Monday, May 16, 2011

The Independent DNA Experts and the Electronic Data Files

Part 28 in the Knox/Sollecito case

Update, 13 June 2011

In the story “Knox appeal: DNA experts to request more time” from the AFP on 20 May 2011, Knox lawyer Carlo Dalla Vedova said “The experts asked the forensic police to hand over information essential to their report on the DNA. They still haven't received it and will therefore request a 40 days extension.” He added, “It's not the first time we've asked for the police to hand over this information,” He also said, “But they need the raw data they have asked for from the police to do so. We first asked for it in 2009 and it's still not been handed over.” This ends the debate about whether or not the forensic files were ever released to the defense during the trial of the first instance.

Judge Hellmann appointed two independent experts to review the DNA forensic evidence in Amanda Knox’s and Raffaele Sollecito’s appeal. Recently, the experts asked for more time, and reports suggested that they did not yet have access to documents the felt were necessary to carry out this task.

According to Candace Dempsey, forensic scientist under whose supervision the tests were carried out, Dr. Patrizia Stefanoni, turned aside this request. She wrote to Judge Hellman, “In reference to the request of acquisition of CD RAW DATA, one is obligated to explain that the information in the form of this file in the sequencer is never an integral part of the technical report, as far as the object being tested by the forensic geneticist, namely the DNA profile, and that it is already reported in the electropherogram printout, connected to the technical report on which all of the useful date and an evaluation of the genetic profile are reported… Finally, the request asked for by the expert consultants relative to the acquisition of the CD RAW DATA appears incomplete in so much as the name of the ‘sample file’ requested was not specified…”

To help me consider Dr. Stefanoni's refusal refusal, I have consulted with DNA forensics professionals Dan Krane and Jason Gilder of Forensic Bioinformatics, and I gratefully acknowledge their help. The continued lack of file release with respect to the DNA profiling of this case has been a recurring theme of this blog.

Her arguments against releasing further information are essentially:
(1) All of the necessary data are already in the paper printouts of the electropherograms.
(2) The request for data files is insufficiently specific.

Let us examine point (1) first. Dr. Stefanoni’s position appears to be the same as it was when Dr. Pascali was refused data, as noted in Raffaele’s appeal. Yet some of the electropherograms only provide the number of repeats, not the peak height for each peak. Peak heights are essential to evaluate peak height imbalance within a locus, which bears on the question of whether or not a sample is in the low-template range, and whether two peaks within a locus belong to the same or to two different individuals. Peak heights can also be used to quantify the severity of degradation when one compares DNA fragments of different lengths. Peak height ratios also help one to decide whether or not a small peak is a type of artifact known as a stutter. A careful examination of these small peaks is especially important in helping to judge what other DNA is present on the bra clasp besides Meredith’s and presumably Raffaele’s.

In addition, having the electronic data files allows one to calculate a run-specific limit of detection (Gilder et al., J. Forensic Science, January 2007, 52 (1), 97). This process sets a lower limit on the size of which peaks to accept, based on the amount of noise.

It can also be helpful in detecting a type of artifact known as a pull-up. There are four types of dyes used in DNA profiling, each with a different wavelength (color) of detection. Each dye is ordinarily detected in its own channel. Sometimes a large peak gives a small spurious signal because of bleeding from one channel into another (Butler, Forensic DNA Typing (2005), pp. 336-337; 384). According to Christine Funk and Dr. Simon Ford, “Pull-up can usually be identified through careful analysis of the position of peaks across the color spectrum, but there is a danger that pull-up will go unrecognized, particularly when the result it produces is consistent with what the analyst expected or wanted to find.”

Dan Krane was asked to give his opinion about the release of such files in a separate legal matter. He wrote, “I believe that a defense expert cannot competently evaluate the results of an STR DNA test without having access to the test’s underlying electronic data. In my experience, review of electronic data has often led directly to the discovery of important problems or limitations in the STR testing, or to alternative theories of the evidence, that would not have been apparent based on a review of laboratory reports or other laboratory records… In my opinion, review of the electronic data is as important as review of the laboratory’s written notes…There is no legitimate reason for a laboratory to refuse a defendant’s request to examine the electronic data.” (bolding mine) Finally, this blog has previously noted that the ABA standards explicitly call for release of the electronic data files.

