Showing posts with label electronic data files. Show all posts
Showing posts with label electronic data files. Show all posts

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.”

Tuesday, July 20, 2010

To those who believe that Amanda Knox and Raffaele Sollecito are guilty, I issue a challenge.

Part 20 in the Knox/Sollecito case

Francesco Maresco, lawyer for the Kercher family, said after the verdict last December, “We are teaching the whole world and the United States how to collect, analyse and evaluate scientific technical aspects of the case.”

I have previously discussed how the electronic data files are used by independent experts in criminal cases. Those arguments are especially compelling in the murder of Meredith Kercher, in which the amount of DNA in two of the most important pieces of DNA evidence fall near or into the low copy number (LCN) range. The profile from the bra clasp is also a mixture, and it is well known that the analysis of mixtures introduces subjectivity into the analysis. I have also previously given my reasons for believing that these critical files were never released to the defense teams. Since that time some additional information has become available that puts this question to rest.

Raffaele Sollecito’s appeal documents indicate that his defense expert Dr. Pascali requested the raw data in 2008 (presumably the electronic data files). This request was prior to the preliminary hearing, and the lawyers supported their request with a reference to article 415. They also requested the log files. The judge granted the defense teams the right to forensic information in the summer of 2009 that they had been denied until that time. However, the prosecutions did not fully comply with this order, according to a source close to the defense, and this was one of the things that precipitated the defense teams’ asking for a mistrial in September of 2009.


An open letter coauthored by Dr. Elizabeth Johnson and Professor Gregory Hampikian noted that the prosecution failed to release the electronic data files (.fsa files) to the defense. Since the time of the letter’s release on 11/19/09, some have assumed that these two DNA forensic scientists were unrelated to the case and therefore had no standing to ask for these files. This argument is false. An article written by Fiona Ness on 25 April 2010 indicates that Professor Hampikian is a consultant for Amanda Knox’s defense team. As such, he has every reason to request the operating procedures of the lab, as well as the electronic data files that produce the electropherograms.

“The importance of DNA evidence in a conviction is highlighted in one of Hampikian’s cases - that of US student Amanda Knox. Knox was convicted of the murder of British student Meredith Kercher after a high-profile trial in Italy in 2009. Knox’s conviction was partly based on a sample of her DNA discovered on a knife found in the house. However, Hampikian says he is appalled by the standard of DNA evidence used by the Italian courts to convict Knox in the case. ‘The amount of DNA present is far below the normal cut-off for many labs that I know of. A one off spurious piece of DNA evidence shouldn’t be treated as a gold standard profile from a high-profile source. The issue of this low-template DNA sample is really troubling me.’ Trying to obtain the evidence to have it retested, however, is proving difficult. ‘The discovery rules in Italy are different to what I’m used to. It’s fairly routine in the US that I send a request and get what I want. But in the Knox case I haven’t been able to get a copy of the standard operating procedures of the lab and without that, it’s hard to see if they even followed their own guidelines.’ Evidence, Hampikian says, is a matter of science, to be reviewed, not protected.” (emphasis added) An article in the Irish Times confirms that a professional relationship exists between Professor Hampikian and the Knox family.

The words of an anonymous forensic DNA expert unconnected with the murder of Meredith Kercher are apropos here. This individual said with reference to a different case, “Honest differences of opinion by qualified experts should be welcomed by the Court. This can only be accomplished if the independent expert is provided full and complete discovery by the government.” Keith Inman and Norah Rudin gave ten ways to improve forensic science. Number five was “Provide transparency. Secrecy and gamesmanship are inappropriate to the work of the forensic scientist. All laboratory notes, data, results, procedures, logs, and records should be open to controlled
and appropriate scrutiny.”

