Conti and Vecchiotti note that samples A-C were actually not tested with the same real-time PCR technique described in the table above. Instead, a Qubit Fluorometer with the dsDNA HS Kit was used. According to Conti and Vecchiotti, this method is not specific for human DNA. I am not familiar with this technique and do not know why it would be used in favor of the standard real-time PCR methodologies.
The results from the Qubit Fluorometer indicate that no DNA was detected in Samples B and C, and that .08 nanograms per microliter of DNA (not necessarily human) was detected in Sample A.
There is therefore a major discrepancy here beyond possibly not reporting the right technique. Why is Sample B reported as being positive for DNA if none was detected in the assay? No DNA was detected for C in the same assay, yet C was reported as being negative for DNA in Stefanonis report.
Conti and Vecchotti further state:
Nor is it comprehensible, considering the negative results on sample B, what Dr. Stefanoni reported during the GUP questioning (page 178) where she stated that the DNA in sample B, quantified with Real Time PCR (it is recalled that such quantification confirmed during the hearing was never carried out or, at least, no documentation was provided to support this claim), was in the order of some hundreds of picograms, a value which does not appear in any of the documents provided to us (SAL, Fluorimeter report, Real Time report, RTIGF).
To tie all of this in to the final result, sample B is from the knife blade and reportedly has a trace level of DNA consistent with Meredith Kercher on it. Sample A is from the knife handle and reportedly has DNA consistent with Amanda Knox on it.
Sample A certainly had an amount of DNA amenable for typing and the final result is as expected with regard to level of DNA detected in the final typing.
There is apparent confusion regarding Sample B, which is best explained in the Conti-Vecchiotti report:
We learn from the transcript of the GUP questioning that Dr. Stefanoni concentrated the volume of the extract from sample B several times.
In particular, she stated first having concentrated the extract from an initial volume of 50 microlitres to around 20, 22, 23 microlitres (GUP page 178), and of having subsequently carried out Real Time quantification of the total [amount of] DNA, and not of the DNA of masculine origin.
Since from the Real Time quantification (never carried out!) she obtained a concentration of some hundreds of picograms of DNA (GUP, page 178) she took steps to further concentrate the extract in order to obtain a final volume of 10 μl which she would have used for the PCR reaction.
We hold that quantification was also not performed on the final volume, since there is no confirmation either in the documentation in the case file (SAL, Real Time report, RTIGF) nor was such a circumstance ever reported by Dr. Stefanoni in the course of her questioning.
In practical terms, an amplification was carried out without knowledge of one of the basic parameters: that is, the concentration of the DNA possibly extracted from sample B.
It sounds like Conti-Vecchiotti were not provided with data on this concentration and only learned about it by reviewing transcripts. Certainly this issue will be vetted in court to determine if Conti-Vecchiotti simply misunderstood the documentation, were not provided with documentation, or if something else is going on. If sample B underwent concentration procedures, it is important that appropriate negative controls were also concentrated to demonstrate that the procedure did not introduce contamination.
At any rate, it appears that Sample B had to be concentrated multiple times, and it is unclear how much, if any DNA was actually introduced into the final typing procedures.