Point (2) is equally difficult to comprehend. Clearly Dr. Stefanoni understands that the electronic data files are being requested, yet apparently wants specific file names. It is difficult to see how the independent scientists would know the file naming convention used in Dr. Stefanoni’s lab. Who does Dr. Stefanoni think can provide the specific file names?

Forensic Bioinformatics has a 10-point standard discovery motion, and point 6 covers files. The material should include:
(6.1) All collection files (such as injection lists and log files for an ABI 310 analysis).
(6.2) All GeneScan® files, including sample files and project files.
(6.3) All Genotyper® files, including templates/macros (see Request 5).
(6.4) All GeneMapper® files, including sample files (.fsa files) and project files (.ser files).
(6.5) If the data you are providing includes files from another case that are not pertinent to the instant case (e.g., sample files from another case included in the same run folder), then please identify those non-pertinent samples by name and laboratory code.

Clearly it is the job of the laboratory that performed the test to provide the file names.

Concluding remarks
The failure of Dr. Stefanoni’s laboratory to provide the data to the independent forensic scientists is a continuation of her refusal to provide them to the defense. There is absolutely no legitimate reason for her to do so. As Dan Krane noted, “It is a fundamental tenet of science that two reasonable experts should be able to independently arrive at the same conclusions after reviewing the same experimental data.”


mdklion said...

It is becoming clearer and clearer that she has something to hide here. Scientists who have a clear conscience welcome colleagues checking their data.

Patrick King said...

My crystal ball sees a well-deserved perjury indictment in Dr. Stefanoni's future.

Eric said...

This was extremely informative.

I'm thinking that we're going to discover that Stefanoni was doing things like counting the stutter peaks as real peaks.

I can't see any other reason for witholding the data.

Michelle Moore said...

If there's nothing to hide, then show them the documents. They are scared out of their minds right now.
Frankly, I think this is very exciting to hear!!! :)

Rose said...

Thanks, Chris.

It appears to me that Stefanoni does not understand the importance of this data, or it least that is what she seems to be saying.

Chris Halkides said...


You may well be correct, but it would suggest that Dr. Stefanoni has a relatively unsophisticated idea of how to analyze electropherograms. It would be as if she only understood the information along the horizontal axis of the graph which is time and which is proportional to how large the DNA fragment is. This tells us how many short tandem repeats are present. However, there is also data in the vertical axis, information on how abundant each fragment is. That is the information that is needed to assess peak height imbalance and the other things I discussed.

Eric said...

@Rose Montague.

Stop being equivocal. It's pretty obvious something is badly wrong if Stefanoni won't release the data.

Why on Earth do you bother posting stupid comments like 'Stefanoni does not understand the importance of this data'.

She's supposed to be a scientist for crying out loud. Not understanding the importance of the data surely disqualifies her from being a scientist? And that still doesn't answer the question of why she is refusing to hand over the data.

You really come out with some crap sometimes Rose.

Chris Halkides said...


One of my favorite saying is along the lines of "Never ascribe to malice what can be explained by incompetence." I have had to trot this out many times during the present case. I admit that I am beginning to wonder whether or not something major is hidden in the files. However, Stefanoni and her boss may just be taking the attitude of why release anything unless absolutely forced. Massei should have forced them, but perhaps Hellmann can't be rolled so easily.

billyryan said...

Hi Chris
Stefanoni is trying to hide something.The rusting of the bra-clip was not an accident either.I would say that when Stefanoni was doing her DNA analysis she done so with the belief that Amanda and Raffaele would soon confess,She had no way of knowing what was being printed in the Italian press was all lies being fed to reporters by Mignini and the police,and she got careless.
Frank Sfarzo does not think Stefanoni acted with any impropriety he believes she just found on the knife blade and the bra clasp what the police planted,his take on the exchange between Hellmann and Stefanoni is an awful loss now that Perugia shock is down

zooks said...