To those who believe Ms. Knox and Mr. Sollecito are guilty, I respectfully issue a challenge: Join me in calling for the release of all of the forensic information that the defense has been denied until now. Some among you have argued that the Italian authorities should not release any more information than that demanded by Italian law. However, it is conceivable that Italian law is not yet settled on the question of whether or not to release the electronic data files. If it is not, why should the precedent be against full disclosure rather than in support of full disclosure? If the case against the defendants is as strong as you say it is, you have nothing to fear. On the contrary, your certainty would be stronger if the release and examination of these files produced nothing.

To the Italian authorities I respectfully issue a related challenge: Make good on Mr. Maresca’s claim. Show the world that forensic evidence is to be shared with the defense. At that point the analysis will be complete. Provide the electronic data files (.fsa files), and the instrument log files, and include the contamination log files if they exist. Then and only then will you indeed be showing the world the right way to treat forensic evidence.

Monday, June 21, 2010

Raffaele Sollecito's Appeal

Part XVIII in the Knox/Sollecito case

Update, 7/12/10

Here is a better translation of a portion of Sollecito’s appeal dealing with the bra clasp, provided by an anonymous translator:

“But there is more. The lack of full discovery was also found during the course of the trial:
- on July 18 2009, during cross-examination of the technical consultant of Raffaele Sollecito’s defence, Prof. Adriano Tagliabracci, there was an astonishing coup de theatre, in which the prosecution formulated a question which generated the suspicion that the Public Minister was in possession of further laboratory data never made available to the defence. In particular, the data relative to the quantity of the extract used for genetic analysis of the biological material found on the bra clasp of the victim;
- confronted with the reaction of the defence, the office of the Public Minister had to admit that there existed documents compiled by the scientific police never deposited at the conclusion of the investigations (contravening in this way the provision of Article 415 bis c.p.p.), nor sent to the Gup with the request for trial (in violation of Article 416, paragraph 2, c.p.p.).
In other words, the office of the PM denied a complete discovery of the documents of the investigation, extending this breach in the rights of the defence into the trial!”

This passage indicates that the prosecution failed to provide the defense with information relating to the single most important piece of evidence against Raffaele Sollecito all through the pre-trial and well into the trial phase. What is unclear from the appeal document alone is whether or not all information was ultimately released. However, other documents indicate that the prosecution never released all of the information that the defense teams sought.
___________________________________________________

The following is Google-translated from Raffaele's appeal document (pp. 51-57) with some minor edits. Although it is hard to decipher the meaning in places, it gives a picture of the defense continually asking for information on the DNA testing all throughout the preliminary hearing and trial, and the prosecution continually refusing. I have previously written about the importance of the electronic data files to a proper defense and about the near universality of this disclosure. I am eager to hear the prosecution’s explanation of how their refusal to hand over log files and electronic data files can be anything other than a trampling upon the right of discovery:


