA approved for diagnosis of infection (only Antibody tests are), but studies suggest that a DNA PCR or RNA PCR test will reveal infection in almost all people after 4 (high confidence) to 8 weeks (very high confidence).

6. Passing a PCR test after 4 weeks is very good news. Passing a PCR test after 8 weeks is excellent news.

7. Passing an Antibody test after 3 months is very good news. Passing an Antibody test after 6 months is excellent news.

8. If 6 and 7 or combinations therof are true, then one is really, extremely unlikely to be infected.

9. If one wants to take a PCR test, consult your doctor to order a test or find a Lab (do an internet search) that specializes in diagnostic tests but which do not require a medical lab requisition.

10. The PCR tests generally cost $150 to $250. The cost of the doctor's appointment, assuming he or she is willing to order a PCR test for you, is extra.

Now for my question:

You have mentioned previously that a "Qualitative" DNA PCR test sacrifices quantitation (accuracy about how many viral copies/ml) at the expense of providing a better answer to the question of infected or not infected.

I asked a doctor, ( I wrote to you previously about which immunosuppressives may inhibit antibody development; thank you very much for your help!!), that I wanted this "Qualitative" DNA PCR test.

He replied that all PCR tests are actually quantitative in nature and not qualitative! He was kind enough to order a RNA PCR test for me, but I am wondering if that was more due to habit (the clinic I went to deals mostly with patients in whom infection is already established, and hence using a "qualitative" test is pointless) or science?

Can you please provide enough detailed information about the Qualitative DNA PCR test, so that I can ask my doctor to order this test please ? I think many other readers of this forum may also be interested in establishing whether they are infected rather than whether they have an accurate viral load count, and hence would be most interested in the "Qualitative DNA PCR test".

Thank you again for your help!!!!! I think I echo the sentiments of many readers when I say that you are being of tremendous help to many people. Thank you!

Response from Dr. Holodniy

Great job on 1-10!!! There are some semantic arguments here regarding quantitation. In some respects all PCR tests are quantitative, in that each cycle of amplification generates ever increasing amounts of DNA copies. The detection systems will only measure quantitative differences in input copy number after a certain number of cycles of amplification. For instance, we can only detect PCR products after 20 cycles of amplification. Between about 20-30 cycles(30 being about where most assays are used), PCR can be "quantitative", that is showing some linearity in output signal from ever increasing amounts of input copy number. Above 30 cycles, PCR loses it's ability to be quantitative because there is just too much product from all the cycles of amplification, so the detection systems become saturated ( unable to detect differences in input copy number). So 10 copies looks the same as 10,000 copies. RNA PCR for plasma viral load works in the 30 cycle range to maximize quantitation ability. DNA PCR works in the 35-40 cycle range to maximize saturated detection so that everything above say 5 input copies will be detected, but not quantitated. That is, it is a yes/no answer. MH



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