I think it's possible you're right that she doesn't know. She didn't know not to wrap to secure evidence with paper found on the scence. She didn't deem it important to collect the victim's clothing. I have not trust in her. As Kaosium would ask - is she incompetent, corrupt or both?

I think it is likely we will hear her say "ooops" very soon. She will be very sorry that she can NO LONGER find the electonic files. It has been many years after all!

Great article Chris !

Kaosium said...

Is Stefanoni a scientist or is she just a glorified lab tech? Grunting it out with the forensics team in the field suggests the latter, as does her education being limited to a biology degree as I recall. Her sole claim to status above that would appear to have been her 'revolutionary' technique used to find incriminating evidence of Raffaele and Amanda, and it sure seems she has about as much idea how to document and prove her claims as did the cold-fusion 'breakthrough...'

She appears to be hoping she can stymie these requests with bureaucratic resistance, but it doesn't appear that's as likely to be successful with this court as it was with Massei's. It seems like she might be in a lose-lose scenario, as those independent experts might just refuse to 'confirm' her findings without those files. If they end up having been 'lost' it's just one more item in the litany of destroyed evidence I will have to remember, so cough them up lady! :)

I don't think she will though. If there was no other reason not to turn them over, they would have been released when the independent experts requested data. I could understand if not sympathize with the idea they might have been withheld from the defense as that wasn't currently practice in Italy, being a bit outside the modern forensic DNA community, however if there was nothing to hide in those files you'd think she'd trumpet her compliance loudly, as other aspects of her work did need disguising as the independent experts have already discovered going by leaked reports and decayed evidence.

LorettaP said...

What I think will happen
Stefanoni never finds , or never did, required paperwork
All DNA evidence is tossed out.
Mignini is all puffed up and mad at Stefanoni for screwing up
Estimated time of death is re-revised to match the evidence.
Amanda is released and RUNS to the airport
Amanda is greeted by a huge crowd that Sea-Tac airport did not expect
Stefanoni is blamed for losing the case and her reputation is ruined. Mignini fires her.
Marresca pushes all the other cases to go forward, including the one by the Kerchers against Amanda
Perugian authorities try to lure Amanda back to Italy. They ask for an extradition. The U.S. replies, “Ptui!”
Amanda goes down in history as the killer who got off on a technicality. The guilters ramp up their outrage.
Mignini gets off scot-free

LorettaP said...

I have a Polyanna version of this if you want a happier ending

Rose Montague said...

Eric said:
Stop being equivocal. It's pretty obvious something is badly wrong if Stefanoni won't release the data.

I think it is clear that I think that there is something wrong, if you have been following my posts at all.

Why on Earth do you bother posting stupid comments like 'Stefanoni does not understand the importance of this data'.

Actually if you read my comment, I was posting on what I believe Stefanoni said in so many words. I would agree that her lack of knowledge defense for not releasing the data is pretty stupid. Perhaps if you had included the rest of my comment, you know the part "that is what she seems to be saying", you might have understood my comment better. Either she doesn't know or she is pretending not to know, those are the two interpretations I give to her excuses.

You really come out with some crap sometimes Rose.

LOL. Your opinion bothers me not at all

Chris Halkides said...

The lack of file release makes it impossible to maintain that the first trial was fair. That may explain why the pro-guilt commenters go to such extremes in trying to explain it away.

Mann said...

Its quite clear that she does not want to release the data because she knows that this is a bogus result and it will be over turned if they get the chance to look at it and if its was a valid result there would be no reason not to release the data she is doing what is called dragging her feet because she knows the gig is up.

Eric said...

@Rose Sorry. I think I misinterpreted your comment, on reflection. In fact it's clear that you were subtly questioning Stefanoni's abilities.

Emotions run high with this case, and sometimes people including myself jump to incorrect conclusions.

billyryan said...