“And there is no doubt that, in terms of 'prosecution, failure to discovery on one of the main aspects of the process has been a considerable advantage over the defense, since the case involved Raffaele Sollecito is building right on genetic testing. In fact, it is useful to make a historical reconstruction of the case at hand:
- Following the conclusion of preliminary investigations, the defense could review the technical report of forensic genetic investigations in the signature of Dr. Patrizia Stefanoni, to which were attached tables who reported only the number of alleles, without which they would specify any other information or scientific data (for clarity, we define each variant allele of a gene, the genotype of an individual gene has a relatively Kit alleles he is in possession);
- Given the extreme importance of this for proof on indication of Prof. Pascali expert defense Raffaele Reminder, on June 24, 2008 - pending the period of 20 days under Article. 415 bis -, was made an initial request to Prosecutor acquisition diagrams in electropherograms whereby the forensic results came in content Technical report on forensic genetics. In particular, this request is have specified the absolute necessity (in order of presentation defensive pleadings and petitions under Article. 415 bis cpp) to have the aforementioned documents available to the consultant of the could examine it in detail;
- However, against all evidence, the prosecutor dismissed the request was deemed inadmissible 'because the option in all.art.415 cpp a cover secured and only those acts ';
- To deal with a similar unjust refusal, the defense made on July 3, 2008, a further instance in which it sought to 'acquire forensic laboratories of the numerical values and RFU peaks on all findings, or alternatively to obtain police Scientific CDROM containing the raw data and peak RFU. It was asked, Moreover, in case it was not possible to obtain copies of these data, that the Prof. Pascali was allowed to go to the police service science for a spot inspection of the data and make it directly computerized copy;
- Even that request, however, was inexplicably rejected on 11 July 2008 with the anodyne statement that 'on the charts of Forensic there are already bars with generic value on fluorescence peaks.
The defense then returned to a preliminary hearing with a serious cognitive gap, due to lack of awareness of scientific data used by the police in their scientific investigations. As we shall see, this story had a further follow:
- Preliminary hearing of 16 September 2008, the defense reiterated request to acquire numerical values RFU and peaks at all findings or, alternatively, to acquire the CD-ROM containing the raw data RFU and peaks. The request filed at that meeting was based upon both the incompleteness detected in the diagrams attached to the report, and by the repeated requests made to the office of the C>P> to obtain the missing data;
- After this request, the Gup could not help but detect need 'for purposes of deciding' to understand 'fully (...) as procedure has been adopted for the analysis in question, and whether there further elaborations that constitute the necessary support conclusions reached. 'Consequently, the Gup has ordered the hearing in heard of Dr. Stefanoni calling 'to accompany their testimony with computer media containing data requested by the defense. "The same judge in that case was aware the extreme importance of data capture whereas the investigations living would receive 'the most important elements all.impianto accusatory;
- On September 25, 2008 in observance of the provision of Gup is was deposited by association. Zugarini on behalf of Dr. Stefanoni, the CD-Rom containing the requested data. In this regard like to highlight as the immediate acceptance of the instance in question proves unequivocally from the outset the importance of having the data available full scientific;
- Hearing on September 27, 2008, was then represented to the Gup need to obtain additional documentation because incomplete data, therefore, was asked to Court to acquire the service files (log files);
- However, the Judge, after seeking an opinion to Dr. Stefanoni has also rejected the application based on an uncritical adherence to its comments, coming to claim that "not be needed information contained in the logs (data nell.esperienza forensic are never identified, resulting standards approved by the parameters internationally and which appear to be in use in all Laboratories engaged in Forensic Genetics).
Such an established procedure is not, of course, acceptable under no point of view, since the unconditional adherence to observations of Dr. Stefanoni, has led to support the contention accusatory, without the technical-scientific comparison of an expert third and impartial.
And indeed, if it had consulted a person not bound by any constraint on the charge (ie a neutral), the parties would certainly have benefitted. And 'quite clear that to ask to review its person (Dr Stefanoni) which produced that result is, in fact, nonsense: can not say, claim of self-discipline science by the same technician who testified that result. Any specialist will of course be pushed, albeit inadvertently, to defend the validity of their work, even in front of a simple request for clarification, and justify - after all, understandably, by his point of view - that all data provided are sufficient.