She must know that she is going to be forced to hand over the files,she must have known this day was coming for a long time and has being planning what to do
Chris according to Candice's article,as we all know their is not enough material on the knife blade to retest but she adds to this by saying their was never enough material on the knife blade to produce a DNA profile in the first place,is this a proven fact or just speculation

RoseMontague said...

No worries Eric. It is already forgotten and I am glad you are here.

Chris Halkides said...

It depends upon what one means. The quantitation run told her "too low." There was some small amount DNA present, or there would not be a profile at all. However, both by how much DNA was present and by how tall the peaks in the e-gram are, I do not think that Meredith's profile on the knife deserves to be considered a complete DNA profile, unlike her profile on the bra clasp. This profile has much more intense peaks and which has near equality of peak height within a locus.

Anonymous said...

This all is so complicated. There is obviously a great deal of cover up about the events surrounding this case. More important is that individuals instinctively surmised such from the onset. Being oblivious to comprehending the topic of "Data Files" my instincts tell me that they were manipulated and fabricated or worse do not exist. It has never been about incompetence, or mishandling, or misconduct it is about protocol. Simply reading through the 1000's of hours of documentation and B.S. from court reports to Judges reasonings there flows this undertone of a convoluted story of fairy-tales and drama created by individuals who are directing the flow of the out come with the belief that if you keep people guessing, under Italian law the accuser wins. WE NO LONGER ARE GUESSING! I do believe that if these files are not turned over by the time court begins Saturday these proceedings should be ended, Amanda and Raffaele released thus setting a precedence to all policing/prosecution proceedings. The tone of these events also could be examples of what the new Egypt, Syria, Libya, can set as examples of rules of authority, Checks and balances. Will the court blow the trumpet over these actions or is it just protocol? Justice? What's it gonna be?

Colin Connaughton said...

The court, i.e. Judge Hellman, has asked for the files. So, Stefanoni should give the files, not excuses or explanations, or she should be held in contempt of court. If the files have been lost or corrupted (which would be not be surprising since the police have already destroyed three, I think, computers relating to the case) then she should say so. Simple.

sandra Olson said...

I as well have been trying to get the files on dna testing done in a paternity matter, One of the labs is orchid cellmark. They had the report, but refused for years to release anything. Then in the spring of 2011, Jennifer Clay, told me that if I got a lawyer, AND paid them 140 and hour they MIGhT release the file to me, I went to the freedom of information office, Jennifer Clay then released a copy of the report, but nothing else, I continued by requests, suddenly, she insisted that the file had been destroyed after the 3 years mandated by law for their destruction. I pointed out that this 3 year mandate is not for private labs and she is a private lab. Suddenly the freedom of information office said that SHE THOUGHT she had to destroy the file and that was it. I now have a public inquiry in the works with the lab at calgary childrens hospital, same problems same situation. Refuse to release etc. It seems to me this problem is a prime example of how the dna industry is acting like god. They say what they want in a report, and then refuse to prove anything they say, insisting they don't have to. I say if you are playing god with people's lives, you should be completely transparent with the public. And what judicial system in the world would let someone flout their orders without consequence?? If they need to release their work for independent review is there, and refused, what is this material doing in a court of law at all???

Anonymous said...

DNA labs have been playing this game forever. What needs to be understood is the ability of a Human lab expert to falsify the reports. Raw DNA data actually has the alleles on the data. Lab technician only have to put it in adobe reader form that is easier to convey. The human link in this process is exactly that.HUMAN. I have had numerous testing done and My DNA and that of the children have kept changing. Courts know this very well and the crown attorneys will not allow you to take these labs down. Stay tuned as i am in process of exposing international lab falsifying records. Labs problem with me is that i understand more than the lab technicians do at this point. They use the general publics lack of knowledge and hide behind accreditations. In Canada, labs get accreditation letters that give them an expiry date of lets say 2018, then they voluntarily pull their accreditations without changing their websites. You also need to consider the opposing party in the cases. My opposing party has family in the justice system and they will not let me win. Corruption is the problem. Human condition is the probelm. As humans, no matter if you are law enforcement, lawyer, judge, or lab technician, we all have greed, envy and many emootional faults.