Was evidence showed the need to provide all documentation scientific defense.
It 'important to note that log files are much scientific data relevant, if not indispensable, especially in situations (such as the case in point) where the peak height must be assessed together with other parameters (such as area) is also higher to determine the plausibility or, conversely, the unlikelihood attribution to a person's DNA. So it is true that during the preliminary hearing in court, the Dr. Stefanoni - at the request of the consultant that the Prosecution asked if it was important given the "peak area" – said "Normally not. "However, what is more surprising is that the very Dr. Stefanoni candidly admitted that it had no other experiences on (p. 68 transcription.'s preliminary hearing Oct. 4, 2009). The opinion of Dr. Stefanoni, in fact, emerged in all its fragility when the consultant has made the defense Reminder noted a recommendation of the International Society of Genetic Lawyers, which states that the method used to interpret traces of mixed DNA and consider l.area l.altezza of peaks "(p. 99 of those transcripts.)
The GUP at this point, he invited Dr. Stefanoni to be received by October 8, 'the data relating to the calculation of peak areas related to the finding 165 / B indicated by prof. Pascali in the third column, in his name, all.allegato referred to the report filed, and diagram on the second run on the sample elettroferografica 36B.
The epilogue of this long run-up occurred on October 8, 2008 with the filing by Dr. Stefanoni the CD-ROM containing the data dell.amplificato electrophoresis sample DNA called 165 / B (finding piece of cloth with hooks), and the CD-Rom containing: Sample data info for the two races dell.amplificato electrophoretic sample of DNA known as 36 / B (Finding knife) electropherograms of the second electrophoresis.
As can be seen from the picture just outlined, the defense did not have provision, at the conclusion of preliminary investigations, all acts of investigation as required by law, so much so that this uncertainty lasted at least for the preliminary hearing stage (and beyond, as you say).
For example, consider the simple analysis of the peak - technical data that was provided to the defense until after the hearing at the hearing Preliminary Dr. Stefanoni, damaging irreparably the rights of defense -revealed that the amount of DNA used for analysis was quite modest, which led the consultant to the defense clarified, that the interpretation given to the forensic graphics has minimally complied with the guidelines laid down by the International Society of Forensic Genetics.
But there is more. The lack of full discovery was also found in during the process:
- On July 18, 2009, during cross-examination technical consultant Defense Raffaele Sollecito, Professor Adriano Tagliabracci, there was an astonishing coup de théâtre, as the accusation made questions that have created the suspicion that the prosecutor had hold additional laboratory data ever made available to parties. It was, in particular, data on the amount of extract used for genetic analysis of biological material found on the hook of the bra of the victim;
- In front of the defense reaction, the Office of Public Prosecutor had to admit that there are acts performed by forensic ever deposited at the conclusion of the investigation (in contravention Thus the provision of art. 415 bis cpp) or sent to Gup with the request of trial (in violation of Article. 416, paragraph 2, cpp).
In other words, the Office of the PM or denied full discovery of documents investigation, pushing this lesion of the right of defense to the debate! We will now give an account of evaluations of the Court of Assizes of Perugia. The sentence I can refer about the motivations of the order of rejection "of All.audience 14/09/2009 defenses of the defendants objected l.avv n the interference with the right defense, arguing in this regard, which were verified the void. After hearing the other party seeking to disregard l.exception, this Court issued l.decree, which read out with which l.exception of nullity was rejected and was available to proceed further "(p.7. above).
Passing the order of 14 September 2009, the Assize Court noted as follows: 'respect of invalidity l.exception advanced and illustrated memory today filed for violation of the right of defense question exception is not admissible, l.activity sampling and comparison of traces biological object activity.exception the nature of prior technical investigation covered with the possibility dall.article 360 for parties to participate in and comment in this context is not apparent that there has been no lesion of the right of defense, for the nullity that would assessed in a case of a 415 dell.article knows nzione not provided by any specific provision or by a 415 Criminal Procedure Code that principle of mandatory nature of the void during preliminary dell.audience compare 1/10/2008 GUP measure included in documents filed today in support the plea of nullity that aspect has been addressed and its exception has not been repeated in terms of which all.article Code 491 Nell.audience of Criminal Procedure also before this Court on 18.7.2009 issue was not raised in terms of the void under the compare the transcripts of the hearing on 18.7.2009, with particular Refer to pages 102 et seq and 114 et seq therefore logical to conclude that l.aspect in all.exception now advances to integrate a nullity ta question But to sanction by the Supreme Court ruled on the matter for example compare Cassation Judgement second section 29573 of 2006 and Section Supreme number 21593 2009 its fifth exception was belatedly raised. As for the broken and also being the subject of advanced today than that penalty is justified in the presence of a omitted on filing all.entire investigations in this case l.omission h a covered part of the supporting documentation'”